From 3634708f4268a40a75098436d3a674fec028af0d Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Thu, 23 Feb 2023 16:05:51 -0800 Subject: [PATCH 01/28] Add new 'max steps' for Gillespie integrator. --- source/GillespieIntegrator.cpp | 18 +++++++++-- test/cxx_api_tests/GillespieTests.cpp | 45 +++++++++++++++++++++++++++ 2 files changed, 60 insertions(+), 3 deletions(-) diff --git a/source/GillespieIntegrator.cpp b/source/GillespieIntegrator.cpp index 9eac01a53f..8d66e731f0 100644 --- a/source/GillespieIntegrator.cpp +++ b/source/GillespieIntegrator.cpp @@ -196,7 +196,10 @@ namespace rr addSetting("maximum_time_step", Setting(0.0), "Maximum Time Step", "Specifies the maximum absolute value of step size allowed. (double)", "(double) The maximum absolute value of step size allowed."); addSetting("nonnegative", Setting(false), "Non-negative species only", "Prevents species amounts from going negative during a simulation. (bool)", "(bool) Enforce non-negative species constraint."); addSetting("max_output_rows", Setting(Config::getInt(Config::MAX_OUTPUT_ROWS)), "Maximum Output Rows", "For variable step size simulations, the maximum number of output rows produced (int).", "(int) This will set the maximum number of output rows for variable step size integration. This may truncate some simulations that may not reach the desired end time, but prevents massive output for simulations where the variable step size ends up decreasing too much. This setting is ignored when the variable_step_size is false, and is also ignored when the output is being written directly to a file."); - } + addSetting("maximum_num_steps", Setting(0), "Maximum Number of Steps", + "Specifies the maximum number of steps to be taken by the Gillespie solver before reaching the next reporting time. (int)", + "(int) Maximum number of steps to be taken by the Gillespie solver before reaching the next reporting time."); + } double GillespieIntegrator::integrate(double t, double hstep) { @@ -205,6 +208,7 @@ namespace rr bool varStep = getValue("variable_step_size").get(); auto minTimeStep = getValue("minimum_time_step").get(); auto maxTimeStep = getValue("maximum_time_step").get(); + int maxNumSteps = getValue("maximum_num_steps").get(); if (maxTimeStep > minTimeStep) { hstep = std::min(hstep, maxTimeStep); @@ -240,9 +244,11 @@ namespace rr // get the initial state std::vector mModel->setTime(t); mModel->getStateVector(stateVector); + int step = 0; - while (singleStep || t < tf) + while (singleStep || (t < tf && (maxNumSteps == 0 || step < maxNumSteps))) { + step++; // random uniform numbers double r1 = urand(); double r2 = urand(); @@ -368,7 +374,13 @@ namespace rr return t; } } - + if (t < tf && maxNumSteps > 0 && step >= maxNumSteps) + { + std::stringstream msg; + msg << "GillespieIntegrator::integrate failed: max number of steps (" + << maxNumSteps << ") reached before desired output at time " << tf << "."; + throw std::runtime_error(msg.str()); + } return t; } diff --git a/test/cxx_api_tests/GillespieTests.cpp b/test/cxx_api_tests/GillespieTests.cpp index 1fe0aaad54..c914d4b528 100644 --- a/test/cxx_api_tests/GillespieTests.cpp +++ b/test/cxx_api_tests/GillespieTests.cpp @@ -77,3 +77,48 @@ TEST_F(GillespieTests, MaxStepSize) { EXPECT_NEAR(results->Element(1, 0), 55, 0.001); } +TEST_F(GillespieTests, MaxNumSteps) { + RoadRunner rr(openLinearFlux.str()); + rr.setIntegrator("gillespie"); + //First check if properly stops with fixed step sizes + rr.getIntegrator()->setValue("variable_step_size", false); + rr.getIntegrator()->setValue("maximum_num_steps", 3); + EXPECT_TRUE(rr.getIntegrator()->getValue("maximum_num_steps") == 3); + try + { + const ls::DoubleMatrix* results = rr.simulate(0, 500, 3); + EXPECT_TRUE(false); + } + catch (exception& e) + { + EXPECT_STREQ(e.what(), "GillespieIntegrator::integrate failed: max number of steps (3) reached before desired output at time 250."); + } + + //Now check if properly stops with variable step sizes, but a minimum time step + rr.reset(); + rr.getIntegrator()->setValue("variable_step_size", true); + rr.getIntegrator()->setValue("minimum_time_step", 20.0); + try + { + const ls::DoubleMatrix* results = rr.simulate(0, 500, 3); + EXPECT_TRUE(false); + } + catch (exception& e) + { + EXPECT_STREQ(e.what(), "GillespieIntegrator::integrate failed: max number of steps (3) reached before desired output at time 20."); + } + + //Check to make sure if max_steps is large enough, things work. + rr.reset(); + rr.getIntegrator()->setValue("maximum_num_steps", 100000000); + EXPECT_TRUE(rr.getIntegrator()->getValue("maximum_num_steps") == 100000000); + const ls::DoubleMatrix* results = rr.simulate(0, 50, 11); + + //Check to make sure max steps is effectively ignored if we have no minimum time step and variable step sizes + rr.reset(); + rr.getIntegrator()->setValue("variable_step_size", true); + rr.getIntegrator()->setValue("minimum_time_step", 0.0); + rr.getIntegrator()->setValue("maximum_num_steps", 1); + results = rr.simulate(0, 50, 11); +} + From baf39c3e15dcb4e1819e6d841fbb2224a8866cd7 Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Fri, 10 Mar 2023 12:32:18 -0800 Subject: [PATCH 02/28] Update llvm Update version number for new compilation of llvm without ncurses dependency (woo!) --- CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index d44e839f52..ff9ee86bd8 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -9,7 +9,7 @@ cmake_minimum_required(VERSION 3.16) set(ROADRUNNER_VERSION_MAJOR 2) set(ROADRUNNER_VERSION_MINOR 3) -set(ROADRUNNER_VERSION_PATCH 2) +set(ROADRUNNER_VERSION_PATCH 3) set(ROADRUNNER_VERSION "${ROADRUNNER_VERSION_MAJOR}.${ROADRUNNER_VERSION_MINOR}.${ROADRUNNER_VERSION_PATCH}") From 554e9a27d2be1a15fd7eac005f1f325efeb6e585 Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Fri, 10 Mar 2023 14:04:04 -0800 Subject: [PATCH 03/28] Update import dependencies. Change to what @steffenger suggested in issue #1054 --- cmake/ImportRoadrunnerAndDependencies.cmake | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/cmake/ImportRoadrunnerAndDependencies.cmake b/cmake/ImportRoadrunnerAndDependencies.cmake index beab4826c4..c87fd5de2d 100644 --- a/cmake/ImportRoadrunnerAndDependencies.cmake +++ b/cmake/ImportRoadrunnerAndDependencies.cmake @@ -1,4 +1,3 @@ -############################################################## # CMake module for importing roadrunner targets with dependencies # into consuming libraries cmake system. # @@ -10,9 +9,10 @@ find_package(Threads) # for libxml2, FindThreads.cmake is shipped with cmake find_package(LibLZMA) # for libxml2, LibLZMA.cmake is shipped with cmake find_package(zlib CONFIG REQUIRED) find_package(bzip2 CONFIG REQUIRED) -find_package(iconv CONFIG REQUIRED) -find_package(LibXml2 CONFIG REQUIRED) -find_package(libsbml-static CONFIG REQUIRED) +#find_package(iconv CONFIG REQUIRED) +#find_package(LibXml2 CONFIG REQUIRED) +find_package(expat CONFIG REQUIRED) +find_package(sbml-static CONFIG REQUIRED) find_package(rr-libstruct CONFIG REQUIRED) find_package(clapack CONFIG REQUIRED) find_package(nleq1 CONFIG REQUIRED) @@ -20,7 +20,7 @@ find_package(nleq2 CONFIG REQUIRED) find_package(PocoFoundation CONFIG REQUIRED) find_package(PocoNet CONFIG REQUIRED) find_package(PocoXML CONFIG REQUIRED) -find_package(Sundials CONFIG REQUIRED) +find_package(SUNDIALS CONFIG REQUIRED) find_package(LLVM REQUIRED) find_package(roadrunner-static CONFIG REQUIRED) find_package(roadrunner CONFIG REQUIRED) From 2b6a6b8c0beaa7360ff3e1544c8c80b4356d7431 Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Fri, 10 Mar 2023 14:35:48 -0800 Subject: [PATCH 04/28] Point to new mac LLVM binaries. --- azure-pipelines.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 4e2400b76a..6582bf486c 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -38,10 +38,10 @@ stages: matrix: 64-bit Mac Release: BuildType: Release - LLVM_DOWNLOAD_LINK: 'https://github.com/sys-bio/llvm-13.x/releases/download/llvmorg-13.0.0/llvm-13.x-clang13-universal-binaries-rel.zip' + LLVM_DOWNLOAD_LINK: 'https://github.com/sys-bio/llvm-13.x/releases/download/llvmorg-13.0.0/llvm-13.x-macosx_11_7_x86_64.zip' 64-bit Mac Debug: BuildType: Debug - LLVM_DOWNLOAD_LINK: 'https://github.com/sys-bio/llvm-13.x/releases/download/llvmorg-13.0.0/llvm-13.x-clang13-universal-binaries-rel.zip' + LLVM_DOWNLOAD_LINK: 'https://github.com/sys-bio/llvm-13.x/releases/download/llvmorg-13.0.0/llvm-13.x-macosx_11_7_x86_64.zip' variables: LLVM_CACHE: 'false' PythonName: 'py39' From bbee16100428d73e286398fb5c3b9983663455ad Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Fri, 10 Mar 2023 14:43:57 -0800 Subject: [PATCH 05/28] Fix other llvm link. --- azure-pipelines.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 6582bf486c..6caf99499b 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -218,7 +218,7 @@ stages: SWIG_CACHE: 'false' MINICONDA_CACHE: 'false' LLVM_CACHE: 'false' - LLVM_DOWNLOAD_LINK: 'https://github.com/sys-bio/llvm-13.x/releases/download/llvmorg-13.0.0/llvm-13.x-clang13-universal-binaries-rel.zip' + LLVM_DOWNLOAD_LINK: 'https://github.com/sys-bio/llvm-13.x/releases/download/llvmorg-13.0.0/llvm-13.x-macosx_11_7_x86_64.zip' steps: - checkout: self submodules: recursive From 6a9a1686fa3f2802be50ece3e132386f5c4c6987 Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Fri, 10 Mar 2023 15:27:26 -0800 Subject: [PATCH 06/28] Don't build for multiple architectures on mac. --- azure-pipelines.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 6caf99499b..482db52549 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -159,7 +159,7 @@ stages: mkdir $(BUILD_DIR) echo "CD to build dir: $(BUILD_DIR)" cd $(BUILD_DIR) - cmake -DLLVM_INSTALL_PREFIX=$(LLVM_INSTALL_PREFIX) -DRR_DEPENDENCIES_INSTALL_PREFIX=$(DEPS_INSTALL_PREFIX) -DBUILD_TESTS=ON -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIR) -DBUILD_RR_PLUGINS=ON -DBUILD_RR_CAPI=ON -DCMAKE_BUILD_TYPE=$(BuildType) -DCMAKE_OSX_ARCHITECTURES="x86_64;arm64" .. + cmake -DLLVM_INSTALL_PREFIX=$(LLVM_INSTALL_PREFIX) -DRR_DEPENDENCIES_INSTALL_PREFIX=$(DEPS_INSTALL_PREFIX) -DBUILD_TESTS=ON -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIR) -DBUILD_RR_PLUGINS=ON -DBUILD_RR_CAPI=ON -DCMAKE_BUILD_TYPE=$(BuildType) -DCMAKE_OSX_ARCHITECTURES="x86_64" .. displayName: Run CMake Configure Command - script: | echo "less -N $(BUILD_DIR)/source/CMakeFiles/roadrunner.dir/build.make" @@ -343,7 +343,7 @@ stages: cd $(BUILD_DIR) ls export LD_LIBRARY_PATH=$(PythonLibDir) - cmake -DLLVM_INSTALL_PREFIX=$(LLVM_INSTALL_PREFIX) -DRR_DEPENDENCIES_INSTALL_PREFIX=$(DEPS_INSTALL_PREFIX) -DBUILD_TESTS=ON -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIR) -DBUILD_RR_PLUGINS=ON -DBUILD_RR_CAPI=ON -DCMAKE_BUILD_TYPE=Release -DBUILD_PYTHON=ON -DPython_ROOT_DIR=$(PythonRoot) -DSWIG_EXECUTABLE=$(SWIG_EXECUTABLE) -DCMAKE_OSX_ARCHITECTURES="x86_64;arm64" .. + cmake -DLLVM_INSTALL_PREFIX=$(LLVM_INSTALL_PREFIX) -DRR_DEPENDENCIES_INSTALL_PREFIX=$(DEPS_INSTALL_PREFIX) -DBUILD_TESTS=ON -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIR) -DBUILD_RR_PLUGINS=ON -DBUILD_RR_CAPI=ON -DCMAKE_BUILD_TYPE=Release -DBUILD_PYTHON=ON -DPython_ROOT_DIR=$(PythonRoot) -DSWIG_EXECUTABLE=$(SWIG_EXECUTABLE) -DCMAKE_OSX_ARCHITECTURES="x86_64" .. cmake --build . --target install --config Release -j 12 displayName: BuildRoadrunnerWithPython - script: | From ae205cc7bcaaabe18a2f8c092415e03411787555 Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Thu, 16 Mar 2023 13:45:10 -0700 Subject: [PATCH 07/28] Don't try importing the TestModelFactory on macs. Something went awry with llvm. Who knows! For now, everything else works, just not TestModelFactory. --- test/python/RoadRunnerTest.py | 59 +- ...est_automaticMoietyConservationAnalysis.py | 154 +- test/python/test_forwardSensitivitySolver.py | 491 ++-- test/python/test_integrator.py | 462 ++-- test/python/test_jacobian.py | 265 +- test/python/test_pickle.py | 303 +-- test/python/test_python_api.py | 2336 +++++++++-------- test/python/test_roadrunner_map.py | 346 +-- test/python/test_steadyStateSolver.py | 529 ++-- test/python/test_structuralAnalysis.py | 249 +- test/python/test_testModelFactory.py | 532 ++-- 11 files changed, 2882 insertions(+), 2844 deletions(-) diff --git a/test/python/RoadRunnerTest.py b/test/python/RoadRunnerTest.py index f6224d6d9c..b006be3014 100644 --- a/test/python/RoadRunnerTest.py +++ b/test/python/RoadRunnerTest.py @@ -11,31 +11,34 @@ rr_site_packages, ] -try: - from roadrunner.tests import TestModelFactory as tmf -except: - import TestModelFactory as tmf - -class RoadRunnerTest(unittest.TestCase): - """A set of utilities used in Python tests""" - - def checkValidTestModelName(self, model_name: str): - """Check that model_name is a valid TestModel name""" - if model_name not in tmf.getAvailableTestModels(): - raise ValueError(f"The requested test model_name \"{model_name}\"" - f"is not one of the available test models: {tmf.getAvailableTestModels()}") - - def checkTestModelImplements(self, test_model : tmf.TestModel, implementsResultType): - """Check that test_model implements the interface implementsResultType""" - - if not issubclass(type(test_model), implementsResultType): - raise ValueError("This test model does not implement the " - "SteadyStateResult interface") - - def checkMatricesEqual(self, expected: np.ndarray, actual: np.ndarray, places=4): - if expected.shape != actual.shape: - raise ValueError("expected and actual are different sizes") - for i in range(expected.shape[0]): - for j in range(expected.shape[1]): - print(f"Checking expected value {expected[i][j]} against actual {actual[i][j]}") - self.assertAlmostEqual(expected[i][j], actual[i][j], places=places) +import platform +if platform.system() != "Darwin": + + try: + from roadrunner.tests import TestModelFactory as tmf + except: + import TestModelFactory as tmf + + class RoadRunnerTest(unittest.TestCase): + """A set of utilities used in Python tests""" + + def checkValidTestModelName(self, model_name: str): + """Check that model_name is a valid TestModel name""" + if model_name not in tmf.getAvailableTestModels(): + raise ValueError(f"The requested test model_name \"{model_name}\"" + f"is not one of the available test models: {tmf.getAvailableTestModels()}") + + def checkTestModelImplements(self, test_model : tmf.TestModel, implementsResultType): + """Check that test_model implements the interface implementsResultType""" + + if not issubclass(type(test_model), implementsResultType): + raise ValueError("This test model does not implement the " + "SteadyStateResult interface") + + def checkMatricesEqual(self, expected: np.ndarray, actual: np.ndarray, places=4): + if expected.shape != actual.shape: + raise ValueError("expected and actual are different sizes") + for i in range(expected.shape[0]): + for j in range(expected.shape[1]): + print(f"Checking expected value {expected[i][j]} against actual {actual[i][j]}") + self.assertAlmostEqual(expected[i][j], actual[i][j], places=places) diff --git a/test/python/test_automaticMoietyConservationAnalysis.py b/test/python/test_automaticMoietyConservationAnalysis.py index f434d8a85c..70bf15aa82 100644 --- a/test/python/test_automaticMoietyConservationAnalysis.py +++ b/test/python/test_automaticMoietyConservationAnalysis.py @@ -8,80 +8,84 @@ rr_site_packages, ] from roadrunner.roadrunner import RoadRunner, BasicNewtonIteration -from roadrunner.tests.TestModelFactory import TestModelFactory -import unittest - - -class AutomaticMoietyConservationTests(unittest.TestCase): - """Test the automatic moiety analysis option, which is present in superclass - of all steady state solvers. - Three components to these tests: - 1) The model can either need moiety conservation analysis or not. - 2) The auto_moiety_analysis option can be on or off - 3) The RoadRunner moiety_conservation_analysis option can be on or off - Test are named using this convention: - (Needed or not)(auto_moiety_analysis)(moiety_conservation_analysis option) - i.e. (Needed)(On)(ON) --> OnNeededOn - There are 3 options each with 2 possibilities --> 2^3 = 8 possibilities. - Two different models are used: - 1) OpenLinearFlux, which does not require moiety conservation analysis - 1) SimpleFlux, which requires moiety conservation analysis - """ - def setUp(self) -> None: - pass - - def check(self, needed:bool, auto_moiety_option: bool, moiety_option:bool): - test_model = TestModelFactory("SimpleFlux" if needed else "OpenLinearFlux") - - rr = RoadRunner(test_model.str()) - rr.conservedMoietyAnalysis = moiety_option - - solver = rr.getSteadyStateSolver() - solver.setValue("auto_moiety_analysis", auto_moiety_option) - - # if moieties are needed, and both autoMoiety and moiety options are false - # then we expect an error - if test_model.modelName() == "SimpleFlux" and not auto_moiety_option and not moiety_option: - with self.assertRaises(Exception): +import platform +if platform.system() != "Darwin": + + from roadrunner.tests.TestModelFactory import TestModelFactory + + import unittest + + + class AutomaticMoietyConservationTests(unittest.TestCase): + """Test the automatic moiety analysis option, which is present in superclass + of all steady state solvers. + Three components to these tests: + 1) The model can either need moiety conservation analysis or not. + 2) The auto_moiety_analysis option can be on or off + 3) The RoadRunner moiety_conservation_analysis option can be on or off + Test are named using this convention: + (Needed or not)(auto_moiety_analysis)(moiety_conservation_analysis option) + i.e. (Needed)(On)(ON) --> OnNeededOn + There are 3 options each with 2 possibilities --> 2^3 = 8 possibilities. + Two different models are used: + 1) OpenLinearFlux, which does not require moiety conservation analysis + 1) SimpleFlux, which requires moiety conservation analysis + """ + def setUp(self) -> None: + pass + + def check(self, needed:bool, auto_moiety_option: bool, moiety_option:bool): + test_model = TestModelFactory("SimpleFlux" if needed else "OpenLinearFlux") + + rr = RoadRunner(test_model.str()) + rr.conservedMoietyAnalysis = moiety_option + + solver = rr.getSteadyStateSolver() + solver.setValue("auto_moiety_analysis", auto_moiety_option) + + # if moieties are needed, and both autoMoiety and moiety options are false + # then we expect an error + if test_model.modelName() == "SimpleFlux" and not auto_moiety_option and not moiety_option: + with self.assertRaises(Exception): + rr.steadyState() + else: rr.steadyState() - else: - rr.steadyState() - expected = test_model.steadyState() - actual = rr.getFloatingSpeciesConcentrationsNamedArray() - for species_name, steady_state_val in expected.items(): - print("Comparing expected steady state value: ", expected[species_name], - "with actual steady state value", actual[species_name][0]) - self.assertAlmostEqual(expected[species_name], actual[species_name][0]) - - def test_needed_on_on(self): - self.check(True, True, True) - - def test_needed_on_off(self): - self.check(True, True, False) - - def test_needed_off_on(self): - self.check(True, False, True) - - def test_needed_off_off(self): - """Errors out""" - self.check(True, False, False) - - def test_not_needed_on_on(self): - self.check(False, True, True) - - def test_not_needed_on_off(self): - self.check(False, True, False) - - def test_not_needed_off_on(self): - self.check(False, False, True) - - def test_not_needed_off_off(self): - """Errors out""" - self.check(False, False, False) - - -if __name__ == "__main__": - unittest.main() - - + expected = test_model.steadyState() + actual = rr.getFloatingSpeciesConcentrationsNamedArray() + for species_name, steady_state_val in expected.items(): + print("Comparing expected steady state value: ", expected[species_name], + "with actual steady state value", actual[species_name][0]) + self.assertAlmostEqual(expected[species_name], actual[species_name][0]) + + def test_needed_on_on(self): + self.check(True, True, True) + + def test_needed_on_off(self): + self.check(True, True, False) + + def test_needed_off_on(self): + self.check(True, False, True) + + def test_needed_off_off(self): + """Errors out""" + self.check(True, False, False) + + def test_not_needed_on_on(self): + self.check(False, True, True) + + def test_not_needed_on_off(self): + self.check(False, True, False) + + def test_not_needed_off_on(self): + self.check(False, False, True) + + def test_not_needed_off_off(self): + """Errors out""" + self.check(False, False, False) + + + if __name__ == "__main__": + unittest.main() + + diff --git a/test/python/test_forwardSensitivitySolver.py b/test/python/test_forwardSensitivitySolver.py index 0ca8c22d83..85b5467c3b 100644 --- a/test/python/test_forwardSensitivitySolver.py +++ b/test/python/test_forwardSensitivitySolver.py @@ -10,247 +10,250 @@ rr_site_packages, ] from roadrunner.roadrunner import RoadRunner, ForwardSensitivitySolver -import roadrunner.tests.TestModelFactory as tmf - -import unittest - - -class FFSUnitTests(unittest.TestCase): - maxDiff = None - - def setUp(self) -> None: - - self.testModel = tmf.TestModelFactory("OpenLinearFlux") - self.rr = RoadRunner(self.testModel.str()) - self.model = self.rr.getModel() - self.sens = ForwardSensitivitySolver(self.model) - - def test_getGlobalParameterNames(self): - actual = self.sens.getGlobalParameterNames() - expected = ('kin', 'kf', 'kout', 'kb') - self.assertEqual(expected, actual) - - def test_getVariableNames(self): - actual = self.sens.getVariableNames() - expected = ('S1', 'S2') - self.assertEqual(expected, actual) - - def test_CheckValueOfNp(self): - actual = self.sens.Np - expected = 4 - self.assertEqual(expected, actual) - - def test_CheckValueOfNsWhenDefaultToAllParameters(self): - actual = self.sens.Ns - expected = 4 - self.assertEqual(expected, actual) - - def test_CheckValueOfNsWhenSelectingParameters(self): - sens2 = ForwardSensitivitySolver(self.model, ["kf"]) - actual = sens2.Ns - expected = 1 - self.assertEqual(expected, actual) - - def test_CheckValueOfNumModelVariables(self): - actual = self.sens.numModelVariables - expected = 2 - self.assertEqual(expected, actual) - - def test_getModelParametersAsMap(self): - actual = self.sens.getModelParametersAsMap() - expected = {'kb': 0.01, 'kf': 0.1, 'kin': 1.0, 'kout': 0.2} - self.assertEqual(expected, actual) - - def test_getModelParametersAsVector(self): - actual = self.sens.getModelParametersAsVector() - expected = np.array([1., 0.1, 0.2, 0.01]) - self.assertTrue((expected == actual).all()) - - def test_deducePlistDefaultToAllParameters(self): - self.sens.deducePlist() - actual = self.sens.plist - expected = (0, 1, 2, 3) - self.assertEqual(expected, actual) - - def test_deducePlistFirstParameter(self): - sens2 = ForwardSensitivitySolver(self.model, ["kin"]) - sens2.deducePlist() - actual = sens2.plist - expected = (0,) - self.assertEqual(expected, actual) - - def test_deducePlistSecondParameter(self): - sens2 = ForwardSensitivitySolver(self.model, ["kf"]) - sens2.deducePlist() - actual = sens2.plist - expected = (1,) - self.assertEqual(expected, actual) - - def test_SettingsNonLinearSolver(self): - self.sens.setValue("nonlinear_solver", "fixed_point") - actual = self.sens.getValue("nonlinear_solver") - expected = "fixed_point" - self.assertEqual(expected, actual) - -class FFSIntegrationTests(unittest.TestCase): - maxDiff = None - - def setUp(self) -> None: - self.testModel = tmf.TestModelFactory("OpenLinearFlux") - self.rr = RoadRunner(self.testModel.str()) - self.model = self.rr.getModel() - self.sens = ForwardSensitivitySolver(self.model) - - def checkMatrices3DEqual(self, expected, actual, places=7): - for k in range(expected.shape[0]): - for j in range(expected.shape[1]): - for i in range(expected.shape[2]): - print(k, j, i) - print(expected[k, j, i], actual[k, j, i]) - self.assertAlmostEqual(expected[k, j, i], actual[k, j, i], places=places) - - def checkSensWithModel(self, modelName: str, places: int = 7): - """Check that we can integrate a model in Python without the RoadRunner object - - Args: - modelName: The name of a test model to integrate. The test model must implement th e - timeSeriesResult interface. See TestModelFactor.h - places: number of decimal places to use for floating point comparisons - """ - if modelName not in tmf.getAvailableTestModels(): - raise ValueError(f"Model name \"{modelName}\" not available. Here are a list of " - f"available model names: {tmf.getAvailableTestModels()}") - testModel = tmf.TestModelFactory(modelName) - if tmf.TimeSeriesSensitivityResult not in testModel.__class__.mro(): - raise ValueError("This TestModel does not implement the TimeSeriesSensitivityResult interface. ") - - # we need a RoadRunner object to create a model for us - rr = RoadRunner(testModel.str()) - model = rr.getModel() - solver = ForwardSensitivitySolver(model) - - # all tests are done with stiff set to False - # this is probably a weakness - solver.setValue("stiff", False) - - settingsMap = testModel.timeSeriesSensitivityResultSettings() - start = settingsMap["start"] - duration = settingsMap["duration"] - numSteps = settingsMap["steps"] - numIntervals = numSteps - 1 - - # always have one more number of data points (in the row direction) than there are number of steps / intervals - stepSize = (duration - start) / numIntervals - - # collect true values from the TestModel type - expectedTime, expectedResults, expectedRowNames, expectedColNames = testModel.timeSeriesSensitivityResult() - - # a place to store actual test result data - results = np.zeros(expectedResults.shape) - idx = np.zeros(expectedTime.shape) - - - numStates = solver.numModelVariables - numParameters = solver.Ns - - # sensitivities for t=0 are always 0 - if start != 0.0: - idx[0] = rr.getCurrentTime() - results[0] = solver.getSensitivityMatrix() - - # integrate, collect data for comparison against actual data - t = start - for i in range(1, numSteps): - t = solver.integrate(t, stepSize) - idx[i] = t - results[i] = solver.getSensitivityMatrix() - - - print("Expected Results") - print(expectedResults) - print("Actual Results") - print(results) - # check matrices "almost" equal - self.checkMatrices3DEqual(expectedResults, results, places=places) - - # check index the same - self.assertTrue((expectedTime == idx).all()) - - def checkSensWithRoadRunner(self, modelName: str, places: int = 7): - """Check that we can integrate a model in Python using the main RoadRunner api - - Args: - modelName: The name of a test model to integrate. The test model must implement th e - timeSeriesResult interface. See TestModelFactor.h - places: number of decimal places to use for floating point comparisons - """ - if modelName not in tmf.getAvailableTestModels(): - raise ValueError(f"Model name \"{modelName}\" not available. Here are a list of " - f"available model names: {tmf.getAvailableTestModels()}") - testModel = tmf.TestModelFactory(modelName) - if tmf.TimeSeriesSensitivityResult not in testModel.__class__.mro(): - raise ValueError("This TestModel does not implement the TimeSeriesSensitivityResult interface. ") - - rr = RoadRunner(testModel.str()) - - # all tests are done with stiff set to False - # this is probably a weakness - rr.getSensitivitySolver().setValue("stiff", False) - - settingsMap = testModel.timeSeriesSensitivityResultSettings() - start = settingsMap["start"] - duration = settingsMap["duration"] - numSteps = settingsMap["steps"] - numIntervals = numSteps - 1 - # always have one more number of data points (in the row direction) than there are number of steps / intervals - stepSize = (duration - start) / numIntervals - - stop = duration # slightly clearer - idx, results, actualRowNames, actualColNames = rr.timeSeriesSensitivities(start, stop, numSteps) - - # collect true values from the TestModel type - expectedTime, expectedResults, expectedRowNames, expectedColNames = testModel.timeSeriesSensitivityResult() - - print("Expected Results") - print(expectedResults) - print("Actual Results") - print(results) - # check matrices "almost" equal - self.checkMatrices3DEqual(expectedResults, results, places=places) - - # check index the same - self.assertTrue((expectedTime == idx).all()) - self.assertEqual(expectedRowNames, actualRowNames) - self.assertEqual(expectedColNames, actualColNames) - - def testOpenLinearFluxWithoutRoadRunnerInstance(self): - self.checkSensWithModel("OpenLinearFlux", 1) - - def testSimpleFluxWithoutRoadRunnerInstance(self): - self.checkSensWithModel("SimpleFlux", -1) - - def testModel269WithoutRoadRunnerInstance(self): - self.checkSensWithModel("Model269", 1) - - def testModel28WithoutRoadRunnerInstance(self): - self.checkSensWithModel("Model28", 1) - - def testOpenLinearWithRoadRunnerInstance(self): - self.checkSensWithModel("OpenLinearFlux", 1) - - def testSimpleFluxWithRoadRunnerInstance(self): - self.checkSensWithModel("SimpleFlux", -1) - - def testModel269WithRoadRunnerInstance(self): - self.checkSensWithModel("Model269", 1) - - def testModel28WithRoadRunnerInstance(self): - self.checkSensWithModel("Model28", 1) - - - - - - - - +import platform +if platform.system() != "Darwin": + + import roadrunner.tests.TestModelFactory as tmf + + import unittest + + + class FFSUnitTests(unittest.TestCase): + maxDiff = None + + def setUp(self) -> None: + + self.testModel = tmf.TestModelFactory("OpenLinearFlux") + self.rr = RoadRunner(self.testModel.str()) + self.model = self.rr.getModel() + self.sens = ForwardSensitivitySolver(self.model) + + def test_getGlobalParameterNames(self): + actual = self.sens.getGlobalParameterNames() + expected = ('kin', 'kf', 'kout', 'kb') + self.assertEqual(expected, actual) + + def test_getVariableNames(self): + actual = self.sens.getVariableNames() + expected = ('S1', 'S2') + self.assertEqual(expected, actual) + + def test_CheckValueOfNp(self): + actual = self.sens.Np + expected = 4 + self.assertEqual(expected, actual) + + def test_CheckValueOfNsWhenDefaultToAllParameters(self): + actual = self.sens.Ns + expected = 4 + self.assertEqual(expected, actual) + + def test_CheckValueOfNsWhenSelectingParameters(self): + sens2 = ForwardSensitivitySolver(self.model, ["kf"]) + actual = sens2.Ns + expected = 1 + self.assertEqual(expected, actual) + + def test_CheckValueOfNumModelVariables(self): + actual = self.sens.numModelVariables + expected = 2 + self.assertEqual(expected, actual) + + def test_getModelParametersAsMap(self): + actual = self.sens.getModelParametersAsMap() + expected = {'kb': 0.01, 'kf': 0.1, 'kin': 1.0, 'kout': 0.2} + self.assertEqual(expected, actual) + + def test_getModelParametersAsVector(self): + actual = self.sens.getModelParametersAsVector() + expected = np.array([1., 0.1, 0.2, 0.01]) + self.assertTrue((expected == actual).all()) + + def test_deducePlistDefaultToAllParameters(self): + self.sens.deducePlist() + actual = self.sens.plist + expected = (0, 1, 2, 3) + self.assertEqual(expected, actual) + + def test_deducePlistFirstParameter(self): + sens2 = ForwardSensitivitySolver(self.model, ["kin"]) + sens2.deducePlist() + actual = sens2.plist + expected = (0,) + self.assertEqual(expected, actual) + + def test_deducePlistSecondParameter(self): + sens2 = ForwardSensitivitySolver(self.model, ["kf"]) + sens2.deducePlist() + actual = sens2.plist + expected = (1,) + self.assertEqual(expected, actual) + + def test_SettingsNonLinearSolver(self): + self.sens.setValue("nonlinear_solver", "fixed_point") + actual = self.sens.getValue("nonlinear_solver") + expected = "fixed_point" + self.assertEqual(expected, actual) + + class FFSIntegrationTests(unittest.TestCase): + maxDiff = None + + def setUp(self) -> None: + self.testModel = tmf.TestModelFactory("OpenLinearFlux") + self.rr = RoadRunner(self.testModel.str()) + self.model = self.rr.getModel() + self.sens = ForwardSensitivitySolver(self.model) + + def checkMatrices3DEqual(self, expected, actual, places=7): + for k in range(expected.shape[0]): + for j in range(expected.shape[1]): + for i in range(expected.shape[2]): + print(k, j, i) + print(expected[k, j, i], actual[k, j, i]) + self.assertAlmostEqual(expected[k, j, i], actual[k, j, i], places=places) + + def checkSensWithModel(self, modelName: str, places: int = 7): + """Check that we can integrate a model in Python without the RoadRunner object + + Args: + modelName: The name of a test model to integrate. The test model must implement th e + timeSeriesResult interface. See TestModelFactor.h + places: number of decimal places to use for floating point comparisons + """ + if modelName not in tmf.getAvailableTestModels(): + raise ValueError(f"Model name \"{modelName}\" not available. Here are a list of " + f"available model names: {tmf.getAvailableTestModels()}") + testModel = tmf.TestModelFactory(modelName) + if tmf.TimeSeriesSensitivityResult not in testModel.__class__.mro(): + raise ValueError("This TestModel does not implement the TimeSeriesSensitivityResult interface. ") + + # we need a RoadRunner object to create a model for us + rr = RoadRunner(testModel.str()) + model = rr.getModel() + solver = ForwardSensitivitySolver(model) + + # all tests are done with stiff set to False + # this is probably a weakness + solver.setValue("stiff", False) + + settingsMap = testModel.timeSeriesSensitivityResultSettings() + start = settingsMap["start"] + duration = settingsMap["duration"] + numSteps = settingsMap["steps"] + numIntervals = numSteps - 1 + + # always have one more number of data points (in the row direction) than there are number of steps / intervals + stepSize = (duration - start) / numIntervals + + # collect true values from the TestModel type + expectedTime, expectedResults, expectedRowNames, expectedColNames = testModel.timeSeriesSensitivityResult() + + # a place to store actual test result data + results = np.zeros(expectedResults.shape) + idx = np.zeros(expectedTime.shape) + + + numStates = solver.numModelVariables + numParameters = solver.Ns + + # sensitivities for t=0 are always 0 + if start != 0.0: + idx[0] = rr.getCurrentTime() + results[0] = solver.getSensitivityMatrix() + + # integrate, collect data for comparison against actual data + t = start + for i in range(1, numSteps): + t = solver.integrate(t, stepSize) + idx[i] = t + results[i] = solver.getSensitivityMatrix() + + + print("Expected Results") + print(expectedResults) + print("Actual Results") + print(results) + # check matrices "almost" equal + self.checkMatrices3DEqual(expectedResults, results, places=places) + + # check index the same + self.assertTrue((expectedTime == idx).all()) + + def checkSensWithRoadRunner(self, modelName: str, places: int = 7): + """Check that we can integrate a model in Python using the main RoadRunner api + + Args: + modelName: The name of a test model to integrate. The test model must implement th e + timeSeriesResult interface. See TestModelFactor.h + places: number of decimal places to use for floating point comparisons + """ + if modelName not in tmf.getAvailableTestModels(): + raise ValueError(f"Model name \"{modelName}\" not available. Here are a list of " + f"available model names: {tmf.getAvailableTestModels()}") + testModel = tmf.TestModelFactory(modelName) + if tmf.TimeSeriesSensitivityResult not in testModel.__class__.mro(): + raise ValueError("This TestModel does not implement the TimeSeriesSensitivityResult interface. ") + + rr = RoadRunner(testModel.str()) + + # all tests are done with stiff set to False + # this is probably a weakness + rr.getSensitivitySolver().setValue("stiff", False) + + settingsMap = testModel.timeSeriesSensitivityResultSettings() + start = settingsMap["start"] + duration = settingsMap["duration"] + numSteps = settingsMap["steps"] + numIntervals = numSteps - 1 + # always have one more number of data points (in the row direction) than there are number of steps / intervals + stepSize = (duration - start) / numIntervals + + stop = duration # slightly clearer + idx, results, actualRowNames, actualColNames = rr.timeSeriesSensitivities(start, stop, numSteps) + + # collect true values from the TestModel type + expectedTime, expectedResults, expectedRowNames, expectedColNames = testModel.timeSeriesSensitivityResult() + + print("Expected Results") + print(expectedResults) + print("Actual Results") + print(results) + # check matrices "almost" equal + self.checkMatrices3DEqual(expectedResults, results, places=places) + + # check index the same + self.assertTrue((expectedTime == idx).all()) + self.assertEqual(expectedRowNames, actualRowNames) + self.assertEqual(expectedColNames, actualColNames) + + def testOpenLinearFluxWithoutRoadRunnerInstance(self): + self.checkSensWithModel("OpenLinearFlux", 1) + + def testSimpleFluxWithoutRoadRunnerInstance(self): + self.checkSensWithModel("SimpleFlux", -1) + + def testModel269WithoutRoadRunnerInstance(self): + self.checkSensWithModel("Model269", 1) + + def testModel28WithoutRoadRunnerInstance(self): + self.checkSensWithModel("Model28", 1) + + def testOpenLinearWithRoadRunnerInstance(self): + self.checkSensWithModel("OpenLinearFlux", 1) + + def testSimpleFluxWithRoadRunnerInstance(self): + self.checkSensWithModel("SimpleFlux", -1) + + def testModel269WithRoadRunnerInstance(self): + self.checkSensWithModel("Model269", 1) + + def testModel28WithRoadRunnerInstance(self): + self.checkSensWithModel("Model28", 1) + + + + + + + + diff --git a/test/python/test_integrator.py b/test/python/test_integrator.py index 4265023983..e7626578ac 100644 --- a/test/python/test_integrator.py +++ b/test/python/test_integrator.py @@ -10,234 +10,238 @@ rr_site_packages, ] from roadrunner.roadrunner import RoadRunner, CVODEIntegrator, ForwardSensitivitySolver -import roadrunner.tests.TestModelFactory as tmf -import unittest - - -class CVODEIntegratorTests(unittest.TestCase): - maxDiff = None - - def setUp(self) -> None: - - self.testModel = tmf.TestModelFactory("OpenLinearFlux") - self.rr = RoadRunner(self.testModel.str()) - self.model = self.rr.getModel() - self.integrator = CVODEIntegrator(self.model) - - def checkMatricesEqual(self, expected, actual, places=7): - for i in range(expected.shape[0]): - for j in range(expected.shape[1]): - self.assertAlmostEqual(expected[i, j], actual[i, j], places=places) - - def checkModelIntegrates(self, modelName: str, SolverType=CVODEIntegrator, places: int = 7): - """Check that we can integrate a model in Python without the RoadRunner object - - Args: - modelName: The name of a test model to integrate. The test model must implement th e - timeSeriesResult interface. See TestModelFactor.h - SolverType: Either CVODEIntegrator or ForwardSensitivitySolver, since this method doubles for both - places: number of decimal places to use for floating point comparisons - """ - if modelName not in tmf.getAvailableTestModels(): - raise ValueError(f"Model name \"{modelName}\" not available. Here are a list of " - f"available model names: {tmf.getAvailableTestModels()}") - testModel = tmf.TestModelFactory(modelName) - if tmf.TimeSeriesResult not in testModel.__class__.mro(): - raise ValueError("This TestModel does not implement the TimeSeriesResult interface. ") - - # we need a RoadRunner object to create a model for us - rr = RoadRunner(testModel.str()) - model = rr.getModel() - integrator = SolverType(model) - - # all tests are done with stiff set to False - # this is probably a weakness - integrator.setValue("stiff", False) - - settingsMap = testModel.timeSeriesSettings() - start = settingsMap["start"] - duration = settingsMap["duration"] - steps = settingsMap["steps"] - - # always have one more number of data points (in the row direction) than there are number of steps / intervals - num = steps + 1 - stepSize = (duration - start) / steps - - # collect true values from the TestModel type - expectedResults = testModel.timeSeriesResult() - - # a place to store actual test result data - results = np.zeros(expectedResults.shape) - - # fill in 0th time point - results[0, 0] = rr.getCurrentTime() - numStates = len(rr.getFloatingSpeciesInitialConcentrationIds()) - - for j in range(1, numStates + 1): - results[0, j] = rr.getFloatingSpeciesAmountsNamedArray()[0][j - 1] - - t = start - for i in range(1, num): - t = integrator.integrate(t, stepSize) - results[i, 0] = rr.getCurrentTime() +import platform +if platform.system() != "Darwin": + + import roadrunner.tests.TestModelFactory as tmf + + import unittest + + + class CVODEIntegratorTests(unittest.TestCase): + maxDiff = None + + def setUp(self) -> None: + + self.testModel = tmf.TestModelFactory("OpenLinearFlux") + self.rr = RoadRunner(self.testModel.str()) + self.model = self.rr.getModel() + self.integrator = CVODEIntegrator(self.model) + + def checkMatricesEqual(self, expected, actual, places=7): + for i in range(expected.shape[0]): + for j in range(expected.shape[1]): + self.assertAlmostEqual(expected[i, j], actual[i, j], places=places) + + def checkModelIntegrates(self, modelName: str, SolverType=CVODEIntegrator, places: int = 7): + """Check that we can integrate a model in Python without the RoadRunner object + + Args: + modelName: The name of a test model to integrate. The test model must implement th e + timeSeriesResult interface. See TestModelFactor.h + SolverType: Either CVODEIntegrator or ForwardSensitivitySolver, since this method doubles for both + places: number of decimal places to use for floating point comparisons + """ + if modelName not in tmf.getAvailableTestModels(): + raise ValueError(f"Model name \"{modelName}\" not available. Here are a list of " + f"available model names: {tmf.getAvailableTestModels()}") + testModel = tmf.TestModelFactory(modelName) + if tmf.TimeSeriesResult not in testModel.__class__.mro(): + raise ValueError("This TestModel does not implement the TimeSeriesResult interface. ") + + # we need a RoadRunner object to create a model for us + rr = RoadRunner(testModel.str()) + model = rr.getModel() + integrator = SolverType(model) + + # all tests are done with stiff set to False + # this is probably a weakness + integrator.setValue("stiff", False) + + settingsMap = testModel.timeSeriesSettings() + start = settingsMap["start"] + duration = settingsMap["duration"] + steps = settingsMap["steps"] + + # always have one more number of data points (in the row direction) than there are number of steps / intervals + num = steps + 1 + stepSize = (duration - start) / steps + + # collect true values from the TestModel type + expectedResults = testModel.timeSeriesResult() + + # a place to store actual test result data + results = np.zeros(expectedResults.shape) + + # fill in 0th time point + results[0, 0] = rr.getCurrentTime() + numStates = len(rr.getFloatingSpeciesInitialConcentrationIds()) + for j in range(1, numStates + 1): - results[i, j] = rr.getFloatingSpeciesAmountsNamedArray()[0][j - 1] - - print(expectedResults) - print(results) - self.checkMatricesEqual(expectedResults, results, places=places) - - def checkRoadRunnerSimulates(self, modelName: str, places: int = 5): - """Check that the RoadRunner.simulate produces correct output""" - - if modelName not in tmf.getAvailableTestModels(): - raise ValueError(f"Model name \"{modelName}\" not available. Here are a list of " - f"available model names: {tmf.getAvailableTestModels()}") - testModel = tmf.TestModelFactory(modelName) - - if tmf.TimeSeriesResult not in testModel.__class__.mro(): - raise ValueError("This TestModel does not implement the TimeSeriesResult interface. ") - - # we need a RoadRunner object to create a model for us - rr = RoadRunner(testModel.str()) - - # all tests are done with stiff set to False - # this is probably a weakness - rr.getIntegrator().setValue("stiff", False) - - settingsMap = testModel.timeSeriesSettings() - start = settingsMap["start"] - duration = settingsMap["duration"] - steps = settingsMap["steps"] - - # always have one more number of data points (in the row direction) than there are number of steps / intervals - num = steps + 1 - stepSize = (duration - start) / steps - - # collect true values from the TestModel type - expectedResults = testModel.timeSeriesResult() - - results = rr.simulate(start, duration, num) - self.checkMatricesEqual(expectedResults, results, places=places) - - # Integration tests - - # With CVODEIntegrator only - - def testOpenLinearFluxWithoutRoadRunnerInstance(self): - self.checkModelIntegrates("OpenLinearFlux", CVODEIntegrator, 5) - - def testSimpleFluxWithoutRoadRunnerInstance(self): - self.checkModelIntegrates("SimpleFlux", CVODEIntegrator, 5) - - def testModel269WithoutRoadRunnerInstance(self): - self.checkModelIntegrates("Model269", CVODEIntegrator, 5) - - def testModel28WithoutRoadRunnerInstance(self): - self.checkModelIntegrates("Model28", CVODEIntegrator, 5) - - def testFactorialInRateLawWithoutRoadRunnerInstance(self): - self.checkModelIntegrates("FactorialInRateLaw", CVODEIntegrator, 4) - - # with ForwardSensitivitySolver only - # Note: This is slight abuse of classification, but the test method - # doubles nicely for the FFS - - def testOpenLinearFluxWithoutRoadRunnerInstanceFFS(self): - self.checkModelIntegrates("OpenLinearFlux", ForwardSensitivitySolver, 5) - - def testSimpleFluxWithoutRoadRunnerInstanceFFS(self): - self.checkModelIntegrates("SimpleFlux", ForwardSensitivitySolver, 5) - - def testModel269WithoutRoadRunnerInstanceFFS(self): - self.checkModelIntegrates("Model269", ForwardSensitivitySolver, 5) - - def testModel28WithoutRoadRunnerInstanceFFS(self): - self.checkModelIntegrates("Model28", ForwardSensitivitySolver, 5) - - def testFactorialInRateLawWithoutRoadRunnerInstanceFFS(self): - self.checkModelIntegrates("FactorialInRateLaw", ForwardSensitivitySolver, 4) - - def testOpenLinearFluxWithRoadRunnerInstance(self): - self.checkRoadRunnerSimulates("OpenLinearFlux", 5) - - def testSimpleFluxWithRoadRunnerInstance(self): - self.checkRoadRunnerSimulates("SimpleFlux", 5) - - def testModel269WithRoadRunnerInstance(self): - self.checkRoadRunnerSimulates("Model269", 5) - - def testModel28WithRoadRunnerInstance(self): - self.checkRoadRunnerSimulates("Model28", 5) - - def testFactorialInRateLawWithRoadRunnerInstance(self): - self.checkRoadRunnerSimulates("FactorialInRateLaw", 4) - - # Unit tests - - def test_relative_tolerance(self): - self.integrator.setValue("relative_tolerance", 1e-07) - self.assertEqual(1e-07, self.integrator.getValue("relative_tolerance")) - - def test_absolute_tolerance(self): - self.integrator.setValue("absolute_tolerance", 1e-13) - self.assertEqual(1e-13, self.integrator.getValue("absolute_tolerance")) - - def test_stiff(self): - self.integrator.setValue("stiff", False) - self.assertFalse(self.integrator.getValue("stiff")) - - def test_set_maximum_bdf_order(self): - self.integrator.setValue("maximum_bdf_order", 3) - self.assertEqual(3, self.integrator.getValue("maximum_bdf_order")) - - def test_set_maximum_adams_order(self): - self.integrator.setValue("maximum_adams_order", 2) - self.assertEqual(2, self.integrator.getValue("maximum_adams_order")) - - def test_set_maximum_num_steps(self): - self.integrator.setValue("maximum_num_steps", 500) - self.assertEqual(500, self.integrator.getValue("maximum_num_steps")) - - def test_set_maximum_time_step(self): - self.integrator.setValue("maximum_time_step", 5) - self.assertEqual(5, self.integrator.getValue("maximum_time_step")) - - def test_set_minimum_time_step(self): - self.integrator.setValue("minimum_time_step", 0.1) - self.assertEqual(0.1, self.integrator.getValue("minimum_time_step")) - - def test_set_initial_time_step(self): - self.integrator.setValue("initial_time_step", 3.56) - self.assertEqual(3.56, self.integrator.getValue("initial_time_step")) - - def test_set_multiple_steps(self): - self.integrator.setValue("multiple_steps", True) - self.assertTrue(self.integrator.getValue("multiple_steps")) - - def test_set_variable_step_size(self): - self.integrator.setValue("variable_step_size", True) - self.assertTrue(self.integrator.getValue("variable_step_size")) - - def test_set_max_output_rows(self): - self.integrator.setValue("max_output_rows", 50) - self.assertEqual(50, self.integrator.getValue("max_output_rows")) - - def test_set_concentration_tolerance(self): - self.integrator.setConcentrationTolerance(1e-8) - - def test_simulate_sequence_with_times(self): - results = self.rr.simulate() - self.assertEqual(len(results), 51); - results = self.rr.simulate(0, 10, 11); - self.assertEqual(len(results), 11); - results = self.rr.simulate(times=[3, 5, 11]); - self.assertEqual(len(results), 3); - results = self.rr.simulate(0, 10, 11); - self.assertEqual(len(results), 11); - results = self.rr.simulate() - self.assertEqual(len(results), 51); - -if __name__ == "__main__": - unittest.main() + results[0, j] = rr.getFloatingSpeciesAmountsNamedArray()[0][j - 1] + + t = start + for i in range(1, num): + t = integrator.integrate(t, stepSize) + results[i, 0] = rr.getCurrentTime() + for j in range(1, numStates + 1): + results[i, j] = rr.getFloatingSpeciesAmountsNamedArray()[0][j - 1] + + print(expectedResults) + print(results) + self.checkMatricesEqual(expectedResults, results, places=places) + + def checkRoadRunnerSimulates(self, modelName: str, places: int = 5): + """Check that the RoadRunner.simulate produces correct output""" + + if modelName not in tmf.getAvailableTestModels(): + raise ValueError(f"Model name \"{modelName}\" not available. Here are a list of " + f"available model names: {tmf.getAvailableTestModels()}") + testModel = tmf.TestModelFactory(modelName) + + if tmf.TimeSeriesResult not in testModel.__class__.mro(): + raise ValueError("This TestModel does not implement the TimeSeriesResult interface. ") + + # we need a RoadRunner object to create a model for us + rr = RoadRunner(testModel.str()) + + # all tests are done with stiff set to False + # this is probably a weakness + rr.getIntegrator().setValue("stiff", False) + + settingsMap = testModel.timeSeriesSettings() + start = settingsMap["start"] + duration = settingsMap["duration"] + steps = settingsMap["steps"] + + # always have one more number of data points (in the row direction) than there are number of steps / intervals + num = steps + 1 + stepSize = (duration - start) / steps + + # collect true values from the TestModel type + expectedResults = testModel.timeSeriesResult() + + results = rr.simulate(start, duration, num) + self.checkMatricesEqual(expectedResults, results, places=places) + + # Integration tests + + # With CVODEIntegrator only + + def testOpenLinearFluxWithoutRoadRunnerInstance(self): + self.checkModelIntegrates("OpenLinearFlux", CVODEIntegrator, 5) + + def testSimpleFluxWithoutRoadRunnerInstance(self): + self.checkModelIntegrates("SimpleFlux", CVODEIntegrator, 5) + + def testModel269WithoutRoadRunnerInstance(self): + self.checkModelIntegrates("Model269", CVODEIntegrator, 5) + + def testModel28WithoutRoadRunnerInstance(self): + self.checkModelIntegrates("Model28", CVODEIntegrator, 5) + + def testFactorialInRateLawWithoutRoadRunnerInstance(self): + self.checkModelIntegrates("FactorialInRateLaw", CVODEIntegrator, 4) + + # with ForwardSensitivitySolver only + # Note: This is slight abuse of classification, but the test method + # doubles nicely for the FFS + + def testOpenLinearFluxWithoutRoadRunnerInstanceFFS(self): + self.checkModelIntegrates("OpenLinearFlux", ForwardSensitivitySolver, 5) + + def testSimpleFluxWithoutRoadRunnerInstanceFFS(self): + self.checkModelIntegrates("SimpleFlux", ForwardSensitivitySolver, 5) + + def testModel269WithoutRoadRunnerInstanceFFS(self): + self.checkModelIntegrates("Model269", ForwardSensitivitySolver, 5) + + def testModel28WithoutRoadRunnerInstanceFFS(self): + self.checkModelIntegrates("Model28", ForwardSensitivitySolver, 5) + + def testFactorialInRateLawWithoutRoadRunnerInstanceFFS(self): + self.checkModelIntegrates("FactorialInRateLaw", ForwardSensitivitySolver, 4) + + def testOpenLinearFluxWithRoadRunnerInstance(self): + self.checkRoadRunnerSimulates("OpenLinearFlux", 5) + + def testSimpleFluxWithRoadRunnerInstance(self): + self.checkRoadRunnerSimulates("SimpleFlux", 5) + + def testModel269WithRoadRunnerInstance(self): + self.checkRoadRunnerSimulates("Model269", 5) + + def testModel28WithRoadRunnerInstance(self): + self.checkRoadRunnerSimulates("Model28", 5) + + def testFactorialInRateLawWithRoadRunnerInstance(self): + self.checkRoadRunnerSimulates("FactorialInRateLaw", 4) + + # Unit tests + + def test_relative_tolerance(self): + self.integrator.setValue("relative_tolerance", 1e-07) + self.assertEqual(1e-07, self.integrator.getValue("relative_tolerance")) + + def test_absolute_tolerance(self): + self.integrator.setValue("absolute_tolerance", 1e-13) + self.assertEqual(1e-13, self.integrator.getValue("absolute_tolerance")) + + def test_stiff(self): + self.integrator.setValue("stiff", False) + self.assertFalse(self.integrator.getValue("stiff")) + + def test_set_maximum_bdf_order(self): + self.integrator.setValue("maximum_bdf_order", 3) + self.assertEqual(3, self.integrator.getValue("maximum_bdf_order")) + + def test_set_maximum_adams_order(self): + self.integrator.setValue("maximum_adams_order", 2) + self.assertEqual(2, self.integrator.getValue("maximum_adams_order")) + + def test_set_maximum_num_steps(self): + self.integrator.setValue("maximum_num_steps", 500) + self.assertEqual(500, self.integrator.getValue("maximum_num_steps")) + + def test_set_maximum_time_step(self): + self.integrator.setValue("maximum_time_step", 5) + self.assertEqual(5, self.integrator.getValue("maximum_time_step")) + + def test_set_minimum_time_step(self): + self.integrator.setValue("minimum_time_step", 0.1) + self.assertEqual(0.1, self.integrator.getValue("minimum_time_step")) + + def test_set_initial_time_step(self): + self.integrator.setValue("initial_time_step", 3.56) + self.assertEqual(3.56, self.integrator.getValue("initial_time_step")) + + def test_set_multiple_steps(self): + self.integrator.setValue("multiple_steps", True) + self.assertTrue(self.integrator.getValue("multiple_steps")) + + def test_set_variable_step_size(self): + self.integrator.setValue("variable_step_size", True) + self.assertTrue(self.integrator.getValue("variable_step_size")) + + def test_set_max_output_rows(self): + self.integrator.setValue("max_output_rows", 50) + self.assertEqual(50, self.integrator.getValue("max_output_rows")) + + def test_set_concentration_tolerance(self): + self.integrator.setConcentrationTolerance(1e-8) + + def test_simulate_sequence_with_times(self): + results = self.rr.simulate() + self.assertEqual(len(results), 51); + results = self.rr.simulate(0, 10, 11); + self.assertEqual(len(results), 11); + results = self.rr.simulate(times=[3, 5, 11]); + self.assertEqual(len(results), 3); + results = self.rr.simulate(0, 10, 11); + self.assertEqual(len(results), 11); + results = self.rr.simulate() + self.assertEqual(len(results), 51); + + if __name__ == "__main__": + unittest.main() diff --git a/test/python/test_jacobian.py b/test/python/test_jacobian.py index a2fb849103..3a62f023d3 100644 --- a/test/python/test_jacobian.py +++ b/test/python/test_jacobian.py @@ -19,135 +19,138 @@ RoadRunner, Config ) -try: - from roadrunner.tests import TestModelFactory as tmf - from roadrunner.tests.RoadRunnerTest import RoadRunnerTest -except: - import TestModelFactory as tmf - from RoadRunnerTest import RoadRunnerTest - -class JacobianTests(RoadRunnerTest): - - def setUp(self) -> None: - pass - - def tearDown(self) -> None: - pass - - def checkMatricesEqualValues(self, expected: np.ndarray, actual: np.ndarray, places=4): - if expected.shape != actual.shape: - if expected.shape == (1,) and actual.shape == (1,1): - self.assertAlmostEqual(expected[0], actual[0][0], places=places) - return - raise ValueError("expected and actual are different sizes") - arr1 = [] - arr2 = [] - for i in range(expected.shape[0]): - for j in range(expected.shape[1]): - arr1.append(expected[i][j]) - arr2.append(actual[i][j]) - arr1.sort() - arr2.sort() - for i in range(len(arr1)): - self.assertAlmostEqual(arr1[i], arr2[i], places=places) - - def _checkJacFull(self, modelName: str, rrJacMode: Config.ROADRUNNER_JACOBIAN_MODE): - """ - check the values of TestModel jacobian interface against those computed by the current model - - If full is set to false, then we turn on moiety conservation - - :param modelName: A valid test model name (See TestModelFactory::getAvailableTestModelNames() - :param tol: degree of tolerance, allowed error - :param rrJacMode: either Config::ROADRUNNER_JACOBIAN_MODE_AMOUNTS or Config::ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS - :param full: true if we are looking at full jacobian, false if were looking at reduced. - """ - self.checkValidTestModelName(modelName) - testModel = tmf.TestModelFactory(modelName) - self.checkTestModelImplements(testModel, tmf.JacobianResultFull) - rr = RoadRunner(testModel.str()) - Config.setValue(Config.ROADRUNNER_JACOBIAN_MODE, rrJacMode) - - expectedJac = None - if rrJacMode == Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS: - expectedJac = testModel.fullJacobianConc() - elif rrJacMode == Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS: - expectedJac = testModel.fullJacobianAmt() - - else: - raise ValueError("Should never reach here") - - jacSettings = testModel.jacobianSettings() - if "steady_state" in jacSettings.keys(): +import platform +if platform.system() != "Darwin": + + try: + from roadrunner.tests import TestModelFactory as tmf + from roadrunner.tests.RoadRunnerTest import RoadRunnerTest + except: + import TestModelFactory as tmf + from RoadRunnerTest import RoadRunnerTest + + class JacobianTests(RoadRunnerTest): + + def setUp(self) -> None: + pass + + def tearDown(self) -> None: + pass + + def checkMatricesEqualValues(self, expected: np.ndarray, actual: np.ndarray, places=4): + if expected.shape != actual.shape: + if expected.shape == (1,) and actual.shape == (1,1): + self.assertAlmostEqual(expected[0], actual[0][0], places=places) + return + raise ValueError("expected and actual are different sizes") + arr1 = [] + arr2 = [] + for i in range(expected.shape[0]): + for j in range(expected.shape[1]): + arr1.append(expected[i][j]) + arr2.append(actual[i][j]) + arr1.sort() + arr2.sort() + for i in range(len(arr1)): + self.assertAlmostEqual(arr1[i], arr2[i], places=places) + + def _checkJacFull(self, modelName: str, rrJacMode: Config.ROADRUNNER_JACOBIAN_MODE): + """ + check the values of TestModel jacobian interface against those computed by the current model + + If full is set to false, then we turn on moiety conservation + + :param modelName: A valid test model name (See TestModelFactory::getAvailableTestModelNames() + :param tol: degree of tolerance, allowed error + :param rrJacMode: either Config::ROADRUNNER_JACOBIAN_MODE_AMOUNTS or Config::ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS + :param full: true if we are looking at full jacobian, false if were looking at reduced. + """ + self.checkValidTestModelName(modelName) + testModel = tmf.TestModelFactory(modelName) + self.checkTestModelImplements(testModel, tmf.JacobianResultFull) + rr = RoadRunner(testModel.str()) + Config.setValue(Config.ROADRUNNER_JACOBIAN_MODE, rrJacMode) + + expectedJac = None + if rrJacMode == Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS: + expectedJac = testModel.fullJacobianConc() + elif rrJacMode == Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS: + expectedJac = testModel.fullJacobianAmt() + + else: + raise ValueError("Should never reach here") + + jacSettings = testModel.jacobianSettings() + if "steady_state" in jacSettings.keys(): + rr.conservedMoietyAnalysis = True + rr.steadyState() + actualJac = rr.getFullJacobian() + + print("\n", expectedJac) + print(actualJac) + + # expectedJac.sortColsByLabels(); + # expectedJac.sortRowsByLabels(); + # actualJac.sortColsByLabels(); + # actualJac.sortRowsByLabels(); + + + self.checkMatricesEqualValues(expectedJac, actualJac) + + def _checkJacReduced(self, modelName: str, rrJacMode: Config.ROADRUNNER_JACOBIAN_MODE): + """ + check the values of TestModel jacobian interface against those computed by the current model + + If full is set to false, then we turn on moiety conservation + + :param modelName: A valid test model name (See TestModelFactory::getAvailableTestModelNames() + :param tol: degree of tolerance, allowed error + :param rrJacMode: either Config::ROADRUNNER_JACOBIAN_MODE_AMOUNTS or Config::ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS + :param full: true if we are looking at full jacobian, false if were looking at reduced. + """ + self.checkValidTestModelName(modelName) + testModel = tmf.TestModelFactory(modelName) + self.checkTestModelImplements(testModel, tmf.JacobianResultReduced) + rr = RoadRunner(testModel.str()) + Config.setValue(Config.ROADRUNNER_JACOBIAN_MODE, rrJacMode) + + expectedJac = None + if rrJacMode == Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS: + expectedJac = testModel.reducedJacobianConc() + elif rrJacMode == Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS: + expectedJac = testModel.reducedJacobianAmt() + else: + raise ValueError("Should never reach here") + rr.conservedMoietyAnalysis = True - rr.steadyState() - actualJac = rr.getFullJacobian() - - print("\n", expectedJac) - print(actualJac) - - # expectedJac.sortColsByLabels(); - # expectedJac.sortRowsByLabels(); - # actualJac.sortColsByLabels(); - # actualJac.sortRowsByLabels(); - - - self.checkMatricesEqualValues(expectedJac, actualJac) - - def _checkJacReduced(self, modelName: str, rrJacMode: Config.ROADRUNNER_JACOBIAN_MODE): - """ - check the values of TestModel jacobian interface against those computed by the current model - - If full is set to false, then we turn on moiety conservation - - :param modelName: A valid test model name (See TestModelFactory::getAvailableTestModelNames() - :param tol: degree of tolerance, allowed error - :param rrJacMode: either Config::ROADRUNNER_JACOBIAN_MODE_AMOUNTS or Config::ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS - :param full: true if we are looking at full jacobian, false if were looking at reduced. - """ - self.checkValidTestModelName(modelName) - testModel = tmf.TestModelFactory(modelName) - self.checkTestModelImplements(testModel, tmf.JacobianResultReduced) - rr = RoadRunner(testModel.str()) - Config.setValue(Config.ROADRUNNER_JACOBIAN_MODE, rrJacMode) - - expectedJac = None - if rrJacMode == Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS: - expectedJac = testModel.reducedJacobianConc() - elif rrJacMode == Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS: - expectedJac = testModel.reducedJacobianAmt() - else: - raise ValueError("Should never reach here") - - rr.conservedMoietyAnalysis = True - jacSettings = testModel.jacobianSettings() - print("jacSettings", jacSettings) - if "steady_state" in jacSettings.keys(): - rr.conservedMoietyAnalysis = True - rr.steadyState() - - actualJac = rr.getReducedJacobian() - - self.checkMatricesEqualValues(expectedJac, actualJac) - - def test_BimolecularEnd_FullAmt(self): - self._checkJacFull("BimolecularEnd", Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS) - - def test_BimolecularEnd_FullConc(self): - self._checkJacFull("BimolecularEnd", Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS) - - def test_SimpleFlux_FullAmt(self): - self._checkJacFull("SimpleFlux", Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS) - - def test_SimpleFlux_FullConc(self): - self._checkJacFull("SimpleFlux", Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS) - - def test_SimpleFlux_ReducedAmt(self): - self._checkJacReduced("SimpleFlux", Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS) - - def test_SimpleFlux_ReducedConc(self): - self._checkJacReduced("SimpleFlux", Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS) - - -if __name__ == "__main__": - unittest.main() + jacSettings = testModel.jacobianSettings() + print("jacSettings", jacSettings) + if "steady_state" in jacSettings.keys(): + rr.conservedMoietyAnalysis = True + rr.steadyState() + + actualJac = rr.getReducedJacobian() + + self.checkMatricesEqualValues(expectedJac, actualJac) + + def test_BimolecularEnd_FullAmt(self): + self._checkJacFull("BimolecularEnd", Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS) + + def test_BimolecularEnd_FullConc(self): + self._checkJacFull("BimolecularEnd", Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS) + + def test_SimpleFlux_FullAmt(self): + self._checkJacFull("SimpleFlux", Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS) + + def test_SimpleFlux_FullConc(self): + self._checkJacFull("SimpleFlux", Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS) + + def test_SimpleFlux_ReducedAmt(self): + self._checkJacReduced("SimpleFlux", Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS) + + def test_SimpleFlux_ReducedConc(self): + self._checkJacReduced("SimpleFlux", Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS) + + + if __name__ == "__main__": + unittest.main() diff --git a/test/python/test_pickle.py b/test/python/test_pickle.py index 9f4a65b58f..7486b44956 100644 --- a/test/python/test_pickle.py +++ b/test/python/test_pickle.py @@ -7,154 +7,157 @@ import os import copy -try: - import ray - - print(f"Python interpreter at: {sys.executable}") - - # sys.path += [ - # # r'/mnt/d/roadrunner/roadrunner/cmake-build-release-wsl/lib/site-packages' - # # r"D:\roadrunner\roadrunner\install-msvc2019-rel\site-packages", - # # r"D:\roadrunner\roadrunner\cmake-build-release-visual-studio\lib\site-packages" - # - # ] - import roadrunner - # from roadrunner import * - - import roadrunner.tests.TestModelFactory as tmf - from roadrunner.roadrunner import RoadRunner - - - def simulate_return_None(r): - r.resetAll() - print(r.simulate(0, 10, 11)) - - - def simulate_return_dataframe(r): - r.resetAll() - data = r.simulate(0, 10, 11) - df = pd.DataFrame(data, columns=data.colnames) - return df - - - def simulate_return_NamedArray(r): - r.resetAll() - return r.simulate(0, 10, 11) - - - @ray.remote - class SimulatorActorPath(object): - """Ray actor to execute simulations.""" - - def __init__(self, r: roadrunner.RoadRunner): - self.r: roadrunner.RoadRunner = r - - def simulate(self, size=1): - num_points = 101 - results = np.ndarray((size, num_points, 2)) # 2 for 1 model species and time - for k in range(size): - self.r.resetAll() - results[k] = self.r.simulate(0, 100, num_points) - return results - - - class RoadRunnerPickleTests(unittest.TestCase): - def setUp(self): - rr = RoadRunner(tmf.SimpleFlux().str()) - rr.setIntegrator("gillespie") - gillespie = rr.getIntegrator() - gillespie.seed = 123 - self.rr = rr - - def tearDown(self): - pass - - # @unittest.skip("Takes too long to run when running all CTest. Not sure why...") - def test_to_pickle_and_back(self): - pfile = os.path.join(os.path.dirname(__file__), "pkl.serialization") - with open(pfile, 'wb') as f: - pickle.dump(self.rr, f) - - self.assertTrue(os.path.isfile(pfile)) - - with open(pfile, "rb") as f: - rr = pickle.load(f) - try: - data = rr.simulate(0, 10, 11) - except Exception: - self.fail("Cannot simulate a serialization loaded model") - - self.assertEqual(data.shape, (11, 3)) - - if os.path.isfile(pfile): - os.remove(pfile) - - # @unittest.skip("Takes too long to run when running all CTest. Not sure why...") - def test_we_can_copy_rr(self): - rr2 = copy.copy(self.rr) - self.assertNotEqual(hex(id(self.rr)), hex(id(rr2))) - - @unittest.skip("""Running a multiprocessing pool in - CTest causes the whole test suite to hang. Therefore - these are skipped. You should manually comment out the unittest.skip - decorator to test pickle stuff""") - def test_pool_returns_None(self): - p = Pool(processes=4) - p.map(simulate_return_None, [self.rr for i in range(10)]) - p.close() - - @unittest.skip("""Running a multiprocessing pool in - CTest causes the whole test suite to hang. Therefore - these are skipped. You should manually comment out the unittest.skip - decorator to test pickle stuff""") - def test_pool_returns_DataFrame(self): - N = 10 - p = Pool(processes=4) - dfs = p.map(simulate_return_dataframe, [self.rr for i in range(N)]) - p.close() - self.assertEqual(len(dfs), 10) - dct = {i: df for i, df in enumerate(dfs)} - df = pd.concat(dct, axis=0) - print(df) - self.assertEqual(df.shape, (N * 11, 3)) - - @unittest.skip("""Running a multiprocessing pool in - CTest causes the whole test suite to hang. Therefore - these are skipped. You should manually comment out the unittest.skip - decorator to test pickle stuff""") - def test_pool_returns_NamedArray(self): - N = 10 - p = Pool(processes=4) - arrs = p.map(simulate_return_NamedArray, [self.rr for i in range(N)]) - p.close() - print(arrs) - data = np.vstack(arrs) - self.assertEqual((110, 3), data.shape) - - @unittest.skip("Works when you run on its own but " - "No module named 'roadrunner' error when " - "in test suite with other tests, on windows only. ") - def test_using_ray_library(self): - import roadrunner - ray.init(ignore_reinit_error=True) - - actor_count = 10 # cores to run this on - - rr = roadrunner.RoadRunner(tmf.SimpleFlux().str()) - simulators = [SimulatorActorPath.remote(rr) for _ in range(actor_count)] - - # run simulations - sim_per_actor = 10 - tc_ids = [] - for k, simulator in enumerate(simulators): - tcs_id = simulator.simulate.remote(size=sim_per_actor) - tc_ids.append(tcs_id) - results = ray.get(tc_ids) - data = np.vstack(results) - self.assertEqual((100, 101, 3), data.shape) - - if __name__ == "__main__": - unittest.main() +import platform +if platform.system() != "Darwin": -except: - pass + try: + import ray + + print(f"Python interpreter at: {sys.executable}") + + # sys.path += [ + # # r'/mnt/d/roadrunner/roadrunner/cmake-build-release-wsl/lib/site-packages' + # # r"D:\roadrunner\roadrunner\install-msvc2019-rel\site-packages", + # # r"D:\roadrunner\roadrunner\cmake-build-release-visual-studio\lib\site-packages" + # + # ] + import roadrunner + # from roadrunner import * + + import roadrunner.tests.TestModelFactory as tmf + from roadrunner.roadrunner import RoadRunner + + + def simulate_return_None(r): + r.resetAll() + print(r.simulate(0, 10, 11)) + + + def simulate_return_dataframe(r): + r.resetAll() + data = r.simulate(0, 10, 11) + df = pd.DataFrame(data, columns=data.colnames) + return df + + + def simulate_return_NamedArray(r): + r.resetAll() + return r.simulate(0, 10, 11) + + + @ray.remote + class SimulatorActorPath(object): + """Ray actor to execute simulations.""" + + def __init__(self, r: roadrunner.RoadRunner): + self.r: roadrunner.RoadRunner = r + + def simulate(self, size=1): + num_points = 101 + results = np.ndarray((size, num_points, 2)) # 2 for 1 model species and time + for k in range(size): + self.r.resetAll() + results[k] = self.r.simulate(0, 100, num_points) + return results + + + class RoadRunnerPickleTests(unittest.TestCase): + def setUp(self): + rr = RoadRunner(tmf.SimpleFlux().str()) + rr.setIntegrator("gillespie") + gillespie = rr.getIntegrator() + gillespie.seed = 123 + self.rr = rr + + def tearDown(self): + pass + + # @unittest.skip("Takes too long to run when running all CTest. Not sure why...") + def test_to_pickle_and_back(self): + pfile = os.path.join(os.path.dirname(__file__), "pkl.serialization") + with open(pfile, 'wb') as f: + pickle.dump(self.rr, f) + + self.assertTrue(os.path.isfile(pfile)) + + with open(pfile, "rb") as f: + rr = pickle.load(f) + try: + data = rr.simulate(0, 10, 11) + except Exception: + self.fail("Cannot simulate a serialization loaded model") + + self.assertEqual(data.shape, (11, 3)) + + if os.path.isfile(pfile): + os.remove(pfile) + + # @unittest.skip("Takes too long to run when running all CTest. Not sure why...") + def test_we_can_copy_rr(self): + rr2 = copy.copy(self.rr) + self.assertNotEqual(hex(id(self.rr)), hex(id(rr2))) + + @unittest.skip("""Running a multiprocessing pool in + CTest causes the whole test suite to hang. Therefore + these are skipped. You should manually comment out the unittest.skip + decorator to test pickle stuff""") + def test_pool_returns_None(self): + p = Pool(processes=4) + p.map(simulate_return_None, [self.rr for i in range(10)]) + p.close() + + @unittest.skip("""Running a multiprocessing pool in + CTest causes the whole test suite to hang. Therefore + these are skipped. You should manually comment out the unittest.skip + decorator to test pickle stuff""") + def test_pool_returns_DataFrame(self): + N = 10 + p = Pool(processes=4) + dfs = p.map(simulate_return_dataframe, [self.rr for i in range(N)]) + p.close() + self.assertEqual(len(dfs), 10) + dct = {i: df for i, df in enumerate(dfs)} + df = pd.concat(dct, axis=0) + print(df) + self.assertEqual(df.shape, (N * 11, 3)) + + @unittest.skip("""Running a multiprocessing pool in + CTest causes the whole test suite to hang. Therefore + these are skipped. You should manually comment out the unittest.skip + decorator to test pickle stuff""") + def test_pool_returns_NamedArray(self): + N = 10 + p = Pool(processes=4) + arrs = p.map(simulate_return_NamedArray, [self.rr for i in range(N)]) + p.close() + print(arrs) + data = np.vstack(arrs) + self.assertEqual((110, 3), data.shape) + + @unittest.skip("Works when you run on its own but " + "No module named 'roadrunner' error when " + "in test suite with other tests, on windows only. ") + def test_using_ray_library(self): + import roadrunner + ray.init(ignore_reinit_error=True) + + actor_count = 10 # cores to run this on + + rr = roadrunner.RoadRunner(tmf.SimpleFlux().str()) + simulators = [SimulatorActorPath.remote(rr) for _ in range(actor_count)] + + # run simulations + sim_per_actor = 10 + tc_ids = [] + for k, simulator in enumerate(simulators): + tcs_id = simulator.simulate.remote(size=sim_per_actor) + tc_ids.append(tcs_id) + results = ray.get(tc_ids) + data = np.vstack(results) + self.assertEqual((100, 101, 3), data.shape) + + if __name__ == "__main__": + unittest.main() + + except: + pass diff --git a/test/python/test_python_api.py b/test/python/test_python_api.py index 36e787f20a..8fd99b58f8 100644 --- a/test/python/test_python_api.py +++ b/test/python/test_python_api.py @@ -42,1170 +42,1174 @@ # tricks some Python unit testing frameworks (such as nose) # into thinking the function TestModelFactory is a test, which will fail. # So we import TestModelFactory as an alias. -import roadrunner.tests.TestModelFactory as tmf -Config.setValue(Config.LLJIT_OPTIMIZATION_LEVEL, Config.NONE) - -class RoadRunnerTests(unittest.TestCase): - maxDiff = None - - def setUp(self) -> None: - # print(getAvailableTestModels()) - self.testModel = tmf.TestModelFactory("SimpleFlux") - self.rr = RoadRunner(self.testModel.str()) - - def tearDown(self) -> None: - pass - - def checkMatricesAlmostEqual(self, expected, actual, places=7): - if len(expected) != len(actual): - raise ValueError("len(expected) != len(actual)") - - if len(expected[0]) != len(actual[0]): - raise ValueError("len(expected[0]) != len(actual[0])") - - for i in range(len(expected)): - for j in range(len(expected[0])): - self.assertAlmostEqual(expected[i][j], actual[i][j], places=places) - - def test_species_attribute(self): - self.assertEqual(self.rr.S1, 10) - - def test_species_attribute_amount(self): - self.assertEqual(self.rr.S1_amt, 10) - - def test_species_attribute_conc(self): - self.assertEqual(self.rr.S1_conc, 10) - - def test_reaction_flux(self): - self.assertEqual(self.rr._J0, 1) - - def test_attribute_access_protocols_setattr(self): - self.rr.__setattr__("cheese", 6) - self.assertTrue(hasattr(self.rr, "cheese")) - self.assertEqual(getattr(self.rr, "cheese"), 6) - - def test_attribute_access_protocols_getattr(self): - self.assertEqual(self.rr.__getattr__("S1"), 10) - - def test___dict__(self): - self.assertEqual( - ["this"], - list(self.rr.__dict__.keys()) - ) - - @unittest.skip("__eq__ may be implemented, may not. If not we should do") - def test___eq__(self): - pass - - def test___getitem__(self): - self.assertEqual(self.rr.__getitem__("S1"), 10.0) - - def test___len__(self): - self.assertEqual(len(self.rr), 62) # Enumerates all possible rr[x] arguments. - - def test___repr__(self): - l = repr([self.rr]) - self.assertIn("roadrunner.RoadRunner()", l) - - def test___setitem__fails_when_key_not_exist(self): - with self.assertRaises(RuntimeError): - self.rr.__setitem__("five", 5) - - def test___setitem__when_key_exists(self): - self.rr.__setitem__("S1", 12) - self.assertEqual(self.rr.__getitem__("S1"), 12) - - # def test___sizeof__(self): - # self.assertEqual(32, self.rr.__sizeof__()) - - def test___str__(self): - s = str(self.rr) - print(s) - self.assertIn("roadrunner", s) - - @unittest.skip("Method not implemented yet (but should be)") - def test_getCompartmentIds(self): - """This method is missing from the rr api""" - pass - - def test_addCompartment(self): - """The rr._addCompartment() method is called by the - rr.addCompartment() method. The difference, is the - latter adds the compartment to the __dict__ as an - attribute. - """ - self.rr.addCompartment("C1", 1, True) - self.assertEqual(self.rr.C1, 1) - - def testAddParameter(self): - self.rr.addParameter("k_new", 25, True) - self.assertEqual(25, self.rr.k_new) - - def testAddReaction(self): - self.rr.addReaction("NewReaction", ["S1"], ["S2"], "kf*S1", True) - self.rr.S1 = 10 - self.assertEqual(self.rr.NewReaction, 1.0) - - def testAddSpeciesConcentrations(self): - self.rr.addSpeciesConcentration("NewSpecies", "default_compartment", 123.3, False, False, "", True) - self.assertEqual(self.rr.NewSpecies, 123.3) - - def testAddSpecies(self): - self.rr.addSpeciesAmount("NewSpecies", "default_compartment", 123.3, False, False, "", True) - self.assertEqual(self.rr.NewSpecies, 123.3) - - @unittest.skip - def test_removeInitialAssignment(self): - self.assertEqual( - self.rr.removeInitialAssignment(), - ) - - @unittest.skip - def test_removeParameter(self): - self.assertEqual( - self.rr.removeParameter(), ) - - @unittest.skip - def test_removeReaction(self): - self.assertEqual( - self.rr.removeReaction(), - ) - - @unittest.skip - def test_removeRules(self): - self.assertEqual( - self.rr.removeRules(), - - ) - - @unittest.skip - def test_removeSpecies(self): - self.assertEqual( - self.rr.removeSpecies(), - ) - - def test_diffstep_getter(self): - self.assertEqual(self.rr._diffstep_getter(), 0.02) - - def test_diffstep_stter(self): - self.rr._diffstep_stter(0.01) - self.assertEqual(self.rr._diffstep_getter(), 0.01) - - def test_getConservedMoietyAnalysis(self): - self.assertFalse(self.rr._getConservedMoietyAnalysis()) - - def test_setConservedMoietyAnalysis(self): - self.rr.conservedMoietyAnalysis = True - self.assertTrue(self.rr._getConservedMoietyAnalysis()) - - def test_addAssignmentRule(self): - self.rr.addSpeciesConcentration("SNew", "default_compartment", 2.5, False, True, "", True) - self.rr.addAssignmentRule("SNew", "S1+5", True) - self.assertEqual(self.rr.SNew, 15) - - @unittest.skip("Not sure how to test this right now") - def test_addDelay(self): - pass - - @unittest.skip("Not sure how to test this right now") - def test_addEvent(self): - pass - - @unittest.skip("Not sure how to test this right now") - def test_addEventAssignment(self): - pass - - @unittest.skip("Not sure how to test this right now") - def test_addInitialAssignment(self): - self.rr.addSpeciesConcentration("NewSpec", "default_compartment", 13.3, False, True, "", False) - self.rr.addInitialAssignment("NewSpec", "S1+S2", True) - - @unittest.skip("Not sure how to test this right now") - def test_addPriority(self): - pass - - @unittest.skip("Not sure how to test this right now") - def test_addRateRule(self): - pass - - @unittest.skip("Not sure how to test this right now") - def test_addTrigger(self): - pass - - def test_clearModel(self): - self.assertTrue(self.rr.clearModel()) - - @unittest.skip("Not sure how to test this right now. Docs are not clear") - def test_createSelection(self): - pass - - def test_default_compartment(self): - self.assertEqual(self.rr.default_compartment, 1) - - def test_diffstep(self): - self.assertEqual(self.rr.diffstep, 0.02) - - @unittest.skip("This API is unclear. ") - def test_ensureSolversRegistered(self): - self.rr.ensureSolversRegistered() - - def test_getAvailableIntegrators(self): - self.assertEqual(self.rr.getAvailableIntegrators(), ("cvode",)) - - def test_getBoundarySpeciesAmountsNamedArray(self): - self.rr.setBoundary("S1", True) - bs = self.rr.getBoundarySpeciesAmountsNamedArray() - self.assertEqual(bs["S1"], 10) - - def test_getBoundarySpeciesConcentrationsNamedArray(self): - self.rr.setBoundary("S1", True) - self.rr.default_compartment = 0.5 - bs = self.rr.getBoundarySpeciesConcentrationsNamedArray() - self.assertEqual(bs["S1"], 20) - - def test_getCC(self): - self.assertAlmostEqual(self.rr.getCC("_J0", "kf"), 0.009090905110435235) - - def test_getCompiler(self): - compiler_string = str(self.rr.getCompiler()) - self.assertIn("Compiler", compiler_string) - - def test_getConservationMatrix(self): - rr2 = RoadRunner(tmf.TestModelFactory("Brown2004").str()) - rr2.conservedMoietyAnalysis = True - print(rr2.getConservationMatrix().shape) - self.assertEqual(rr2.getConservationMatrix().shape, (15, 28)) - - def test_getConservedMoietyIds(self): - """This mode has no conserved moieties so poor model for testing this feature""" - rr2 = RoadRunner(tmf.TestModelFactory("Brown2004").str()) - rr2.conservedMoietyAnalysis = True - expected = tuple([f"_CSUM{i}" for i in range(15)]) - self.assertEqual(rr2.getConservedMoietyIds(), expected) - - def test_getConservedMoietyValues(self): - """This mode has no conserved moieties so poor model for testing this feature""" - rr2 = RoadRunner(tmf.TestModelFactory("Brown2004").str()) - rr2.conservedMoietyAnalysis = True - print(rr2.getConservedMoietyValues()) - expected = [1.2000e+05, 6.0000e+05, 1.2000e+05, 1.2000e+05, 6.0000e+05, 1.2000e+05, 1.0000e+04, 1.2000e+05, - 1.2000e+05, 4.4600e+05, 1.2000e+05, 1.0002e+07, 1.2000e+05, 1.2000e+05, 8.0000e+04] - actual = rr2.getConservedMoietyValues() - for i in range(len(expected)): - self.assertAlmostEqual(expected[i], actual[i]) - - def test_getCurrentSBML(self): - self.assertIsInstance(self.rr.getCurrentSBML(), str) - - def test_getDependentFloatingSpeciesIds(self): - """No dependents in this model""" - self.assertTrue(callable(self.rr.getDependentFloatingSpeciesIds)) - - def test_getDependentRatesOfChange(self): - """No dependents in this model so we'll just check callable""" - self.assertTrue(callable(self.rr.getDependentRatesOfChange)) - - def test_getDependentRatesOfChangeNamedArray(self): - """No dependents in this model""" - self.assertTrue(callable(self.rr.getDependentRatesOfChangeNamedArray)) - - def test_getDiffStepSize(self): - self.assertEqual(0.02, self.rr.getDiffStepSize()) - - def test_getEE(self): - self.assertAlmostEqual(self.rr.getEE("_J0", "kf"), 1.0000000000000024) - - def test_getEigenValueIds(self): - expected = ('eigen(S1)', 'eigenReal(S1)', 'eigenImag(S1)', 'eigen(S2)', 'eigenReal(S2)', 'eigenImag(S2)') - self.assertEqual(self.rr.getEigenValueIds(), expected) - - def test_getExistingIntegratorNames(self): - expected = ('cvode',) - self.assertEqual(expected, self.rr.getExistingIntegratorNames()) - - def test_getExtendedStoichiometryMatrix(self): - rr2 = RoadRunner(tmf.TestModelFactory("OpenLinearFlux").str()) - mat = rr2.getExtendedStoichiometryMatrix() - print(mat) - expected = [ - [1, -1, 0], - [0, 1, -1], - [-1, 0, 0], - [0, 0, 1], - ] - # todo implement proper equality operators - print(mat.shape) - for i in range(mat.shape[0]): - for j in range(mat.shape[1]): - self.assertEqual(expected[i][j], mat[i][j]) - - def test_getFloatingSpeciesAmountsNamedArray(self): - x = self.rr.getFloatingSpeciesAmountsNamedArray() - self.assertEqual(x["S2"], 1) - - def test_getFloatingSpeciesConcentrationsNamedArray(self): - self.rr.default_compartment = 0.33 - x = self.rr.getFloatingSpeciesConcentrationsNamedArray() - self.assertAlmostEqual(3.0303030303030303, x["S2"][0]) - - def test_getFloatingSpeciesInitialConcentrationIds(self): - x = self.rr.getFloatingSpeciesInitialConcentrationIds() - self.assertEqual(x, ("init([S1])", "init([S2])",)) - - @unittest.skip("figure out how to use") - def test_getFrequencyResponse(self): - pass - - def test_getFullEigenValues(self): - print(dir(self.testModel)) - expected = self.testModel.fullEigenValues() - actual = self.rr.getFullEigenValues() - print(expected) - print(actual) - self.assertAlmostEqual(expected[0], actual[0]) - self.assertAlmostEqual(expected[1], actual[1]) - - def test_getFullJacobian(self): - print(dir(self.testModel)) - expected = self.testModel.fullJacobianAmt() - actual = self.rr.getFullJacobian() - for i in range(expected.shape[0]): - for j in range(expected.shape[1]): - self.assertAlmostEqual(expected[i][j], actual[i][j]) - - def test_getFullJacobianConc(self): - Config.setValue(Config.ROADRUNNER_JACOBIAN_MODE, Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS) - expected = self.testModel.fullJacobianConc() - actual = self.rr.getFullJacobian() - for i in range(expected.shape[0]): - for j in range(expected.shape[1]): - self.assertAlmostEqual(expected[i][j], actual[i][j]) - - def test_getFullJacobianAmt(self): - expected = self.testModel.fullJacobianAmt() - Config.setValue(Config.ROADRUNNER_JACOBIAN_MODE, Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS) - actual = self.rr.getFullJacobian() - for i in range(expected.shape[0]): - for j in range(expected.shape[1]): - self.assertAlmostEqual(expected[i][j], actual[i][j]) - - def test_getFullStoichiometryMatrix(self): - expected = self.testModel.fullStoicMatrix() - self.checkMatricesAlmostEqual(expected, self.rr.getFullStoichiometryMatrix()) - - def test_getGlobalParameterByName(self): - self.assertEqual(self.rr.getGlobalParameterByName("kf"), 0.1) - - @unittest.skip("No way to use this method from Python - it " - "requires an out parameter as input") - def test_getIds(self): - pass - - def test_getIndependentFloatingSpeciesIds(self): - self.assertEqual(self.rr.getIndependentFloatingSpeciesIds(), ["S1"]) - - def test_getIndependentRatesOfChange(self): - self.assertEqual(-0.99, self.rr.getIndependentRatesOfChange()) - - def test_getIndependentRatesOfChangeNamedArray(self): - self.assertEqual( - self.rr.getIndependentRatesOfChangeNamedArray(), - [[-0.99]] - ) - - def test_getInfo(self): - self.assertIn( - "jacobianStepSize", - self.rr.getInfo(), - ) - - def test_getIntegrator(self): - self.assertEqual( - self.rr.getIntegrator().getName(), - "cvode" - ) - - def test_getIntegratorByName(self): - self.assertIsInstance( - self.rr.getIntegratorByName("cvode"), - Integrator - ) - - def test_getKMatrix(self): - expected = [[1], [1]] - self.checkMatricesAlmostEqual( - expected, - self.rr.getKMatrix(), - ) - - def test_getKineticLaw(self): - self.assertEqual( - self.rr.getKineticLaw("_J0"), - "kf * S1" - ) - - def test_getL0Matrix(self): - print(dir(self.testModel)) - expected = self.testModel.L0Matrix() - actual = self.rr.getL0Matrix() - self.assertEqual(expected, actual) - - def test_getLinkMatrix(self): - # roadrunner automatically trasposes column vectors - # into row vectors - expected = self.testModel.linkMatrix() - actual = self.rr.getLinkMatrix().T[0] - print(expected) - print(actual) - self.assertTrue((expected == actual).all()) - - def test_getModel(self): - self.assertIsInstance( - self.rr.getModel(), - ExecutableModel - ) - - def test_getNrMatrix(self): - expected = self.testModel.NrMatrix() - self.checkMatricesAlmostEqual( - expected, - self.rr.getNrMatrix(), - ) - - @unittest.skip("No idea what the argument for this method should be?") - def test_getParamPromotedSBML(self): - self.assertEqual( - self.rr.getParamPromotedSBML(), - ) - - def test_getRatesOfChange(self): - print(self.rr.getRatesOfChange()) - self.assertSequenceEqual( - list(self.rr.getRatesOfChange()), - [-0.99, 0.99] - ) - - def test_getRatesOfChangeNamedArray(self): - print(self.rr.getRatesOfChangeNamedArray()) - self.assertSequenceEqual( - list(self.rr.getRatesOfChangeNamedArray()[0]), - [-0.99, 0.99] - ) - - def test_getReactionRates(self): - self.assertEqual(1.0, self.rr.getReactionRates()[0]) - self.assertEqual(0.01, self.rr.getReactionRates()[1]) - - def test_getReducedEigenValues(self): - expected = self.testModel.reducedEigenValues() - self.rr.conservedMoietyAnalysis = True - actual = self.rr.getReducedEigenValues() - print("expected: ", expected) - print("actual: ", actual) - self.assertEqual(expected.shape, actual.shape) - self.assertAlmostEqual(expected[0], actual[0]) - - def test_getReducedJacobian(self): - self.rr.conservedMoietyAnalysis = True - expected = self.testModel.reducedJacobianConc() - actual = self.rr.getReducedJacobian() - print(expected) - print(actual) - - self.assertAlmostEqual( - -0.11, - self.rr.getReducedJacobian()["S1"][0], - ) - - def test_getReducedStoichiometryMatrix(self): - self.rr.conservedMoietyAnalysis = True - expected = self.testModel.reducedStoicMatrix() - self.checkMatricesAlmostEqual( - expected, - self.rr.getReducedStoichiometryMatrix(), - ) - - def test_getRegisteredIntegratorNames(self): - self.assertEqual( - ('cvode', 'gillespie', 'rk4', 'rk45', 'euler'), - self.rr.getRegisteredIntegratorNames(), - ) - - def test_getRegisteredSteadyStateSolverNames(self): - self.assertEqual( - ('nleq1', 'nleq2', 'newton', "newton_linesearch"), - self.rr.getRegisteredSteadyStateSolverNames(), - ) - - def test_getRegisteredSensitivitySolverNames(self): - print(dir(self.rr)) - self.assertEqual( - ("forward",), - self.rr.getRegisteredSensitivitySolverNames(), - ) - - def test_getSBML(self): - self.assertIsInstance( - self.rr.getSBML(), - str - ) - - def test_getScaledConcentrationControlCoefficientMatrix(self): - expected = self.testModel.scaledConcentrationControlCoefficientMatrix() - actual = self.rr.getScaledConcentrationControlCoefficientMatrix() - self.checkMatricesAlmostEqual( - expected, actual, 5 - ) - - def test_getScaledElasticityMatrix(self): - actual = self.rr.getScaledElasticityMatrix() - expected = self.testModel.scaledElasticityMatrix() - print(actual) - self.checkMatricesAlmostEqual( - expected, actual - ) - - def test_getScaledFloatingSpeciesElasticity(self): - self.assertAlmostEqual( - 1.0, - self.rr.getScaledFloatingSpeciesElasticity("_J1", "S2"), - ) - - def test_getScaledFluxControlCoefficientMatrix(self): - expected = self.testModel.scaledFluxControlCoefficientMatrix() - actual = self.rr.getScaledFluxControlCoefficientMatrix() - self.checkMatricesAlmostEqual( - expected, actual, 5 - ) - - def test_getSelectedValues(self): - self.assertEqual(self.rr.getSelectedValues()[0], 0) - self.assertEqual(self.rr.getSelectedValues()[1], 10) - - def test_getSimulationData(self): - self.assertTrue( - self.rr.getSimulationData().size == 0 - ) - self.rr.simulate(0, 10, 11) - actual = self.rr.getSimulationData() - expected = self.testModel.timeSeriesResult() - self.checkMatricesAlmostEqual(actual, expected, places=4) - - def test_getSteadyStateSelectionStrings(self): - self.assertEqual( - self.rr.getSteadyStateSelectionStrings(), - ("[S1]", "[S2]") - ) - - def test_getSteadyStateSolver(self): - solver = self.rr.getSteadyStateSolver() - self.assertEqual("nleq2", solver.getName()) - - def test_getSteadyStateThreshold(self): - self.assertEqual( - self.rr.getSteadyStateThreshold(), - 0.01 - ) - - def test_getSteadyStateValues(self): - expected = self.testModel.steadyState() - actual = self.rr.getSteadyStateValues() - print(expected) - print(actual) - self.assertEqual(expected["S1"], actual[0]) - self.assertEqual(expected["S2"], actual[1]) - - def test_getSteadyStateValuesNamedArray(self): - expected = self.testModel.steadyState() - actual = self.rr.getSteadyStateValuesNamedArray() - print(expected) - self.assertAlmostEqual(expected["S1"], actual[0, 0]) - self.assertAlmostEqual(expected["S2"], actual[0, 1]) - - def test_getSensitivitySolver(self): - self.assertEqual( - "forward", - self.rr.getSensitivitySolver().getName() - ) - - @unittest.skip("This method should be not be visible in Python") - def test_getSupportedIdTypes(self): - """returns a bit field of the ids that this class supports.""" - - def test_getUnscaledConcentrationControlCoefficientMatrix(self): - expected = self.testModel.unscaledConcentrationControlCoefficientMatrix() - actual = self.rr.getUnscaledConcentrationControlCoefficientMatrix() - self.checkMatricesAlmostEqual( - expected, actual, 5 - ) - - def test_getUnscaledElasticityMatrix(self): - expected = self.testModel.unscaledElasticityMatrix() - actual = self.rr.getUnscaledElasticityMatrix() - self.checkMatricesAlmostEqual( - expected, actual, 5 - ) - - def test_getUnscaledFluxControlCoefficientMatrix(self): - expected = self.testModel.unscaledFluxControlCoefficientMatrix() - actual = self.rr.getUnscaledFluxControlCoefficientMatrix() - self.checkMatricesAlmostEqual( - expected, actual, 5 - ) - - def test_getUnscaledParameterElasticity(self): - self.assertAlmostEqual( - 10, - self.rr.getUnscaledParameterElasticity("_J0", "kf"), - ) - - def test_getUnscaledSpeciesElasticity(self): - self.assertEqual( - 0.10000000000000007, - self.rr.getUnscaledSpeciesElasticity(0, 0), - ) - - def test_getValue(self): - self.assertEqual( - self.rr.getValue("kb"), - 0.01 - ) - - def test_getuCC(self): - self.assertAlmostEqual( - 0.09090905110435235, - self.rr.getuCC("_J0", "kf"), - ) - - def test_getuEE(self): - self.assertAlmostEqual( - self.rr.getuEE("_J0", "kf"), - 10 - ) - - def test_integrator(self): - self.assertIsInstance( - self.rr.integrator, - Integrator - ) - - def test_integratorExists(self): - self.assertTrue( - self.rr.integratorExists("cvode"), - ) - - def test_internalOneStep(self): - before = self.rr.S2 - self.rr.internalOneStep(0, 10) - after = self.rr.S2 - self.assertNotEqual(before, after) - - def test_isModelLoaded(self): - self.assertTrue( - self.rr.isModelLoaded(), - ) - - def test_items(self): - expected = [('S1', 10.0), - ('S2', 1.0), - ('[S1]', 10.0), - ('[S2]', 1.0), - ('default_compartment', 1.0), - ('kf', 0.1), - ('kb', 0.01), - ('_J0', 1.0), - ('_J1', 0.01), - ('init([S1])', 10.0), - ('init([S2])', 1.0), - ('init(S1)', 10.0), - ('init(S2)', 1.0), - ('init(default_compartment)', 1.0), - ('init(kf)', 0.1), - ('init(kb)', 0.01), - ("S1'", -0.99), - ("S2'", 0.99), - ("[S1]'", -0.99), - ("[S2]'", 0.99), - ('stoich(S1, _J0)', -1.0), - ('stoich(S1, _J1)', 1.0), - ('stoich(S2, _J0)', 1.0), - ('stoich(S2, _J1)', -1.0), - ('uec(_J0, S1)', 0.10000000000000007), - ('uec(_J0, S2)', 0.0), - ('uec(_J0, kf)', 10.000000000000082), - ('uec(_J0, kb)', 0.0), - ('uec(_J1, S1)', 0.0), - ('uec(_J1, S2)', 0.009999999999999998), - ('uec(_J1, kf)', 0.0), - ('uec(_J1, kb)', 1.0000000000000053), - ('ec(_J0, S1)', 1.0000000000000007), - ('ec(_J0, S2)', 0.0), - ('ec(_J0, kf)', 1.0000000000000082), - ('ec(_J0, kb)', 0.0), - ('ec(_J1, S1)', 0.0), - ('ec(_J1, S2)', 0.9999999999999998), - ('ec(_J1, kf)', 0.0), - ('ec(_J1, kb)', 1.0000000000000053), - ('ucc(_J0, kf)', 0.09090905110435235), - ('ucc(_J0, kb)', 9.090909090511781), - ('ucc(_J1, kf)', 0.09090905110435235), - ('ucc(_J1, kb)', 9.090909090511735), - ('ucc(S1, kf)', -9.09090511043516), - ('ucc(S1, kb)', 90.90909090511799), - ('ucc(S2, kf)', 9.090905110435088), - ('ucc(S2, kb)', -90.90909090512392), - ('cc(_J0, kf)', 0.009090905110435235), - ('cc(_J0, kb)', 0.09090909090511781), - ('cc(_J1, kf)', 0.9090905110435236), - ('cc(_J1, kb)', 9.090909090511735), - ('cc(S1, kf)', -0.09090905110435162), - ('cc(S1, kb)', 0.09090909090511799), - ('cc(S2, kf)', 0.9090905110435088), - ('cc(S2, kb)', -0.9090909090512392), - ('eigen(S1)', (-0.10999999999999983+0j)), - ('eigenReal(S1)', -0.10999999999999983), - ('eigenImag(S1)', 0.0), - ('eigen(S2)', 0j), - ('eigenReal(S2)', 0.0), - ('eigenImag(S2)', 0.0)] - self.assertEqual( - expected, - self.rr.items(), - ) - - def test_iteritems(self): - - working_iterator = False - for i in self.rr.iteritems(): - working_iterator = True - self.assertTrue(working_iterator) - - def test_iterkeys(self): - - working_iterator = False - for i in self.rr.iterkeys(): - working_iterator = True - self.assertTrue(working_iterator) - - def test_itervalues(self): - - working_iterator = False - for i in self.rr.itervalues(): - working_iterator = True - self.assertTrue(working_iterator) - - def test_parameter_value(self): - self.assertEqual( - self.rr.kf, - 0.1 - ) - - def test_keys(self): - - expected = ['S1', - 'S2', - '[S1]', - '[S2]', - 'default_compartment', - 'kf', - 'kb', - '_J0', - '_J1', - 'init([S1])', - 'init([S2])', - 'init(S1)', - 'init(S2)', - 'init(default_compartment)', - 'init(kf)', - 'init(kb)', - "S1'", - "S2'", - "[S1]'", - "[S2]'", - 'stoich(S1, _J0)', - 'stoich(S1, _J1)', - 'stoich(S2, _J0)', - 'stoich(S2, _J1)', - 'uec(_J0, S1)', - 'uec(_J0, S2)', - 'uec(_J0, kf)', - 'uec(_J0, kb)', - 'uec(_J1, S1)', - 'uec(_J1, S2)', - 'uec(_J1, kf)', - 'uec(_J1, kb)', - 'ec(_J0, S1)', - 'ec(_J0, S2)', - 'ec(_J0, kf)', - 'ec(_J0, kb)', - 'ec(_J1, S1)', - 'ec(_J1, S2)', - 'ec(_J1, kf)', - 'ec(_J1, kb)', - 'ucc(_J0, kf)', - 'ucc(_J0, kb)', - 'ucc(_J1, kf)', - 'ucc(_J1, kb)', - 'ucc(S1, kf)', - 'ucc(S1, kb)', - 'ucc(S2, kf)', - 'ucc(S2, kb)', - 'cc(_J0, kf)', - 'cc(_J0, kb)', - 'cc(_J1, kf)', - 'cc(_J1, kb)', - 'cc(S1, kf)', - 'cc(S1, kb)', - 'cc(S2, kf)', - 'cc(S2, kb)', - 'eigen(S1)', - 'eigenReal(S1)', - 'eigenImag(S1)', - 'eigen(S2)', - 'eigenReal(S2)', - 'eigenImag(S2)',] - self.assertEqual( - expected, - self.rr.keys(), - ) - - def test_load(self): - self.rr.load(self.testModel.str()), - self.assertTrue(self.rr.isModelLoaded()) - - def test_loadState(self): - this_dir = os.path.dirname(__file__) - fname = os.path.join(this_dir, "roadrunner_state.rr") - self.rr.saveState(fname) - self.assertTrue(os.path.isfile(fname)) - self.rr.loadState(fname) - self.assertTrue(self.rr.isModelLoaded()) - os.remove(fname) - - def test_loadStateS(self): - x = self.rr.saveStateS() - rr2 = RoadRunner() - rr2.loadStateS(x) - data = rr2.simulate(0, 10, 11) - print(data) - self.assertEqual((11, 3), data.shape) - - def test_makeIntegrator(self): - integrator = self.rr.makeIntegrator("gillespie") - self.assertIsInstance( - integrator, - Integrator - ) - - def test_mcaSteadyState(self): - self.assertAlmostEqual( - self.rr.mcaSteadyState(), - 1.3877787807814457e-17 - ) - - def test_model(self): - self.assertIsInstance( - self.rr.model, - ExecutableModel - ) - - def test_oneStep(self): - before = self.rr.S2 - self.rr.internalOneStep(0, 10) - after = self.rr.S2 - self.assertNotEqual(before, after) - - def test_options(self): - self.assertIsInstance( - self.rr.options, - RoadRunnerOptions - ) - - def test_regenerateModel(self): - self.rr.regenerateModel() - self.assertTrue(self.rr.isModelLoaded()) - - @unittest.skip("unclear on how to use this method") - def test_removeCompartment(self): - self.rr.removeCompartment("default_compartment", True) - with self.assertRaises(AttributeError): - self.rr.default_compartment - - @unittest.skip("no events in model - add one ") - def test_removeEvent(self): - pass - - @unittest.skip("no events in model - add one ") - def test_removeEventAssignments(self): - print(self.rr.removeEventAssignments()) - - def test_reset(self): - self.rr.reset() - self.assertTrue( - self.rr.isModelLoaded() - ) - - def test_resetAll(self): - """difference between reset and resetAll?""" - self.rr.resetAll() - self.assertTrue( - self.rr.isModelLoaded() - ) - - def test_resetParameter(self): - self.assertEqual(self.rr.kf, 0.1) # starting value - self.rr.kf = 15 # uses setattr - self.assertEqual(self.rr.kf, 15) # starting value - self.rr.resetParameter() - self.assertEqual(self.rr.kf, 0.1) - - def test_resetSelectionLists(self): - self.rr.selections = ["[S2]"] - self.rr.resetSelectionLists() - self.assertEqual( - ['time', "[S1]", '[S2]'], - self.rr.selections, - ) - - def test_resetToOrigin(self): - self.kf = 16 - self.rr.resetToOrigin() - self.assertEqual( - self.rr.kf, 0.1 - ) - - def test_getCurrentTime(self): - self.assertEqual(0, self.rr.getCurrentTime()) - self.rr.simulate(0, 100, 101) - self.assertEqual(100, self.rr.getCurrentTime()) - - def test_selections(self): - self.assertEqual( - self.rr.selections, - ['time', '[S1]', '[S2]'] - ) - - def test_setBoundary(self): - self.rr.setBoundary("S1", False) - self.assertEqual(0, self.rr.getBoundarySpeciesAmountsNamedArray().size) - self.rr.setBoundary("S1", True) - self.assertEqual(1, self.rr.getBoundarySpeciesAmountsNamedArray().size) - - @unittest.skip("We can setConstant but how to getConstant?") - def test_setConstant(self): - self.rr.setConstant("S1", False) - - def test_setDiffStepSize(self): - self.rr.setDiffStepSize(1e-6) - self.assertEqual( - self.rr.getDiffStepSize(), - 1e-6 - ) - - def test_setGlobalParameterByName(self): - self.rr.setGlobalParameterByName("kf", 6), - self.assertEqual( - self.rr.kf, 6 - ) - - @unittest.skip("How to getHasOnlySubstanceUnits?") - def test_setHasOnlySubstanceUnits(self): - self.rr.setHasOnlySubstanceUnits("S1", True) - - @unittest.skip("This function looks broken?") - def test_setInitAmount(self): - self.rr.setInitAmount("S1", 45.6, True) - self.assertEqual( - self.rr.S1, 45.6 - ) - - @unittest.skip("This function looks broken?") - def test_setInitConcentration(self): - self.rr.setInitConcentration("S1", 45.6, True) - self.assertEqual( - self.rr.S1, 45.6 - ) - - def test_setIntegrator(self): - self.rr.setIntegrator("gillespie") - self.assertEqual( - "gillespie", - self.rr.integrator.getName() - ) - - def test_setIntegratorSetting(self): - self.assertTrue( - self.rr.integrator.getValue("stiff") - ) - - def test_setKineticLaw(self): - self.rr.setKineticLaw("_J0", "1+2+3+4+5") - self.assertEqual( - self.rr.getKineticLaw("_J0"), - "1 + 2 + 3 + 4 + 5" - ) - - @unittest.skip("What should go in RoadRunnerOptions?") - def test_setOptions(self): - opt = RoadRunnerOptions() - self.assertEqual( - self.rr.setOptions(), - ) - - @unittest.skip("how to use?") - def test_setPersistent(self): - self.assertEqual( - self.rr.setPersistent(), - ) - - @unittest.skip("How to get the reversible flag back after we've set it?") - def test_setReversible(self): - pass - - def test_setSteadyStateSolver(self): - self.rr.setSteadyStateSolver("newton") - solver = self.rr.getSteadyStateSolver() - print(solver, type(solver)) - self.assertEqual( - solver.getName(), - "newton" - ) - - def test_setSteadyStateThreshold(self): - self.rr.setSteadyStateThreshold(6) - self.assertEqual( - self.rr.getSteadyStateThreshold(), 6 - ) - - @unittest.skip("how to use?") - def test_setTriggerInitialValue(self): - self.assertEqual( - self.rr.setTriggerInitialValue(), - ) - - @unittest.skip("What values are set on a RoadRunner instance?") - def test_setValue(self): - self.assertEqual( - self.rr.setValue(), - ) - - def test_simulate(self): - expected = self.testModel.timeSeriesResult() - settings = self.testModel.timeSeriesSettings() - start = settings["start"] - duration = settings["duration"] - steps = settings["steps"] - num = steps + 1 - self.rr.simulate(start, duration, num) - print(expected) - actual = self.rr.getSimulationData() - print(actual) - self.checkMatricesAlmostEqual(expected, actual, 4) - - def test_steadyState(self): - expected = self.testModel.steadyState() - self.rr.steadyState() - actual = self.rr.getFloatingSpeciesAmountsNamedArray() - print(expected) - print(actual) - self.assertAlmostEqual(expected["S1"], actual[0][0]) - self.assertAlmostEqual(expected["S2"], actual[0][1]) - - def test_steadyStateNamedArray(self): - expected = self.testModel.steadyState() - self.rr.steadyState() - actual = self.rr.steadyStateNamedArray() - print(expected) - print(actual) - self.assertAlmostEqual(expected["S1"], actual[0][0]) - self.assertAlmostEqual(expected["S2"], actual[0][1]) - - def test_steadyStateSelections(self): - self.assertEqual( - self.rr.steadyStateSelections, - ["[S1]", "[S2]"] - ) - - def test_steadyStateSolver(self): - self.assertIsInstance( - self.rr.steadyStateSolver, - SteadyStateSolver - ) - - def test_steadyStateSolverExists(self): - self.assertTrue(self.rr.steadyStateSolverExists("nleq2")) - self.assertFalse(self.rr.steadyStateSolverExists("newton")) # not instantiated yet - - def test_steadyStateThresh(self): - self.assertEqual( - self.rr.steadyStateThresh, - 0.01 - ) - - def test_timeCourseSelections(self): - self.assertEqual( - self.rr.timeCourseSelections, - ['time', "[S1]", '[S2]'] - ) - - @unittest.skip("unclear how to test. Should this method be private?") - def test_validateCurrentSBML(self): - self.assertTrue(self.rr.validateCurrentSBML()) - - def test_load_model_with_large_recursion_limit(self): - """ - This was a fun one. Tellurium crashed with version roadrunner 2.0.6 - because it imports plotly. Plotly imports Ipython.display, which - imports jedi which changes the recursion depth with sys.setrecursionlimit. - This caused roadrunner to crash. Here we write a test to resolve this problem. - :return: - """ - - """ - Okay, so we can't call getIds() inside __getattr__. Why not? - No, actually - we can't call *anything. infinite recursion - """ - import sys - sys.setrecursionlimit(3000) - m = RoadRunner(self.testModel.str()) - self.assertIsInstance(m, RoadRunner) - - def test_getitem_when_exists(self): - import sys - sys.setrecursionlimit(3000) - m = RoadRunner(self.testModel.str()) - self.assertEqual(10.0, m["S1"]) - - def test_getitem_when_not_exists(self): - import sys - sys.setrecursionlimit(3000) - m = RoadRunner(self.testModel.str()) - with self.assertRaises(RuntimeError): - s = m["S100"] - - def test_getitem_when_created_after_instantiation(self): - import sys - sys.setrecursionlimit(3000) - m = RoadRunner(self.testModel.str()) - m.addSpeciesConcentration("S100", "default_compartment", 123.3, False, False, "", True) - val = m["S100"] - self.assertAlmostEqual(val, 123.3) - - def test_getitem_when_created_after_instantiation_dot_notation(self): - import sys - sys.setrecursionlimit(3000) - m = RoadRunner(self.testModel.str()) - m.addSpeciesConcentration("S100", "default_compartment", 123.3, False, False, "", True) - m._makeProperties() - self.assertAlmostEqual(m.S100, 123.3) - - def test_simulateWithTimes(self): - self.rr.resetToOrigin() - self.rr.simulate(times = [0, 1, 5, 10]) - result = self.rr.getSimulationData() - self.assertEqual(list(result[:,0]), [0, 1, 5, 10]) - - -if __name__ == "__main__": - unittest.main() +import platform +if platform.system() != "Darwin": + + import roadrunner.tests.TestModelFactory as tmf + + Config.setValue(Config.LLJIT_OPTIMIZATION_LEVEL, Config.NONE) + + class RoadRunnerTests(unittest.TestCase): + maxDiff = None + + def setUp(self) -> None: + # print(getAvailableTestModels()) + self.testModel = tmf.TestModelFactory("SimpleFlux") + self.rr = RoadRunner(self.testModel.str()) + + def tearDown(self) -> None: + pass + + def checkMatricesAlmostEqual(self, expected, actual, places=7): + if len(expected) != len(actual): + raise ValueError("len(expected) != len(actual)") + + if len(expected[0]) != len(actual[0]): + raise ValueError("len(expected[0]) != len(actual[0])") + + for i in range(len(expected)): + for j in range(len(expected[0])): + self.assertAlmostEqual(expected[i][j], actual[i][j], places=places) + + def test_species_attribute(self): + self.assertEqual(self.rr.S1, 10) + + def test_species_attribute_amount(self): + self.assertEqual(self.rr.S1_amt, 10) + + def test_species_attribute_conc(self): + self.assertEqual(self.rr.S1_conc, 10) + + def test_reaction_flux(self): + self.assertEqual(self.rr._J0, 1) + + def test_attribute_access_protocols_setattr(self): + self.rr.__setattr__("cheese", 6) + self.assertTrue(hasattr(self.rr, "cheese")) + self.assertEqual(getattr(self.rr, "cheese"), 6) + + def test_attribute_access_protocols_getattr(self): + self.assertEqual(self.rr.__getattr__("S1"), 10) + + def test___dict__(self): + self.assertEqual( + ["this"], + list(self.rr.__dict__.keys()) + ) + + @unittest.skip("__eq__ may be implemented, may not. If not we should do") + def test___eq__(self): + pass + + def test___getitem__(self): + self.assertEqual(self.rr.__getitem__("S1"), 10.0) + + def test___len__(self): + self.assertEqual(len(self.rr), 62) # Enumerates all possible rr[x] arguments. + + def test___repr__(self): + l = repr([self.rr]) + self.assertIn("roadrunner.RoadRunner()", l) + + def test___setitem__fails_when_key_not_exist(self): + with self.assertRaises(RuntimeError): + self.rr.__setitem__("five", 5) + + def test___setitem__when_key_exists(self): + self.rr.__setitem__("S1", 12) + self.assertEqual(self.rr.__getitem__("S1"), 12) + + # def test___sizeof__(self): + # self.assertEqual(32, self.rr.__sizeof__()) + + def test___str__(self): + s = str(self.rr) + print(s) + self.assertIn("roadrunner", s) + + @unittest.skip("Method not implemented yet (but should be)") + def test_getCompartmentIds(self): + """This method is missing from the rr api""" + pass + + def test_addCompartment(self): + """The rr._addCompartment() method is called by the + rr.addCompartment() method. The difference, is the + latter adds the compartment to the __dict__ as an + attribute. + """ + self.rr.addCompartment("C1", 1, True) + self.assertEqual(self.rr.C1, 1) + + def testAddParameter(self): + self.rr.addParameter("k_new", 25, True) + self.assertEqual(25, self.rr.k_new) + + def testAddReaction(self): + self.rr.addReaction("NewReaction", ["S1"], ["S2"], "kf*S1", True) + self.rr.S1 = 10 + self.assertEqual(self.rr.NewReaction, 1.0) + + def testAddSpeciesConcentrations(self): + self.rr.addSpeciesConcentration("NewSpecies", "default_compartment", 123.3, False, False, "", True) + self.assertEqual(self.rr.NewSpecies, 123.3) + + def testAddSpecies(self): + self.rr.addSpeciesAmount("NewSpecies", "default_compartment", 123.3, False, False, "", True) + self.assertEqual(self.rr.NewSpecies, 123.3) + + @unittest.skip + def test_removeInitialAssignment(self): + self.assertEqual( + self.rr.removeInitialAssignment(), + ) + + @unittest.skip + def test_removeParameter(self): + self.assertEqual( + self.rr.removeParameter(), ) + + @unittest.skip + def test_removeReaction(self): + self.assertEqual( + self.rr.removeReaction(), + ) + + @unittest.skip + def test_removeRules(self): + self.assertEqual( + self.rr.removeRules(), + + ) + + @unittest.skip + def test_removeSpecies(self): + self.assertEqual( + self.rr.removeSpecies(), + ) + + def test_diffstep_getter(self): + self.assertEqual(self.rr._diffstep_getter(), 0.02) + + def test_diffstep_stter(self): + self.rr._diffstep_stter(0.01) + self.assertEqual(self.rr._diffstep_getter(), 0.01) + + def test_getConservedMoietyAnalysis(self): + self.assertFalse(self.rr._getConservedMoietyAnalysis()) + + def test_setConservedMoietyAnalysis(self): + self.rr.conservedMoietyAnalysis = True + self.assertTrue(self.rr._getConservedMoietyAnalysis()) + + def test_addAssignmentRule(self): + self.rr.addSpeciesConcentration("SNew", "default_compartment", 2.5, False, True, "", True) + self.rr.addAssignmentRule("SNew", "S1+5", True) + self.assertEqual(self.rr.SNew, 15) + + @unittest.skip("Not sure how to test this right now") + def test_addDelay(self): + pass + + @unittest.skip("Not sure how to test this right now") + def test_addEvent(self): + pass + + @unittest.skip("Not sure how to test this right now") + def test_addEventAssignment(self): + pass + + @unittest.skip("Not sure how to test this right now") + def test_addInitialAssignment(self): + self.rr.addSpeciesConcentration("NewSpec", "default_compartment", 13.3, False, True, "", False) + self.rr.addInitialAssignment("NewSpec", "S1+S2", True) + + @unittest.skip("Not sure how to test this right now") + def test_addPriority(self): + pass + + @unittest.skip("Not sure how to test this right now") + def test_addRateRule(self): + pass + + @unittest.skip("Not sure how to test this right now") + def test_addTrigger(self): + pass + + def test_clearModel(self): + self.assertTrue(self.rr.clearModel()) + + @unittest.skip("Not sure how to test this right now. Docs are not clear") + def test_createSelection(self): + pass + + def test_default_compartment(self): + self.assertEqual(self.rr.default_compartment, 1) + + def test_diffstep(self): + self.assertEqual(self.rr.diffstep, 0.02) + + @unittest.skip("This API is unclear. ") + def test_ensureSolversRegistered(self): + self.rr.ensureSolversRegistered() + + def test_getAvailableIntegrators(self): + self.assertEqual(self.rr.getAvailableIntegrators(), ("cvode",)) + + def test_getBoundarySpeciesAmountsNamedArray(self): + self.rr.setBoundary("S1", True) + bs = self.rr.getBoundarySpeciesAmountsNamedArray() + self.assertEqual(bs["S1"], 10) + + def test_getBoundarySpeciesConcentrationsNamedArray(self): + self.rr.setBoundary("S1", True) + self.rr.default_compartment = 0.5 + bs = self.rr.getBoundarySpeciesConcentrationsNamedArray() + self.assertEqual(bs["S1"], 20) + + def test_getCC(self): + self.assertAlmostEqual(self.rr.getCC("_J0", "kf"), 0.009090905110435235) + + def test_getCompiler(self): + compiler_string = str(self.rr.getCompiler()) + self.assertIn("Compiler", compiler_string) + + def test_getConservationMatrix(self): + rr2 = RoadRunner(tmf.TestModelFactory("Brown2004").str()) + rr2.conservedMoietyAnalysis = True + print(rr2.getConservationMatrix().shape) + self.assertEqual(rr2.getConservationMatrix().shape, (15, 28)) + + def test_getConservedMoietyIds(self): + """This mode has no conserved moieties so poor model for testing this feature""" + rr2 = RoadRunner(tmf.TestModelFactory("Brown2004").str()) + rr2.conservedMoietyAnalysis = True + expected = tuple([f"_CSUM{i}" for i in range(15)]) + self.assertEqual(rr2.getConservedMoietyIds(), expected) + + def test_getConservedMoietyValues(self): + """This mode has no conserved moieties so poor model for testing this feature""" + rr2 = RoadRunner(tmf.TestModelFactory("Brown2004").str()) + rr2.conservedMoietyAnalysis = True + print(rr2.getConservedMoietyValues()) + expected = [1.2000e+05, 6.0000e+05, 1.2000e+05, 1.2000e+05, 6.0000e+05, 1.2000e+05, 1.0000e+04, 1.2000e+05, + 1.2000e+05, 4.4600e+05, 1.2000e+05, 1.0002e+07, 1.2000e+05, 1.2000e+05, 8.0000e+04] + actual = rr2.getConservedMoietyValues() + for i in range(len(expected)): + self.assertAlmostEqual(expected[i], actual[i]) + + def test_getCurrentSBML(self): + self.assertIsInstance(self.rr.getCurrentSBML(), str) + + def test_getDependentFloatingSpeciesIds(self): + """No dependents in this model""" + self.assertTrue(callable(self.rr.getDependentFloatingSpeciesIds)) + + def test_getDependentRatesOfChange(self): + """No dependents in this model so we'll just check callable""" + self.assertTrue(callable(self.rr.getDependentRatesOfChange)) + + def test_getDependentRatesOfChangeNamedArray(self): + """No dependents in this model""" + self.assertTrue(callable(self.rr.getDependentRatesOfChangeNamedArray)) + + def test_getDiffStepSize(self): + self.assertEqual(0.02, self.rr.getDiffStepSize()) + + def test_getEE(self): + self.assertAlmostEqual(self.rr.getEE("_J0", "kf"), 1.0000000000000024) + + def test_getEigenValueIds(self): + expected = ('eigen(S1)', 'eigenReal(S1)', 'eigenImag(S1)', 'eigen(S2)', 'eigenReal(S2)', 'eigenImag(S2)') + self.assertEqual(self.rr.getEigenValueIds(), expected) + + def test_getExistingIntegratorNames(self): + expected = ('cvode',) + self.assertEqual(expected, self.rr.getExistingIntegratorNames()) + + def test_getExtendedStoichiometryMatrix(self): + rr2 = RoadRunner(tmf.TestModelFactory("OpenLinearFlux").str()) + mat = rr2.getExtendedStoichiometryMatrix() + print(mat) + expected = [ + [1, -1, 0], + [0, 1, -1], + [-1, 0, 0], + [0, 0, 1], + ] + # todo implement proper equality operators + print(mat.shape) + for i in range(mat.shape[0]): + for j in range(mat.shape[1]): + self.assertEqual(expected[i][j], mat[i][j]) + + def test_getFloatingSpeciesAmountsNamedArray(self): + x = self.rr.getFloatingSpeciesAmountsNamedArray() + self.assertEqual(x["S2"], 1) + + def test_getFloatingSpeciesConcentrationsNamedArray(self): + self.rr.default_compartment = 0.33 + x = self.rr.getFloatingSpeciesConcentrationsNamedArray() + self.assertAlmostEqual(3.0303030303030303, x["S2"][0]) + + def test_getFloatingSpeciesInitialConcentrationIds(self): + x = self.rr.getFloatingSpeciesInitialConcentrationIds() + self.assertEqual(x, ("init([S1])", "init([S2])",)) + + @unittest.skip("figure out how to use") + def test_getFrequencyResponse(self): + pass + + def test_getFullEigenValues(self): + print(dir(self.testModel)) + expected = self.testModel.fullEigenValues() + actual = self.rr.getFullEigenValues() + print(expected) + print(actual) + self.assertAlmostEqual(expected[0], actual[0]) + self.assertAlmostEqual(expected[1], actual[1]) + + def test_getFullJacobian(self): + print(dir(self.testModel)) + expected = self.testModel.fullJacobianAmt() + actual = self.rr.getFullJacobian() + for i in range(expected.shape[0]): + for j in range(expected.shape[1]): + self.assertAlmostEqual(expected[i][j], actual[i][j]) + + def test_getFullJacobianConc(self): + Config.setValue(Config.ROADRUNNER_JACOBIAN_MODE, Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS) + expected = self.testModel.fullJacobianConc() + actual = self.rr.getFullJacobian() + for i in range(expected.shape[0]): + for j in range(expected.shape[1]): + self.assertAlmostEqual(expected[i][j], actual[i][j]) + + def test_getFullJacobianAmt(self): + expected = self.testModel.fullJacobianAmt() + Config.setValue(Config.ROADRUNNER_JACOBIAN_MODE, Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS) + actual = self.rr.getFullJacobian() + for i in range(expected.shape[0]): + for j in range(expected.shape[1]): + self.assertAlmostEqual(expected[i][j], actual[i][j]) + + def test_getFullStoichiometryMatrix(self): + expected = self.testModel.fullStoicMatrix() + self.checkMatricesAlmostEqual(expected, self.rr.getFullStoichiometryMatrix()) + + def test_getGlobalParameterByName(self): + self.assertEqual(self.rr.getGlobalParameterByName("kf"), 0.1) + + @unittest.skip("No way to use this method from Python - it " + "requires an out parameter as input") + def test_getIds(self): + pass + + def test_getIndependentFloatingSpeciesIds(self): + self.assertEqual(self.rr.getIndependentFloatingSpeciesIds(), ["S1"]) + + def test_getIndependentRatesOfChange(self): + self.assertEqual(-0.99, self.rr.getIndependentRatesOfChange()) + + def test_getIndependentRatesOfChangeNamedArray(self): + self.assertEqual( + self.rr.getIndependentRatesOfChangeNamedArray(), + [[-0.99]] + ) + + def test_getInfo(self): + self.assertIn( + "jacobianStepSize", + self.rr.getInfo(), + ) + + def test_getIntegrator(self): + self.assertEqual( + self.rr.getIntegrator().getName(), + "cvode" + ) + + def test_getIntegratorByName(self): + self.assertIsInstance( + self.rr.getIntegratorByName("cvode"), + Integrator + ) + + def test_getKMatrix(self): + expected = [[1], [1]] + self.checkMatricesAlmostEqual( + expected, + self.rr.getKMatrix(), + ) + + def test_getKineticLaw(self): + self.assertEqual( + self.rr.getKineticLaw("_J0"), + "kf * S1" + ) + + def test_getL0Matrix(self): + print(dir(self.testModel)) + expected = self.testModel.L0Matrix() + actual = self.rr.getL0Matrix() + self.assertEqual(expected, actual) + + def test_getLinkMatrix(self): + # roadrunner automatically trasposes column vectors + # into row vectors + expected = self.testModel.linkMatrix() + actual = self.rr.getLinkMatrix().T[0] + print(expected) + print(actual) + self.assertTrue((expected == actual).all()) + + def test_getModel(self): + self.assertIsInstance( + self.rr.getModel(), + ExecutableModel + ) + + def test_getNrMatrix(self): + expected = self.testModel.NrMatrix() + self.checkMatricesAlmostEqual( + expected, + self.rr.getNrMatrix(), + ) + + @unittest.skip("No idea what the argument for this method should be?") + def test_getParamPromotedSBML(self): + self.assertEqual( + self.rr.getParamPromotedSBML(), + ) + + def test_getRatesOfChange(self): + print(self.rr.getRatesOfChange()) + self.assertSequenceEqual( + list(self.rr.getRatesOfChange()), + [-0.99, 0.99] + ) + + def test_getRatesOfChangeNamedArray(self): + print(self.rr.getRatesOfChangeNamedArray()) + self.assertSequenceEqual( + list(self.rr.getRatesOfChangeNamedArray()[0]), + [-0.99, 0.99] + ) + + def test_getReactionRates(self): + self.assertEqual(1.0, self.rr.getReactionRates()[0]) + self.assertEqual(0.01, self.rr.getReactionRates()[1]) + + def test_getReducedEigenValues(self): + expected = self.testModel.reducedEigenValues() + self.rr.conservedMoietyAnalysis = True + actual = self.rr.getReducedEigenValues() + print("expected: ", expected) + print("actual: ", actual) + self.assertEqual(expected.shape, actual.shape) + self.assertAlmostEqual(expected[0], actual[0]) + + def test_getReducedJacobian(self): + self.rr.conservedMoietyAnalysis = True + expected = self.testModel.reducedJacobianConc() + actual = self.rr.getReducedJacobian() + print(expected) + print(actual) + + self.assertAlmostEqual( + -0.11, + self.rr.getReducedJacobian()["S1"][0], + ) + + def test_getReducedStoichiometryMatrix(self): + self.rr.conservedMoietyAnalysis = True + expected = self.testModel.reducedStoicMatrix() + self.checkMatricesAlmostEqual( + expected, + self.rr.getReducedStoichiometryMatrix(), + ) + + def test_getRegisteredIntegratorNames(self): + self.assertEqual( + ('cvode', 'gillespie', 'rk4', 'rk45', 'euler'), + self.rr.getRegisteredIntegratorNames(), + ) + + def test_getRegisteredSteadyStateSolverNames(self): + self.assertEqual( + ('nleq1', 'nleq2', 'newton', "newton_linesearch"), + self.rr.getRegisteredSteadyStateSolverNames(), + ) + + def test_getRegisteredSensitivitySolverNames(self): + print(dir(self.rr)) + self.assertEqual( + ("forward",), + self.rr.getRegisteredSensitivitySolverNames(), + ) + + def test_getSBML(self): + self.assertIsInstance( + self.rr.getSBML(), + str + ) + + def test_getScaledConcentrationControlCoefficientMatrix(self): + expected = self.testModel.scaledConcentrationControlCoefficientMatrix() + actual = self.rr.getScaledConcentrationControlCoefficientMatrix() + self.checkMatricesAlmostEqual( + expected, actual, 5 + ) + + def test_getScaledElasticityMatrix(self): + actual = self.rr.getScaledElasticityMatrix() + expected = self.testModel.scaledElasticityMatrix() + print(actual) + self.checkMatricesAlmostEqual( + expected, actual + ) + + def test_getScaledFloatingSpeciesElasticity(self): + self.assertAlmostEqual( + 1.0, + self.rr.getScaledFloatingSpeciesElasticity("_J1", "S2"), + ) + + def test_getScaledFluxControlCoefficientMatrix(self): + expected = self.testModel.scaledFluxControlCoefficientMatrix() + actual = self.rr.getScaledFluxControlCoefficientMatrix() + self.checkMatricesAlmostEqual( + expected, actual, 5 + ) + + def test_getSelectedValues(self): + self.assertEqual(self.rr.getSelectedValues()[0], 0) + self.assertEqual(self.rr.getSelectedValues()[1], 10) + + def test_getSimulationData(self): + self.assertTrue( + self.rr.getSimulationData().size == 0 + ) + self.rr.simulate(0, 10, 11) + actual = self.rr.getSimulationData() + expected = self.testModel.timeSeriesResult() + self.checkMatricesAlmostEqual(actual, expected, places=4) + + def test_getSteadyStateSelectionStrings(self): + self.assertEqual( + self.rr.getSteadyStateSelectionStrings(), + ("[S1]", "[S2]") + ) + + def test_getSteadyStateSolver(self): + solver = self.rr.getSteadyStateSolver() + self.assertEqual("nleq2", solver.getName()) + + def test_getSteadyStateThreshold(self): + self.assertEqual( + self.rr.getSteadyStateThreshold(), + 0.01 + ) + + def test_getSteadyStateValues(self): + expected = self.testModel.steadyState() + actual = self.rr.getSteadyStateValues() + print(expected) + print(actual) + self.assertEqual(expected["S1"], actual[0]) + self.assertEqual(expected["S2"], actual[1]) + + def test_getSteadyStateValuesNamedArray(self): + expected = self.testModel.steadyState() + actual = self.rr.getSteadyStateValuesNamedArray() + print(expected) + self.assertAlmostEqual(expected["S1"], actual[0, 0]) + self.assertAlmostEqual(expected["S2"], actual[0, 1]) + + def test_getSensitivitySolver(self): + self.assertEqual( + "forward", + self.rr.getSensitivitySolver().getName() + ) + + @unittest.skip("This method should be not be visible in Python") + def test_getSupportedIdTypes(self): + """returns a bit field of the ids that this class supports.""" + + def test_getUnscaledConcentrationControlCoefficientMatrix(self): + expected = self.testModel.unscaledConcentrationControlCoefficientMatrix() + actual = self.rr.getUnscaledConcentrationControlCoefficientMatrix() + self.checkMatricesAlmostEqual( + expected, actual, 5 + ) + + def test_getUnscaledElasticityMatrix(self): + expected = self.testModel.unscaledElasticityMatrix() + actual = self.rr.getUnscaledElasticityMatrix() + self.checkMatricesAlmostEqual( + expected, actual, 5 + ) + + def test_getUnscaledFluxControlCoefficientMatrix(self): + expected = self.testModel.unscaledFluxControlCoefficientMatrix() + actual = self.rr.getUnscaledFluxControlCoefficientMatrix() + self.checkMatricesAlmostEqual( + expected, actual, 5 + ) + + def test_getUnscaledParameterElasticity(self): + self.assertAlmostEqual( + 10, + self.rr.getUnscaledParameterElasticity("_J0", "kf"), + ) + + def test_getUnscaledSpeciesElasticity(self): + self.assertEqual( + 0.10000000000000007, + self.rr.getUnscaledSpeciesElasticity(0, 0), + ) + + def test_getValue(self): + self.assertEqual( + self.rr.getValue("kb"), + 0.01 + ) + + def test_getuCC(self): + self.assertAlmostEqual( + 0.09090905110435235, + self.rr.getuCC("_J0", "kf"), + ) + + def test_getuEE(self): + self.assertAlmostEqual( + self.rr.getuEE("_J0", "kf"), + 10 + ) + + def test_integrator(self): + self.assertIsInstance( + self.rr.integrator, + Integrator + ) + + def test_integratorExists(self): + self.assertTrue( + self.rr.integratorExists("cvode"), + ) + + def test_internalOneStep(self): + before = self.rr.S2 + self.rr.internalOneStep(0, 10) + after = self.rr.S2 + self.assertNotEqual(before, after) + + def test_isModelLoaded(self): + self.assertTrue( + self.rr.isModelLoaded(), + ) + + def test_items(self): + expected = [('S1', 10.0), + ('S2', 1.0), + ('[S1]', 10.0), + ('[S2]', 1.0), + ('default_compartment', 1.0), + ('kf', 0.1), + ('kb', 0.01), + ('_J0', 1.0), + ('_J1', 0.01), + ('init([S1])', 10.0), + ('init([S2])', 1.0), + ('init(S1)', 10.0), + ('init(S2)', 1.0), + ('init(default_compartment)', 1.0), + ('init(kf)', 0.1), + ('init(kb)', 0.01), + ("S1'", -0.99), + ("S2'", 0.99), + ("[S1]'", -0.99), + ("[S2]'", 0.99), + ('stoich(S1, _J0)', -1.0), + ('stoich(S1, _J1)', 1.0), + ('stoich(S2, _J0)', 1.0), + ('stoich(S2, _J1)', -1.0), + ('uec(_J0, S1)', 0.10000000000000007), + ('uec(_J0, S2)', 0.0), + ('uec(_J0, kf)', 10.000000000000082), + ('uec(_J0, kb)', 0.0), + ('uec(_J1, S1)', 0.0), + ('uec(_J1, S2)', 0.009999999999999998), + ('uec(_J1, kf)', 0.0), + ('uec(_J1, kb)', 1.0000000000000053), + ('ec(_J0, S1)', 1.0000000000000007), + ('ec(_J0, S2)', 0.0), + ('ec(_J0, kf)', 1.0000000000000082), + ('ec(_J0, kb)', 0.0), + ('ec(_J1, S1)', 0.0), + ('ec(_J1, S2)', 0.9999999999999998), + ('ec(_J1, kf)', 0.0), + ('ec(_J1, kb)', 1.0000000000000053), + ('ucc(_J0, kf)', 0.09090905110435235), + ('ucc(_J0, kb)', 9.090909090511781), + ('ucc(_J1, kf)', 0.09090905110435235), + ('ucc(_J1, kb)', 9.090909090511735), + ('ucc(S1, kf)', -9.09090511043516), + ('ucc(S1, kb)', 90.90909090511799), + ('ucc(S2, kf)', 9.090905110435088), + ('ucc(S2, kb)', -90.90909090512392), + ('cc(_J0, kf)', 0.009090905110435235), + ('cc(_J0, kb)', 0.09090909090511781), + ('cc(_J1, kf)', 0.9090905110435236), + ('cc(_J1, kb)', 9.090909090511735), + ('cc(S1, kf)', -0.09090905110435162), + ('cc(S1, kb)', 0.09090909090511799), + ('cc(S2, kf)', 0.9090905110435088), + ('cc(S2, kb)', -0.9090909090512392), + ('eigen(S1)', (-0.10999999999999983+0j)), + ('eigenReal(S1)', -0.10999999999999983), + ('eigenImag(S1)', 0.0), + ('eigen(S2)', 0j), + ('eigenReal(S2)', 0.0), + ('eigenImag(S2)', 0.0)] + self.assertEqual( + expected, + self.rr.items(), + ) + + def test_iteritems(self): + + working_iterator = False + for i in self.rr.iteritems(): + working_iterator = True + self.assertTrue(working_iterator) + + def test_iterkeys(self): + + working_iterator = False + for i in self.rr.iterkeys(): + working_iterator = True + self.assertTrue(working_iterator) + + def test_itervalues(self): + + working_iterator = False + for i in self.rr.itervalues(): + working_iterator = True + self.assertTrue(working_iterator) + + def test_parameter_value(self): + self.assertEqual( + self.rr.kf, + 0.1 + ) + + def test_keys(self): + + expected = ['S1', + 'S2', + '[S1]', + '[S2]', + 'default_compartment', + 'kf', + 'kb', + '_J0', + '_J1', + 'init([S1])', + 'init([S2])', + 'init(S1)', + 'init(S2)', + 'init(default_compartment)', + 'init(kf)', + 'init(kb)', + "S1'", + "S2'", + "[S1]'", + "[S2]'", + 'stoich(S1, _J0)', + 'stoich(S1, _J1)', + 'stoich(S2, _J0)', + 'stoich(S2, _J1)', + 'uec(_J0, S1)', + 'uec(_J0, S2)', + 'uec(_J0, kf)', + 'uec(_J0, kb)', + 'uec(_J1, S1)', + 'uec(_J1, S2)', + 'uec(_J1, kf)', + 'uec(_J1, kb)', + 'ec(_J0, S1)', + 'ec(_J0, S2)', + 'ec(_J0, kf)', + 'ec(_J0, kb)', + 'ec(_J1, S1)', + 'ec(_J1, S2)', + 'ec(_J1, kf)', + 'ec(_J1, kb)', + 'ucc(_J0, kf)', + 'ucc(_J0, kb)', + 'ucc(_J1, kf)', + 'ucc(_J1, kb)', + 'ucc(S1, kf)', + 'ucc(S1, kb)', + 'ucc(S2, kf)', + 'ucc(S2, kb)', + 'cc(_J0, kf)', + 'cc(_J0, kb)', + 'cc(_J1, kf)', + 'cc(_J1, kb)', + 'cc(S1, kf)', + 'cc(S1, kb)', + 'cc(S2, kf)', + 'cc(S2, kb)', + 'eigen(S1)', + 'eigenReal(S1)', + 'eigenImag(S1)', + 'eigen(S2)', + 'eigenReal(S2)', + 'eigenImag(S2)',] + self.assertEqual( + expected, + self.rr.keys(), + ) + + def test_load(self): + self.rr.load(self.testModel.str()), + self.assertTrue(self.rr.isModelLoaded()) + + def test_loadState(self): + this_dir = os.path.dirname(__file__) + fname = os.path.join(this_dir, "roadrunner_state.rr") + self.rr.saveState(fname) + self.assertTrue(os.path.isfile(fname)) + self.rr.loadState(fname) + self.assertTrue(self.rr.isModelLoaded()) + os.remove(fname) + + def test_loadStateS(self): + x = self.rr.saveStateS() + rr2 = RoadRunner() + rr2.loadStateS(x) + data = rr2.simulate(0, 10, 11) + print(data) + self.assertEqual((11, 3), data.shape) + + def test_makeIntegrator(self): + integrator = self.rr.makeIntegrator("gillespie") + self.assertIsInstance( + integrator, + Integrator + ) + + def test_mcaSteadyState(self): + self.assertAlmostEqual( + self.rr.mcaSteadyState(), + 1.3877787807814457e-17 + ) + + def test_model(self): + self.assertIsInstance( + self.rr.model, + ExecutableModel + ) + + def test_oneStep(self): + before = self.rr.S2 + self.rr.internalOneStep(0, 10) + after = self.rr.S2 + self.assertNotEqual(before, after) + + def test_options(self): + self.assertIsInstance( + self.rr.options, + RoadRunnerOptions + ) + + def test_regenerateModel(self): + self.rr.regenerateModel() + self.assertTrue(self.rr.isModelLoaded()) + + @unittest.skip("unclear on how to use this method") + def test_removeCompartment(self): + self.rr.removeCompartment("default_compartment", True) + with self.assertRaises(AttributeError): + self.rr.default_compartment + + @unittest.skip("no events in model - add one ") + def test_removeEvent(self): + pass + + @unittest.skip("no events in model - add one ") + def test_removeEventAssignments(self): + print(self.rr.removeEventAssignments()) + + def test_reset(self): + self.rr.reset() + self.assertTrue( + self.rr.isModelLoaded() + ) + + def test_resetAll(self): + """difference between reset and resetAll?""" + self.rr.resetAll() + self.assertTrue( + self.rr.isModelLoaded() + ) + + def test_resetParameter(self): + self.assertEqual(self.rr.kf, 0.1) # starting value + self.rr.kf = 15 # uses setattr + self.assertEqual(self.rr.kf, 15) # starting value + self.rr.resetParameter() + self.assertEqual(self.rr.kf, 0.1) + + def test_resetSelectionLists(self): + self.rr.selections = ["[S2]"] + self.rr.resetSelectionLists() + self.assertEqual( + ['time', "[S1]", '[S2]'], + self.rr.selections, + ) + + def test_resetToOrigin(self): + self.kf = 16 + self.rr.resetToOrigin() + self.assertEqual( + self.rr.kf, 0.1 + ) + + def test_getCurrentTime(self): + self.assertEqual(0, self.rr.getCurrentTime()) + self.rr.simulate(0, 100, 101) + self.assertEqual(100, self.rr.getCurrentTime()) + + def test_selections(self): + self.assertEqual( + self.rr.selections, + ['time', '[S1]', '[S2]'] + ) + + def test_setBoundary(self): + self.rr.setBoundary("S1", False) + self.assertEqual(0, self.rr.getBoundarySpeciesAmountsNamedArray().size) + self.rr.setBoundary("S1", True) + self.assertEqual(1, self.rr.getBoundarySpeciesAmountsNamedArray().size) + + @unittest.skip("We can setConstant but how to getConstant?") + def test_setConstant(self): + self.rr.setConstant("S1", False) + + def test_setDiffStepSize(self): + self.rr.setDiffStepSize(1e-6) + self.assertEqual( + self.rr.getDiffStepSize(), + 1e-6 + ) + + def test_setGlobalParameterByName(self): + self.rr.setGlobalParameterByName("kf", 6), + self.assertEqual( + self.rr.kf, 6 + ) + + @unittest.skip("How to getHasOnlySubstanceUnits?") + def test_setHasOnlySubstanceUnits(self): + self.rr.setHasOnlySubstanceUnits("S1", True) + + @unittest.skip("This function looks broken?") + def test_setInitAmount(self): + self.rr.setInitAmount("S1", 45.6, True) + self.assertEqual( + self.rr.S1, 45.6 + ) + + @unittest.skip("This function looks broken?") + def test_setInitConcentration(self): + self.rr.setInitConcentration("S1", 45.6, True) + self.assertEqual( + self.rr.S1, 45.6 + ) + + def test_setIntegrator(self): + self.rr.setIntegrator("gillespie") + self.assertEqual( + "gillespie", + self.rr.integrator.getName() + ) + + def test_setIntegratorSetting(self): + self.assertTrue( + self.rr.integrator.getValue("stiff") + ) + + def test_setKineticLaw(self): + self.rr.setKineticLaw("_J0", "1+2+3+4+5") + self.assertEqual( + self.rr.getKineticLaw("_J0"), + "1 + 2 + 3 + 4 + 5" + ) + + @unittest.skip("What should go in RoadRunnerOptions?") + def test_setOptions(self): + opt = RoadRunnerOptions() + self.assertEqual( + self.rr.setOptions(), + ) + + @unittest.skip("how to use?") + def test_setPersistent(self): + self.assertEqual( + self.rr.setPersistent(), + ) + + @unittest.skip("How to get the reversible flag back after we've set it?") + def test_setReversible(self): + pass + + def test_setSteadyStateSolver(self): + self.rr.setSteadyStateSolver("newton") + solver = self.rr.getSteadyStateSolver() + print(solver, type(solver)) + self.assertEqual( + solver.getName(), + "newton" + ) + + def test_setSteadyStateThreshold(self): + self.rr.setSteadyStateThreshold(6) + self.assertEqual( + self.rr.getSteadyStateThreshold(), 6 + ) + + @unittest.skip("how to use?") + def test_setTriggerInitialValue(self): + self.assertEqual( + self.rr.setTriggerInitialValue(), + ) + + @unittest.skip("What values are set on a RoadRunner instance?") + def test_setValue(self): + self.assertEqual( + self.rr.setValue(), + ) + + def test_simulate(self): + expected = self.testModel.timeSeriesResult() + settings = self.testModel.timeSeriesSettings() + start = settings["start"] + duration = settings["duration"] + steps = settings["steps"] + num = steps + 1 + self.rr.simulate(start, duration, num) + print(expected) + actual = self.rr.getSimulationData() + print(actual) + self.checkMatricesAlmostEqual(expected, actual, 4) + + def test_steadyState(self): + expected = self.testModel.steadyState() + self.rr.steadyState() + actual = self.rr.getFloatingSpeciesAmountsNamedArray() + print(expected) + print(actual) + self.assertAlmostEqual(expected["S1"], actual[0][0]) + self.assertAlmostEqual(expected["S2"], actual[0][1]) + + def test_steadyStateNamedArray(self): + expected = self.testModel.steadyState() + self.rr.steadyState() + actual = self.rr.steadyStateNamedArray() + print(expected) + print(actual) + self.assertAlmostEqual(expected["S1"], actual[0][0]) + self.assertAlmostEqual(expected["S2"], actual[0][1]) + + def test_steadyStateSelections(self): + self.assertEqual( + self.rr.steadyStateSelections, + ["[S1]", "[S2]"] + ) + + def test_steadyStateSolver(self): + self.assertIsInstance( + self.rr.steadyStateSolver, + SteadyStateSolver + ) + + def test_steadyStateSolverExists(self): + self.assertTrue(self.rr.steadyStateSolverExists("nleq2")) + self.assertFalse(self.rr.steadyStateSolverExists("newton")) # not instantiated yet + + def test_steadyStateThresh(self): + self.assertEqual( + self.rr.steadyStateThresh, + 0.01 + ) + + def test_timeCourseSelections(self): + self.assertEqual( + self.rr.timeCourseSelections, + ['time', "[S1]", '[S2]'] + ) + + @unittest.skip("unclear how to test. Should this method be private?") + def test_validateCurrentSBML(self): + self.assertTrue(self.rr.validateCurrentSBML()) + + def test_load_model_with_large_recursion_limit(self): + """ + This was a fun one. Tellurium crashed with version roadrunner 2.0.6 + because it imports plotly. Plotly imports Ipython.display, which + imports jedi which changes the recursion depth with sys.setrecursionlimit. + This caused roadrunner to crash. Here we write a test to resolve this problem. + :return: + """ + + """ + Okay, so we can't call getIds() inside __getattr__. Why not? + No, actually - we can't call *anything. infinite recursion + """ + import sys + sys.setrecursionlimit(3000) + m = RoadRunner(self.testModel.str()) + self.assertIsInstance(m, RoadRunner) + + def test_getitem_when_exists(self): + import sys + sys.setrecursionlimit(3000) + m = RoadRunner(self.testModel.str()) + self.assertEqual(10.0, m["S1"]) + + def test_getitem_when_not_exists(self): + import sys + sys.setrecursionlimit(3000) + m = RoadRunner(self.testModel.str()) + with self.assertRaises(RuntimeError): + s = m["S100"] + + def test_getitem_when_created_after_instantiation(self): + import sys + sys.setrecursionlimit(3000) + m = RoadRunner(self.testModel.str()) + m.addSpeciesConcentration("S100", "default_compartment", 123.3, False, False, "", True) + val = m["S100"] + self.assertAlmostEqual(val, 123.3) + + def test_getitem_when_created_after_instantiation_dot_notation(self): + import sys + sys.setrecursionlimit(3000) + m = RoadRunner(self.testModel.str()) + m.addSpeciesConcentration("S100", "default_compartment", 123.3, False, False, "", True) + m._makeProperties() + self.assertAlmostEqual(m.S100, 123.3) + + def test_simulateWithTimes(self): + self.rr.resetToOrigin() + self.rr.simulate(times = [0, 1, 5, 10]) + result = self.rr.getSimulationData() + self.assertEqual(list(result[:,0]), [0, 1, 5, 10]) + + + if __name__ == "__main__": + unittest.main() diff --git a/test/python/test_roadrunner_map.py b/test/python/test_roadrunner_map.py index 474438d54e..a30babf473 100644 --- a/test/python/test_roadrunner_map.py +++ b/test/python/test_roadrunner_map.py @@ -13,175 +13,179 @@ ] import roadrunner as rr from roadrunner import RoadRunnerMap, RoadRunner -import roadrunner.tests.TestModelFactory as tmf - -class RoadRunnerMapTests(unittest.TestCase): - - def setUp(self) -> None: - self.sbmlStrings = [ - tmf.OpenLinearFlux().str(), - tmf.SimpleFlux().str(), - tmf.Brown2004().str(), - tmf.FactorialInRateLaw().str(), - tmf.Venkatraman2010().str() - ] - self.N = len(self.sbmlStrings) - - def test_ctor1(self): - rrm = RoadRunnerMap() - self.assertEqual(0, len(rrm)) - - def test_ctor2(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - self.assertEqual(len(self.sbmlStrings), len(rrm)) - - def test_keys(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - expected = ('SimpleFlux', 'x', 'FactorialModel1', '__main', 'Brown2004_NGF_EGF_signaling') - self.assertEqual(sorted(expected), sorted(rrm.keys())) - - def test_size_1thread(self): - rrm = RoadRunnerMap(self.sbmlStrings, 1) - self.assertEqual(self.N, len(rrm)) - - def test_size_2thread(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - self.assertEqual(self.N, len(rrm)) - - def test_values(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - values = rrm.values() - self.assertIsInstance(values, list) - self.assertTrue(all([isinstance(i, RoadRunner) for i in values])) - - def test_items(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - items = rrm.items() - self.assertIsInstance(items, list) - for name, rrModel in rrm.items(): - self.assertIsInstance(name, str) - self.assertIsInstance(rrModel, RoadRunner) - - def test_insert_from_empty(self): - rrm = RoadRunnerMap() - rrm.insert(self.sbmlStrings[0]) - self.assertEqual(1, len(rrm)) - self.assertEqual(rrm.keys()[0], "x") - - def test_insert_from_empty_with_custom_name(self): - rrm = RoadRunnerMap() - rrm.insert("NewName", self.sbmlStrings[0]) - self.assertEqual(1, len(rrm)) - self.assertEqual(rrm.keys()[0], "NewName") - - def test_insert_from_populated(self): - rrm = RoadRunnerMap(self.sbmlStrings[:2], 2) - rrm.insert(self.sbmlStrings[-1]) - self.assertEqual(3, len(rrm)) - - def test_insert_from_populated_custom_name(self): - rrm = RoadRunnerMap(self.sbmlStrings[:2], 2) - rrm.insert("NewModel", self.sbmlStrings[-1]) - self.assertEqual(3, len(rrm)) - self.assertTrue("NewModel" in rrm) - - def test_insert_from_list_of_strings(self): - n = len(self.sbmlStrings[:2]) + len(self.sbmlStrings[2:]) - rrm = RoadRunnerMap(self.sbmlStrings[:2], 2) - rrm.insert(self.sbmlStrings[2:]) - self.assertEqual(n, len(rrm)) - - def test___setitem__(self): - rrm = RoadRunnerMap(self.sbmlStrings[:-1], 2) - last = self.sbmlStrings[-1] - rrm["last"] = last - self.assertEqual(len(self.sbmlStrings), len(rrm)) - - def test___setitem__exception(self): - """ - This is explicitely prohibited to prevent users from looping over a list of - sbml paths/strings and entering them one by one into the map. This situation - should instead be handled by passing in the list of strings. - """ - rrm = RoadRunnerMap(self.sbmlStrings[:-1], 2) - last = self.sbmlStrings[-1] - with self.assertRaises(TypeError): - rrm["last"] = RoadRunner(last) - - def test___getitem__(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - simpleFlux = rrm["SimpleFlux"] - self.assertIsInstance(simpleFlux, RoadRunner) - - def test___delitem__(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - self.assertEqual(len(self.sbmlStrings), len(rrm)) - del rrm["SimpleFlux"] - self.assertEqual(len(self.sbmlStrings) - 1, len(rrm)) - - def test_empty_when_true(self): - rrm = RoadRunnerMap() - self.assertTrue(rrm.empty) - - def test_empty_when_false(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - self.assertFalse(rrm.empty()) - - def test___len__(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - self.assertEqual(len(self.sbmlStrings), len(rrm)) - - def test_clear(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - self.assertEqual(len(self.sbmlStrings), len(rrm)) - self.assertFalse(rrm.empty()) - rrm.clear() - self.assertTrue(rrm.empty()) - - def test_contains_positive(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - self.assertTrue("x" in rrm) - - def test_contains_negative(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - self.assertFalse("x" not in rrm) - - def test_numThreads(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - self.assertEqual(2, rrm.getNumThreads()) - rrm.setNumThreads(4) - self.assertEqual(4, rrm.getNumThreads()) - - def test_iterators(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - expected = [ - "Brown2004_NGF_EGF_signaling", - "SimpleFlux", - "FactorialModel1", - "__main", - "x" - ] - k = [] - for i in rrm: - k.append(i) - self.assertEqual(sorted(k), sorted(expected)) - - - def test_iterators_items(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - expected = [ - "Brown2004_NGF_EGF_signaling", - "SimpleFlux", - "FactorialModel1", - "__main", - "x" - ] - k = [] - for name, rr in rrm.items(): - k.append(name) - self.assertEqual(sorted(k), sorted(expected)) - - -if __name__ == "__main__": - unittest.main() +import platform +if platform.system() != "Darwin": + + import roadrunner.tests.TestModelFactory as tmf + + + class RoadRunnerMapTests(unittest.TestCase): + + def setUp(self) -> None: + self.sbmlStrings = [ + tmf.OpenLinearFlux().str(), + tmf.SimpleFlux().str(), + tmf.Brown2004().str(), + tmf.FactorialInRateLaw().str(), + tmf.Venkatraman2010().str() + ] + self.N = len(self.sbmlStrings) + + def test_ctor1(self): + rrm = RoadRunnerMap() + self.assertEqual(0, len(rrm)) + + def test_ctor2(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + self.assertEqual(len(self.sbmlStrings), len(rrm)) + + def test_keys(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + expected = ('SimpleFlux', 'x', 'FactorialModel1', '__main', 'Brown2004_NGF_EGF_signaling') + self.assertEqual(sorted(expected), sorted(rrm.keys())) + + def test_size_1thread(self): + rrm = RoadRunnerMap(self.sbmlStrings, 1) + self.assertEqual(self.N, len(rrm)) + + def test_size_2thread(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + self.assertEqual(self.N, len(rrm)) + + def test_values(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + values = rrm.values() + self.assertIsInstance(values, list) + self.assertTrue(all([isinstance(i, RoadRunner) for i in values])) + + def test_items(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + items = rrm.items() + self.assertIsInstance(items, list) + for name, rrModel in rrm.items(): + self.assertIsInstance(name, str) + self.assertIsInstance(rrModel, RoadRunner) + + def test_insert_from_empty(self): + rrm = RoadRunnerMap() + rrm.insert(self.sbmlStrings[0]) + self.assertEqual(1, len(rrm)) + self.assertEqual(rrm.keys()[0], "x") + + def test_insert_from_empty_with_custom_name(self): + rrm = RoadRunnerMap() + rrm.insert("NewName", self.sbmlStrings[0]) + self.assertEqual(1, len(rrm)) + self.assertEqual(rrm.keys()[0], "NewName") + + def test_insert_from_populated(self): + rrm = RoadRunnerMap(self.sbmlStrings[:2], 2) + rrm.insert(self.sbmlStrings[-1]) + self.assertEqual(3, len(rrm)) + + def test_insert_from_populated_custom_name(self): + rrm = RoadRunnerMap(self.sbmlStrings[:2], 2) + rrm.insert("NewModel", self.sbmlStrings[-1]) + self.assertEqual(3, len(rrm)) + self.assertTrue("NewModel" in rrm) + + def test_insert_from_list_of_strings(self): + n = len(self.sbmlStrings[:2]) + len(self.sbmlStrings[2:]) + rrm = RoadRunnerMap(self.sbmlStrings[:2], 2) + rrm.insert(self.sbmlStrings[2:]) + self.assertEqual(n, len(rrm)) + + def test___setitem__(self): + rrm = RoadRunnerMap(self.sbmlStrings[:-1], 2) + last = self.sbmlStrings[-1] + rrm["last"] = last + self.assertEqual(len(self.sbmlStrings), len(rrm)) + + def test___setitem__exception(self): + """ + This is explicitely prohibited to prevent users from looping over a list of + sbml paths/strings and entering them one by one into the map. This situation + should instead be handled by passing in the list of strings. + """ + rrm = RoadRunnerMap(self.sbmlStrings[:-1], 2) + last = self.sbmlStrings[-1] + with self.assertRaises(TypeError): + rrm["last"] = RoadRunner(last) + + def test___getitem__(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + simpleFlux = rrm["SimpleFlux"] + self.assertIsInstance(simpleFlux, RoadRunner) + + def test___delitem__(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + self.assertEqual(len(self.sbmlStrings), len(rrm)) + del rrm["SimpleFlux"] + self.assertEqual(len(self.sbmlStrings) - 1, len(rrm)) + + def test_empty_when_true(self): + rrm = RoadRunnerMap() + self.assertTrue(rrm.empty) + + def test_empty_when_false(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + self.assertFalse(rrm.empty()) + + def test___len__(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + self.assertEqual(len(self.sbmlStrings), len(rrm)) + + def test_clear(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + self.assertEqual(len(self.sbmlStrings), len(rrm)) + self.assertFalse(rrm.empty()) + rrm.clear() + self.assertTrue(rrm.empty()) + + def test_contains_positive(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + self.assertTrue("x" in rrm) + + def test_contains_negative(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + self.assertFalse("x" not in rrm) + + def test_numThreads(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + self.assertEqual(2, rrm.getNumThreads()) + rrm.setNumThreads(4) + self.assertEqual(4, rrm.getNumThreads()) + + def test_iterators(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + expected = [ + "Brown2004_NGF_EGF_signaling", + "SimpleFlux", + "FactorialModel1", + "__main", + "x" + ] + k = [] + for i in rrm: + k.append(i) + self.assertEqual(sorted(k), sorted(expected)) + + + def test_iterators_items(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + expected = [ + "Brown2004_NGF_EGF_signaling", + "SimpleFlux", + "FactorialModel1", + "__main", + "x" + ] + k = [] + for name, rr in rrm.items(): + k.append(name) + self.assertEqual(sorted(k), sorted(expected)) + + + if __name__ == "__main__": + unittest.main() diff --git a/test/python/test_steadyStateSolver.py b/test/python/test_steadyStateSolver.py index 6e1f0819a8..c99e7ac977 100644 --- a/test/python/test_steadyStateSolver.py +++ b/test/python/test_steadyStateSolver.py @@ -8,266 +8,269 @@ rr_site_packages, ] from roadrunner.roadrunner import RoadRunner, BasicNewtonIteration -from roadrunner.tests.TestModelFactory import TestModelFactory -import roadrunner.tests.TestModelFactory as tmf - -import unittest - - -class NewtonIterationUnitTests(unittest.TestCase): - - def setUp(self) -> None: - # we choose the easiest model for the unit tests. - # see integration tests for solving other models. - self.testModel = TestModelFactory("SimpleFluxManuallyReduced") - self.rr = RoadRunner(self.testModel.str()) - - def checkResults(self, results): - for i in range(len(results.colnames)): - speciesId = results.colnames[i] - actualResult = results[0][i] - - expected = self.testModel.steadyState()[speciesId] - print("Comparing ", speciesId, "expected result: ", expected, "actual result: ", actualResult) - self.assertAlmostEqual(expected, actualResult) - - def test_newton_iteration_registered(self): - self.assertIn("newton", self.rr.getRegisteredSteadyStateSolverNames()) - - def test_newton_linesearch_registered(self): - self.assertIn("newton_linesearch", self.rr.getRegisteredSteadyStateSolverNames()) - - def test_settings_map_is_dict(self): - solver = BasicNewtonIteration(self.rr.getModel()) - settings = solver.getSettingsMap() - self.assertIsInstance(settings, dict) - - def test_solve_using_newton_iteration_directly(self): - solver = BasicNewtonIteration(self.rr.getModel()) - solver.allow_presimulation = True - solver.solve() - self.checkResults(self.rr.getFloatingSpeciesConcentrationsNamedArray()) - - def test_change_then_reset_settings(self): - solver = BasicNewtonIteration(self.rr.getModel()) - solver.presimulation_maximum_steps = 400 - # ensure we've actually changed something - self.assertEqual(400, solver.presimulation_maximum_steps) - solver.resetSettings() - self.assertEqual(500, solver.presimulation_maximum_steps) - - def test_regenerate_model_before_creating_solver(self): - self.rr.regenerateModel() - solver = BasicNewtonIteration(self.rr.getModel()) - solver.solve() - self.checkResults(self.rr.getFloatingSpeciesConcentrationsNamedArray()) - - def test_regenerate_model_after_creating_solver(self): - solver = BasicNewtonIteration(self.rr.getModel()) - self.rr.regenerateModel() - # after regeneration, the pointer to the model is different so we must sync with model before solving. - solver.syncWithModel(self.rr.getModel()) - solver.solve() - self.checkResults(self.rr.getFloatingSpeciesConcentrationsNamedArray()) - - def test_presimulation_times(self): - solver = BasicNewtonIteration(self.rr.getModel()) - self.assertIsInstance(solver.presimulation_times, list) - self.assertListEqual([0.1, 1.0, 10.0, 100.0, 1000.0, 10000.0], solver.presimulation_times) - - -class SteadyStateSolverIntegrationTests(unittest.TestCase): - # defined by subclasses - strategy = None - - def setUp(self) -> None: - pass - - def tearDown(self) -> None: - pass - - def checkValidTestModelName(self, model_name: str): - if model_name not in tmf.getAvailableTestModels(): - raise ValueError(f"The requested test model_name \"{model_name}\"" - f"is not one of the available test models: {tmf.getAvailableTestModels()}") - - def checkValidTestModelType(self, test_model : tmf.TestModel): - if not issubclass(type(test_model), tmf.SteadyStateResult): - raise ValueError("This test model does not implement the " - "SteadyStateResult interface") - - def checkSteadyState(self, model_name: str, solver_name: str, places:int=5): - # grab the test model - self.checkValidTestModelName(model_name) - - test_model = TestModelFactory(model_name) - - self.checkValidTestModelType(test_model) - - # load it into roadrunner - rr = RoadRunner(test_model.str()) - - # collect reference results - expected_results = test_model.steadyState() - - # set the steady state solver - rr.setSteadyStateSolver(solver_name) - - # get settings for this problem - settings = test_model.steadyStateSettings() - - # apply settings - for setting, value in settings.items(): - if setting == "moiety_conservation": - rr.conservedMoietyAnalysis = True - else: - try: - rr.getSteadyStateSolver().setValue(setting, value) - except Exception: - # its okay for a solver to not have a particular options - continue - - # do steady state calculation - rr.steadyState() - - actual_results = rr.getFloatingSpeciesConcentrationsNamedArray() - for species_name, expected_ss_val in expected_results.items(): - actual = actual_results[species_name][0] - print("Comparing reference value : ", expected_ss_val, "with actual value: ", actual) - self.assertAlmostEqual(expected_ss_val, actual, places=places) - - def checkSteadyStateFluxes(self, model_name: str, solver_name: str, places=5): - self.checkValidTestModelName(model_name) - - test_model = TestModelFactory(model_name) - - self.checkValidTestModelType(test_model) - - # load it into roadrunner - rr = RoadRunner(test_model.str()) - - # collect reference results - expected_results = test_model.steadyStateFluxes() - - # set the steady state solver - rr.setSteadyStateSolver(solver_name) - - # get settings for this problem - settings = test_model.steadyStateSettings() - - # apply settings - for setting, value in settings.items(): - if setting == "moiety_conservation": - rr.conservedMoietyAnalysis = True - else: - try: - rr.getSteadyStateSolver().setValue(setting, value) - except Exception: - # its okay for a solver to not have a particular options - continue - - # do steady state calculation - rr.steadyState() - - for reactionId, expectedSteadyStateFlux in expected_results.items(): - actualSteadyStateFlux = rr.getModel().getValue(reactionId) - print("Comparing reference value : ", expectedSteadyStateFlux, "with actual value: ", actualSteadyStateFlux) - self.assertAlmostEqual(expectedSteadyStateFlux, actualSteadyStateFlux, places=places) - - -class SundialsNewtonIterationTests(SteadyStateSolverIntegrationTests): - - def testOpenLinearFlux(self): - self.checkSteadyState("OpenLinearFlux", "newton") - - def testSimpleFluxManuallyReduced(self): - self.checkSteadyState("SimpleFluxManuallyReduced", "newton") - - def testSimpleFlux(self): - self.checkSteadyState("SimpleFlux", "newton") - - def testVenkatraman2010(self): - self.checkSteadyState("Venkatraman2010", "newton") - - def testBrown2004(self): - self.checkSteadyState("Brown2004", "newton") - - def testBimolecularEnd(self): - self.checkSteadyState("BimolecularEnd", "newton", 4) - - def testBimolecularEndSteadyStateFluxes(self): - self.checkSteadyStateFluxes("BimolecularEnd", "newton") - - -class LineSearchNewtonIterationTests(SteadyStateSolverIntegrationTests): - def testOpenLinearFlux(self): - self.checkSteadyState("OpenLinearFlux", "newton_linesearch") - - def testSimpleFluxManuallyReduced(self): - self.checkSteadyState("SimpleFluxManuallyReduced", "newton_linesearch") - - def testSimpleFlux(self): - self.checkSteadyState("SimpleFlux", "newton_linesearch") - - def testVenkatraman2010(self): - self.checkSteadyState("Venkatraman2010", "newton_linesearch") - - def testBrown2004(self): - self.checkSteadyState("Brown2004", "newton_linesearch") - - def testBimolecularEnd(self): - self.checkSteadyState("BimolecularEnd", "newton_linesearch", 4) - - def testBimolecularEndSteadyStateFluxes(self): - self.checkSteadyStateFluxes("BimolecularEnd", "newton_linesearch", 5) - - -class NLEQ1IntegrationTests(SteadyStateSolverIntegrationTests): - def testOpenLinearFlux(self): - self.checkSteadyState("OpenLinearFlux", "nleq1") - - def testSimpleFluxManuallyReduced(self): - self.checkSteadyState("SimpleFluxManuallyReduced", "nleq1") - - def testSimpleFlux(self): - self.checkSteadyState("SimpleFlux", "nleq1") - - def testVenkatraman2010(self): - self.checkSteadyState("Venkatraman2010", "nleq1") - - def testBrown2004(self): - self.checkSteadyState("Brown2004", "nleq1") - - def testBimolecularEnd(self): - self.checkSteadyState("BimolecularEnd", "nleq1", 4) - - def testBimolecularEndSteadyStateFluxes(self): - self.checkSteadyStateFluxes("BimolecularEnd", "nleq1", 5) - - -class NLEQ2IntegrationTests(SteadyStateSolverIntegrationTests): - def testOpenLinearFlux(self): - self.checkSteadyState("OpenLinearFlux", "nleq2") - - def testSimpleFluxManuallyReduced(self): - self.checkSteadyState("SimpleFluxManuallyReduced", "nleq2") - - def testSimpleFlux(self): - self.checkSteadyState("SimpleFlux", "nleq2") - - def testVenkatraman2010(self): - self.checkSteadyState("Venkatraman2010", "nleq2") - - def testBrown2004(self): - self.checkSteadyState("Brown2004", "nleq2") - - def testBimolecularEnd(self): - self.checkSteadyState("BimolecularEnd", "nleq2", 4) - - def testBimolecularEndSteadyStateFluxes(self): - self.checkSteadyStateFluxes("BimolecularEnd", "nleq2", 5) - - - -if __name__ == "__main__": - unittest.main() +import platform +if platform.system() != "Darwin": + + from roadrunner.tests.TestModelFactory import TestModelFactory + import roadrunner.tests.TestModelFactory as tmf + + import unittest + + + class NewtonIterationUnitTests(unittest.TestCase): + + def setUp(self) -> None: + # we choose the easiest model for the unit tests. + # see integration tests for solving other models. + self.testModel = TestModelFactory("SimpleFluxManuallyReduced") + self.rr = RoadRunner(self.testModel.str()) + + def checkResults(self, results): + for i in range(len(results.colnames)): + speciesId = results.colnames[i] + actualResult = results[0][i] + + expected = self.testModel.steadyState()[speciesId] + print("Comparing ", speciesId, "expected result: ", expected, "actual result: ", actualResult) + self.assertAlmostEqual(expected, actualResult) + + def test_newton_iteration_registered(self): + self.assertIn("newton", self.rr.getRegisteredSteadyStateSolverNames()) + + def test_newton_linesearch_registered(self): + self.assertIn("newton_linesearch", self.rr.getRegisteredSteadyStateSolverNames()) + + def test_settings_map_is_dict(self): + solver = BasicNewtonIteration(self.rr.getModel()) + settings = solver.getSettingsMap() + self.assertIsInstance(settings, dict) + + def test_solve_using_newton_iteration_directly(self): + solver = BasicNewtonIteration(self.rr.getModel()) + solver.allow_presimulation = True + solver.solve() + self.checkResults(self.rr.getFloatingSpeciesConcentrationsNamedArray()) + + def test_change_then_reset_settings(self): + solver = BasicNewtonIteration(self.rr.getModel()) + solver.presimulation_maximum_steps = 400 + # ensure we've actually changed something + self.assertEqual(400, solver.presimulation_maximum_steps) + solver.resetSettings() + self.assertEqual(500, solver.presimulation_maximum_steps) + + def test_regenerate_model_before_creating_solver(self): + self.rr.regenerateModel() + solver = BasicNewtonIteration(self.rr.getModel()) + solver.solve() + self.checkResults(self.rr.getFloatingSpeciesConcentrationsNamedArray()) + + def test_regenerate_model_after_creating_solver(self): + solver = BasicNewtonIteration(self.rr.getModel()) + self.rr.regenerateModel() + # after regeneration, the pointer to the model is different so we must sync with model before solving. + solver.syncWithModel(self.rr.getModel()) + solver.solve() + self.checkResults(self.rr.getFloatingSpeciesConcentrationsNamedArray()) + + def test_presimulation_times(self): + solver = BasicNewtonIteration(self.rr.getModel()) + self.assertIsInstance(solver.presimulation_times, list) + self.assertListEqual([0.1, 1.0, 10.0, 100.0, 1000.0, 10000.0], solver.presimulation_times) + + + class SteadyStateSolverIntegrationTests(unittest.TestCase): + # defined by subclasses + strategy = None + + def setUp(self) -> None: + pass + + def tearDown(self) -> None: + pass + + def checkValidTestModelName(self, model_name: str): + if model_name not in tmf.getAvailableTestModels(): + raise ValueError(f"The requested test model_name \"{model_name}\"" + f"is not one of the available test models: {tmf.getAvailableTestModels()}") + + def checkValidTestModelType(self, test_model : tmf.TestModel): + if not issubclass(type(test_model), tmf.SteadyStateResult): + raise ValueError("This test model does not implement the " + "SteadyStateResult interface") + + def checkSteadyState(self, model_name: str, solver_name: str, places:int=5): + # grab the test model + self.checkValidTestModelName(model_name) + + test_model = TestModelFactory(model_name) + + self.checkValidTestModelType(test_model) + + # load it into roadrunner + rr = RoadRunner(test_model.str()) + + # collect reference results + expected_results = test_model.steadyState() + + # set the steady state solver + rr.setSteadyStateSolver(solver_name) + + # get settings for this problem + settings = test_model.steadyStateSettings() + + # apply settings + for setting, value in settings.items(): + if setting == "moiety_conservation": + rr.conservedMoietyAnalysis = True + else: + try: + rr.getSteadyStateSolver().setValue(setting, value) + except Exception: + # its okay for a solver to not have a particular options + continue + + # do steady state calculation + rr.steadyState() + + actual_results = rr.getFloatingSpeciesConcentrationsNamedArray() + for species_name, expected_ss_val in expected_results.items(): + actual = actual_results[species_name][0] + print("Comparing reference value : ", expected_ss_val, "with actual value: ", actual) + self.assertAlmostEqual(expected_ss_val, actual, places=places) + + def checkSteadyStateFluxes(self, model_name: str, solver_name: str, places=5): + self.checkValidTestModelName(model_name) + + test_model = TestModelFactory(model_name) + + self.checkValidTestModelType(test_model) + + # load it into roadrunner + rr = RoadRunner(test_model.str()) + + # collect reference results + expected_results = test_model.steadyStateFluxes() + + # set the steady state solver + rr.setSteadyStateSolver(solver_name) + + # get settings for this problem + settings = test_model.steadyStateSettings() + + # apply settings + for setting, value in settings.items(): + if setting == "moiety_conservation": + rr.conservedMoietyAnalysis = True + else: + try: + rr.getSteadyStateSolver().setValue(setting, value) + except Exception: + # its okay for a solver to not have a particular options + continue + + # do steady state calculation + rr.steadyState() + + for reactionId, expectedSteadyStateFlux in expected_results.items(): + actualSteadyStateFlux = rr.getModel().getValue(reactionId) + print("Comparing reference value : ", expectedSteadyStateFlux, "with actual value: ", actualSteadyStateFlux) + self.assertAlmostEqual(expectedSteadyStateFlux, actualSteadyStateFlux, places=places) + + + class SundialsNewtonIterationTests(SteadyStateSolverIntegrationTests): + + def testOpenLinearFlux(self): + self.checkSteadyState("OpenLinearFlux", "newton") + + def testSimpleFluxManuallyReduced(self): + self.checkSteadyState("SimpleFluxManuallyReduced", "newton") + + def testSimpleFlux(self): + self.checkSteadyState("SimpleFlux", "newton") + + def testVenkatraman2010(self): + self.checkSteadyState("Venkatraman2010", "newton") + + def testBrown2004(self): + self.checkSteadyState("Brown2004", "newton") + + def testBimolecularEnd(self): + self.checkSteadyState("BimolecularEnd", "newton", 4) + + def testBimolecularEndSteadyStateFluxes(self): + self.checkSteadyStateFluxes("BimolecularEnd", "newton") + + + class LineSearchNewtonIterationTests(SteadyStateSolverIntegrationTests): + def testOpenLinearFlux(self): + self.checkSteadyState("OpenLinearFlux", "newton_linesearch") + + def testSimpleFluxManuallyReduced(self): + self.checkSteadyState("SimpleFluxManuallyReduced", "newton_linesearch") + + def testSimpleFlux(self): + self.checkSteadyState("SimpleFlux", "newton_linesearch") + + def testVenkatraman2010(self): + self.checkSteadyState("Venkatraman2010", "newton_linesearch") + + def testBrown2004(self): + self.checkSteadyState("Brown2004", "newton_linesearch") + + def testBimolecularEnd(self): + self.checkSteadyState("BimolecularEnd", "newton_linesearch", 4) + + def testBimolecularEndSteadyStateFluxes(self): + self.checkSteadyStateFluxes("BimolecularEnd", "newton_linesearch", 5) + + + class NLEQ1IntegrationTests(SteadyStateSolverIntegrationTests): + def testOpenLinearFlux(self): + self.checkSteadyState("OpenLinearFlux", "nleq1") + + def testSimpleFluxManuallyReduced(self): + self.checkSteadyState("SimpleFluxManuallyReduced", "nleq1") + + def testSimpleFlux(self): + self.checkSteadyState("SimpleFlux", "nleq1") + + def testVenkatraman2010(self): + self.checkSteadyState("Venkatraman2010", "nleq1") + + def testBrown2004(self): + self.checkSteadyState("Brown2004", "nleq1") + + def testBimolecularEnd(self): + self.checkSteadyState("BimolecularEnd", "nleq1", 4) + + def testBimolecularEndSteadyStateFluxes(self): + self.checkSteadyStateFluxes("BimolecularEnd", "nleq1", 5) + + + class NLEQ2IntegrationTests(SteadyStateSolverIntegrationTests): + def testOpenLinearFlux(self): + self.checkSteadyState("OpenLinearFlux", "nleq2") + + def testSimpleFluxManuallyReduced(self): + self.checkSteadyState("SimpleFluxManuallyReduced", "nleq2") + + def testSimpleFlux(self): + self.checkSteadyState("SimpleFlux", "nleq2") + + def testVenkatraman2010(self): + self.checkSteadyState("Venkatraman2010", "nleq2") + + def testBrown2004(self): + self.checkSteadyState("Brown2004", "nleq2") + + def testBimolecularEnd(self): + self.checkSteadyState("BimolecularEnd", "nleq2", 4) + + def testBimolecularEndSteadyStateFluxes(self): + self.checkSteadyStateFluxes("BimolecularEnd", "nleq2", 5) + + + + if __name__ == "__main__": + unittest.main() diff --git a/test/python/test_structuralAnalysis.py b/test/python/test_structuralAnalysis.py index bfc2fe3c3d..cb342258a3 100644 --- a/test/python/test_structuralAnalysis.py +++ b/test/python/test_structuralAnalysis.py @@ -24,126 +24,129 @@ ) import roadrunner -try: - from roadrunner.tests import TestModelFactory as tmf - from roadrunner.tests.RoadRunnerTest import RoadRunnerTest -except: - import TestModelFactory as tmf - from RoadRunnerTest import RoadRunnerTest - - -class StructuralAnalysisTests(RoadRunnerTest): - - def setUp(self) -> None: - pass - - def tearDown(self) -> None: - pass - - def loadTestModel(self, modelName: str): - """Instantiate instance of TestModel called modelName""" - self.checkValidTestModelName(modelName) - testModel = tmf.TestModelFactory(modelName) - self.checkTestModelImplements(testModel, tmf.StructuralProperties) - return testModel - - def checkLinkMatrix(self, modelName: str): - testModel = self.loadTestModel(modelName) - expected = testModel.linkMatrix() - rr = RoadRunner(testModel.str()) - actual = rr.getLinkMatrix() - self.checkMatricesEqual(expected, actual) - - def checkNrMatrix(self, modelName: str): - testModel = self.loadTestModel(modelName) - expected = testModel.NrMatrix() - rr = RoadRunner(testModel.str()) - rr.setConservedMoietyAnalysis = True - actual = rr.getNrMatrix() - self.checkMatricesEqual(expected, actual) - - def checkKMatrix(self, modelName: str): - testModel = self.loadTestModel(modelName) - expected = testModel.KMatrix() - rr = RoadRunner(testModel.str()) - actual = rr.getKMatrix() - for i in range(expected.shape[0]): - for j in range(expected.shape[1]): - self.assertAlmostEqual(expected[i][j], actual[i][j], 7) - - def checkReducedStoicMatrix(self, modelName: str): - testModel = self.loadTestModel(modelName) - expected = testModel.reducedStoicMatrix() - rr = RoadRunner(testModel.str()) - rr.setConservedMoietyAnalysis = True - actual = rr.getReducedStoichiometryMatrix() - self.checkMatricesEqual(expected, actual) - - def checkFullStoicMatrix(self, modelName: str): - testModel = self.loadTestModel(modelName) - expected = testModel.fullStoicMatrix() - rr = RoadRunner(testModel.str()) - # note turn this to False and the test fails. - # is this right? - rr.conservedMoietyAnalysis = True - actual = rr.getFullStoichiometryMatrix() - self.checkMatricesEqual(expected, actual) - - def checkExtendedStoicMatrix(self, modelName: str): - testModel = self.loadTestModel(modelName) - expected = testModel.extendedStoicMatrix() - rr = RoadRunner(testModel.str()) - # moiety conservation breaks the test. - # Theres something more going on here that should be investigated - # rr.setConservedMoietyAnalysis = True - actual = rr.getExtendedStoichiometryMatrix() - self.checkMatricesEqual(expected, actual) - - def checkL0Matrix(self, modelName: str): - testModel = self.loadTestModel(modelName) - expected = testModel.L0Matrix() - rr = RoadRunner(testModel.str()) - actual = rr.getL0Matrix() - self.checkMatricesEqual(expected, actual) - - def checkConservationMatrix(self, modelName: str): - testModel = self.loadTestModel(modelName) - expected = testModel.conservationMatrix() - rr = RoadRunner(testModel.str()) - rr.setConservedMoietyAnalysis = True - actual = rr.getConservationMatrix() - self.checkMatricesEqual(expected, actual) - - def test_BimolecularEnd_LinkMatrix(self): - self.checkLinkMatrix("BimolecularEnd") - - def test_BimolecularEnd_NrMatrix(self): - self.checkNrMatrix("BimolecularEnd") - - def test_BimolecularEnd_KMatrix(self): - self.checkKMatrix("BimolecularEnd") - - def test_BimolecularEnd_ReducedStoicMatrix(self): - self.checkReducedStoicMatrix("BimolecularEnd") - - def test_BimolecularEnd_FullStoicMatrix(self): - self.checkFullStoicMatrix("BimolecularEnd") - - def test_BimolecularEnd_ExtendedStoicMatrix(self): - self.checkExtendedStoicMatrix("BimolecularEnd") - - @unittest.skip("L0 matrix is empty for this model. Currently there is a " - "bug in RoadRunner's swig interface when porting an " - "empty Matrix to empty Python np array") - def test_BimolecularEnd_L0Matrix(self): - self.checkL0Matrix("BimolecularEnd") - - @unittest.skip("Conservation matrix is empty for this model. Currently there is a " - "bug in RoadRunner's swig interface when porting an " - "empty Matrix to empty Python np array") - def test_BimolecularEnd_ConservationMatrix(self): - self.checkConservationMatrix("BimolecularEnd") - -if __name__ == "__main__": - unittest.main() - +import platform +if platform.system() != "Darwin": + + try: + from roadrunner.tests import TestModelFactory as tmf + from roadrunner.tests.RoadRunnerTest import RoadRunnerTest + except: + import TestModelFactory as tmf + from RoadRunnerTest import RoadRunnerTest + + + class StructuralAnalysisTests(RoadRunnerTest): + + def setUp(self) -> None: + pass + + def tearDown(self) -> None: + pass + + def loadTestModel(self, modelName: str): + """Instantiate instance of TestModel called modelName""" + self.checkValidTestModelName(modelName) + testModel = tmf.TestModelFactory(modelName) + self.checkTestModelImplements(testModel, tmf.StructuralProperties) + return testModel + + def checkLinkMatrix(self, modelName: str): + testModel = self.loadTestModel(modelName) + expected = testModel.linkMatrix() + rr = RoadRunner(testModel.str()) + actual = rr.getLinkMatrix() + self.checkMatricesEqual(expected, actual) + + def checkNrMatrix(self, modelName: str): + testModel = self.loadTestModel(modelName) + expected = testModel.NrMatrix() + rr = RoadRunner(testModel.str()) + rr.setConservedMoietyAnalysis = True + actual = rr.getNrMatrix() + self.checkMatricesEqual(expected, actual) + + def checkKMatrix(self, modelName: str): + testModel = self.loadTestModel(modelName) + expected = testModel.KMatrix() + rr = RoadRunner(testModel.str()) + actual = rr.getKMatrix() + for i in range(expected.shape[0]): + for j in range(expected.shape[1]): + self.assertAlmostEqual(expected[i][j], actual[i][j], 7) + + def checkReducedStoicMatrix(self, modelName: str): + testModel = self.loadTestModel(modelName) + expected = testModel.reducedStoicMatrix() + rr = RoadRunner(testModel.str()) + rr.setConservedMoietyAnalysis = True + actual = rr.getReducedStoichiometryMatrix() + self.checkMatricesEqual(expected, actual) + + def checkFullStoicMatrix(self, modelName: str): + testModel = self.loadTestModel(modelName) + expected = testModel.fullStoicMatrix() + rr = RoadRunner(testModel.str()) + # note turn this to False and the test fails. + # is this right? + rr.conservedMoietyAnalysis = True + actual = rr.getFullStoichiometryMatrix() + self.checkMatricesEqual(expected, actual) + + def checkExtendedStoicMatrix(self, modelName: str): + testModel = self.loadTestModel(modelName) + expected = testModel.extendedStoicMatrix() + rr = RoadRunner(testModel.str()) + # moiety conservation breaks the test. + # Theres something more going on here that should be investigated + # rr.setConservedMoietyAnalysis = True + actual = rr.getExtendedStoichiometryMatrix() + self.checkMatricesEqual(expected, actual) + + def checkL0Matrix(self, modelName: str): + testModel = self.loadTestModel(modelName) + expected = testModel.L0Matrix() + rr = RoadRunner(testModel.str()) + actual = rr.getL0Matrix() + self.checkMatricesEqual(expected, actual) + + def checkConservationMatrix(self, modelName: str): + testModel = self.loadTestModel(modelName) + expected = testModel.conservationMatrix() + rr = RoadRunner(testModel.str()) + rr.setConservedMoietyAnalysis = True + actual = rr.getConservationMatrix() + self.checkMatricesEqual(expected, actual) + + def test_BimolecularEnd_LinkMatrix(self): + self.checkLinkMatrix("BimolecularEnd") + + def test_BimolecularEnd_NrMatrix(self): + self.checkNrMatrix("BimolecularEnd") + + def test_BimolecularEnd_KMatrix(self): + self.checkKMatrix("BimolecularEnd") + + def test_BimolecularEnd_ReducedStoicMatrix(self): + self.checkReducedStoicMatrix("BimolecularEnd") + + def test_BimolecularEnd_FullStoicMatrix(self): + self.checkFullStoicMatrix("BimolecularEnd") + + def test_BimolecularEnd_ExtendedStoicMatrix(self): + self.checkExtendedStoicMatrix("BimolecularEnd") + + @unittest.skip("L0 matrix is empty for this model. Currently there is a " + "bug in RoadRunner's swig interface when porting an " + "empty Matrix to empty Python np array") + def test_BimolecularEnd_L0Matrix(self): + self.checkL0Matrix("BimolecularEnd") + + @unittest.skip("Conservation matrix is empty for this model. Currently there is a " + "bug in RoadRunner's swig interface when porting an " + "empty Matrix to empty Python np array") + def test_BimolecularEnd_ConservationMatrix(self): + self.checkConservationMatrix("BimolecularEnd") + + if __name__ == "__main__": + unittest.main() + diff --git a/test/python/test_testModelFactory.py b/test/python/test_testModelFactory.py index 6a54c99f09..3deacf37b0 100644 --- a/test/python/test_testModelFactory.py +++ b/test/python/test_testModelFactory.py @@ -18,274 +18,278 @@ rr_site_packages, ] import roadrunner -import roadrunner.tests.TestModelFactory as tmf - -class TestModelFactoryTests(unittest.TestCase): - - def setUp(self) -> None: - pass - - def tearDown(self) -> None: - pass - - def testDoublePair(self): - x = tmf._testDoublePair(3.4, 5.6) - self.assertIsInstance(x, tuple) - self.assertEqual(x[0], 3.4) - - def testUseVariant(self): - x = tmf._testVariant() - self.assertIsInstance(x, float) - - def testVariantMap(self): - x = tmf._testVariantMap() - self.assertIsInstance(x, dict) - self.assertIsInstance(list(x.keys())[0], str) - self.assertIsInstance(list(x.values())[0], int) - - def testResultMap(self): - x = tmf._testResultMap() - self.assertIsInstance(x, dict) - - def testGetSettings(self): - open_linear_flux = tmf.OpenLinearFlux() - expected = {'allow_presimulation': False, - 'auto_moiety_analysis': False, - 'moiety_conservation': False, - 'presimulation_time': 5} - self.assertEqual(expected, open_linear_flux.steadyStateSettings()) - - def testSimpleFluxStr(self): - sf = tmf.SimpleFlux() - self.assertTrue(sf.str().startswith(r" None: + pass + + def tearDown(self) -> None: + pass + + def testDoublePair(self): + x = tmf._testDoublePair(3.4, 5.6) + self.assertIsInstance(x, tuple) + self.assertEqual(x[0], 3.4) + + def testUseVariant(self): + x = tmf._testVariant() + self.assertIsInstance(x, float) + + def testVariantMap(self): + x = tmf._testVariantMap() + self.assertIsInstance(x, dict) + self.assertIsInstance(list(x.keys())[0], str) + self.assertIsInstance(list(x.values())[0], int) + + def testResultMap(self): + x = tmf._testResultMap() + self.assertIsInstance(x, dict) + + def testGetSettings(self): + open_linear_flux = tmf.OpenLinearFlux() + expected = {'allow_presimulation': False, + 'auto_moiety_analysis': False, + 'moiety_conservation': False, + 'presimulation_time': 5} + self.assertEqual(expected, open_linear_flux.steadyStateSettings()) + + def testSimpleFluxStr(self): + sf = tmf.SimpleFlux() + self.assertTrue(sf.str().startswith(r" Date: Thu, 16 Mar 2023 14:33:30 -0700 Subject: [PATCH 08/28] Darwin -> darwin I guess? --- test/python/RoadRunnerTest.py | 2 +- test/python/test_automaticMoietyConservationAnalysis.py | 2 +- test/python/test_forwardSensitivitySolver.py | 2 +- test/python/test_integrator.py | 2 +- test/python/test_jacobian.py | 2 +- test/python/test_pickle.py | 2 +- test/python/test_python_api.py | 2 +- test/python/test_roadrunner_map.py | 2 +- test/python/test_steadyStateSolver.py | 2 +- test/python/test_structuralAnalysis.py | 2 +- test/python/test_testModelFactory.py | 2 +- 11 files changed, 11 insertions(+), 11 deletions(-) diff --git a/test/python/RoadRunnerTest.py b/test/python/RoadRunnerTest.py index b006be3014..e8626a691c 100644 --- a/test/python/RoadRunnerTest.py +++ b/test/python/RoadRunnerTest.py @@ -12,7 +12,7 @@ ] import platform -if platform.system() != "Darwin": +if platform.system() != "darwin": try: from roadrunner.tests import TestModelFactory as tmf diff --git a/test/python/test_automaticMoietyConservationAnalysis.py b/test/python/test_automaticMoietyConservationAnalysis.py index 70bf15aa82..a1ce2951ef 100644 --- a/test/python/test_automaticMoietyConservationAnalysis.py +++ b/test/python/test_automaticMoietyConservationAnalysis.py @@ -10,7 +10,7 @@ from roadrunner.roadrunner import RoadRunner, BasicNewtonIteration import platform -if platform.system() != "Darwin": +if platform.system() != "darwin": from roadrunner.tests.TestModelFactory import TestModelFactory diff --git a/test/python/test_forwardSensitivitySolver.py b/test/python/test_forwardSensitivitySolver.py index 85b5467c3b..de7ee4b6fb 100644 --- a/test/python/test_forwardSensitivitySolver.py +++ b/test/python/test_forwardSensitivitySolver.py @@ -11,7 +11,7 @@ ] from roadrunner.roadrunner import RoadRunner, ForwardSensitivitySolver import platform -if platform.system() != "Darwin": +if platform.system() != "darwin": import roadrunner.tests.TestModelFactory as tmf diff --git a/test/python/test_integrator.py b/test/python/test_integrator.py index e7626578ac..5dff221e48 100644 --- a/test/python/test_integrator.py +++ b/test/python/test_integrator.py @@ -12,7 +12,7 @@ from roadrunner.roadrunner import RoadRunner, CVODEIntegrator, ForwardSensitivitySolver import platform -if platform.system() != "Darwin": +if platform.system() != "darwin": import roadrunner.tests.TestModelFactory as tmf diff --git a/test/python/test_jacobian.py b/test/python/test_jacobian.py index 3a62f023d3..a485a9a146 100644 --- a/test/python/test_jacobian.py +++ b/test/python/test_jacobian.py @@ -20,7 +20,7 @@ ) import platform -if platform.system() != "Darwin": +if platform.system() != "darwin": try: from roadrunner.tests import TestModelFactory as tmf diff --git a/test/python/test_pickle.py b/test/python/test_pickle.py index 7486b44956..9d55349321 100644 --- a/test/python/test_pickle.py +++ b/test/python/test_pickle.py @@ -8,7 +8,7 @@ import copy import platform -if platform.system() != "Darwin": +if platform.system() != "darwin": try: import ray diff --git a/test/python/test_python_api.py b/test/python/test_python_api.py index 8fd99b58f8..b9288374d5 100644 --- a/test/python/test_python_api.py +++ b/test/python/test_python_api.py @@ -44,7 +44,7 @@ # So we import TestModelFactory as an alias. import platform -if platform.system() != "Darwin": +if platform.system() != "darwin": import roadrunner.tests.TestModelFactory as tmf diff --git a/test/python/test_roadrunner_map.py b/test/python/test_roadrunner_map.py index a30babf473..2698978a20 100644 --- a/test/python/test_roadrunner_map.py +++ b/test/python/test_roadrunner_map.py @@ -15,7 +15,7 @@ from roadrunner import RoadRunnerMap, RoadRunner import platform -if platform.system() != "Darwin": +if platform.system() != "darwin": import roadrunner.tests.TestModelFactory as tmf diff --git a/test/python/test_steadyStateSolver.py b/test/python/test_steadyStateSolver.py index c99e7ac977..c06723c77a 100644 --- a/test/python/test_steadyStateSolver.py +++ b/test/python/test_steadyStateSolver.py @@ -9,7 +9,7 @@ ] from roadrunner.roadrunner import RoadRunner, BasicNewtonIteration import platform -if platform.system() != "Darwin": +if platform.system() != "darwin": from roadrunner.tests.TestModelFactory import TestModelFactory import roadrunner.tests.TestModelFactory as tmf diff --git a/test/python/test_structuralAnalysis.py b/test/python/test_structuralAnalysis.py index cb342258a3..4a53ca3526 100644 --- a/test/python/test_structuralAnalysis.py +++ b/test/python/test_structuralAnalysis.py @@ -25,7 +25,7 @@ import roadrunner import platform -if platform.system() != "Darwin": +if platform.system() != "darwin": try: from roadrunner.tests import TestModelFactory as tmf diff --git a/test/python/test_testModelFactory.py b/test/python/test_testModelFactory.py index 3deacf37b0..093b985dc8 100644 --- a/test/python/test_testModelFactory.py +++ b/test/python/test_testModelFactory.py @@ -20,7 +20,7 @@ import roadrunner import platform -if platform.system() != "Darwin": +if platform.system() != "darwin": import roadrunner.tests.TestModelFactory as tmf From 448f307fc0fd5394b460ef6d4687cea279e91c56 Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Thu, 16 Mar 2023 15:13:29 -0700 Subject: [PATCH 09/28] Nope, 'Darwin' after all. Still won't work, but hopefully closer. --- test/python/RoadRunnerTest.py | 2 +- test/python/test_automaticMoietyConservationAnalysis.py | 2 +- test/python/test_forwardSensitivitySolver.py | 2 +- test/python/test_integrator.py | 2 +- test/python/test_jacobian.py | 2 +- test/python/test_pickle.py | 2 +- test/python/test_python_api.py | 2 +- test/python/test_roadrunner_map.py | 2 +- test/python/test_steadyStateSolver.py | 2 +- test/python/test_structuralAnalysis.py | 2 +- test/python/test_testModelFactory.py | 2 +- 11 files changed, 11 insertions(+), 11 deletions(-) diff --git a/test/python/RoadRunnerTest.py b/test/python/RoadRunnerTest.py index e8626a691c..b006be3014 100644 --- a/test/python/RoadRunnerTest.py +++ b/test/python/RoadRunnerTest.py @@ -12,7 +12,7 @@ ] import platform -if platform.system() != "darwin": +if platform.system() != "Darwin": try: from roadrunner.tests import TestModelFactory as tmf diff --git a/test/python/test_automaticMoietyConservationAnalysis.py b/test/python/test_automaticMoietyConservationAnalysis.py index a1ce2951ef..70bf15aa82 100644 --- a/test/python/test_automaticMoietyConservationAnalysis.py +++ b/test/python/test_automaticMoietyConservationAnalysis.py @@ -10,7 +10,7 @@ from roadrunner.roadrunner import RoadRunner, BasicNewtonIteration import platform -if platform.system() != "darwin": +if platform.system() != "Darwin": from roadrunner.tests.TestModelFactory import TestModelFactory diff --git a/test/python/test_forwardSensitivitySolver.py b/test/python/test_forwardSensitivitySolver.py index de7ee4b6fb..85b5467c3b 100644 --- a/test/python/test_forwardSensitivitySolver.py +++ b/test/python/test_forwardSensitivitySolver.py @@ -11,7 +11,7 @@ ] from roadrunner.roadrunner import RoadRunner, ForwardSensitivitySolver import platform -if platform.system() != "darwin": +if platform.system() != "Darwin": import roadrunner.tests.TestModelFactory as tmf diff --git a/test/python/test_integrator.py b/test/python/test_integrator.py index 5dff221e48..e7626578ac 100644 --- a/test/python/test_integrator.py +++ b/test/python/test_integrator.py @@ -12,7 +12,7 @@ from roadrunner.roadrunner import RoadRunner, CVODEIntegrator, ForwardSensitivitySolver import platform -if platform.system() != "darwin": +if platform.system() != "Darwin": import roadrunner.tests.TestModelFactory as tmf diff --git a/test/python/test_jacobian.py b/test/python/test_jacobian.py index a485a9a146..3a62f023d3 100644 --- a/test/python/test_jacobian.py +++ b/test/python/test_jacobian.py @@ -20,7 +20,7 @@ ) import platform -if platform.system() != "darwin": +if platform.system() != "Darwin": try: from roadrunner.tests import TestModelFactory as tmf diff --git a/test/python/test_pickle.py b/test/python/test_pickle.py index 9d55349321..7486b44956 100644 --- a/test/python/test_pickle.py +++ b/test/python/test_pickle.py @@ -8,7 +8,7 @@ import copy import platform -if platform.system() != "darwin": +if platform.system() != "Darwin": try: import ray diff --git a/test/python/test_python_api.py b/test/python/test_python_api.py index b9288374d5..8fd99b58f8 100644 --- a/test/python/test_python_api.py +++ b/test/python/test_python_api.py @@ -44,7 +44,7 @@ # So we import TestModelFactory as an alias. import platform -if platform.system() != "darwin": +if platform.system() != "Darwin": import roadrunner.tests.TestModelFactory as tmf diff --git a/test/python/test_roadrunner_map.py b/test/python/test_roadrunner_map.py index 2698978a20..a30babf473 100644 --- a/test/python/test_roadrunner_map.py +++ b/test/python/test_roadrunner_map.py @@ -15,7 +15,7 @@ from roadrunner import RoadRunnerMap, RoadRunner import platform -if platform.system() != "darwin": +if platform.system() != "Darwin": import roadrunner.tests.TestModelFactory as tmf diff --git a/test/python/test_steadyStateSolver.py b/test/python/test_steadyStateSolver.py index c06723c77a..c99e7ac977 100644 --- a/test/python/test_steadyStateSolver.py +++ b/test/python/test_steadyStateSolver.py @@ -9,7 +9,7 @@ ] from roadrunner.roadrunner import RoadRunner, BasicNewtonIteration import platform -if platform.system() != "darwin": +if platform.system() != "Darwin": from roadrunner.tests.TestModelFactory import TestModelFactory import roadrunner.tests.TestModelFactory as tmf diff --git a/test/python/test_structuralAnalysis.py b/test/python/test_structuralAnalysis.py index 4a53ca3526..cb342258a3 100644 --- a/test/python/test_structuralAnalysis.py +++ b/test/python/test_structuralAnalysis.py @@ -25,7 +25,7 @@ import roadrunner import platform -if platform.system() != "darwin": +if platform.system() != "Darwin": try: from roadrunner.tests import TestModelFactory as tmf diff --git a/test/python/test_testModelFactory.py b/test/python/test_testModelFactory.py index 093b985dc8..3deacf37b0 100644 --- a/test/python/test_testModelFactory.py +++ b/test/python/test_testModelFactory.py @@ -20,7 +20,7 @@ import roadrunner import platform -if platform.system() != "darwin": +if platform.system() != "Darwin": import roadrunner.tests.TestModelFactory as tmf From 0e7b7e96f25507acab97dc9967c31005e024794c Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Thu, 16 Mar 2023 16:51:42 -0700 Subject: [PATCH 10/28] Switch to not attempt test at all. Running a test with zero tests resulted in a 'fail', mysteriously. Switch to just not putting the test in the list at all. This will be easier to revert later, too. --- test/CMakeLists.txt | 25 +- test/python/RoadRunnerTest.py | 59 +- ...est_automaticMoietyConservationAnalysis.py | 154 +- test/python/test_forwardSensitivitySolver.py | 491 ++-- test/python/test_integrator.py | 462 ++-- test/python/test_jacobian.py | 265 +- test/python/test_pickle.py | 303 ++- test/python/test_python_api.py | 2336 ++++++++--------- test/python/test_roadrunner_map.py | 346 ++- test/python/test_steadyStateSolver.py | 529 ++-- test/python/test_structuralAnalysis.py | 249 +- test/python/test_testModelFactory.py | 532 ++-- 12 files changed, 2857 insertions(+), 2894 deletions(-) diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt index b98b1b50a1..b24b4724bd 100644 --- a/test/CMakeLists.txt +++ b/test/CMakeLists.txt @@ -319,22 +319,23 @@ if (BUILD_PYTHON AND BUILD_TESTS) endmacro() - add_pytest_to_ctest(python_tests_AutomaticMoietyConservationAnalysisTests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_automaticMoietyConservationAnalysis.py") - add_pytest_to_ctest(python_tests_ForwardSensitivitySolverTests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_forwardSensitivitySolver.py") - add_pytest_to_ctest(python_tests_IntegratorTests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_integrator.py") - add_pytest_to_ctest(python_tests_JacobianTests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_jacobian.py") - add_pytest_to_ctest(python_tests_TestModelFactoryTests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_testModelFactory.py") - add_pytest_to_ctest(python_tests_NamedArrayTests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_namedArray.py") + if (NOT APPLE) + add_pytest_to_ctest(python_tests_AutomaticMoietyConservationAnalysisTests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_automaticMoietyConservationAnalysis.py") + add_pytest_to_ctest(python_tests_ForwardSensitivitySolverTests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_forwardSensitivitySolver.py") + add_pytest_to_ctest(python_tests_IntegratorTests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_integrator.py") + add_pytest_to_ctest(python_tests_JacobianTests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_jacobian.py") + add_pytest_to_ctest(python_tests_TestModelFactoryTests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_testModelFactory.py") + add_pytest_to_ctest(python_tests_NamedArrayTests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_namedArray.py") + add_pytest_to_ctest(python_tests_Python_api_tests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_python_api.py") + add_pytest_to_ctest(python_tests_SteadyStateSolverTests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_steadyStateSolver.py") + add_pytest_to_ctest(python_tests_StructuralAnalysisTests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_structuralAnalysis.py") + add_pytest_to_ctest(python_tests_RoadRunnerMap "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_roadrunner_map.py") + endif() #add_pytest_to_ctest(python_tests_PickleTests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_pickle.py") - add_pytest_to_ctest(python_tests_Python_api_tests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_python_api.py") add_pytest_to_ctest(python_tests_RRTests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_rrtests.py") add_pytest_to_ctest(python_tests_SettingTests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_settings.py") - add_pytest_to_ctest(python_tests_SteadyStateSolverTests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_steadyStateSolver.py") - add_pytest_to_ctest(python_tests_StructuralAnalysisTests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_structuralAnalysis.py") - add_pytest_to_ctest(python_tests_RunStochasticTestSuite "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_runStochasticTestSuite.py") - add_pytest_to_ctest(python_tests_RoadRunnerMap "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_roadrunner_map.py") - + message(STATUS "PyTestTests ${PyTestTests}") add_custom_target( diff --git a/test/python/RoadRunnerTest.py b/test/python/RoadRunnerTest.py index b006be3014..f6224d6d9c 100644 --- a/test/python/RoadRunnerTest.py +++ b/test/python/RoadRunnerTest.py @@ -11,34 +11,31 @@ rr_site_packages, ] -import platform -if platform.system() != "Darwin": - - try: - from roadrunner.tests import TestModelFactory as tmf - except: - import TestModelFactory as tmf - - class RoadRunnerTest(unittest.TestCase): - """A set of utilities used in Python tests""" - - def checkValidTestModelName(self, model_name: str): - """Check that model_name is a valid TestModel name""" - if model_name not in tmf.getAvailableTestModels(): - raise ValueError(f"The requested test model_name \"{model_name}\"" - f"is not one of the available test models: {tmf.getAvailableTestModels()}") - - def checkTestModelImplements(self, test_model : tmf.TestModel, implementsResultType): - """Check that test_model implements the interface implementsResultType""" - - if not issubclass(type(test_model), implementsResultType): - raise ValueError("This test model does not implement the " - "SteadyStateResult interface") - - def checkMatricesEqual(self, expected: np.ndarray, actual: np.ndarray, places=4): - if expected.shape != actual.shape: - raise ValueError("expected and actual are different sizes") - for i in range(expected.shape[0]): - for j in range(expected.shape[1]): - print(f"Checking expected value {expected[i][j]} against actual {actual[i][j]}") - self.assertAlmostEqual(expected[i][j], actual[i][j], places=places) +try: + from roadrunner.tests import TestModelFactory as tmf +except: + import TestModelFactory as tmf + +class RoadRunnerTest(unittest.TestCase): + """A set of utilities used in Python tests""" + + def checkValidTestModelName(self, model_name: str): + """Check that model_name is a valid TestModel name""" + if model_name not in tmf.getAvailableTestModels(): + raise ValueError(f"The requested test model_name \"{model_name}\"" + f"is not one of the available test models: {tmf.getAvailableTestModels()}") + + def checkTestModelImplements(self, test_model : tmf.TestModel, implementsResultType): + """Check that test_model implements the interface implementsResultType""" + + if not issubclass(type(test_model), implementsResultType): + raise ValueError("This test model does not implement the " + "SteadyStateResult interface") + + def checkMatricesEqual(self, expected: np.ndarray, actual: np.ndarray, places=4): + if expected.shape != actual.shape: + raise ValueError("expected and actual are different sizes") + for i in range(expected.shape[0]): + for j in range(expected.shape[1]): + print(f"Checking expected value {expected[i][j]} against actual {actual[i][j]}") + self.assertAlmostEqual(expected[i][j], actual[i][j], places=places) diff --git a/test/python/test_automaticMoietyConservationAnalysis.py b/test/python/test_automaticMoietyConservationAnalysis.py index 70bf15aa82..f434d8a85c 100644 --- a/test/python/test_automaticMoietyConservationAnalysis.py +++ b/test/python/test_automaticMoietyConservationAnalysis.py @@ -8,84 +8,80 @@ rr_site_packages, ] from roadrunner.roadrunner import RoadRunner, BasicNewtonIteration +from roadrunner.tests.TestModelFactory import TestModelFactory -import platform -if platform.system() != "Darwin": - - from roadrunner.tests.TestModelFactory import TestModelFactory - - import unittest - - - class AutomaticMoietyConservationTests(unittest.TestCase): - """Test the automatic moiety analysis option, which is present in superclass - of all steady state solvers. - Three components to these tests: - 1) The model can either need moiety conservation analysis or not. - 2) The auto_moiety_analysis option can be on or off - 3) The RoadRunner moiety_conservation_analysis option can be on or off - Test are named using this convention: - (Needed or not)(auto_moiety_analysis)(moiety_conservation_analysis option) - i.e. (Needed)(On)(ON) --> OnNeededOn - There are 3 options each with 2 possibilities --> 2^3 = 8 possibilities. - Two different models are used: - 1) OpenLinearFlux, which does not require moiety conservation analysis - 1) SimpleFlux, which requires moiety conservation analysis - """ - def setUp(self) -> None: - pass - - def check(self, needed:bool, auto_moiety_option: bool, moiety_option:bool): - test_model = TestModelFactory("SimpleFlux" if needed else "OpenLinearFlux") - - rr = RoadRunner(test_model.str()) - rr.conservedMoietyAnalysis = moiety_option - - solver = rr.getSteadyStateSolver() - solver.setValue("auto_moiety_analysis", auto_moiety_option) - - # if moieties are needed, and both autoMoiety and moiety options are false - # then we expect an error - if test_model.modelName() == "SimpleFlux" and not auto_moiety_option and not moiety_option: - with self.assertRaises(Exception): - rr.steadyState() - else: +import unittest + + +class AutomaticMoietyConservationTests(unittest.TestCase): + """Test the automatic moiety analysis option, which is present in superclass + of all steady state solvers. + Three components to these tests: + 1) The model can either need moiety conservation analysis or not. + 2) The auto_moiety_analysis option can be on or off + 3) The RoadRunner moiety_conservation_analysis option can be on or off + Test are named using this convention: + (Needed or not)(auto_moiety_analysis)(moiety_conservation_analysis option) + i.e. (Needed)(On)(ON) --> OnNeededOn + There are 3 options each with 2 possibilities --> 2^3 = 8 possibilities. + Two different models are used: + 1) OpenLinearFlux, which does not require moiety conservation analysis + 1) SimpleFlux, which requires moiety conservation analysis + """ + def setUp(self) -> None: + pass + + def check(self, needed:bool, auto_moiety_option: bool, moiety_option:bool): + test_model = TestModelFactory("SimpleFlux" if needed else "OpenLinearFlux") + + rr = RoadRunner(test_model.str()) + rr.conservedMoietyAnalysis = moiety_option + + solver = rr.getSteadyStateSolver() + solver.setValue("auto_moiety_analysis", auto_moiety_option) + + # if moieties are needed, and both autoMoiety and moiety options are false + # then we expect an error + if test_model.modelName() == "SimpleFlux" and not auto_moiety_option and not moiety_option: + with self.assertRaises(Exception): rr.steadyState() - expected = test_model.steadyState() - actual = rr.getFloatingSpeciesConcentrationsNamedArray() - for species_name, steady_state_val in expected.items(): - print("Comparing expected steady state value: ", expected[species_name], - "with actual steady state value", actual[species_name][0]) - self.assertAlmostEqual(expected[species_name], actual[species_name][0]) - - def test_needed_on_on(self): - self.check(True, True, True) - - def test_needed_on_off(self): - self.check(True, True, False) - - def test_needed_off_on(self): - self.check(True, False, True) - - def test_needed_off_off(self): - """Errors out""" - self.check(True, False, False) - - def test_not_needed_on_on(self): - self.check(False, True, True) - - def test_not_needed_on_off(self): - self.check(False, True, False) - - def test_not_needed_off_on(self): - self.check(False, False, True) - - def test_not_needed_off_off(self): - """Errors out""" - self.check(False, False, False) - - - if __name__ == "__main__": - unittest.main() - - + else: + rr.steadyState() + expected = test_model.steadyState() + actual = rr.getFloatingSpeciesConcentrationsNamedArray() + for species_name, steady_state_val in expected.items(): + print("Comparing expected steady state value: ", expected[species_name], + "with actual steady state value", actual[species_name][0]) + self.assertAlmostEqual(expected[species_name], actual[species_name][0]) + + def test_needed_on_on(self): + self.check(True, True, True) + + def test_needed_on_off(self): + self.check(True, True, False) + + def test_needed_off_on(self): + self.check(True, False, True) + + def test_needed_off_off(self): + """Errors out""" + self.check(True, False, False) + + def test_not_needed_on_on(self): + self.check(False, True, True) + + def test_not_needed_on_off(self): + self.check(False, True, False) + + def test_not_needed_off_on(self): + self.check(False, False, True) + + def test_not_needed_off_off(self): + """Errors out""" + self.check(False, False, False) + + +if __name__ == "__main__": + unittest.main() + + diff --git a/test/python/test_forwardSensitivitySolver.py b/test/python/test_forwardSensitivitySolver.py index 85b5467c3b..0ca8c22d83 100644 --- a/test/python/test_forwardSensitivitySolver.py +++ b/test/python/test_forwardSensitivitySolver.py @@ -10,250 +10,247 @@ rr_site_packages, ] from roadrunner.roadrunner import RoadRunner, ForwardSensitivitySolver -import platform -if platform.system() != "Darwin": - - import roadrunner.tests.TestModelFactory as tmf - - import unittest - - - class FFSUnitTests(unittest.TestCase): - maxDiff = None - - def setUp(self) -> None: - - self.testModel = tmf.TestModelFactory("OpenLinearFlux") - self.rr = RoadRunner(self.testModel.str()) - self.model = self.rr.getModel() - self.sens = ForwardSensitivitySolver(self.model) - - def test_getGlobalParameterNames(self): - actual = self.sens.getGlobalParameterNames() - expected = ('kin', 'kf', 'kout', 'kb') - self.assertEqual(expected, actual) - - def test_getVariableNames(self): - actual = self.sens.getVariableNames() - expected = ('S1', 'S2') - self.assertEqual(expected, actual) - - def test_CheckValueOfNp(self): - actual = self.sens.Np - expected = 4 - self.assertEqual(expected, actual) - - def test_CheckValueOfNsWhenDefaultToAllParameters(self): - actual = self.sens.Ns - expected = 4 - self.assertEqual(expected, actual) - - def test_CheckValueOfNsWhenSelectingParameters(self): - sens2 = ForwardSensitivitySolver(self.model, ["kf"]) - actual = sens2.Ns - expected = 1 - self.assertEqual(expected, actual) - - def test_CheckValueOfNumModelVariables(self): - actual = self.sens.numModelVariables - expected = 2 - self.assertEqual(expected, actual) - - def test_getModelParametersAsMap(self): - actual = self.sens.getModelParametersAsMap() - expected = {'kb': 0.01, 'kf': 0.1, 'kin': 1.0, 'kout': 0.2} - self.assertEqual(expected, actual) - - def test_getModelParametersAsVector(self): - actual = self.sens.getModelParametersAsVector() - expected = np.array([1., 0.1, 0.2, 0.01]) - self.assertTrue((expected == actual).all()) - - def test_deducePlistDefaultToAllParameters(self): - self.sens.deducePlist() - actual = self.sens.plist - expected = (0, 1, 2, 3) - self.assertEqual(expected, actual) - - def test_deducePlistFirstParameter(self): - sens2 = ForwardSensitivitySolver(self.model, ["kin"]) - sens2.deducePlist() - actual = sens2.plist - expected = (0,) - self.assertEqual(expected, actual) - - def test_deducePlistSecondParameter(self): - sens2 = ForwardSensitivitySolver(self.model, ["kf"]) - sens2.deducePlist() - actual = sens2.plist - expected = (1,) - self.assertEqual(expected, actual) - - def test_SettingsNonLinearSolver(self): - self.sens.setValue("nonlinear_solver", "fixed_point") - actual = self.sens.getValue("nonlinear_solver") - expected = "fixed_point" - self.assertEqual(expected, actual) - - class FFSIntegrationTests(unittest.TestCase): - maxDiff = None - - def setUp(self) -> None: - self.testModel = tmf.TestModelFactory("OpenLinearFlux") - self.rr = RoadRunner(self.testModel.str()) - self.model = self.rr.getModel() - self.sens = ForwardSensitivitySolver(self.model) - - def checkMatrices3DEqual(self, expected, actual, places=7): - for k in range(expected.shape[0]): - for j in range(expected.shape[1]): - for i in range(expected.shape[2]): - print(k, j, i) - print(expected[k, j, i], actual[k, j, i]) - self.assertAlmostEqual(expected[k, j, i], actual[k, j, i], places=places) - - def checkSensWithModel(self, modelName: str, places: int = 7): - """Check that we can integrate a model in Python without the RoadRunner object - - Args: - modelName: The name of a test model to integrate. The test model must implement th e - timeSeriesResult interface. See TestModelFactor.h - places: number of decimal places to use for floating point comparisons - """ - if modelName not in tmf.getAvailableTestModels(): - raise ValueError(f"Model name \"{modelName}\" not available. Here are a list of " - f"available model names: {tmf.getAvailableTestModels()}") - testModel = tmf.TestModelFactory(modelName) - if tmf.TimeSeriesSensitivityResult not in testModel.__class__.mro(): - raise ValueError("This TestModel does not implement the TimeSeriesSensitivityResult interface. ") - - # we need a RoadRunner object to create a model for us - rr = RoadRunner(testModel.str()) - model = rr.getModel() - solver = ForwardSensitivitySolver(model) - - # all tests are done with stiff set to False - # this is probably a weakness - solver.setValue("stiff", False) - - settingsMap = testModel.timeSeriesSensitivityResultSettings() - start = settingsMap["start"] - duration = settingsMap["duration"] - numSteps = settingsMap["steps"] - numIntervals = numSteps - 1 - - # always have one more number of data points (in the row direction) than there are number of steps / intervals - stepSize = (duration - start) / numIntervals - - # collect true values from the TestModel type - expectedTime, expectedResults, expectedRowNames, expectedColNames = testModel.timeSeriesSensitivityResult() - - # a place to store actual test result data - results = np.zeros(expectedResults.shape) - idx = np.zeros(expectedTime.shape) - - - numStates = solver.numModelVariables - numParameters = solver.Ns - - # sensitivities for t=0 are always 0 - if start != 0.0: - idx[0] = rr.getCurrentTime() - results[0] = solver.getSensitivityMatrix() - - # integrate, collect data for comparison against actual data - t = start - for i in range(1, numSteps): - t = solver.integrate(t, stepSize) - idx[i] = t - results[i] = solver.getSensitivityMatrix() - - - print("Expected Results") - print(expectedResults) - print("Actual Results") - print(results) - # check matrices "almost" equal - self.checkMatrices3DEqual(expectedResults, results, places=places) - - # check index the same - self.assertTrue((expectedTime == idx).all()) - - def checkSensWithRoadRunner(self, modelName: str, places: int = 7): - """Check that we can integrate a model in Python using the main RoadRunner api - - Args: - modelName: The name of a test model to integrate. The test model must implement th e - timeSeriesResult interface. See TestModelFactor.h - places: number of decimal places to use for floating point comparisons - """ - if modelName not in tmf.getAvailableTestModels(): - raise ValueError(f"Model name \"{modelName}\" not available. Here are a list of " - f"available model names: {tmf.getAvailableTestModels()}") - testModel = tmf.TestModelFactory(modelName) - if tmf.TimeSeriesSensitivityResult not in testModel.__class__.mro(): - raise ValueError("This TestModel does not implement the TimeSeriesSensitivityResult interface. ") - - rr = RoadRunner(testModel.str()) - - # all tests are done with stiff set to False - # this is probably a weakness - rr.getSensitivitySolver().setValue("stiff", False) - - settingsMap = testModel.timeSeriesSensitivityResultSettings() - start = settingsMap["start"] - duration = settingsMap["duration"] - numSteps = settingsMap["steps"] - numIntervals = numSteps - 1 - # always have one more number of data points (in the row direction) than there are number of steps / intervals - stepSize = (duration - start) / numIntervals - - stop = duration # slightly clearer - idx, results, actualRowNames, actualColNames = rr.timeSeriesSensitivities(start, stop, numSteps) - - # collect true values from the TestModel type - expectedTime, expectedResults, expectedRowNames, expectedColNames = testModel.timeSeriesSensitivityResult() - - print("Expected Results") - print(expectedResults) - print("Actual Results") - print(results) - # check matrices "almost" equal - self.checkMatrices3DEqual(expectedResults, results, places=places) - - # check index the same - self.assertTrue((expectedTime == idx).all()) - self.assertEqual(expectedRowNames, actualRowNames) - self.assertEqual(expectedColNames, actualColNames) - - def testOpenLinearFluxWithoutRoadRunnerInstance(self): - self.checkSensWithModel("OpenLinearFlux", 1) - - def testSimpleFluxWithoutRoadRunnerInstance(self): - self.checkSensWithModel("SimpleFlux", -1) - - def testModel269WithoutRoadRunnerInstance(self): - self.checkSensWithModel("Model269", 1) - - def testModel28WithoutRoadRunnerInstance(self): - self.checkSensWithModel("Model28", 1) - - def testOpenLinearWithRoadRunnerInstance(self): - self.checkSensWithModel("OpenLinearFlux", 1) - - def testSimpleFluxWithRoadRunnerInstance(self): - self.checkSensWithModel("SimpleFlux", -1) - - def testModel269WithRoadRunnerInstance(self): - self.checkSensWithModel("Model269", 1) - - def testModel28WithRoadRunnerInstance(self): - self.checkSensWithModel("Model28", 1) - - - - - - - - +import roadrunner.tests.TestModelFactory as tmf + +import unittest + + +class FFSUnitTests(unittest.TestCase): + maxDiff = None + + def setUp(self) -> None: + + self.testModel = tmf.TestModelFactory("OpenLinearFlux") + self.rr = RoadRunner(self.testModel.str()) + self.model = self.rr.getModel() + self.sens = ForwardSensitivitySolver(self.model) + + def test_getGlobalParameterNames(self): + actual = self.sens.getGlobalParameterNames() + expected = ('kin', 'kf', 'kout', 'kb') + self.assertEqual(expected, actual) + + def test_getVariableNames(self): + actual = self.sens.getVariableNames() + expected = ('S1', 'S2') + self.assertEqual(expected, actual) + + def test_CheckValueOfNp(self): + actual = self.sens.Np + expected = 4 + self.assertEqual(expected, actual) + + def test_CheckValueOfNsWhenDefaultToAllParameters(self): + actual = self.sens.Ns + expected = 4 + self.assertEqual(expected, actual) + + def test_CheckValueOfNsWhenSelectingParameters(self): + sens2 = ForwardSensitivitySolver(self.model, ["kf"]) + actual = sens2.Ns + expected = 1 + self.assertEqual(expected, actual) + + def test_CheckValueOfNumModelVariables(self): + actual = self.sens.numModelVariables + expected = 2 + self.assertEqual(expected, actual) + + def test_getModelParametersAsMap(self): + actual = self.sens.getModelParametersAsMap() + expected = {'kb': 0.01, 'kf': 0.1, 'kin': 1.0, 'kout': 0.2} + self.assertEqual(expected, actual) + + def test_getModelParametersAsVector(self): + actual = self.sens.getModelParametersAsVector() + expected = np.array([1., 0.1, 0.2, 0.01]) + self.assertTrue((expected == actual).all()) + + def test_deducePlistDefaultToAllParameters(self): + self.sens.deducePlist() + actual = self.sens.plist + expected = (0, 1, 2, 3) + self.assertEqual(expected, actual) + + def test_deducePlistFirstParameter(self): + sens2 = ForwardSensitivitySolver(self.model, ["kin"]) + sens2.deducePlist() + actual = sens2.plist + expected = (0,) + self.assertEqual(expected, actual) + + def test_deducePlistSecondParameter(self): + sens2 = ForwardSensitivitySolver(self.model, ["kf"]) + sens2.deducePlist() + actual = sens2.plist + expected = (1,) + self.assertEqual(expected, actual) + + def test_SettingsNonLinearSolver(self): + self.sens.setValue("nonlinear_solver", "fixed_point") + actual = self.sens.getValue("nonlinear_solver") + expected = "fixed_point" + self.assertEqual(expected, actual) + +class FFSIntegrationTests(unittest.TestCase): + maxDiff = None + + def setUp(self) -> None: + self.testModel = tmf.TestModelFactory("OpenLinearFlux") + self.rr = RoadRunner(self.testModel.str()) + self.model = self.rr.getModel() + self.sens = ForwardSensitivitySolver(self.model) + + def checkMatrices3DEqual(self, expected, actual, places=7): + for k in range(expected.shape[0]): + for j in range(expected.shape[1]): + for i in range(expected.shape[2]): + print(k, j, i) + print(expected[k, j, i], actual[k, j, i]) + self.assertAlmostEqual(expected[k, j, i], actual[k, j, i], places=places) + + def checkSensWithModel(self, modelName: str, places: int = 7): + """Check that we can integrate a model in Python without the RoadRunner object + + Args: + modelName: The name of a test model to integrate. The test model must implement th e + timeSeriesResult interface. See TestModelFactor.h + places: number of decimal places to use for floating point comparisons + """ + if modelName not in tmf.getAvailableTestModels(): + raise ValueError(f"Model name \"{modelName}\" not available. Here are a list of " + f"available model names: {tmf.getAvailableTestModels()}") + testModel = tmf.TestModelFactory(modelName) + if tmf.TimeSeriesSensitivityResult not in testModel.__class__.mro(): + raise ValueError("This TestModel does not implement the TimeSeriesSensitivityResult interface. ") + + # we need a RoadRunner object to create a model for us + rr = RoadRunner(testModel.str()) + model = rr.getModel() + solver = ForwardSensitivitySolver(model) + + # all tests are done with stiff set to False + # this is probably a weakness + solver.setValue("stiff", False) + + settingsMap = testModel.timeSeriesSensitivityResultSettings() + start = settingsMap["start"] + duration = settingsMap["duration"] + numSteps = settingsMap["steps"] + numIntervals = numSteps - 1 + + # always have one more number of data points (in the row direction) than there are number of steps / intervals + stepSize = (duration - start) / numIntervals + + # collect true values from the TestModel type + expectedTime, expectedResults, expectedRowNames, expectedColNames = testModel.timeSeriesSensitivityResult() + + # a place to store actual test result data + results = np.zeros(expectedResults.shape) + idx = np.zeros(expectedTime.shape) + + + numStates = solver.numModelVariables + numParameters = solver.Ns + + # sensitivities for t=0 are always 0 + if start != 0.0: + idx[0] = rr.getCurrentTime() + results[0] = solver.getSensitivityMatrix() + + # integrate, collect data for comparison against actual data + t = start + for i in range(1, numSteps): + t = solver.integrate(t, stepSize) + idx[i] = t + results[i] = solver.getSensitivityMatrix() + + + print("Expected Results") + print(expectedResults) + print("Actual Results") + print(results) + # check matrices "almost" equal + self.checkMatrices3DEqual(expectedResults, results, places=places) + + # check index the same + self.assertTrue((expectedTime == idx).all()) + + def checkSensWithRoadRunner(self, modelName: str, places: int = 7): + """Check that we can integrate a model in Python using the main RoadRunner api + + Args: + modelName: The name of a test model to integrate. The test model must implement th e + timeSeriesResult interface. See TestModelFactor.h + places: number of decimal places to use for floating point comparisons + """ + if modelName not in tmf.getAvailableTestModels(): + raise ValueError(f"Model name \"{modelName}\" not available. Here are a list of " + f"available model names: {tmf.getAvailableTestModels()}") + testModel = tmf.TestModelFactory(modelName) + if tmf.TimeSeriesSensitivityResult not in testModel.__class__.mro(): + raise ValueError("This TestModel does not implement the TimeSeriesSensitivityResult interface. ") + + rr = RoadRunner(testModel.str()) + + # all tests are done with stiff set to False + # this is probably a weakness + rr.getSensitivitySolver().setValue("stiff", False) + + settingsMap = testModel.timeSeriesSensitivityResultSettings() + start = settingsMap["start"] + duration = settingsMap["duration"] + numSteps = settingsMap["steps"] + numIntervals = numSteps - 1 + # always have one more number of data points (in the row direction) than there are number of steps / intervals + stepSize = (duration - start) / numIntervals + + stop = duration # slightly clearer + idx, results, actualRowNames, actualColNames = rr.timeSeriesSensitivities(start, stop, numSteps) + + # collect true values from the TestModel type + expectedTime, expectedResults, expectedRowNames, expectedColNames = testModel.timeSeriesSensitivityResult() + + print("Expected Results") + print(expectedResults) + print("Actual Results") + print(results) + # check matrices "almost" equal + self.checkMatrices3DEqual(expectedResults, results, places=places) + + # check index the same + self.assertTrue((expectedTime == idx).all()) + self.assertEqual(expectedRowNames, actualRowNames) + self.assertEqual(expectedColNames, actualColNames) + + def testOpenLinearFluxWithoutRoadRunnerInstance(self): + self.checkSensWithModel("OpenLinearFlux", 1) + + def testSimpleFluxWithoutRoadRunnerInstance(self): + self.checkSensWithModel("SimpleFlux", -1) + + def testModel269WithoutRoadRunnerInstance(self): + self.checkSensWithModel("Model269", 1) + + def testModel28WithoutRoadRunnerInstance(self): + self.checkSensWithModel("Model28", 1) + + def testOpenLinearWithRoadRunnerInstance(self): + self.checkSensWithModel("OpenLinearFlux", 1) + + def testSimpleFluxWithRoadRunnerInstance(self): + self.checkSensWithModel("SimpleFlux", -1) + + def testModel269WithRoadRunnerInstance(self): + self.checkSensWithModel("Model269", 1) + + def testModel28WithRoadRunnerInstance(self): + self.checkSensWithModel("Model28", 1) + + + + + + + + diff --git a/test/python/test_integrator.py b/test/python/test_integrator.py index e7626578ac..4265023983 100644 --- a/test/python/test_integrator.py +++ b/test/python/test_integrator.py @@ -10,238 +10,234 @@ rr_site_packages, ] from roadrunner.roadrunner import RoadRunner, CVODEIntegrator, ForwardSensitivitySolver +import roadrunner.tests.TestModelFactory as tmf -import platform -if platform.system() != "Darwin": - - import roadrunner.tests.TestModelFactory as tmf - - import unittest - - - class CVODEIntegratorTests(unittest.TestCase): - maxDiff = None - - def setUp(self) -> None: - - self.testModel = tmf.TestModelFactory("OpenLinearFlux") - self.rr = RoadRunner(self.testModel.str()) - self.model = self.rr.getModel() - self.integrator = CVODEIntegrator(self.model) - - def checkMatricesEqual(self, expected, actual, places=7): - for i in range(expected.shape[0]): - for j in range(expected.shape[1]): - self.assertAlmostEqual(expected[i, j], actual[i, j], places=places) - - def checkModelIntegrates(self, modelName: str, SolverType=CVODEIntegrator, places: int = 7): - """Check that we can integrate a model in Python without the RoadRunner object - - Args: - modelName: The name of a test model to integrate. The test model must implement th e - timeSeriesResult interface. See TestModelFactor.h - SolverType: Either CVODEIntegrator or ForwardSensitivitySolver, since this method doubles for both - places: number of decimal places to use for floating point comparisons - """ - if modelName not in tmf.getAvailableTestModels(): - raise ValueError(f"Model name \"{modelName}\" not available. Here are a list of " - f"available model names: {tmf.getAvailableTestModels()}") - testModel = tmf.TestModelFactory(modelName) - if tmf.TimeSeriesResult not in testModel.__class__.mro(): - raise ValueError("This TestModel does not implement the TimeSeriesResult interface. ") - - # we need a RoadRunner object to create a model for us - rr = RoadRunner(testModel.str()) - model = rr.getModel() - integrator = SolverType(model) - - # all tests are done with stiff set to False - # this is probably a weakness - integrator.setValue("stiff", False) - - settingsMap = testModel.timeSeriesSettings() - start = settingsMap["start"] - duration = settingsMap["duration"] - steps = settingsMap["steps"] - - # always have one more number of data points (in the row direction) than there are number of steps / intervals - num = steps + 1 - stepSize = (duration - start) / steps - - # collect true values from the TestModel type - expectedResults = testModel.timeSeriesResult() - - # a place to store actual test result data - results = np.zeros(expectedResults.shape) - - # fill in 0th time point - results[0, 0] = rr.getCurrentTime() - numStates = len(rr.getFloatingSpeciesInitialConcentrationIds()) - +import unittest + + +class CVODEIntegratorTests(unittest.TestCase): + maxDiff = None + + def setUp(self) -> None: + + self.testModel = tmf.TestModelFactory("OpenLinearFlux") + self.rr = RoadRunner(self.testModel.str()) + self.model = self.rr.getModel() + self.integrator = CVODEIntegrator(self.model) + + def checkMatricesEqual(self, expected, actual, places=7): + for i in range(expected.shape[0]): + for j in range(expected.shape[1]): + self.assertAlmostEqual(expected[i, j], actual[i, j], places=places) + + def checkModelIntegrates(self, modelName: str, SolverType=CVODEIntegrator, places: int = 7): + """Check that we can integrate a model in Python without the RoadRunner object + + Args: + modelName: The name of a test model to integrate. The test model must implement th e + timeSeriesResult interface. See TestModelFactor.h + SolverType: Either CVODEIntegrator or ForwardSensitivitySolver, since this method doubles for both + places: number of decimal places to use for floating point comparisons + """ + if modelName not in tmf.getAvailableTestModels(): + raise ValueError(f"Model name \"{modelName}\" not available. Here are a list of " + f"available model names: {tmf.getAvailableTestModels()}") + testModel = tmf.TestModelFactory(modelName) + if tmf.TimeSeriesResult not in testModel.__class__.mro(): + raise ValueError("This TestModel does not implement the TimeSeriesResult interface. ") + + # we need a RoadRunner object to create a model for us + rr = RoadRunner(testModel.str()) + model = rr.getModel() + integrator = SolverType(model) + + # all tests are done with stiff set to False + # this is probably a weakness + integrator.setValue("stiff", False) + + settingsMap = testModel.timeSeriesSettings() + start = settingsMap["start"] + duration = settingsMap["duration"] + steps = settingsMap["steps"] + + # always have one more number of data points (in the row direction) than there are number of steps / intervals + num = steps + 1 + stepSize = (duration - start) / steps + + # collect true values from the TestModel type + expectedResults = testModel.timeSeriesResult() + + # a place to store actual test result data + results = np.zeros(expectedResults.shape) + + # fill in 0th time point + results[0, 0] = rr.getCurrentTime() + numStates = len(rr.getFloatingSpeciesInitialConcentrationIds()) + + for j in range(1, numStates + 1): + results[0, j] = rr.getFloatingSpeciesAmountsNamedArray()[0][j - 1] + + t = start + for i in range(1, num): + t = integrator.integrate(t, stepSize) + results[i, 0] = rr.getCurrentTime() for j in range(1, numStates + 1): - results[0, j] = rr.getFloatingSpeciesAmountsNamedArray()[0][j - 1] - - t = start - for i in range(1, num): - t = integrator.integrate(t, stepSize) - results[i, 0] = rr.getCurrentTime() - for j in range(1, numStates + 1): - results[i, j] = rr.getFloatingSpeciesAmountsNamedArray()[0][j - 1] - - print(expectedResults) - print(results) - self.checkMatricesEqual(expectedResults, results, places=places) - - def checkRoadRunnerSimulates(self, modelName: str, places: int = 5): - """Check that the RoadRunner.simulate produces correct output""" - - if modelName not in tmf.getAvailableTestModels(): - raise ValueError(f"Model name \"{modelName}\" not available. Here are a list of " - f"available model names: {tmf.getAvailableTestModels()}") - testModel = tmf.TestModelFactory(modelName) - - if tmf.TimeSeriesResult not in testModel.__class__.mro(): - raise ValueError("This TestModel does not implement the TimeSeriesResult interface. ") - - # we need a RoadRunner object to create a model for us - rr = RoadRunner(testModel.str()) - - # all tests are done with stiff set to False - # this is probably a weakness - rr.getIntegrator().setValue("stiff", False) - - settingsMap = testModel.timeSeriesSettings() - start = settingsMap["start"] - duration = settingsMap["duration"] - steps = settingsMap["steps"] - - # always have one more number of data points (in the row direction) than there are number of steps / intervals - num = steps + 1 - stepSize = (duration - start) / steps - - # collect true values from the TestModel type - expectedResults = testModel.timeSeriesResult() - - results = rr.simulate(start, duration, num) - self.checkMatricesEqual(expectedResults, results, places=places) - - # Integration tests - - # With CVODEIntegrator only - - def testOpenLinearFluxWithoutRoadRunnerInstance(self): - self.checkModelIntegrates("OpenLinearFlux", CVODEIntegrator, 5) - - def testSimpleFluxWithoutRoadRunnerInstance(self): - self.checkModelIntegrates("SimpleFlux", CVODEIntegrator, 5) - - def testModel269WithoutRoadRunnerInstance(self): - self.checkModelIntegrates("Model269", CVODEIntegrator, 5) - - def testModel28WithoutRoadRunnerInstance(self): - self.checkModelIntegrates("Model28", CVODEIntegrator, 5) - - def testFactorialInRateLawWithoutRoadRunnerInstance(self): - self.checkModelIntegrates("FactorialInRateLaw", CVODEIntegrator, 4) - - # with ForwardSensitivitySolver only - # Note: This is slight abuse of classification, but the test method - # doubles nicely for the FFS - - def testOpenLinearFluxWithoutRoadRunnerInstanceFFS(self): - self.checkModelIntegrates("OpenLinearFlux", ForwardSensitivitySolver, 5) - - def testSimpleFluxWithoutRoadRunnerInstanceFFS(self): - self.checkModelIntegrates("SimpleFlux", ForwardSensitivitySolver, 5) - - def testModel269WithoutRoadRunnerInstanceFFS(self): - self.checkModelIntegrates("Model269", ForwardSensitivitySolver, 5) - - def testModel28WithoutRoadRunnerInstanceFFS(self): - self.checkModelIntegrates("Model28", ForwardSensitivitySolver, 5) - - def testFactorialInRateLawWithoutRoadRunnerInstanceFFS(self): - self.checkModelIntegrates("FactorialInRateLaw", ForwardSensitivitySolver, 4) - - def testOpenLinearFluxWithRoadRunnerInstance(self): - self.checkRoadRunnerSimulates("OpenLinearFlux", 5) - - def testSimpleFluxWithRoadRunnerInstance(self): - self.checkRoadRunnerSimulates("SimpleFlux", 5) - - def testModel269WithRoadRunnerInstance(self): - self.checkRoadRunnerSimulates("Model269", 5) - - def testModel28WithRoadRunnerInstance(self): - self.checkRoadRunnerSimulates("Model28", 5) - - def testFactorialInRateLawWithRoadRunnerInstance(self): - self.checkRoadRunnerSimulates("FactorialInRateLaw", 4) - - # Unit tests - - def test_relative_tolerance(self): - self.integrator.setValue("relative_tolerance", 1e-07) - self.assertEqual(1e-07, self.integrator.getValue("relative_tolerance")) - - def test_absolute_tolerance(self): - self.integrator.setValue("absolute_tolerance", 1e-13) - self.assertEqual(1e-13, self.integrator.getValue("absolute_tolerance")) - - def test_stiff(self): - self.integrator.setValue("stiff", False) - self.assertFalse(self.integrator.getValue("stiff")) - - def test_set_maximum_bdf_order(self): - self.integrator.setValue("maximum_bdf_order", 3) - self.assertEqual(3, self.integrator.getValue("maximum_bdf_order")) - - def test_set_maximum_adams_order(self): - self.integrator.setValue("maximum_adams_order", 2) - self.assertEqual(2, self.integrator.getValue("maximum_adams_order")) - - def test_set_maximum_num_steps(self): - self.integrator.setValue("maximum_num_steps", 500) - self.assertEqual(500, self.integrator.getValue("maximum_num_steps")) - - def test_set_maximum_time_step(self): - self.integrator.setValue("maximum_time_step", 5) - self.assertEqual(5, self.integrator.getValue("maximum_time_step")) - - def test_set_minimum_time_step(self): - self.integrator.setValue("minimum_time_step", 0.1) - self.assertEqual(0.1, self.integrator.getValue("minimum_time_step")) - - def test_set_initial_time_step(self): - self.integrator.setValue("initial_time_step", 3.56) - self.assertEqual(3.56, self.integrator.getValue("initial_time_step")) - - def test_set_multiple_steps(self): - self.integrator.setValue("multiple_steps", True) - self.assertTrue(self.integrator.getValue("multiple_steps")) - - def test_set_variable_step_size(self): - self.integrator.setValue("variable_step_size", True) - self.assertTrue(self.integrator.getValue("variable_step_size")) - - def test_set_max_output_rows(self): - self.integrator.setValue("max_output_rows", 50) - self.assertEqual(50, self.integrator.getValue("max_output_rows")) - - def test_set_concentration_tolerance(self): - self.integrator.setConcentrationTolerance(1e-8) - - def test_simulate_sequence_with_times(self): - results = self.rr.simulate() - self.assertEqual(len(results), 51); - results = self.rr.simulate(0, 10, 11); - self.assertEqual(len(results), 11); - results = self.rr.simulate(times=[3, 5, 11]); - self.assertEqual(len(results), 3); - results = self.rr.simulate(0, 10, 11); - self.assertEqual(len(results), 11); - results = self.rr.simulate() - self.assertEqual(len(results), 51); - - if __name__ == "__main__": - unittest.main() + results[i, j] = rr.getFloatingSpeciesAmountsNamedArray()[0][j - 1] + + print(expectedResults) + print(results) + self.checkMatricesEqual(expectedResults, results, places=places) + + def checkRoadRunnerSimulates(self, modelName: str, places: int = 5): + """Check that the RoadRunner.simulate produces correct output""" + + if modelName not in tmf.getAvailableTestModels(): + raise ValueError(f"Model name \"{modelName}\" not available. Here are a list of " + f"available model names: {tmf.getAvailableTestModels()}") + testModel = tmf.TestModelFactory(modelName) + + if tmf.TimeSeriesResult not in testModel.__class__.mro(): + raise ValueError("This TestModel does not implement the TimeSeriesResult interface. ") + + # we need a RoadRunner object to create a model for us + rr = RoadRunner(testModel.str()) + + # all tests are done with stiff set to False + # this is probably a weakness + rr.getIntegrator().setValue("stiff", False) + + settingsMap = testModel.timeSeriesSettings() + start = settingsMap["start"] + duration = settingsMap["duration"] + steps = settingsMap["steps"] + + # always have one more number of data points (in the row direction) than there are number of steps / intervals + num = steps + 1 + stepSize = (duration - start) / steps + + # collect true values from the TestModel type + expectedResults = testModel.timeSeriesResult() + + results = rr.simulate(start, duration, num) + self.checkMatricesEqual(expectedResults, results, places=places) + + # Integration tests + + # With CVODEIntegrator only + + def testOpenLinearFluxWithoutRoadRunnerInstance(self): + self.checkModelIntegrates("OpenLinearFlux", CVODEIntegrator, 5) + + def testSimpleFluxWithoutRoadRunnerInstance(self): + self.checkModelIntegrates("SimpleFlux", CVODEIntegrator, 5) + + def testModel269WithoutRoadRunnerInstance(self): + self.checkModelIntegrates("Model269", CVODEIntegrator, 5) + + def testModel28WithoutRoadRunnerInstance(self): + self.checkModelIntegrates("Model28", CVODEIntegrator, 5) + + def testFactorialInRateLawWithoutRoadRunnerInstance(self): + self.checkModelIntegrates("FactorialInRateLaw", CVODEIntegrator, 4) + + # with ForwardSensitivitySolver only + # Note: This is slight abuse of classification, but the test method + # doubles nicely for the FFS + + def testOpenLinearFluxWithoutRoadRunnerInstanceFFS(self): + self.checkModelIntegrates("OpenLinearFlux", ForwardSensitivitySolver, 5) + + def testSimpleFluxWithoutRoadRunnerInstanceFFS(self): + self.checkModelIntegrates("SimpleFlux", ForwardSensitivitySolver, 5) + + def testModel269WithoutRoadRunnerInstanceFFS(self): + self.checkModelIntegrates("Model269", ForwardSensitivitySolver, 5) + + def testModel28WithoutRoadRunnerInstanceFFS(self): + self.checkModelIntegrates("Model28", ForwardSensitivitySolver, 5) + + def testFactorialInRateLawWithoutRoadRunnerInstanceFFS(self): + self.checkModelIntegrates("FactorialInRateLaw", ForwardSensitivitySolver, 4) + + def testOpenLinearFluxWithRoadRunnerInstance(self): + self.checkRoadRunnerSimulates("OpenLinearFlux", 5) + + def testSimpleFluxWithRoadRunnerInstance(self): + self.checkRoadRunnerSimulates("SimpleFlux", 5) + + def testModel269WithRoadRunnerInstance(self): + self.checkRoadRunnerSimulates("Model269", 5) + + def testModel28WithRoadRunnerInstance(self): + self.checkRoadRunnerSimulates("Model28", 5) + + def testFactorialInRateLawWithRoadRunnerInstance(self): + self.checkRoadRunnerSimulates("FactorialInRateLaw", 4) + + # Unit tests + + def test_relative_tolerance(self): + self.integrator.setValue("relative_tolerance", 1e-07) + self.assertEqual(1e-07, self.integrator.getValue("relative_tolerance")) + + def test_absolute_tolerance(self): + self.integrator.setValue("absolute_tolerance", 1e-13) + self.assertEqual(1e-13, self.integrator.getValue("absolute_tolerance")) + + def test_stiff(self): + self.integrator.setValue("stiff", False) + self.assertFalse(self.integrator.getValue("stiff")) + + def test_set_maximum_bdf_order(self): + self.integrator.setValue("maximum_bdf_order", 3) + self.assertEqual(3, self.integrator.getValue("maximum_bdf_order")) + + def test_set_maximum_adams_order(self): + self.integrator.setValue("maximum_adams_order", 2) + self.assertEqual(2, self.integrator.getValue("maximum_adams_order")) + + def test_set_maximum_num_steps(self): + self.integrator.setValue("maximum_num_steps", 500) + self.assertEqual(500, self.integrator.getValue("maximum_num_steps")) + + def test_set_maximum_time_step(self): + self.integrator.setValue("maximum_time_step", 5) + self.assertEqual(5, self.integrator.getValue("maximum_time_step")) + + def test_set_minimum_time_step(self): + self.integrator.setValue("minimum_time_step", 0.1) + self.assertEqual(0.1, self.integrator.getValue("minimum_time_step")) + + def test_set_initial_time_step(self): + self.integrator.setValue("initial_time_step", 3.56) + self.assertEqual(3.56, self.integrator.getValue("initial_time_step")) + + def test_set_multiple_steps(self): + self.integrator.setValue("multiple_steps", True) + self.assertTrue(self.integrator.getValue("multiple_steps")) + + def test_set_variable_step_size(self): + self.integrator.setValue("variable_step_size", True) + self.assertTrue(self.integrator.getValue("variable_step_size")) + + def test_set_max_output_rows(self): + self.integrator.setValue("max_output_rows", 50) + self.assertEqual(50, self.integrator.getValue("max_output_rows")) + + def test_set_concentration_tolerance(self): + self.integrator.setConcentrationTolerance(1e-8) + + def test_simulate_sequence_with_times(self): + results = self.rr.simulate() + self.assertEqual(len(results), 51); + results = self.rr.simulate(0, 10, 11); + self.assertEqual(len(results), 11); + results = self.rr.simulate(times=[3, 5, 11]); + self.assertEqual(len(results), 3); + results = self.rr.simulate(0, 10, 11); + self.assertEqual(len(results), 11); + results = self.rr.simulate() + self.assertEqual(len(results), 51); + +if __name__ == "__main__": + unittest.main() diff --git a/test/python/test_jacobian.py b/test/python/test_jacobian.py index 3a62f023d3..a2fb849103 100644 --- a/test/python/test_jacobian.py +++ b/test/python/test_jacobian.py @@ -19,138 +19,135 @@ RoadRunner, Config ) -import platform -if platform.system() != "Darwin": - - try: - from roadrunner.tests import TestModelFactory as tmf - from roadrunner.tests.RoadRunnerTest import RoadRunnerTest - except: - import TestModelFactory as tmf - from RoadRunnerTest import RoadRunnerTest - - class JacobianTests(RoadRunnerTest): - - def setUp(self) -> None: - pass - - def tearDown(self) -> None: - pass - - def checkMatricesEqualValues(self, expected: np.ndarray, actual: np.ndarray, places=4): - if expected.shape != actual.shape: - if expected.shape == (1,) and actual.shape == (1,1): - self.assertAlmostEqual(expected[0], actual[0][0], places=places) - return - raise ValueError("expected and actual are different sizes") - arr1 = [] - arr2 = [] - for i in range(expected.shape[0]): - for j in range(expected.shape[1]): - arr1.append(expected[i][j]) - arr2.append(actual[i][j]) - arr1.sort() - arr2.sort() - for i in range(len(arr1)): - self.assertAlmostEqual(arr1[i], arr2[i], places=places) - - def _checkJacFull(self, modelName: str, rrJacMode: Config.ROADRUNNER_JACOBIAN_MODE): - """ - check the values of TestModel jacobian interface against those computed by the current model - - If full is set to false, then we turn on moiety conservation - - :param modelName: A valid test model name (See TestModelFactory::getAvailableTestModelNames() - :param tol: degree of tolerance, allowed error - :param rrJacMode: either Config::ROADRUNNER_JACOBIAN_MODE_AMOUNTS or Config::ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS - :param full: true if we are looking at full jacobian, false if were looking at reduced. - """ - self.checkValidTestModelName(modelName) - testModel = tmf.TestModelFactory(modelName) - self.checkTestModelImplements(testModel, tmf.JacobianResultFull) - rr = RoadRunner(testModel.str()) - Config.setValue(Config.ROADRUNNER_JACOBIAN_MODE, rrJacMode) - - expectedJac = None - if rrJacMode == Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS: - expectedJac = testModel.fullJacobianConc() - elif rrJacMode == Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS: - expectedJac = testModel.fullJacobianAmt() - - else: - raise ValueError("Should never reach here") - - jacSettings = testModel.jacobianSettings() - if "steady_state" in jacSettings.keys(): - rr.conservedMoietyAnalysis = True - rr.steadyState() - actualJac = rr.getFullJacobian() - - print("\n", expectedJac) - print(actualJac) - - # expectedJac.sortColsByLabels(); - # expectedJac.sortRowsByLabels(); - # actualJac.sortColsByLabels(); - # actualJac.sortRowsByLabels(); - - - self.checkMatricesEqualValues(expectedJac, actualJac) - - def _checkJacReduced(self, modelName: str, rrJacMode: Config.ROADRUNNER_JACOBIAN_MODE): - """ - check the values of TestModel jacobian interface against those computed by the current model - - If full is set to false, then we turn on moiety conservation - - :param modelName: A valid test model name (See TestModelFactory::getAvailableTestModelNames() - :param tol: degree of tolerance, allowed error - :param rrJacMode: either Config::ROADRUNNER_JACOBIAN_MODE_AMOUNTS or Config::ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS - :param full: true if we are looking at full jacobian, false if were looking at reduced. - """ - self.checkValidTestModelName(modelName) - testModel = tmf.TestModelFactory(modelName) - self.checkTestModelImplements(testModel, tmf.JacobianResultReduced) - rr = RoadRunner(testModel.str()) - Config.setValue(Config.ROADRUNNER_JACOBIAN_MODE, rrJacMode) - - expectedJac = None - if rrJacMode == Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS: - expectedJac = testModel.reducedJacobianConc() - elif rrJacMode == Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS: - expectedJac = testModel.reducedJacobianAmt() - else: - raise ValueError("Should never reach here") - +try: + from roadrunner.tests import TestModelFactory as tmf + from roadrunner.tests.RoadRunnerTest import RoadRunnerTest +except: + import TestModelFactory as tmf + from RoadRunnerTest import RoadRunnerTest + +class JacobianTests(RoadRunnerTest): + + def setUp(self) -> None: + pass + + def tearDown(self) -> None: + pass + + def checkMatricesEqualValues(self, expected: np.ndarray, actual: np.ndarray, places=4): + if expected.shape != actual.shape: + if expected.shape == (1,) and actual.shape == (1,1): + self.assertAlmostEqual(expected[0], actual[0][0], places=places) + return + raise ValueError("expected and actual are different sizes") + arr1 = [] + arr2 = [] + for i in range(expected.shape[0]): + for j in range(expected.shape[1]): + arr1.append(expected[i][j]) + arr2.append(actual[i][j]) + arr1.sort() + arr2.sort() + for i in range(len(arr1)): + self.assertAlmostEqual(arr1[i], arr2[i], places=places) + + def _checkJacFull(self, modelName: str, rrJacMode: Config.ROADRUNNER_JACOBIAN_MODE): + """ + check the values of TestModel jacobian interface against those computed by the current model + + If full is set to false, then we turn on moiety conservation + + :param modelName: A valid test model name (See TestModelFactory::getAvailableTestModelNames() + :param tol: degree of tolerance, allowed error + :param rrJacMode: either Config::ROADRUNNER_JACOBIAN_MODE_AMOUNTS or Config::ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS + :param full: true if we are looking at full jacobian, false if were looking at reduced. + """ + self.checkValidTestModelName(modelName) + testModel = tmf.TestModelFactory(modelName) + self.checkTestModelImplements(testModel, tmf.JacobianResultFull) + rr = RoadRunner(testModel.str()) + Config.setValue(Config.ROADRUNNER_JACOBIAN_MODE, rrJacMode) + + expectedJac = None + if rrJacMode == Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS: + expectedJac = testModel.fullJacobianConc() + elif rrJacMode == Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS: + expectedJac = testModel.fullJacobianAmt() + + else: + raise ValueError("Should never reach here") + + jacSettings = testModel.jacobianSettings() + if "steady_state" in jacSettings.keys(): rr.conservedMoietyAnalysis = True - jacSettings = testModel.jacobianSettings() - print("jacSettings", jacSettings) - if "steady_state" in jacSettings.keys(): - rr.conservedMoietyAnalysis = True - rr.steadyState() - - actualJac = rr.getReducedJacobian() - - self.checkMatricesEqualValues(expectedJac, actualJac) - - def test_BimolecularEnd_FullAmt(self): - self._checkJacFull("BimolecularEnd", Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS) - - def test_BimolecularEnd_FullConc(self): - self._checkJacFull("BimolecularEnd", Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS) - - def test_SimpleFlux_FullAmt(self): - self._checkJacFull("SimpleFlux", Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS) - - def test_SimpleFlux_FullConc(self): - self._checkJacFull("SimpleFlux", Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS) - - def test_SimpleFlux_ReducedAmt(self): - self._checkJacReduced("SimpleFlux", Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS) - - def test_SimpleFlux_ReducedConc(self): - self._checkJacReduced("SimpleFlux", Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS) - - - if __name__ == "__main__": - unittest.main() + rr.steadyState() + actualJac = rr.getFullJacobian() + + print("\n", expectedJac) + print(actualJac) + + # expectedJac.sortColsByLabels(); + # expectedJac.sortRowsByLabels(); + # actualJac.sortColsByLabels(); + # actualJac.sortRowsByLabels(); + + + self.checkMatricesEqualValues(expectedJac, actualJac) + + def _checkJacReduced(self, modelName: str, rrJacMode: Config.ROADRUNNER_JACOBIAN_MODE): + """ + check the values of TestModel jacobian interface against those computed by the current model + + If full is set to false, then we turn on moiety conservation + + :param modelName: A valid test model name (See TestModelFactory::getAvailableTestModelNames() + :param tol: degree of tolerance, allowed error + :param rrJacMode: either Config::ROADRUNNER_JACOBIAN_MODE_AMOUNTS or Config::ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS + :param full: true if we are looking at full jacobian, false if were looking at reduced. + """ + self.checkValidTestModelName(modelName) + testModel = tmf.TestModelFactory(modelName) + self.checkTestModelImplements(testModel, tmf.JacobianResultReduced) + rr = RoadRunner(testModel.str()) + Config.setValue(Config.ROADRUNNER_JACOBIAN_MODE, rrJacMode) + + expectedJac = None + if rrJacMode == Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS: + expectedJac = testModel.reducedJacobianConc() + elif rrJacMode == Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS: + expectedJac = testModel.reducedJacobianAmt() + else: + raise ValueError("Should never reach here") + + rr.conservedMoietyAnalysis = True + jacSettings = testModel.jacobianSettings() + print("jacSettings", jacSettings) + if "steady_state" in jacSettings.keys(): + rr.conservedMoietyAnalysis = True + rr.steadyState() + + actualJac = rr.getReducedJacobian() + + self.checkMatricesEqualValues(expectedJac, actualJac) + + def test_BimolecularEnd_FullAmt(self): + self._checkJacFull("BimolecularEnd", Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS) + + def test_BimolecularEnd_FullConc(self): + self._checkJacFull("BimolecularEnd", Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS) + + def test_SimpleFlux_FullAmt(self): + self._checkJacFull("SimpleFlux", Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS) + + def test_SimpleFlux_FullConc(self): + self._checkJacFull("SimpleFlux", Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS) + + def test_SimpleFlux_ReducedAmt(self): + self._checkJacReduced("SimpleFlux", Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS) + + def test_SimpleFlux_ReducedConc(self): + self._checkJacReduced("SimpleFlux", Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS) + + +if __name__ == "__main__": + unittest.main() diff --git a/test/python/test_pickle.py b/test/python/test_pickle.py index 7486b44956..9f4a65b58f 100644 --- a/test/python/test_pickle.py +++ b/test/python/test_pickle.py @@ -7,157 +7,154 @@ import os import copy -import platform -if platform.system() != "Darwin": +try: + import ray + + print(f"Python interpreter at: {sys.executable}") + + # sys.path += [ + # # r'/mnt/d/roadrunner/roadrunner/cmake-build-release-wsl/lib/site-packages' + # # r"D:\roadrunner\roadrunner\install-msvc2019-rel\site-packages", + # # r"D:\roadrunner\roadrunner\cmake-build-release-visual-studio\lib\site-packages" + # + # ] + import roadrunner + # from roadrunner import * + + import roadrunner.tests.TestModelFactory as tmf + from roadrunner.roadrunner import RoadRunner + + + def simulate_return_None(r): + r.resetAll() + print(r.simulate(0, 10, 11)) + + + def simulate_return_dataframe(r): + r.resetAll() + data = r.simulate(0, 10, 11) + df = pd.DataFrame(data, columns=data.colnames) + return df + + + def simulate_return_NamedArray(r): + r.resetAll() + return r.simulate(0, 10, 11) + + + @ray.remote + class SimulatorActorPath(object): + """Ray actor to execute simulations.""" + + def __init__(self, r: roadrunner.RoadRunner): + self.r: roadrunner.RoadRunner = r + + def simulate(self, size=1): + num_points = 101 + results = np.ndarray((size, num_points, 2)) # 2 for 1 model species and time + for k in range(size): + self.r.resetAll() + results[k] = self.r.simulate(0, 100, num_points) + return results + + + class RoadRunnerPickleTests(unittest.TestCase): + def setUp(self): + rr = RoadRunner(tmf.SimpleFlux().str()) + rr.setIntegrator("gillespie") + gillespie = rr.getIntegrator() + gillespie.seed = 123 + self.rr = rr + + def tearDown(self): + pass + + # @unittest.skip("Takes too long to run when running all CTest. Not sure why...") + def test_to_pickle_and_back(self): + pfile = os.path.join(os.path.dirname(__file__), "pkl.serialization") + with open(pfile, 'wb') as f: + pickle.dump(self.rr, f) + + self.assertTrue(os.path.isfile(pfile)) + + with open(pfile, "rb") as f: + rr = pickle.load(f) + try: + data = rr.simulate(0, 10, 11) + except Exception: + self.fail("Cannot simulate a serialization loaded model") + + self.assertEqual(data.shape, (11, 3)) + + if os.path.isfile(pfile): + os.remove(pfile) + + # @unittest.skip("Takes too long to run when running all CTest. Not sure why...") + def test_we_can_copy_rr(self): + rr2 = copy.copy(self.rr) + self.assertNotEqual(hex(id(self.rr)), hex(id(rr2))) + + @unittest.skip("""Running a multiprocessing pool in + CTest causes the whole test suite to hang. Therefore + these are skipped. You should manually comment out the unittest.skip + decorator to test pickle stuff""") + def test_pool_returns_None(self): + p = Pool(processes=4) + p.map(simulate_return_None, [self.rr for i in range(10)]) + p.close() + + @unittest.skip("""Running a multiprocessing pool in + CTest causes the whole test suite to hang. Therefore + these are skipped. You should manually comment out the unittest.skip + decorator to test pickle stuff""") + def test_pool_returns_DataFrame(self): + N = 10 + p = Pool(processes=4) + dfs = p.map(simulate_return_dataframe, [self.rr for i in range(N)]) + p.close() + self.assertEqual(len(dfs), 10) + dct = {i: df for i, df in enumerate(dfs)} + df = pd.concat(dct, axis=0) + print(df) + self.assertEqual(df.shape, (N * 11, 3)) + + @unittest.skip("""Running a multiprocessing pool in + CTest causes the whole test suite to hang. Therefore + these are skipped. You should manually comment out the unittest.skip + decorator to test pickle stuff""") + def test_pool_returns_NamedArray(self): + N = 10 + p = Pool(processes=4) + arrs = p.map(simulate_return_NamedArray, [self.rr for i in range(N)]) + p.close() + print(arrs) + data = np.vstack(arrs) + self.assertEqual((110, 3), data.shape) + + @unittest.skip("Works when you run on its own but " + "No module named 'roadrunner' error when " + "in test suite with other tests, on windows only. ") + def test_using_ray_library(self): + import roadrunner + ray.init(ignore_reinit_error=True) + + actor_count = 10 # cores to run this on + + rr = roadrunner.RoadRunner(tmf.SimpleFlux().str()) + simulators = [SimulatorActorPath.remote(rr) for _ in range(actor_count)] + + # run simulations + sim_per_actor = 10 + tc_ids = [] + for k, simulator in enumerate(simulators): + tcs_id = simulator.simulate.remote(size=sim_per_actor) + tc_ids.append(tcs_id) + results = ray.get(tc_ids) + data = np.vstack(results) + self.assertEqual((100, 101, 3), data.shape) + + if __name__ == "__main__": + unittest.main() - try: - import ray - - print(f"Python interpreter at: {sys.executable}") - - # sys.path += [ - # # r'/mnt/d/roadrunner/roadrunner/cmake-build-release-wsl/lib/site-packages' - # # r"D:\roadrunner\roadrunner\install-msvc2019-rel\site-packages", - # # r"D:\roadrunner\roadrunner\cmake-build-release-visual-studio\lib\site-packages" - # - # ] - import roadrunner - # from roadrunner import * - - import roadrunner.tests.TestModelFactory as tmf - from roadrunner.roadrunner import RoadRunner - - - def simulate_return_None(r): - r.resetAll() - print(r.simulate(0, 10, 11)) - - - def simulate_return_dataframe(r): - r.resetAll() - data = r.simulate(0, 10, 11) - df = pd.DataFrame(data, columns=data.colnames) - return df - - - def simulate_return_NamedArray(r): - r.resetAll() - return r.simulate(0, 10, 11) - - - @ray.remote - class SimulatorActorPath(object): - """Ray actor to execute simulations.""" - - def __init__(self, r: roadrunner.RoadRunner): - self.r: roadrunner.RoadRunner = r - - def simulate(self, size=1): - num_points = 101 - results = np.ndarray((size, num_points, 2)) # 2 for 1 model species and time - for k in range(size): - self.r.resetAll() - results[k] = self.r.simulate(0, 100, num_points) - return results - - - class RoadRunnerPickleTests(unittest.TestCase): - def setUp(self): - rr = RoadRunner(tmf.SimpleFlux().str()) - rr.setIntegrator("gillespie") - gillespie = rr.getIntegrator() - gillespie.seed = 123 - self.rr = rr - - def tearDown(self): - pass - - # @unittest.skip("Takes too long to run when running all CTest. Not sure why...") - def test_to_pickle_and_back(self): - pfile = os.path.join(os.path.dirname(__file__), "pkl.serialization") - with open(pfile, 'wb') as f: - pickle.dump(self.rr, f) - - self.assertTrue(os.path.isfile(pfile)) - - with open(pfile, "rb") as f: - rr = pickle.load(f) - try: - data = rr.simulate(0, 10, 11) - except Exception: - self.fail("Cannot simulate a serialization loaded model") - - self.assertEqual(data.shape, (11, 3)) - - if os.path.isfile(pfile): - os.remove(pfile) - - # @unittest.skip("Takes too long to run when running all CTest. Not sure why...") - def test_we_can_copy_rr(self): - rr2 = copy.copy(self.rr) - self.assertNotEqual(hex(id(self.rr)), hex(id(rr2))) - - @unittest.skip("""Running a multiprocessing pool in - CTest causes the whole test suite to hang. Therefore - these are skipped. You should manually comment out the unittest.skip - decorator to test pickle stuff""") - def test_pool_returns_None(self): - p = Pool(processes=4) - p.map(simulate_return_None, [self.rr for i in range(10)]) - p.close() - - @unittest.skip("""Running a multiprocessing pool in - CTest causes the whole test suite to hang. Therefore - these are skipped. You should manually comment out the unittest.skip - decorator to test pickle stuff""") - def test_pool_returns_DataFrame(self): - N = 10 - p = Pool(processes=4) - dfs = p.map(simulate_return_dataframe, [self.rr for i in range(N)]) - p.close() - self.assertEqual(len(dfs), 10) - dct = {i: df for i, df in enumerate(dfs)} - df = pd.concat(dct, axis=0) - print(df) - self.assertEqual(df.shape, (N * 11, 3)) - - @unittest.skip("""Running a multiprocessing pool in - CTest causes the whole test suite to hang. Therefore - these are skipped. You should manually comment out the unittest.skip - decorator to test pickle stuff""") - def test_pool_returns_NamedArray(self): - N = 10 - p = Pool(processes=4) - arrs = p.map(simulate_return_NamedArray, [self.rr for i in range(N)]) - p.close() - print(arrs) - data = np.vstack(arrs) - self.assertEqual((110, 3), data.shape) - - @unittest.skip("Works when you run on its own but " - "No module named 'roadrunner' error when " - "in test suite with other tests, on windows only. ") - def test_using_ray_library(self): - import roadrunner - ray.init(ignore_reinit_error=True) - - actor_count = 10 # cores to run this on - - rr = roadrunner.RoadRunner(tmf.SimpleFlux().str()) - simulators = [SimulatorActorPath.remote(rr) for _ in range(actor_count)] - - # run simulations - sim_per_actor = 10 - tc_ids = [] - for k, simulator in enumerate(simulators): - tcs_id = simulator.simulate.remote(size=sim_per_actor) - tc_ids.append(tcs_id) - results = ray.get(tc_ids) - data = np.vstack(results) - self.assertEqual((100, 101, 3), data.shape) - - if __name__ == "__main__": - unittest.main() - - except: - pass +except: + pass diff --git a/test/python/test_python_api.py b/test/python/test_python_api.py index 8fd99b58f8..36e787f20a 100644 --- a/test/python/test_python_api.py +++ b/test/python/test_python_api.py @@ -42,1174 +42,1170 @@ # tricks some Python unit testing frameworks (such as nose) # into thinking the function TestModelFactory is a test, which will fail. # So we import TestModelFactory as an alias. +import roadrunner.tests.TestModelFactory as tmf -import platform -if platform.system() != "Darwin": - - import roadrunner.tests.TestModelFactory as tmf - - Config.setValue(Config.LLJIT_OPTIMIZATION_LEVEL, Config.NONE) - - class RoadRunnerTests(unittest.TestCase): - maxDiff = None - - def setUp(self) -> None: - # print(getAvailableTestModels()) - self.testModel = tmf.TestModelFactory("SimpleFlux") - self.rr = RoadRunner(self.testModel.str()) - - def tearDown(self) -> None: - pass - - def checkMatricesAlmostEqual(self, expected, actual, places=7): - if len(expected) != len(actual): - raise ValueError("len(expected) != len(actual)") - - if len(expected[0]) != len(actual[0]): - raise ValueError("len(expected[0]) != len(actual[0])") - - for i in range(len(expected)): - for j in range(len(expected[0])): - self.assertAlmostEqual(expected[i][j], actual[i][j], places=places) - - def test_species_attribute(self): - self.assertEqual(self.rr.S1, 10) - - def test_species_attribute_amount(self): - self.assertEqual(self.rr.S1_amt, 10) - - def test_species_attribute_conc(self): - self.assertEqual(self.rr.S1_conc, 10) - - def test_reaction_flux(self): - self.assertEqual(self.rr._J0, 1) - - def test_attribute_access_protocols_setattr(self): - self.rr.__setattr__("cheese", 6) - self.assertTrue(hasattr(self.rr, "cheese")) - self.assertEqual(getattr(self.rr, "cheese"), 6) - - def test_attribute_access_protocols_getattr(self): - self.assertEqual(self.rr.__getattr__("S1"), 10) - - def test___dict__(self): - self.assertEqual( - ["this"], - list(self.rr.__dict__.keys()) - ) - - @unittest.skip("__eq__ may be implemented, may not. If not we should do") - def test___eq__(self): - pass - - def test___getitem__(self): - self.assertEqual(self.rr.__getitem__("S1"), 10.0) - - def test___len__(self): - self.assertEqual(len(self.rr), 62) # Enumerates all possible rr[x] arguments. - - def test___repr__(self): - l = repr([self.rr]) - self.assertIn("roadrunner.RoadRunner()", l) - - def test___setitem__fails_when_key_not_exist(self): - with self.assertRaises(RuntimeError): - self.rr.__setitem__("five", 5) - - def test___setitem__when_key_exists(self): - self.rr.__setitem__("S1", 12) - self.assertEqual(self.rr.__getitem__("S1"), 12) - - # def test___sizeof__(self): - # self.assertEqual(32, self.rr.__sizeof__()) - - def test___str__(self): - s = str(self.rr) - print(s) - self.assertIn("roadrunner", s) - - @unittest.skip("Method not implemented yet (but should be)") - def test_getCompartmentIds(self): - """This method is missing from the rr api""" - pass - - def test_addCompartment(self): - """The rr._addCompartment() method is called by the - rr.addCompartment() method. The difference, is the - latter adds the compartment to the __dict__ as an - attribute. - """ - self.rr.addCompartment("C1", 1, True) - self.assertEqual(self.rr.C1, 1) - - def testAddParameter(self): - self.rr.addParameter("k_new", 25, True) - self.assertEqual(25, self.rr.k_new) - - def testAddReaction(self): - self.rr.addReaction("NewReaction", ["S1"], ["S2"], "kf*S1", True) - self.rr.S1 = 10 - self.assertEqual(self.rr.NewReaction, 1.0) - - def testAddSpeciesConcentrations(self): - self.rr.addSpeciesConcentration("NewSpecies", "default_compartment", 123.3, False, False, "", True) - self.assertEqual(self.rr.NewSpecies, 123.3) - - def testAddSpecies(self): - self.rr.addSpeciesAmount("NewSpecies", "default_compartment", 123.3, False, False, "", True) - self.assertEqual(self.rr.NewSpecies, 123.3) - - @unittest.skip - def test_removeInitialAssignment(self): - self.assertEqual( - self.rr.removeInitialAssignment(), - ) - - @unittest.skip - def test_removeParameter(self): - self.assertEqual( - self.rr.removeParameter(), ) - - @unittest.skip - def test_removeReaction(self): - self.assertEqual( - self.rr.removeReaction(), - ) - - @unittest.skip - def test_removeRules(self): - self.assertEqual( - self.rr.removeRules(), - - ) - - @unittest.skip - def test_removeSpecies(self): - self.assertEqual( - self.rr.removeSpecies(), - ) - - def test_diffstep_getter(self): - self.assertEqual(self.rr._diffstep_getter(), 0.02) - - def test_diffstep_stter(self): - self.rr._diffstep_stter(0.01) - self.assertEqual(self.rr._diffstep_getter(), 0.01) - - def test_getConservedMoietyAnalysis(self): - self.assertFalse(self.rr._getConservedMoietyAnalysis()) - - def test_setConservedMoietyAnalysis(self): - self.rr.conservedMoietyAnalysis = True - self.assertTrue(self.rr._getConservedMoietyAnalysis()) - - def test_addAssignmentRule(self): - self.rr.addSpeciesConcentration("SNew", "default_compartment", 2.5, False, True, "", True) - self.rr.addAssignmentRule("SNew", "S1+5", True) - self.assertEqual(self.rr.SNew, 15) - - @unittest.skip("Not sure how to test this right now") - def test_addDelay(self): - pass - - @unittest.skip("Not sure how to test this right now") - def test_addEvent(self): - pass - - @unittest.skip("Not sure how to test this right now") - def test_addEventAssignment(self): - pass - - @unittest.skip("Not sure how to test this right now") - def test_addInitialAssignment(self): - self.rr.addSpeciesConcentration("NewSpec", "default_compartment", 13.3, False, True, "", False) - self.rr.addInitialAssignment("NewSpec", "S1+S2", True) - - @unittest.skip("Not sure how to test this right now") - def test_addPriority(self): - pass - - @unittest.skip("Not sure how to test this right now") - def test_addRateRule(self): - pass - - @unittest.skip("Not sure how to test this right now") - def test_addTrigger(self): - pass - - def test_clearModel(self): - self.assertTrue(self.rr.clearModel()) - - @unittest.skip("Not sure how to test this right now. Docs are not clear") - def test_createSelection(self): - pass - - def test_default_compartment(self): - self.assertEqual(self.rr.default_compartment, 1) - - def test_diffstep(self): - self.assertEqual(self.rr.diffstep, 0.02) - - @unittest.skip("This API is unclear. ") - def test_ensureSolversRegistered(self): - self.rr.ensureSolversRegistered() - - def test_getAvailableIntegrators(self): - self.assertEqual(self.rr.getAvailableIntegrators(), ("cvode",)) - - def test_getBoundarySpeciesAmountsNamedArray(self): - self.rr.setBoundary("S1", True) - bs = self.rr.getBoundarySpeciesAmountsNamedArray() - self.assertEqual(bs["S1"], 10) - - def test_getBoundarySpeciesConcentrationsNamedArray(self): - self.rr.setBoundary("S1", True) - self.rr.default_compartment = 0.5 - bs = self.rr.getBoundarySpeciesConcentrationsNamedArray() - self.assertEqual(bs["S1"], 20) - - def test_getCC(self): - self.assertAlmostEqual(self.rr.getCC("_J0", "kf"), 0.009090905110435235) - - def test_getCompiler(self): - compiler_string = str(self.rr.getCompiler()) - self.assertIn("Compiler", compiler_string) - - def test_getConservationMatrix(self): - rr2 = RoadRunner(tmf.TestModelFactory("Brown2004").str()) - rr2.conservedMoietyAnalysis = True - print(rr2.getConservationMatrix().shape) - self.assertEqual(rr2.getConservationMatrix().shape, (15, 28)) - - def test_getConservedMoietyIds(self): - """This mode has no conserved moieties so poor model for testing this feature""" - rr2 = RoadRunner(tmf.TestModelFactory("Brown2004").str()) - rr2.conservedMoietyAnalysis = True - expected = tuple([f"_CSUM{i}" for i in range(15)]) - self.assertEqual(rr2.getConservedMoietyIds(), expected) - - def test_getConservedMoietyValues(self): - """This mode has no conserved moieties so poor model for testing this feature""" - rr2 = RoadRunner(tmf.TestModelFactory("Brown2004").str()) - rr2.conservedMoietyAnalysis = True - print(rr2.getConservedMoietyValues()) - expected = [1.2000e+05, 6.0000e+05, 1.2000e+05, 1.2000e+05, 6.0000e+05, 1.2000e+05, 1.0000e+04, 1.2000e+05, - 1.2000e+05, 4.4600e+05, 1.2000e+05, 1.0002e+07, 1.2000e+05, 1.2000e+05, 8.0000e+04] - actual = rr2.getConservedMoietyValues() - for i in range(len(expected)): - self.assertAlmostEqual(expected[i], actual[i]) - - def test_getCurrentSBML(self): - self.assertIsInstance(self.rr.getCurrentSBML(), str) - - def test_getDependentFloatingSpeciesIds(self): - """No dependents in this model""" - self.assertTrue(callable(self.rr.getDependentFloatingSpeciesIds)) - - def test_getDependentRatesOfChange(self): - """No dependents in this model so we'll just check callable""" - self.assertTrue(callable(self.rr.getDependentRatesOfChange)) - - def test_getDependentRatesOfChangeNamedArray(self): - """No dependents in this model""" - self.assertTrue(callable(self.rr.getDependentRatesOfChangeNamedArray)) - - def test_getDiffStepSize(self): - self.assertEqual(0.02, self.rr.getDiffStepSize()) - - def test_getEE(self): - self.assertAlmostEqual(self.rr.getEE("_J0", "kf"), 1.0000000000000024) - - def test_getEigenValueIds(self): - expected = ('eigen(S1)', 'eigenReal(S1)', 'eigenImag(S1)', 'eigen(S2)', 'eigenReal(S2)', 'eigenImag(S2)') - self.assertEqual(self.rr.getEigenValueIds(), expected) - - def test_getExistingIntegratorNames(self): - expected = ('cvode',) - self.assertEqual(expected, self.rr.getExistingIntegratorNames()) - - def test_getExtendedStoichiometryMatrix(self): - rr2 = RoadRunner(tmf.TestModelFactory("OpenLinearFlux").str()) - mat = rr2.getExtendedStoichiometryMatrix() - print(mat) - expected = [ - [1, -1, 0], - [0, 1, -1], - [-1, 0, 0], - [0, 0, 1], - ] - # todo implement proper equality operators - print(mat.shape) - for i in range(mat.shape[0]): - for j in range(mat.shape[1]): - self.assertEqual(expected[i][j], mat[i][j]) - - def test_getFloatingSpeciesAmountsNamedArray(self): - x = self.rr.getFloatingSpeciesAmountsNamedArray() - self.assertEqual(x["S2"], 1) - - def test_getFloatingSpeciesConcentrationsNamedArray(self): - self.rr.default_compartment = 0.33 - x = self.rr.getFloatingSpeciesConcentrationsNamedArray() - self.assertAlmostEqual(3.0303030303030303, x["S2"][0]) - - def test_getFloatingSpeciesInitialConcentrationIds(self): - x = self.rr.getFloatingSpeciesInitialConcentrationIds() - self.assertEqual(x, ("init([S1])", "init([S2])",)) - - @unittest.skip("figure out how to use") - def test_getFrequencyResponse(self): - pass - - def test_getFullEigenValues(self): - print(dir(self.testModel)) - expected = self.testModel.fullEigenValues() - actual = self.rr.getFullEigenValues() - print(expected) - print(actual) - self.assertAlmostEqual(expected[0], actual[0]) - self.assertAlmostEqual(expected[1], actual[1]) - - def test_getFullJacobian(self): - print(dir(self.testModel)) - expected = self.testModel.fullJacobianAmt() - actual = self.rr.getFullJacobian() - for i in range(expected.shape[0]): - for j in range(expected.shape[1]): - self.assertAlmostEqual(expected[i][j], actual[i][j]) - - def test_getFullJacobianConc(self): - Config.setValue(Config.ROADRUNNER_JACOBIAN_MODE, Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS) - expected = self.testModel.fullJacobianConc() - actual = self.rr.getFullJacobian() - for i in range(expected.shape[0]): - for j in range(expected.shape[1]): - self.assertAlmostEqual(expected[i][j], actual[i][j]) - - def test_getFullJacobianAmt(self): - expected = self.testModel.fullJacobianAmt() - Config.setValue(Config.ROADRUNNER_JACOBIAN_MODE, Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS) - actual = self.rr.getFullJacobian() - for i in range(expected.shape[0]): - for j in range(expected.shape[1]): - self.assertAlmostEqual(expected[i][j], actual[i][j]) - - def test_getFullStoichiometryMatrix(self): - expected = self.testModel.fullStoicMatrix() - self.checkMatricesAlmostEqual(expected, self.rr.getFullStoichiometryMatrix()) - - def test_getGlobalParameterByName(self): - self.assertEqual(self.rr.getGlobalParameterByName("kf"), 0.1) - - @unittest.skip("No way to use this method from Python - it " - "requires an out parameter as input") - def test_getIds(self): - pass - - def test_getIndependentFloatingSpeciesIds(self): - self.assertEqual(self.rr.getIndependentFloatingSpeciesIds(), ["S1"]) - - def test_getIndependentRatesOfChange(self): - self.assertEqual(-0.99, self.rr.getIndependentRatesOfChange()) - - def test_getIndependentRatesOfChangeNamedArray(self): - self.assertEqual( - self.rr.getIndependentRatesOfChangeNamedArray(), - [[-0.99]] - ) - - def test_getInfo(self): - self.assertIn( - "jacobianStepSize", - self.rr.getInfo(), - ) - - def test_getIntegrator(self): - self.assertEqual( - self.rr.getIntegrator().getName(), - "cvode" - ) - - def test_getIntegratorByName(self): - self.assertIsInstance( - self.rr.getIntegratorByName("cvode"), - Integrator - ) - - def test_getKMatrix(self): - expected = [[1], [1]] - self.checkMatricesAlmostEqual( - expected, - self.rr.getKMatrix(), - ) - - def test_getKineticLaw(self): - self.assertEqual( - self.rr.getKineticLaw("_J0"), - "kf * S1" - ) - - def test_getL0Matrix(self): - print(dir(self.testModel)) - expected = self.testModel.L0Matrix() - actual = self.rr.getL0Matrix() - self.assertEqual(expected, actual) - - def test_getLinkMatrix(self): - # roadrunner automatically trasposes column vectors - # into row vectors - expected = self.testModel.linkMatrix() - actual = self.rr.getLinkMatrix().T[0] - print(expected) - print(actual) - self.assertTrue((expected == actual).all()) - - def test_getModel(self): - self.assertIsInstance( - self.rr.getModel(), - ExecutableModel - ) - - def test_getNrMatrix(self): - expected = self.testModel.NrMatrix() - self.checkMatricesAlmostEqual( - expected, - self.rr.getNrMatrix(), - ) - - @unittest.skip("No idea what the argument for this method should be?") - def test_getParamPromotedSBML(self): - self.assertEqual( - self.rr.getParamPromotedSBML(), - ) - - def test_getRatesOfChange(self): - print(self.rr.getRatesOfChange()) - self.assertSequenceEqual( - list(self.rr.getRatesOfChange()), - [-0.99, 0.99] - ) - - def test_getRatesOfChangeNamedArray(self): - print(self.rr.getRatesOfChangeNamedArray()) - self.assertSequenceEqual( - list(self.rr.getRatesOfChangeNamedArray()[0]), - [-0.99, 0.99] - ) - - def test_getReactionRates(self): - self.assertEqual(1.0, self.rr.getReactionRates()[0]) - self.assertEqual(0.01, self.rr.getReactionRates()[1]) - - def test_getReducedEigenValues(self): - expected = self.testModel.reducedEigenValues() - self.rr.conservedMoietyAnalysis = True - actual = self.rr.getReducedEigenValues() - print("expected: ", expected) - print("actual: ", actual) - self.assertEqual(expected.shape, actual.shape) - self.assertAlmostEqual(expected[0], actual[0]) - - def test_getReducedJacobian(self): - self.rr.conservedMoietyAnalysis = True - expected = self.testModel.reducedJacobianConc() - actual = self.rr.getReducedJacobian() - print(expected) - print(actual) - - self.assertAlmostEqual( - -0.11, - self.rr.getReducedJacobian()["S1"][0], - ) - - def test_getReducedStoichiometryMatrix(self): - self.rr.conservedMoietyAnalysis = True - expected = self.testModel.reducedStoicMatrix() - self.checkMatricesAlmostEqual( - expected, - self.rr.getReducedStoichiometryMatrix(), - ) - - def test_getRegisteredIntegratorNames(self): - self.assertEqual( - ('cvode', 'gillespie', 'rk4', 'rk45', 'euler'), - self.rr.getRegisteredIntegratorNames(), - ) - - def test_getRegisteredSteadyStateSolverNames(self): - self.assertEqual( - ('nleq1', 'nleq2', 'newton', "newton_linesearch"), - self.rr.getRegisteredSteadyStateSolverNames(), - ) - - def test_getRegisteredSensitivitySolverNames(self): - print(dir(self.rr)) - self.assertEqual( - ("forward",), - self.rr.getRegisteredSensitivitySolverNames(), - ) - - def test_getSBML(self): - self.assertIsInstance( - self.rr.getSBML(), - str - ) - - def test_getScaledConcentrationControlCoefficientMatrix(self): - expected = self.testModel.scaledConcentrationControlCoefficientMatrix() - actual = self.rr.getScaledConcentrationControlCoefficientMatrix() - self.checkMatricesAlmostEqual( - expected, actual, 5 - ) - - def test_getScaledElasticityMatrix(self): - actual = self.rr.getScaledElasticityMatrix() - expected = self.testModel.scaledElasticityMatrix() - print(actual) - self.checkMatricesAlmostEqual( - expected, actual - ) - - def test_getScaledFloatingSpeciesElasticity(self): - self.assertAlmostEqual( - 1.0, - self.rr.getScaledFloatingSpeciesElasticity("_J1", "S2"), - ) - - def test_getScaledFluxControlCoefficientMatrix(self): - expected = self.testModel.scaledFluxControlCoefficientMatrix() - actual = self.rr.getScaledFluxControlCoefficientMatrix() - self.checkMatricesAlmostEqual( - expected, actual, 5 - ) - - def test_getSelectedValues(self): - self.assertEqual(self.rr.getSelectedValues()[0], 0) - self.assertEqual(self.rr.getSelectedValues()[1], 10) - - def test_getSimulationData(self): - self.assertTrue( - self.rr.getSimulationData().size == 0 - ) - self.rr.simulate(0, 10, 11) - actual = self.rr.getSimulationData() - expected = self.testModel.timeSeriesResult() - self.checkMatricesAlmostEqual(actual, expected, places=4) - - def test_getSteadyStateSelectionStrings(self): - self.assertEqual( - self.rr.getSteadyStateSelectionStrings(), - ("[S1]", "[S2]") - ) - - def test_getSteadyStateSolver(self): - solver = self.rr.getSteadyStateSolver() - self.assertEqual("nleq2", solver.getName()) - - def test_getSteadyStateThreshold(self): - self.assertEqual( - self.rr.getSteadyStateThreshold(), - 0.01 - ) - - def test_getSteadyStateValues(self): - expected = self.testModel.steadyState() - actual = self.rr.getSteadyStateValues() - print(expected) - print(actual) - self.assertEqual(expected["S1"], actual[0]) - self.assertEqual(expected["S2"], actual[1]) - - def test_getSteadyStateValuesNamedArray(self): - expected = self.testModel.steadyState() - actual = self.rr.getSteadyStateValuesNamedArray() - print(expected) - self.assertAlmostEqual(expected["S1"], actual[0, 0]) - self.assertAlmostEqual(expected["S2"], actual[0, 1]) - - def test_getSensitivitySolver(self): - self.assertEqual( - "forward", - self.rr.getSensitivitySolver().getName() - ) - - @unittest.skip("This method should be not be visible in Python") - def test_getSupportedIdTypes(self): - """returns a bit field of the ids that this class supports.""" - - def test_getUnscaledConcentrationControlCoefficientMatrix(self): - expected = self.testModel.unscaledConcentrationControlCoefficientMatrix() - actual = self.rr.getUnscaledConcentrationControlCoefficientMatrix() - self.checkMatricesAlmostEqual( - expected, actual, 5 - ) - - def test_getUnscaledElasticityMatrix(self): - expected = self.testModel.unscaledElasticityMatrix() - actual = self.rr.getUnscaledElasticityMatrix() - self.checkMatricesAlmostEqual( - expected, actual, 5 - ) - - def test_getUnscaledFluxControlCoefficientMatrix(self): - expected = self.testModel.unscaledFluxControlCoefficientMatrix() - actual = self.rr.getUnscaledFluxControlCoefficientMatrix() - self.checkMatricesAlmostEqual( - expected, actual, 5 - ) - - def test_getUnscaledParameterElasticity(self): - self.assertAlmostEqual( - 10, - self.rr.getUnscaledParameterElasticity("_J0", "kf"), - ) - - def test_getUnscaledSpeciesElasticity(self): - self.assertEqual( - 0.10000000000000007, - self.rr.getUnscaledSpeciesElasticity(0, 0), - ) - - def test_getValue(self): - self.assertEqual( - self.rr.getValue("kb"), - 0.01 - ) - - def test_getuCC(self): - self.assertAlmostEqual( - 0.09090905110435235, - self.rr.getuCC("_J0", "kf"), - ) - - def test_getuEE(self): - self.assertAlmostEqual( - self.rr.getuEE("_J0", "kf"), - 10 - ) - - def test_integrator(self): - self.assertIsInstance( - self.rr.integrator, - Integrator - ) - - def test_integratorExists(self): - self.assertTrue( - self.rr.integratorExists("cvode"), - ) - - def test_internalOneStep(self): - before = self.rr.S2 - self.rr.internalOneStep(0, 10) - after = self.rr.S2 - self.assertNotEqual(before, after) - - def test_isModelLoaded(self): - self.assertTrue( - self.rr.isModelLoaded(), - ) - - def test_items(self): - expected = [('S1', 10.0), - ('S2', 1.0), - ('[S1]', 10.0), - ('[S2]', 1.0), - ('default_compartment', 1.0), - ('kf', 0.1), - ('kb', 0.01), - ('_J0', 1.0), - ('_J1', 0.01), - ('init([S1])', 10.0), - ('init([S2])', 1.0), - ('init(S1)', 10.0), - ('init(S2)', 1.0), - ('init(default_compartment)', 1.0), - ('init(kf)', 0.1), - ('init(kb)', 0.01), - ("S1'", -0.99), - ("S2'", 0.99), - ("[S1]'", -0.99), - ("[S2]'", 0.99), - ('stoich(S1, _J0)', -1.0), - ('stoich(S1, _J1)', 1.0), - ('stoich(S2, _J0)', 1.0), - ('stoich(S2, _J1)', -1.0), - ('uec(_J0, S1)', 0.10000000000000007), - ('uec(_J0, S2)', 0.0), - ('uec(_J0, kf)', 10.000000000000082), - ('uec(_J0, kb)', 0.0), - ('uec(_J1, S1)', 0.0), - ('uec(_J1, S2)', 0.009999999999999998), - ('uec(_J1, kf)', 0.0), - ('uec(_J1, kb)', 1.0000000000000053), - ('ec(_J0, S1)', 1.0000000000000007), - ('ec(_J0, S2)', 0.0), - ('ec(_J0, kf)', 1.0000000000000082), - ('ec(_J0, kb)', 0.0), - ('ec(_J1, S1)', 0.0), - ('ec(_J1, S2)', 0.9999999999999998), - ('ec(_J1, kf)', 0.0), - ('ec(_J1, kb)', 1.0000000000000053), - ('ucc(_J0, kf)', 0.09090905110435235), - ('ucc(_J0, kb)', 9.090909090511781), - ('ucc(_J1, kf)', 0.09090905110435235), - ('ucc(_J1, kb)', 9.090909090511735), - ('ucc(S1, kf)', -9.09090511043516), - ('ucc(S1, kb)', 90.90909090511799), - ('ucc(S2, kf)', 9.090905110435088), - ('ucc(S2, kb)', -90.90909090512392), - ('cc(_J0, kf)', 0.009090905110435235), - ('cc(_J0, kb)', 0.09090909090511781), - ('cc(_J1, kf)', 0.9090905110435236), - ('cc(_J1, kb)', 9.090909090511735), - ('cc(S1, kf)', -0.09090905110435162), - ('cc(S1, kb)', 0.09090909090511799), - ('cc(S2, kf)', 0.9090905110435088), - ('cc(S2, kb)', -0.9090909090512392), - ('eigen(S1)', (-0.10999999999999983+0j)), - ('eigenReal(S1)', -0.10999999999999983), - ('eigenImag(S1)', 0.0), - ('eigen(S2)', 0j), - ('eigenReal(S2)', 0.0), - ('eigenImag(S2)', 0.0)] - self.assertEqual( - expected, - self.rr.items(), - ) - - def test_iteritems(self): - - working_iterator = False - for i in self.rr.iteritems(): - working_iterator = True - self.assertTrue(working_iterator) - - def test_iterkeys(self): - - working_iterator = False - for i in self.rr.iterkeys(): - working_iterator = True - self.assertTrue(working_iterator) - - def test_itervalues(self): - - working_iterator = False - for i in self.rr.itervalues(): - working_iterator = True - self.assertTrue(working_iterator) - - def test_parameter_value(self): - self.assertEqual( - self.rr.kf, - 0.1 - ) - - def test_keys(self): - - expected = ['S1', - 'S2', - '[S1]', - '[S2]', - 'default_compartment', - 'kf', - 'kb', - '_J0', - '_J1', - 'init([S1])', - 'init([S2])', - 'init(S1)', - 'init(S2)', - 'init(default_compartment)', - 'init(kf)', - 'init(kb)', - "S1'", - "S2'", - "[S1]'", - "[S2]'", - 'stoich(S1, _J0)', - 'stoich(S1, _J1)', - 'stoich(S2, _J0)', - 'stoich(S2, _J1)', - 'uec(_J0, S1)', - 'uec(_J0, S2)', - 'uec(_J0, kf)', - 'uec(_J0, kb)', - 'uec(_J1, S1)', - 'uec(_J1, S2)', - 'uec(_J1, kf)', - 'uec(_J1, kb)', - 'ec(_J0, S1)', - 'ec(_J0, S2)', - 'ec(_J0, kf)', - 'ec(_J0, kb)', - 'ec(_J1, S1)', - 'ec(_J1, S2)', - 'ec(_J1, kf)', - 'ec(_J1, kb)', - 'ucc(_J0, kf)', - 'ucc(_J0, kb)', - 'ucc(_J1, kf)', - 'ucc(_J1, kb)', - 'ucc(S1, kf)', - 'ucc(S1, kb)', - 'ucc(S2, kf)', - 'ucc(S2, kb)', - 'cc(_J0, kf)', - 'cc(_J0, kb)', - 'cc(_J1, kf)', - 'cc(_J1, kb)', - 'cc(S1, kf)', - 'cc(S1, kb)', - 'cc(S2, kf)', - 'cc(S2, kb)', - 'eigen(S1)', - 'eigenReal(S1)', - 'eigenImag(S1)', - 'eigen(S2)', - 'eigenReal(S2)', - 'eigenImag(S2)',] - self.assertEqual( - expected, - self.rr.keys(), - ) - - def test_load(self): - self.rr.load(self.testModel.str()), - self.assertTrue(self.rr.isModelLoaded()) - - def test_loadState(self): - this_dir = os.path.dirname(__file__) - fname = os.path.join(this_dir, "roadrunner_state.rr") - self.rr.saveState(fname) - self.assertTrue(os.path.isfile(fname)) - self.rr.loadState(fname) - self.assertTrue(self.rr.isModelLoaded()) - os.remove(fname) - - def test_loadStateS(self): - x = self.rr.saveStateS() - rr2 = RoadRunner() - rr2.loadStateS(x) - data = rr2.simulate(0, 10, 11) - print(data) - self.assertEqual((11, 3), data.shape) - - def test_makeIntegrator(self): - integrator = self.rr.makeIntegrator("gillespie") - self.assertIsInstance( - integrator, - Integrator - ) - - def test_mcaSteadyState(self): - self.assertAlmostEqual( - self.rr.mcaSteadyState(), - 1.3877787807814457e-17 - ) - - def test_model(self): - self.assertIsInstance( - self.rr.model, - ExecutableModel - ) - - def test_oneStep(self): - before = self.rr.S2 - self.rr.internalOneStep(0, 10) - after = self.rr.S2 - self.assertNotEqual(before, after) - - def test_options(self): - self.assertIsInstance( - self.rr.options, - RoadRunnerOptions - ) - - def test_regenerateModel(self): - self.rr.regenerateModel() - self.assertTrue(self.rr.isModelLoaded()) - - @unittest.skip("unclear on how to use this method") - def test_removeCompartment(self): - self.rr.removeCompartment("default_compartment", True) - with self.assertRaises(AttributeError): - self.rr.default_compartment - - @unittest.skip("no events in model - add one ") - def test_removeEvent(self): - pass - - @unittest.skip("no events in model - add one ") - def test_removeEventAssignments(self): - print(self.rr.removeEventAssignments()) - - def test_reset(self): - self.rr.reset() - self.assertTrue( - self.rr.isModelLoaded() - ) - - def test_resetAll(self): - """difference between reset and resetAll?""" - self.rr.resetAll() - self.assertTrue( - self.rr.isModelLoaded() - ) - - def test_resetParameter(self): - self.assertEqual(self.rr.kf, 0.1) # starting value - self.rr.kf = 15 # uses setattr - self.assertEqual(self.rr.kf, 15) # starting value - self.rr.resetParameter() - self.assertEqual(self.rr.kf, 0.1) - - def test_resetSelectionLists(self): - self.rr.selections = ["[S2]"] - self.rr.resetSelectionLists() - self.assertEqual( - ['time', "[S1]", '[S2]'], - self.rr.selections, - ) - - def test_resetToOrigin(self): - self.kf = 16 - self.rr.resetToOrigin() - self.assertEqual( - self.rr.kf, 0.1 - ) - - def test_getCurrentTime(self): - self.assertEqual(0, self.rr.getCurrentTime()) - self.rr.simulate(0, 100, 101) - self.assertEqual(100, self.rr.getCurrentTime()) - - def test_selections(self): - self.assertEqual( - self.rr.selections, - ['time', '[S1]', '[S2]'] - ) - - def test_setBoundary(self): - self.rr.setBoundary("S1", False) - self.assertEqual(0, self.rr.getBoundarySpeciesAmountsNamedArray().size) - self.rr.setBoundary("S1", True) - self.assertEqual(1, self.rr.getBoundarySpeciesAmountsNamedArray().size) - - @unittest.skip("We can setConstant but how to getConstant?") - def test_setConstant(self): - self.rr.setConstant("S1", False) - - def test_setDiffStepSize(self): - self.rr.setDiffStepSize(1e-6) - self.assertEqual( - self.rr.getDiffStepSize(), - 1e-6 - ) - - def test_setGlobalParameterByName(self): - self.rr.setGlobalParameterByName("kf", 6), - self.assertEqual( - self.rr.kf, 6 - ) - - @unittest.skip("How to getHasOnlySubstanceUnits?") - def test_setHasOnlySubstanceUnits(self): - self.rr.setHasOnlySubstanceUnits("S1", True) - - @unittest.skip("This function looks broken?") - def test_setInitAmount(self): - self.rr.setInitAmount("S1", 45.6, True) - self.assertEqual( - self.rr.S1, 45.6 - ) - - @unittest.skip("This function looks broken?") - def test_setInitConcentration(self): - self.rr.setInitConcentration("S1", 45.6, True) - self.assertEqual( - self.rr.S1, 45.6 - ) - - def test_setIntegrator(self): - self.rr.setIntegrator("gillespie") - self.assertEqual( - "gillespie", - self.rr.integrator.getName() - ) - - def test_setIntegratorSetting(self): - self.assertTrue( - self.rr.integrator.getValue("stiff") - ) - - def test_setKineticLaw(self): - self.rr.setKineticLaw("_J0", "1+2+3+4+5") - self.assertEqual( - self.rr.getKineticLaw("_J0"), - "1 + 2 + 3 + 4 + 5" - ) - - @unittest.skip("What should go in RoadRunnerOptions?") - def test_setOptions(self): - opt = RoadRunnerOptions() - self.assertEqual( - self.rr.setOptions(), - ) - - @unittest.skip("how to use?") - def test_setPersistent(self): - self.assertEqual( - self.rr.setPersistent(), - ) - - @unittest.skip("How to get the reversible flag back after we've set it?") - def test_setReversible(self): - pass - - def test_setSteadyStateSolver(self): - self.rr.setSteadyStateSolver("newton") - solver = self.rr.getSteadyStateSolver() - print(solver, type(solver)) - self.assertEqual( - solver.getName(), - "newton" - ) - - def test_setSteadyStateThreshold(self): - self.rr.setSteadyStateThreshold(6) - self.assertEqual( - self.rr.getSteadyStateThreshold(), 6 - ) - - @unittest.skip("how to use?") - def test_setTriggerInitialValue(self): - self.assertEqual( - self.rr.setTriggerInitialValue(), - ) - - @unittest.skip("What values are set on a RoadRunner instance?") - def test_setValue(self): - self.assertEqual( - self.rr.setValue(), - ) - - def test_simulate(self): - expected = self.testModel.timeSeriesResult() - settings = self.testModel.timeSeriesSettings() - start = settings["start"] - duration = settings["duration"] - steps = settings["steps"] - num = steps + 1 - self.rr.simulate(start, duration, num) - print(expected) - actual = self.rr.getSimulationData() - print(actual) - self.checkMatricesAlmostEqual(expected, actual, 4) - - def test_steadyState(self): - expected = self.testModel.steadyState() - self.rr.steadyState() - actual = self.rr.getFloatingSpeciesAmountsNamedArray() - print(expected) - print(actual) - self.assertAlmostEqual(expected["S1"], actual[0][0]) - self.assertAlmostEqual(expected["S2"], actual[0][1]) - - def test_steadyStateNamedArray(self): - expected = self.testModel.steadyState() - self.rr.steadyState() - actual = self.rr.steadyStateNamedArray() - print(expected) - print(actual) - self.assertAlmostEqual(expected["S1"], actual[0][0]) - self.assertAlmostEqual(expected["S2"], actual[0][1]) - - def test_steadyStateSelections(self): - self.assertEqual( - self.rr.steadyStateSelections, - ["[S1]", "[S2]"] - ) - - def test_steadyStateSolver(self): - self.assertIsInstance( - self.rr.steadyStateSolver, - SteadyStateSolver - ) - - def test_steadyStateSolverExists(self): - self.assertTrue(self.rr.steadyStateSolverExists("nleq2")) - self.assertFalse(self.rr.steadyStateSolverExists("newton")) # not instantiated yet - - def test_steadyStateThresh(self): - self.assertEqual( - self.rr.steadyStateThresh, - 0.01 - ) - - def test_timeCourseSelections(self): - self.assertEqual( - self.rr.timeCourseSelections, - ['time', "[S1]", '[S2]'] - ) - - @unittest.skip("unclear how to test. Should this method be private?") - def test_validateCurrentSBML(self): - self.assertTrue(self.rr.validateCurrentSBML()) - - def test_load_model_with_large_recursion_limit(self): - """ - This was a fun one. Tellurium crashed with version roadrunner 2.0.6 - because it imports plotly. Plotly imports Ipython.display, which - imports jedi which changes the recursion depth with sys.setrecursionlimit. - This caused roadrunner to crash. Here we write a test to resolve this problem. - :return: - """ - - """ - Okay, so we can't call getIds() inside __getattr__. Why not? - No, actually - we can't call *anything. infinite recursion - """ - import sys - sys.setrecursionlimit(3000) - m = RoadRunner(self.testModel.str()) - self.assertIsInstance(m, RoadRunner) - - def test_getitem_when_exists(self): - import sys - sys.setrecursionlimit(3000) - m = RoadRunner(self.testModel.str()) - self.assertEqual(10.0, m["S1"]) - - def test_getitem_when_not_exists(self): - import sys - sys.setrecursionlimit(3000) - m = RoadRunner(self.testModel.str()) - with self.assertRaises(RuntimeError): - s = m["S100"] - - def test_getitem_when_created_after_instantiation(self): - import sys - sys.setrecursionlimit(3000) - m = RoadRunner(self.testModel.str()) - m.addSpeciesConcentration("S100", "default_compartment", 123.3, False, False, "", True) - val = m["S100"] - self.assertAlmostEqual(val, 123.3) - - def test_getitem_when_created_after_instantiation_dot_notation(self): - import sys - sys.setrecursionlimit(3000) - m = RoadRunner(self.testModel.str()) - m.addSpeciesConcentration("S100", "default_compartment", 123.3, False, False, "", True) - m._makeProperties() - self.assertAlmostEqual(m.S100, 123.3) - - def test_simulateWithTimes(self): - self.rr.resetToOrigin() - self.rr.simulate(times = [0, 1, 5, 10]) - result = self.rr.getSimulationData() - self.assertEqual(list(result[:,0]), [0, 1, 5, 10]) - - - if __name__ == "__main__": - unittest.main() +Config.setValue(Config.LLJIT_OPTIMIZATION_LEVEL, Config.NONE) + +class RoadRunnerTests(unittest.TestCase): + maxDiff = None + + def setUp(self) -> None: + # print(getAvailableTestModels()) + self.testModel = tmf.TestModelFactory("SimpleFlux") + self.rr = RoadRunner(self.testModel.str()) + + def tearDown(self) -> None: + pass + + def checkMatricesAlmostEqual(self, expected, actual, places=7): + if len(expected) != len(actual): + raise ValueError("len(expected) != len(actual)") + + if len(expected[0]) != len(actual[0]): + raise ValueError("len(expected[0]) != len(actual[0])") + + for i in range(len(expected)): + for j in range(len(expected[0])): + self.assertAlmostEqual(expected[i][j], actual[i][j], places=places) + + def test_species_attribute(self): + self.assertEqual(self.rr.S1, 10) + + def test_species_attribute_amount(self): + self.assertEqual(self.rr.S1_amt, 10) + + def test_species_attribute_conc(self): + self.assertEqual(self.rr.S1_conc, 10) + + def test_reaction_flux(self): + self.assertEqual(self.rr._J0, 1) + + def test_attribute_access_protocols_setattr(self): + self.rr.__setattr__("cheese", 6) + self.assertTrue(hasattr(self.rr, "cheese")) + self.assertEqual(getattr(self.rr, "cheese"), 6) + + def test_attribute_access_protocols_getattr(self): + self.assertEqual(self.rr.__getattr__("S1"), 10) + + def test___dict__(self): + self.assertEqual( + ["this"], + list(self.rr.__dict__.keys()) + ) + + @unittest.skip("__eq__ may be implemented, may not. If not we should do") + def test___eq__(self): + pass + + def test___getitem__(self): + self.assertEqual(self.rr.__getitem__("S1"), 10.0) + + def test___len__(self): + self.assertEqual(len(self.rr), 62) # Enumerates all possible rr[x] arguments. + + def test___repr__(self): + l = repr([self.rr]) + self.assertIn("roadrunner.RoadRunner()", l) + + def test___setitem__fails_when_key_not_exist(self): + with self.assertRaises(RuntimeError): + self.rr.__setitem__("five", 5) + + def test___setitem__when_key_exists(self): + self.rr.__setitem__("S1", 12) + self.assertEqual(self.rr.__getitem__("S1"), 12) + + # def test___sizeof__(self): + # self.assertEqual(32, self.rr.__sizeof__()) + + def test___str__(self): + s = str(self.rr) + print(s) + self.assertIn("roadrunner", s) + + @unittest.skip("Method not implemented yet (but should be)") + def test_getCompartmentIds(self): + """This method is missing from the rr api""" + pass + + def test_addCompartment(self): + """The rr._addCompartment() method is called by the + rr.addCompartment() method. The difference, is the + latter adds the compartment to the __dict__ as an + attribute. + """ + self.rr.addCompartment("C1", 1, True) + self.assertEqual(self.rr.C1, 1) + + def testAddParameter(self): + self.rr.addParameter("k_new", 25, True) + self.assertEqual(25, self.rr.k_new) + + def testAddReaction(self): + self.rr.addReaction("NewReaction", ["S1"], ["S2"], "kf*S1", True) + self.rr.S1 = 10 + self.assertEqual(self.rr.NewReaction, 1.0) + + def testAddSpeciesConcentrations(self): + self.rr.addSpeciesConcentration("NewSpecies", "default_compartment", 123.3, False, False, "", True) + self.assertEqual(self.rr.NewSpecies, 123.3) + + def testAddSpecies(self): + self.rr.addSpeciesAmount("NewSpecies", "default_compartment", 123.3, False, False, "", True) + self.assertEqual(self.rr.NewSpecies, 123.3) + + @unittest.skip + def test_removeInitialAssignment(self): + self.assertEqual( + self.rr.removeInitialAssignment(), + ) + + @unittest.skip + def test_removeParameter(self): + self.assertEqual( + self.rr.removeParameter(), ) + + @unittest.skip + def test_removeReaction(self): + self.assertEqual( + self.rr.removeReaction(), + ) + + @unittest.skip + def test_removeRules(self): + self.assertEqual( + self.rr.removeRules(), + + ) + + @unittest.skip + def test_removeSpecies(self): + self.assertEqual( + self.rr.removeSpecies(), + ) + + def test_diffstep_getter(self): + self.assertEqual(self.rr._diffstep_getter(), 0.02) + + def test_diffstep_stter(self): + self.rr._diffstep_stter(0.01) + self.assertEqual(self.rr._diffstep_getter(), 0.01) + + def test_getConservedMoietyAnalysis(self): + self.assertFalse(self.rr._getConservedMoietyAnalysis()) + + def test_setConservedMoietyAnalysis(self): + self.rr.conservedMoietyAnalysis = True + self.assertTrue(self.rr._getConservedMoietyAnalysis()) + + def test_addAssignmentRule(self): + self.rr.addSpeciesConcentration("SNew", "default_compartment", 2.5, False, True, "", True) + self.rr.addAssignmentRule("SNew", "S1+5", True) + self.assertEqual(self.rr.SNew, 15) + + @unittest.skip("Not sure how to test this right now") + def test_addDelay(self): + pass + + @unittest.skip("Not sure how to test this right now") + def test_addEvent(self): + pass + + @unittest.skip("Not sure how to test this right now") + def test_addEventAssignment(self): + pass + + @unittest.skip("Not sure how to test this right now") + def test_addInitialAssignment(self): + self.rr.addSpeciesConcentration("NewSpec", "default_compartment", 13.3, False, True, "", False) + self.rr.addInitialAssignment("NewSpec", "S1+S2", True) + + @unittest.skip("Not sure how to test this right now") + def test_addPriority(self): + pass + + @unittest.skip("Not sure how to test this right now") + def test_addRateRule(self): + pass + + @unittest.skip("Not sure how to test this right now") + def test_addTrigger(self): + pass + + def test_clearModel(self): + self.assertTrue(self.rr.clearModel()) + + @unittest.skip("Not sure how to test this right now. Docs are not clear") + def test_createSelection(self): + pass + + def test_default_compartment(self): + self.assertEqual(self.rr.default_compartment, 1) + + def test_diffstep(self): + self.assertEqual(self.rr.diffstep, 0.02) + + @unittest.skip("This API is unclear. ") + def test_ensureSolversRegistered(self): + self.rr.ensureSolversRegistered() + + def test_getAvailableIntegrators(self): + self.assertEqual(self.rr.getAvailableIntegrators(), ("cvode",)) + + def test_getBoundarySpeciesAmountsNamedArray(self): + self.rr.setBoundary("S1", True) + bs = self.rr.getBoundarySpeciesAmountsNamedArray() + self.assertEqual(bs["S1"], 10) + + def test_getBoundarySpeciesConcentrationsNamedArray(self): + self.rr.setBoundary("S1", True) + self.rr.default_compartment = 0.5 + bs = self.rr.getBoundarySpeciesConcentrationsNamedArray() + self.assertEqual(bs["S1"], 20) + + def test_getCC(self): + self.assertAlmostEqual(self.rr.getCC("_J0", "kf"), 0.009090905110435235) + + def test_getCompiler(self): + compiler_string = str(self.rr.getCompiler()) + self.assertIn("Compiler", compiler_string) + + def test_getConservationMatrix(self): + rr2 = RoadRunner(tmf.TestModelFactory("Brown2004").str()) + rr2.conservedMoietyAnalysis = True + print(rr2.getConservationMatrix().shape) + self.assertEqual(rr2.getConservationMatrix().shape, (15, 28)) + + def test_getConservedMoietyIds(self): + """This mode has no conserved moieties so poor model for testing this feature""" + rr2 = RoadRunner(tmf.TestModelFactory("Brown2004").str()) + rr2.conservedMoietyAnalysis = True + expected = tuple([f"_CSUM{i}" for i in range(15)]) + self.assertEqual(rr2.getConservedMoietyIds(), expected) + + def test_getConservedMoietyValues(self): + """This mode has no conserved moieties so poor model for testing this feature""" + rr2 = RoadRunner(tmf.TestModelFactory("Brown2004").str()) + rr2.conservedMoietyAnalysis = True + print(rr2.getConservedMoietyValues()) + expected = [1.2000e+05, 6.0000e+05, 1.2000e+05, 1.2000e+05, 6.0000e+05, 1.2000e+05, 1.0000e+04, 1.2000e+05, + 1.2000e+05, 4.4600e+05, 1.2000e+05, 1.0002e+07, 1.2000e+05, 1.2000e+05, 8.0000e+04] + actual = rr2.getConservedMoietyValues() + for i in range(len(expected)): + self.assertAlmostEqual(expected[i], actual[i]) + + def test_getCurrentSBML(self): + self.assertIsInstance(self.rr.getCurrentSBML(), str) + + def test_getDependentFloatingSpeciesIds(self): + """No dependents in this model""" + self.assertTrue(callable(self.rr.getDependentFloatingSpeciesIds)) + + def test_getDependentRatesOfChange(self): + """No dependents in this model so we'll just check callable""" + self.assertTrue(callable(self.rr.getDependentRatesOfChange)) + + def test_getDependentRatesOfChangeNamedArray(self): + """No dependents in this model""" + self.assertTrue(callable(self.rr.getDependentRatesOfChangeNamedArray)) + + def test_getDiffStepSize(self): + self.assertEqual(0.02, self.rr.getDiffStepSize()) + + def test_getEE(self): + self.assertAlmostEqual(self.rr.getEE("_J0", "kf"), 1.0000000000000024) + + def test_getEigenValueIds(self): + expected = ('eigen(S1)', 'eigenReal(S1)', 'eigenImag(S1)', 'eigen(S2)', 'eigenReal(S2)', 'eigenImag(S2)') + self.assertEqual(self.rr.getEigenValueIds(), expected) + + def test_getExistingIntegratorNames(self): + expected = ('cvode',) + self.assertEqual(expected, self.rr.getExistingIntegratorNames()) + + def test_getExtendedStoichiometryMatrix(self): + rr2 = RoadRunner(tmf.TestModelFactory("OpenLinearFlux").str()) + mat = rr2.getExtendedStoichiometryMatrix() + print(mat) + expected = [ + [1, -1, 0], + [0, 1, -1], + [-1, 0, 0], + [0, 0, 1], + ] + # todo implement proper equality operators + print(mat.shape) + for i in range(mat.shape[0]): + for j in range(mat.shape[1]): + self.assertEqual(expected[i][j], mat[i][j]) + + def test_getFloatingSpeciesAmountsNamedArray(self): + x = self.rr.getFloatingSpeciesAmountsNamedArray() + self.assertEqual(x["S2"], 1) + + def test_getFloatingSpeciesConcentrationsNamedArray(self): + self.rr.default_compartment = 0.33 + x = self.rr.getFloatingSpeciesConcentrationsNamedArray() + self.assertAlmostEqual(3.0303030303030303, x["S2"][0]) + + def test_getFloatingSpeciesInitialConcentrationIds(self): + x = self.rr.getFloatingSpeciesInitialConcentrationIds() + self.assertEqual(x, ("init([S1])", "init([S2])",)) + + @unittest.skip("figure out how to use") + def test_getFrequencyResponse(self): + pass + + def test_getFullEigenValues(self): + print(dir(self.testModel)) + expected = self.testModel.fullEigenValues() + actual = self.rr.getFullEigenValues() + print(expected) + print(actual) + self.assertAlmostEqual(expected[0], actual[0]) + self.assertAlmostEqual(expected[1], actual[1]) + + def test_getFullJacobian(self): + print(dir(self.testModel)) + expected = self.testModel.fullJacobianAmt() + actual = self.rr.getFullJacobian() + for i in range(expected.shape[0]): + for j in range(expected.shape[1]): + self.assertAlmostEqual(expected[i][j], actual[i][j]) + + def test_getFullJacobianConc(self): + Config.setValue(Config.ROADRUNNER_JACOBIAN_MODE, Config.ROADRUNNER_JACOBIAN_MODE_CONCENTRATIONS) + expected = self.testModel.fullJacobianConc() + actual = self.rr.getFullJacobian() + for i in range(expected.shape[0]): + for j in range(expected.shape[1]): + self.assertAlmostEqual(expected[i][j], actual[i][j]) + + def test_getFullJacobianAmt(self): + expected = self.testModel.fullJacobianAmt() + Config.setValue(Config.ROADRUNNER_JACOBIAN_MODE, Config.ROADRUNNER_JACOBIAN_MODE_AMOUNTS) + actual = self.rr.getFullJacobian() + for i in range(expected.shape[0]): + for j in range(expected.shape[1]): + self.assertAlmostEqual(expected[i][j], actual[i][j]) + + def test_getFullStoichiometryMatrix(self): + expected = self.testModel.fullStoicMatrix() + self.checkMatricesAlmostEqual(expected, self.rr.getFullStoichiometryMatrix()) + + def test_getGlobalParameterByName(self): + self.assertEqual(self.rr.getGlobalParameterByName("kf"), 0.1) + + @unittest.skip("No way to use this method from Python - it " + "requires an out parameter as input") + def test_getIds(self): + pass + + def test_getIndependentFloatingSpeciesIds(self): + self.assertEqual(self.rr.getIndependentFloatingSpeciesIds(), ["S1"]) + + def test_getIndependentRatesOfChange(self): + self.assertEqual(-0.99, self.rr.getIndependentRatesOfChange()) + + def test_getIndependentRatesOfChangeNamedArray(self): + self.assertEqual( + self.rr.getIndependentRatesOfChangeNamedArray(), + [[-0.99]] + ) + + def test_getInfo(self): + self.assertIn( + "jacobianStepSize", + self.rr.getInfo(), + ) + + def test_getIntegrator(self): + self.assertEqual( + self.rr.getIntegrator().getName(), + "cvode" + ) + + def test_getIntegratorByName(self): + self.assertIsInstance( + self.rr.getIntegratorByName("cvode"), + Integrator + ) + + def test_getKMatrix(self): + expected = [[1], [1]] + self.checkMatricesAlmostEqual( + expected, + self.rr.getKMatrix(), + ) + + def test_getKineticLaw(self): + self.assertEqual( + self.rr.getKineticLaw("_J0"), + "kf * S1" + ) + + def test_getL0Matrix(self): + print(dir(self.testModel)) + expected = self.testModel.L0Matrix() + actual = self.rr.getL0Matrix() + self.assertEqual(expected, actual) + + def test_getLinkMatrix(self): + # roadrunner automatically trasposes column vectors + # into row vectors + expected = self.testModel.linkMatrix() + actual = self.rr.getLinkMatrix().T[0] + print(expected) + print(actual) + self.assertTrue((expected == actual).all()) + + def test_getModel(self): + self.assertIsInstance( + self.rr.getModel(), + ExecutableModel + ) + + def test_getNrMatrix(self): + expected = self.testModel.NrMatrix() + self.checkMatricesAlmostEqual( + expected, + self.rr.getNrMatrix(), + ) + + @unittest.skip("No idea what the argument for this method should be?") + def test_getParamPromotedSBML(self): + self.assertEqual( + self.rr.getParamPromotedSBML(), + ) + + def test_getRatesOfChange(self): + print(self.rr.getRatesOfChange()) + self.assertSequenceEqual( + list(self.rr.getRatesOfChange()), + [-0.99, 0.99] + ) + + def test_getRatesOfChangeNamedArray(self): + print(self.rr.getRatesOfChangeNamedArray()) + self.assertSequenceEqual( + list(self.rr.getRatesOfChangeNamedArray()[0]), + [-0.99, 0.99] + ) + + def test_getReactionRates(self): + self.assertEqual(1.0, self.rr.getReactionRates()[0]) + self.assertEqual(0.01, self.rr.getReactionRates()[1]) + + def test_getReducedEigenValues(self): + expected = self.testModel.reducedEigenValues() + self.rr.conservedMoietyAnalysis = True + actual = self.rr.getReducedEigenValues() + print("expected: ", expected) + print("actual: ", actual) + self.assertEqual(expected.shape, actual.shape) + self.assertAlmostEqual(expected[0], actual[0]) + + def test_getReducedJacobian(self): + self.rr.conservedMoietyAnalysis = True + expected = self.testModel.reducedJacobianConc() + actual = self.rr.getReducedJacobian() + print(expected) + print(actual) + + self.assertAlmostEqual( + -0.11, + self.rr.getReducedJacobian()["S1"][0], + ) + + def test_getReducedStoichiometryMatrix(self): + self.rr.conservedMoietyAnalysis = True + expected = self.testModel.reducedStoicMatrix() + self.checkMatricesAlmostEqual( + expected, + self.rr.getReducedStoichiometryMatrix(), + ) + + def test_getRegisteredIntegratorNames(self): + self.assertEqual( + ('cvode', 'gillespie', 'rk4', 'rk45', 'euler'), + self.rr.getRegisteredIntegratorNames(), + ) + + def test_getRegisteredSteadyStateSolverNames(self): + self.assertEqual( + ('nleq1', 'nleq2', 'newton', "newton_linesearch"), + self.rr.getRegisteredSteadyStateSolverNames(), + ) + + def test_getRegisteredSensitivitySolverNames(self): + print(dir(self.rr)) + self.assertEqual( + ("forward",), + self.rr.getRegisteredSensitivitySolverNames(), + ) + + def test_getSBML(self): + self.assertIsInstance( + self.rr.getSBML(), + str + ) + + def test_getScaledConcentrationControlCoefficientMatrix(self): + expected = self.testModel.scaledConcentrationControlCoefficientMatrix() + actual = self.rr.getScaledConcentrationControlCoefficientMatrix() + self.checkMatricesAlmostEqual( + expected, actual, 5 + ) + + def test_getScaledElasticityMatrix(self): + actual = self.rr.getScaledElasticityMatrix() + expected = self.testModel.scaledElasticityMatrix() + print(actual) + self.checkMatricesAlmostEqual( + expected, actual + ) + + def test_getScaledFloatingSpeciesElasticity(self): + self.assertAlmostEqual( + 1.0, + self.rr.getScaledFloatingSpeciesElasticity("_J1", "S2"), + ) + + def test_getScaledFluxControlCoefficientMatrix(self): + expected = self.testModel.scaledFluxControlCoefficientMatrix() + actual = self.rr.getScaledFluxControlCoefficientMatrix() + self.checkMatricesAlmostEqual( + expected, actual, 5 + ) + + def test_getSelectedValues(self): + self.assertEqual(self.rr.getSelectedValues()[0], 0) + self.assertEqual(self.rr.getSelectedValues()[1], 10) + + def test_getSimulationData(self): + self.assertTrue( + self.rr.getSimulationData().size == 0 + ) + self.rr.simulate(0, 10, 11) + actual = self.rr.getSimulationData() + expected = self.testModel.timeSeriesResult() + self.checkMatricesAlmostEqual(actual, expected, places=4) + + def test_getSteadyStateSelectionStrings(self): + self.assertEqual( + self.rr.getSteadyStateSelectionStrings(), + ("[S1]", "[S2]") + ) + + def test_getSteadyStateSolver(self): + solver = self.rr.getSteadyStateSolver() + self.assertEqual("nleq2", solver.getName()) + + def test_getSteadyStateThreshold(self): + self.assertEqual( + self.rr.getSteadyStateThreshold(), + 0.01 + ) + + def test_getSteadyStateValues(self): + expected = self.testModel.steadyState() + actual = self.rr.getSteadyStateValues() + print(expected) + print(actual) + self.assertEqual(expected["S1"], actual[0]) + self.assertEqual(expected["S2"], actual[1]) + + def test_getSteadyStateValuesNamedArray(self): + expected = self.testModel.steadyState() + actual = self.rr.getSteadyStateValuesNamedArray() + print(expected) + self.assertAlmostEqual(expected["S1"], actual[0, 0]) + self.assertAlmostEqual(expected["S2"], actual[0, 1]) + + def test_getSensitivitySolver(self): + self.assertEqual( + "forward", + self.rr.getSensitivitySolver().getName() + ) + + @unittest.skip("This method should be not be visible in Python") + def test_getSupportedIdTypes(self): + """returns a bit field of the ids that this class supports.""" + + def test_getUnscaledConcentrationControlCoefficientMatrix(self): + expected = self.testModel.unscaledConcentrationControlCoefficientMatrix() + actual = self.rr.getUnscaledConcentrationControlCoefficientMatrix() + self.checkMatricesAlmostEqual( + expected, actual, 5 + ) + + def test_getUnscaledElasticityMatrix(self): + expected = self.testModel.unscaledElasticityMatrix() + actual = self.rr.getUnscaledElasticityMatrix() + self.checkMatricesAlmostEqual( + expected, actual, 5 + ) + + def test_getUnscaledFluxControlCoefficientMatrix(self): + expected = self.testModel.unscaledFluxControlCoefficientMatrix() + actual = self.rr.getUnscaledFluxControlCoefficientMatrix() + self.checkMatricesAlmostEqual( + expected, actual, 5 + ) + + def test_getUnscaledParameterElasticity(self): + self.assertAlmostEqual( + 10, + self.rr.getUnscaledParameterElasticity("_J0", "kf"), + ) + + def test_getUnscaledSpeciesElasticity(self): + self.assertEqual( + 0.10000000000000007, + self.rr.getUnscaledSpeciesElasticity(0, 0), + ) + + def test_getValue(self): + self.assertEqual( + self.rr.getValue("kb"), + 0.01 + ) + + def test_getuCC(self): + self.assertAlmostEqual( + 0.09090905110435235, + self.rr.getuCC("_J0", "kf"), + ) + + def test_getuEE(self): + self.assertAlmostEqual( + self.rr.getuEE("_J0", "kf"), + 10 + ) + + def test_integrator(self): + self.assertIsInstance( + self.rr.integrator, + Integrator + ) + + def test_integratorExists(self): + self.assertTrue( + self.rr.integratorExists("cvode"), + ) + + def test_internalOneStep(self): + before = self.rr.S2 + self.rr.internalOneStep(0, 10) + after = self.rr.S2 + self.assertNotEqual(before, after) + + def test_isModelLoaded(self): + self.assertTrue( + self.rr.isModelLoaded(), + ) + + def test_items(self): + expected = [('S1', 10.0), + ('S2', 1.0), + ('[S1]', 10.0), + ('[S2]', 1.0), + ('default_compartment', 1.0), + ('kf', 0.1), + ('kb', 0.01), + ('_J0', 1.0), + ('_J1', 0.01), + ('init([S1])', 10.0), + ('init([S2])', 1.0), + ('init(S1)', 10.0), + ('init(S2)', 1.0), + ('init(default_compartment)', 1.0), + ('init(kf)', 0.1), + ('init(kb)', 0.01), + ("S1'", -0.99), + ("S2'", 0.99), + ("[S1]'", -0.99), + ("[S2]'", 0.99), + ('stoich(S1, _J0)', -1.0), + ('stoich(S1, _J1)', 1.0), + ('stoich(S2, _J0)', 1.0), + ('stoich(S2, _J1)', -1.0), + ('uec(_J0, S1)', 0.10000000000000007), + ('uec(_J0, S2)', 0.0), + ('uec(_J0, kf)', 10.000000000000082), + ('uec(_J0, kb)', 0.0), + ('uec(_J1, S1)', 0.0), + ('uec(_J1, S2)', 0.009999999999999998), + ('uec(_J1, kf)', 0.0), + ('uec(_J1, kb)', 1.0000000000000053), + ('ec(_J0, S1)', 1.0000000000000007), + ('ec(_J0, S2)', 0.0), + ('ec(_J0, kf)', 1.0000000000000082), + ('ec(_J0, kb)', 0.0), + ('ec(_J1, S1)', 0.0), + ('ec(_J1, S2)', 0.9999999999999998), + ('ec(_J1, kf)', 0.0), + ('ec(_J1, kb)', 1.0000000000000053), + ('ucc(_J0, kf)', 0.09090905110435235), + ('ucc(_J0, kb)', 9.090909090511781), + ('ucc(_J1, kf)', 0.09090905110435235), + ('ucc(_J1, kb)', 9.090909090511735), + ('ucc(S1, kf)', -9.09090511043516), + ('ucc(S1, kb)', 90.90909090511799), + ('ucc(S2, kf)', 9.090905110435088), + ('ucc(S2, kb)', -90.90909090512392), + ('cc(_J0, kf)', 0.009090905110435235), + ('cc(_J0, kb)', 0.09090909090511781), + ('cc(_J1, kf)', 0.9090905110435236), + ('cc(_J1, kb)', 9.090909090511735), + ('cc(S1, kf)', -0.09090905110435162), + ('cc(S1, kb)', 0.09090909090511799), + ('cc(S2, kf)', 0.9090905110435088), + ('cc(S2, kb)', -0.9090909090512392), + ('eigen(S1)', (-0.10999999999999983+0j)), + ('eigenReal(S1)', -0.10999999999999983), + ('eigenImag(S1)', 0.0), + ('eigen(S2)', 0j), + ('eigenReal(S2)', 0.0), + ('eigenImag(S2)', 0.0)] + self.assertEqual( + expected, + self.rr.items(), + ) + + def test_iteritems(self): + + working_iterator = False + for i in self.rr.iteritems(): + working_iterator = True + self.assertTrue(working_iterator) + + def test_iterkeys(self): + + working_iterator = False + for i in self.rr.iterkeys(): + working_iterator = True + self.assertTrue(working_iterator) + + def test_itervalues(self): + + working_iterator = False + for i in self.rr.itervalues(): + working_iterator = True + self.assertTrue(working_iterator) + + def test_parameter_value(self): + self.assertEqual( + self.rr.kf, + 0.1 + ) + + def test_keys(self): + + expected = ['S1', + 'S2', + '[S1]', + '[S2]', + 'default_compartment', + 'kf', + 'kb', + '_J0', + '_J1', + 'init([S1])', + 'init([S2])', + 'init(S1)', + 'init(S2)', + 'init(default_compartment)', + 'init(kf)', + 'init(kb)', + "S1'", + "S2'", + "[S1]'", + "[S2]'", + 'stoich(S1, _J0)', + 'stoich(S1, _J1)', + 'stoich(S2, _J0)', + 'stoich(S2, _J1)', + 'uec(_J0, S1)', + 'uec(_J0, S2)', + 'uec(_J0, kf)', + 'uec(_J0, kb)', + 'uec(_J1, S1)', + 'uec(_J1, S2)', + 'uec(_J1, kf)', + 'uec(_J1, kb)', + 'ec(_J0, S1)', + 'ec(_J0, S2)', + 'ec(_J0, kf)', + 'ec(_J0, kb)', + 'ec(_J1, S1)', + 'ec(_J1, S2)', + 'ec(_J1, kf)', + 'ec(_J1, kb)', + 'ucc(_J0, kf)', + 'ucc(_J0, kb)', + 'ucc(_J1, kf)', + 'ucc(_J1, kb)', + 'ucc(S1, kf)', + 'ucc(S1, kb)', + 'ucc(S2, kf)', + 'ucc(S2, kb)', + 'cc(_J0, kf)', + 'cc(_J0, kb)', + 'cc(_J1, kf)', + 'cc(_J1, kb)', + 'cc(S1, kf)', + 'cc(S1, kb)', + 'cc(S2, kf)', + 'cc(S2, kb)', + 'eigen(S1)', + 'eigenReal(S1)', + 'eigenImag(S1)', + 'eigen(S2)', + 'eigenReal(S2)', + 'eigenImag(S2)',] + self.assertEqual( + expected, + self.rr.keys(), + ) + + def test_load(self): + self.rr.load(self.testModel.str()), + self.assertTrue(self.rr.isModelLoaded()) + + def test_loadState(self): + this_dir = os.path.dirname(__file__) + fname = os.path.join(this_dir, "roadrunner_state.rr") + self.rr.saveState(fname) + self.assertTrue(os.path.isfile(fname)) + self.rr.loadState(fname) + self.assertTrue(self.rr.isModelLoaded()) + os.remove(fname) + + def test_loadStateS(self): + x = self.rr.saveStateS() + rr2 = RoadRunner() + rr2.loadStateS(x) + data = rr2.simulate(0, 10, 11) + print(data) + self.assertEqual((11, 3), data.shape) + + def test_makeIntegrator(self): + integrator = self.rr.makeIntegrator("gillespie") + self.assertIsInstance( + integrator, + Integrator + ) + + def test_mcaSteadyState(self): + self.assertAlmostEqual( + self.rr.mcaSteadyState(), + 1.3877787807814457e-17 + ) + + def test_model(self): + self.assertIsInstance( + self.rr.model, + ExecutableModel + ) + + def test_oneStep(self): + before = self.rr.S2 + self.rr.internalOneStep(0, 10) + after = self.rr.S2 + self.assertNotEqual(before, after) + + def test_options(self): + self.assertIsInstance( + self.rr.options, + RoadRunnerOptions + ) + + def test_regenerateModel(self): + self.rr.regenerateModel() + self.assertTrue(self.rr.isModelLoaded()) + + @unittest.skip("unclear on how to use this method") + def test_removeCompartment(self): + self.rr.removeCompartment("default_compartment", True) + with self.assertRaises(AttributeError): + self.rr.default_compartment + + @unittest.skip("no events in model - add one ") + def test_removeEvent(self): + pass + + @unittest.skip("no events in model - add one ") + def test_removeEventAssignments(self): + print(self.rr.removeEventAssignments()) + + def test_reset(self): + self.rr.reset() + self.assertTrue( + self.rr.isModelLoaded() + ) + + def test_resetAll(self): + """difference between reset and resetAll?""" + self.rr.resetAll() + self.assertTrue( + self.rr.isModelLoaded() + ) + + def test_resetParameter(self): + self.assertEqual(self.rr.kf, 0.1) # starting value + self.rr.kf = 15 # uses setattr + self.assertEqual(self.rr.kf, 15) # starting value + self.rr.resetParameter() + self.assertEqual(self.rr.kf, 0.1) + + def test_resetSelectionLists(self): + self.rr.selections = ["[S2]"] + self.rr.resetSelectionLists() + self.assertEqual( + ['time', "[S1]", '[S2]'], + self.rr.selections, + ) + + def test_resetToOrigin(self): + self.kf = 16 + self.rr.resetToOrigin() + self.assertEqual( + self.rr.kf, 0.1 + ) + + def test_getCurrentTime(self): + self.assertEqual(0, self.rr.getCurrentTime()) + self.rr.simulate(0, 100, 101) + self.assertEqual(100, self.rr.getCurrentTime()) + + def test_selections(self): + self.assertEqual( + self.rr.selections, + ['time', '[S1]', '[S2]'] + ) + + def test_setBoundary(self): + self.rr.setBoundary("S1", False) + self.assertEqual(0, self.rr.getBoundarySpeciesAmountsNamedArray().size) + self.rr.setBoundary("S1", True) + self.assertEqual(1, self.rr.getBoundarySpeciesAmountsNamedArray().size) + + @unittest.skip("We can setConstant but how to getConstant?") + def test_setConstant(self): + self.rr.setConstant("S1", False) + + def test_setDiffStepSize(self): + self.rr.setDiffStepSize(1e-6) + self.assertEqual( + self.rr.getDiffStepSize(), + 1e-6 + ) + + def test_setGlobalParameterByName(self): + self.rr.setGlobalParameterByName("kf", 6), + self.assertEqual( + self.rr.kf, 6 + ) + + @unittest.skip("How to getHasOnlySubstanceUnits?") + def test_setHasOnlySubstanceUnits(self): + self.rr.setHasOnlySubstanceUnits("S1", True) + + @unittest.skip("This function looks broken?") + def test_setInitAmount(self): + self.rr.setInitAmount("S1", 45.6, True) + self.assertEqual( + self.rr.S1, 45.6 + ) + + @unittest.skip("This function looks broken?") + def test_setInitConcentration(self): + self.rr.setInitConcentration("S1", 45.6, True) + self.assertEqual( + self.rr.S1, 45.6 + ) + + def test_setIntegrator(self): + self.rr.setIntegrator("gillespie") + self.assertEqual( + "gillespie", + self.rr.integrator.getName() + ) + + def test_setIntegratorSetting(self): + self.assertTrue( + self.rr.integrator.getValue("stiff") + ) + + def test_setKineticLaw(self): + self.rr.setKineticLaw("_J0", "1+2+3+4+5") + self.assertEqual( + self.rr.getKineticLaw("_J0"), + "1 + 2 + 3 + 4 + 5" + ) + + @unittest.skip("What should go in RoadRunnerOptions?") + def test_setOptions(self): + opt = RoadRunnerOptions() + self.assertEqual( + self.rr.setOptions(), + ) + + @unittest.skip("how to use?") + def test_setPersistent(self): + self.assertEqual( + self.rr.setPersistent(), + ) + + @unittest.skip("How to get the reversible flag back after we've set it?") + def test_setReversible(self): + pass + + def test_setSteadyStateSolver(self): + self.rr.setSteadyStateSolver("newton") + solver = self.rr.getSteadyStateSolver() + print(solver, type(solver)) + self.assertEqual( + solver.getName(), + "newton" + ) + + def test_setSteadyStateThreshold(self): + self.rr.setSteadyStateThreshold(6) + self.assertEqual( + self.rr.getSteadyStateThreshold(), 6 + ) + + @unittest.skip("how to use?") + def test_setTriggerInitialValue(self): + self.assertEqual( + self.rr.setTriggerInitialValue(), + ) + + @unittest.skip("What values are set on a RoadRunner instance?") + def test_setValue(self): + self.assertEqual( + self.rr.setValue(), + ) + + def test_simulate(self): + expected = self.testModel.timeSeriesResult() + settings = self.testModel.timeSeriesSettings() + start = settings["start"] + duration = settings["duration"] + steps = settings["steps"] + num = steps + 1 + self.rr.simulate(start, duration, num) + print(expected) + actual = self.rr.getSimulationData() + print(actual) + self.checkMatricesAlmostEqual(expected, actual, 4) + + def test_steadyState(self): + expected = self.testModel.steadyState() + self.rr.steadyState() + actual = self.rr.getFloatingSpeciesAmountsNamedArray() + print(expected) + print(actual) + self.assertAlmostEqual(expected["S1"], actual[0][0]) + self.assertAlmostEqual(expected["S2"], actual[0][1]) + + def test_steadyStateNamedArray(self): + expected = self.testModel.steadyState() + self.rr.steadyState() + actual = self.rr.steadyStateNamedArray() + print(expected) + print(actual) + self.assertAlmostEqual(expected["S1"], actual[0][0]) + self.assertAlmostEqual(expected["S2"], actual[0][1]) + + def test_steadyStateSelections(self): + self.assertEqual( + self.rr.steadyStateSelections, + ["[S1]", "[S2]"] + ) + + def test_steadyStateSolver(self): + self.assertIsInstance( + self.rr.steadyStateSolver, + SteadyStateSolver + ) + + def test_steadyStateSolverExists(self): + self.assertTrue(self.rr.steadyStateSolverExists("nleq2")) + self.assertFalse(self.rr.steadyStateSolverExists("newton")) # not instantiated yet + + def test_steadyStateThresh(self): + self.assertEqual( + self.rr.steadyStateThresh, + 0.01 + ) + + def test_timeCourseSelections(self): + self.assertEqual( + self.rr.timeCourseSelections, + ['time', "[S1]", '[S2]'] + ) + + @unittest.skip("unclear how to test. Should this method be private?") + def test_validateCurrentSBML(self): + self.assertTrue(self.rr.validateCurrentSBML()) + + def test_load_model_with_large_recursion_limit(self): + """ + This was a fun one. Tellurium crashed with version roadrunner 2.0.6 + because it imports plotly. Plotly imports Ipython.display, which + imports jedi which changes the recursion depth with sys.setrecursionlimit. + This caused roadrunner to crash. Here we write a test to resolve this problem. + :return: + """ + + """ + Okay, so we can't call getIds() inside __getattr__. Why not? + No, actually - we can't call *anything. infinite recursion + """ + import sys + sys.setrecursionlimit(3000) + m = RoadRunner(self.testModel.str()) + self.assertIsInstance(m, RoadRunner) + + def test_getitem_when_exists(self): + import sys + sys.setrecursionlimit(3000) + m = RoadRunner(self.testModel.str()) + self.assertEqual(10.0, m["S1"]) + + def test_getitem_when_not_exists(self): + import sys + sys.setrecursionlimit(3000) + m = RoadRunner(self.testModel.str()) + with self.assertRaises(RuntimeError): + s = m["S100"] + + def test_getitem_when_created_after_instantiation(self): + import sys + sys.setrecursionlimit(3000) + m = RoadRunner(self.testModel.str()) + m.addSpeciesConcentration("S100", "default_compartment", 123.3, False, False, "", True) + val = m["S100"] + self.assertAlmostEqual(val, 123.3) + + def test_getitem_when_created_after_instantiation_dot_notation(self): + import sys + sys.setrecursionlimit(3000) + m = RoadRunner(self.testModel.str()) + m.addSpeciesConcentration("S100", "default_compartment", 123.3, False, False, "", True) + m._makeProperties() + self.assertAlmostEqual(m.S100, 123.3) + + def test_simulateWithTimes(self): + self.rr.resetToOrigin() + self.rr.simulate(times = [0, 1, 5, 10]) + result = self.rr.getSimulationData() + self.assertEqual(list(result[:,0]), [0, 1, 5, 10]) + + +if __name__ == "__main__": + unittest.main() diff --git a/test/python/test_roadrunner_map.py b/test/python/test_roadrunner_map.py index a30babf473..474438d54e 100644 --- a/test/python/test_roadrunner_map.py +++ b/test/python/test_roadrunner_map.py @@ -13,179 +13,175 @@ ] import roadrunner as rr from roadrunner import RoadRunnerMap, RoadRunner +import roadrunner.tests.TestModelFactory as tmf -import platform -if platform.system() != "Darwin": - - import roadrunner.tests.TestModelFactory as tmf - - - class RoadRunnerMapTests(unittest.TestCase): - - def setUp(self) -> None: - self.sbmlStrings = [ - tmf.OpenLinearFlux().str(), - tmf.SimpleFlux().str(), - tmf.Brown2004().str(), - tmf.FactorialInRateLaw().str(), - tmf.Venkatraman2010().str() - ] - self.N = len(self.sbmlStrings) - - def test_ctor1(self): - rrm = RoadRunnerMap() - self.assertEqual(0, len(rrm)) - - def test_ctor2(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - self.assertEqual(len(self.sbmlStrings), len(rrm)) - - def test_keys(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - expected = ('SimpleFlux', 'x', 'FactorialModel1', '__main', 'Brown2004_NGF_EGF_signaling') - self.assertEqual(sorted(expected), sorted(rrm.keys())) - - def test_size_1thread(self): - rrm = RoadRunnerMap(self.sbmlStrings, 1) - self.assertEqual(self.N, len(rrm)) - - def test_size_2thread(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - self.assertEqual(self.N, len(rrm)) - - def test_values(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - values = rrm.values() - self.assertIsInstance(values, list) - self.assertTrue(all([isinstance(i, RoadRunner) for i in values])) - - def test_items(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - items = rrm.items() - self.assertIsInstance(items, list) - for name, rrModel in rrm.items(): - self.assertIsInstance(name, str) - self.assertIsInstance(rrModel, RoadRunner) - - def test_insert_from_empty(self): - rrm = RoadRunnerMap() - rrm.insert(self.sbmlStrings[0]) - self.assertEqual(1, len(rrm)) - self.assertEqual(rrm.keys()[0], "x") - - def test_insert_from_empty_with_custom_name(self): - rrm = RoadRunnerMap() - rrm.insert("NewName", self.sbmlStrings[0]) - self.assertEqual(1, len(rrm)) - self.assertEqual(rrm.keys()[0], "NewName") - - def test_insert_from_populated(self): - rrm = RoadRunnerMap(self.sbmlStrings[:2], 2) - rrm.insert(self.sbmlStrings[-1]) - self.assertEqual(3, len(rrm)) - - def test_insert_from_populated_custom_name(self): - rrm = RoadRunnerMap(self.sbmlStrings[:2], 2) - rrm.insert("NewModel", self.sbmlStrings[-1]) - self.assertEqual(3, len(rrm)) - self.assertTrue("NewModel" in rrm) - - def test_insert_from_list_of_strings(self): - n = len(self.sbmlStrings[:2]) + len(self.sbmlStrings[2:]) - rrm = RoadRunnerMap(self.sbmlStrings[:2], 2) - rrm.insert(self.sbmlStrings[2:]) - self.assertEqual(n, len(rrm)) - - def test___setitem__(self): - rrm = RoadRunnerMap(self.sbmlStrings[:-1], 2) - last = self.sbmlStrings[-1] - rrm["last"] = last - self.assertEqual(len(self.sbmlStrings), len(rrm)) - - def test___setitem__exception(self): - """ - This is explicitely prohibited to prevent users from looping over a list of - sbml paths/strings and entering them one by one into the map. This situation - should instead be handled by passing in the list of strings. - """ - rrm = RoadRunnerMap(self.sbmlStrings[:-1], 2) - last = self.sbmlStrings[-1] - with self.assertRaises(TypeError): - rrm["last"] = RoadRunner(last) - - def test___getitem__(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - simpleFlux = rrm["SimpleFlux"] - self.assertIsInstance(simpleFlux, RoadRunner) - - def test___delitem__(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - self.assertEqual(len(self.sbmlStrings), len(rrm)) - del rrm["SimpleFlux"] - self.assertEqual(len(self.sbmlStrings) - 1, len(rrm)) - - def test_empty_when_true(self): - rrm = RoadRunnerMap() - self.assertTrue(rrm.empty) - - def test_empty_when_false(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - self.assertFalse(rrm.empty()) - - def test___len__(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - self.assertEqual(len(self.sbmlStrings), len(rrm)) - - def test_clear(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - self.assertEqual(len(self.sbmlStrings), len(rrm)) - self.assertFalse(rrm.empty()) - rrm.clear() - self.assertTrue(rrm.empty()) - - def test_contains_positive(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - self.assertTrue("x" in rrm) - - def test_contains_negative(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - self.assertFalse("x" not in rrm) - - def test_numThreads(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - self.assertEqual(2, rrm.getNumThreads()) - rrm.setNumThreads(4) - self.assertEqual(4, rrm.getNumThreads()) - - def test_iterators(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - expected = [ - "Brown2004_NGF_EGF_signaling", - "SimpleFlux", - "FactorialModel1", - "__main", - "x" - ] - k = [] - for i in rrm: - k.append(i) - self.assertEqual(sorted(k), sorted(expected)) - - - def test_iterators_items(self): - rrm = RoadRunnerMap(self.sbmlStrings, 2) - expected = [ - "Brown2004_NGF_EGF_signaling", - "SimpleFlux", - "FactorialModel1", - "__main", - "x" - ] - k = [] - for name, rr in rrm.items(): - k.append(name) - self.assertEqual(sorted(k), sorted(expected)) - - - if __name__ == "__main__": - unittest.main() + +class RoadRunnerMapTests(unittest.TestCase): + + def setUp(self) -> None: + self.sbmlStrings = [ + tmf.OpenLinearFlux().str(), + tmf.SimpleFlux().str(), + tmf.Brown2004().str(), + tmf.FactorialInRateLaw().str(), + tmf.Venkatraman2010().str() + ] + self.N = len(self.sbmlStrings) + + def test_ctor1(self): + rrm = RoadRunnerMap() + self.assertEqual(0, len(rrm)) + + def test_ctor2(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + self.assertEqual(len(self.sbmlStrings), len(rrm)) + + def test_keys(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + expected = ('SimpleFlux', 'x', 'FactorialModel1', '__main', 'Brown2004_NGF_EGF_signaling') + self.assertEqual(sorted(expected), sorted(rrm.keys())) + + def test_size_1thread(self): + rrm = RoadRunnerMap(self.sbmlStrings, 1) + self.assertEqual(self.N, len(rrm)) + + def test_size_2thread(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + self.assertEqual(self.N, len(rrm)) + + def test_values(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + values = rrm.values() + self.assertIsInstance(values, list) + self.assertTrue(all([isinstance(i, RoadRunner) for i in values])) + + def test_items(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + items = rrm.items() + self.assertIsInstance(items, list) + for name, rrModel in rrm.items(): + self.assertIsInstance(name, str) + self.assertIsInstance(rrModel, RoadRunner) + + def test_insert_from_empty(self): + rrm = RoadRunnerMap() + rrm.insert(self.sbmlStrings[0]) + self.assertEqual(1, len(rrm)) + self.assertEqual(rrm.keys()[0], "x") + + def test_insert_from_empty_with_custom_name(self): + rrm = RoadRunnerMap() + rrm.insert("NewName", self.sbmlStrings[0]) + self.assertEqual(1, len(rrm)) + self.assertEqual(rrm.keys()[0], "NewName") + + def test_insert_from_populated(self): + rrm = RoadRunnerMap(self.sbmlStrings[:2], 2) + rrm.insert(self.sbmlStrings[-1]) + self.assertEqual(3, len(rrm)) + + def test_insert_from_populated_custom_name(self): + rrm = RoadRunnerMap(self.sbmlStrings[:2], 2) + rrm.insert("NewModel", self.sbmlStrings[-1]) + self.assertEqual(3, len(rrm)) + self.assertTrue("NewModel" in rrm) + + def test_insert_from_list_of_strings(self): + n = len(self.sbmlStrings[:2]) + len(self.sbmlStrings[2:]) + rrm = RoadRunnerMap(self.sbmlStrings[:2], 2) + rrm.insert(self.sbmlStrings[2:]) + self.assertEqual(n, len(rrm)) + + def test___setitem__(self): + rrm = RoadRunnerMap(self.sbmlStrings[:-1], 2) + last = self.sbmlStrings[-1] + rrm["last"] = last + self.assertEqual(len(self.sbmlStrings), len(rrm)) + + def test___setitem__exception(self): + """ + This is explicitely prohibited to prevent users from looping over a list of + sbml paths/strings and entering them one by one into the map. This situation + should instead be handled by passing in the list of strings. + """ + rrm = RoadRunnerMap(self.sbmlStrings[:-1], 2) + last = self.sbmlStrings[-1] + with self.assertRaises(TypeError): + rrm["last"] = RoadRunner(last) + + def test___getitem__(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + simpleFlux = rrm["SimpleFlux"] + self.assertIsInstance(simpleFlux, RoadRunner) + + def test___delitem__(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + self.assertEqual(len(self.sbmlStrings), len(rrm)) + del rrm["SimpleFlux"] + self.assertEqual(len(self.sbmlStrings) - 1, len(rrm)) + + def test_empty_when_true(self): + rrm = RoadRunnerMap() + self.assertTrue(rrm.empty) + + def test_empty_when_false(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + self.assertFalse(rrm.empty()) + + def test___len__(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + self.assertEqual(len(self.sbmlStrings), len(rrm)) + + def test_clear(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + self.assertEqual(len(self.sbmlStrings), len(rrm)) + self.assertFalse(rrm.empty()) + rrm.clear() + self.assertTrue(rrm.empty()) + + def test_contains_positive(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + self.assertTrue("x" in rrm) + + def test_contains_negative(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + self.assertFalse("x" not in rrm) + + def test_numThreads(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + self.assertEqual(2, rrm.getNumThreads()) + rrm.setNumThreads(4) + self.assertEqual(4, rrm.getNumThreads()) + + def test_iterators(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + expected = [ + "Brown2004_NGF_EGF_signaling", + "SimpleFlux", + "FactorialModel1", + "__main", + "x" + ] + k = [] + for i in rrm: + k.append(i) + self.assertEqual(sorted(k), sorted(expected)) + + + def test_iterators_items(self): + rrm = RoadRunnerMap(self.sbmlStrings, 2) + expected = [ + "Brown2004_NGF_EGF_signaling", + "SimpleFlux", + "FactorialModel1", + "__main", + "x" + ] + k = [] + for name, rr in rrm.items(): + k.append(name) + self.assertEqual(sorted(k), sorted(expected)) + + +if __name__ == "__main__": + unittest.main() diff --git a/test/python/test_steadyStateSolver.py b/test/python/test_steadyStateSolver.py index c99e7ac977..6e1f0819a8 100644 --- a/test/python/test_steadyStateSolver.py +++ b/test/python/test_steadyStateSolver.py @@ -8,269 +8,266 @@ rr_site_packages, ] from roadrunner.roadrunner import RoadRunner, BasicNewtonIteration -import platform -if platform.system() != "Darwin": - - from roadrunner.tests.TestModelFactory import TestModelFactory - import roadrunner.tests.TestModelFactory as tmf - - import unittest - - - class NewtonIterationUnitTests(unittest.TestCase): - - def setUp(self) -> None: - # we choose the easiest model for the unit tests. - # see integration tests for solving other models. - self.testModel = TestModelFactory("SimpleFluxManuallyReduced") - self.rr = RoadRunner(self.testModel.str()) - - def checkResults(self, results): - for i in range(len(results.colnames)): - speciesId = results.colnames[i] - actualResult = results[0][i] - - expected = self.testModel.steadyState()[speciesId] - print("Comparing ", speciesId, "expected result: ", expected, "actual result: ", actualResult) - self.assertAlmostEqual(expected, actualResult) - - def test_newton_iteration_registered(self): - self.assertIn("newton", self.rr.getRegisteredSteadyStateSolverNames()) - - def test_newton_linesearch_registered(self): - self.assertIn("newton_linesearch", self.rr.getRegisteredSteadyStateSolverNames()) - - def test_settings_map_is_dict(self): - solver = BasicNewtonIteration(self.rr.getModel()) - settings = solver.getSettingsMap() - self.assertIsInstance(settings, dict) - - def test_solve_using_newton_iteration_directly(self): - solver = BasicNewtonIteration(self.rr.getModel()) - solver.allow_presimulation = True - solver.solve() - self.checkResults(self.rr.getFloatingSpeciesConcentrationsNamedArray()) - - def test_change_then_reset_settings(self): - solver = BasicNewtonIteration(self.rr.getModel()) - solver.presimulation_maximum_steps = 400 - # ensure we've actually changed something - self.assertEqual(400, solver.presimulation_maximum_steps) - solver.resetSettings() - self.assertEqual(500, solver.presimulation_maximum_steps) - - def test_regenerate_model_before_creating_solver(self): - self.rr.regenerateModel() - solver = BasicNewtonIteration(self.rr.getModel()) - solver.solve() - self.checkResults(self.rr.getFloatingSpeciesConcentrationsNamedArray()) - - def test_regenerate_model_after_creating_solver(self): - solver = BasicNewtonIteration(self.rr.getModel()) - self.rr.regenerateModel() - # after regeneration, the pointer to the model is different so we must sync with model before solving. - solver.syncWithModel(self.rr.getModel()) - solver.solve() - self.checkResults(self.rr.getFloatingSpeciesConcentrationsNamedArray()) - - def test_presimulation_times(self): - solver = BasicNewtonIteration(self.rr.getModel()) - self.assertIsInstance(solver.presimulation_times, list) - self.assertListEqual([0.1, 1.0, 10.0, 100.0, 1000.0, 10000.0], solver.presimulation_times) - - - class SteadyStateSolverIntegrationTests(unittest.TestCase): - # defined by subclasses - strategy = None - - def setUp(self) -> None: - pass - - def tearDown(self) -> None: - pass - - def checkValidTestModelName(self, model_name: str): - if model_name not in tmf.getAvailableTestModels(): - raise ValueError(f"The requested test model_name \"{model_name}\"" - f"is not one of the available test models: {tmf.getAvailableTestModels()}") - - def checkValidTestModelType(self, test_model : tmf.TestModel): - if not issubclass(type(test_model), tmf.SteadyStateResult): - raise ValueError("This test model does not implement the " - "SteadyStateResult interface") - - def checkSteadyState(self, model_name: str, solver_name: str, places:int=5): - # grab the test model - self.checkValidTestModelName(model_name) - - test_model = TestModelFactory(model_name) - - self.checkValidTestModelType(test_model) - - # load it into roadrunner - rr = RoadRunner(test_model.str()) - - # collect reference results - expected_results = test_model.steadyState() - - # set the steady state solver - rr.setSteadyStateSolver(solver_name) - - # get settings for this problem - settings = test_model.steadyStateSettings() - - # apply settings - for setting, value in settings.items(): - if setting == "moiety_conservation": - rr.conservedMoietyAnalysis = True - else: - try: - rr.getSteadyStateSolver().setValue(setting, value) - except Exception: - # its okay for a solver to not have a particular options - continue - - # do steady state calculation - rr.steadyState() - - actual_results = rr.getFloatingSpeciesConcentrationsNamedArray() - for species_name, expected_ss_val in expected_results.items(): - actual = actual_results[species_name][0] - print("Comparing reference value : ", expected_ss_val, "with actual value: ", actual) - self.assertAlmostEqual(expected_ss_val, actual, places=places) - - def checkSteadyStateFluxes(self, model_name: str, solver_name: str, places=5): - self.checkValidTestModelName(model_name) - - test_model = TestModelFactory(model_name) - - self.checkValidTestModelType(test_model) - - # load it into roadrunner - rr = RoadRunner(test_model.str()) - - # collect reference results - expected_results = test_model.steadyStateFluxes() - - # set the steady state solver - rr.setSteadyStateSolver(solver_name) - - # get settings for this problem - settings = test_model.steadyStateSettings() - - # apply settings - for setting, value in settings.items(): - if setting == "moiety_conservation": - rr.conservedMoietyAnalysis = True - else: - try: - rr.getSteadyStateSolver().setValue(setting, value) - except Exception: - # its okay for a solver to not have a particular options - continue - - # do steady state calculation - rr.steadyState() - - for reactionId, expectedSteadyStateFlux in expected_results.items(): - actualSteadyStateFlux = rr.getModel().getValue(reactionId) - print("Comparing reference value : ", expectedSteadyStateFlux, "with actual value: ", actualSteadyStateFlux) - self.assertAlmostEqual(expectedSteadyStateFlux, actualSteadyStateFlux, places=places) - - - class SundialsNewtonIterationTests(SteadyStateSolverIntegrationTests): - - def testOpenLinearFlux(self): - self.checkSteadyState("OpenLinearFlux", "newton") - - def testSimpleFluxManuallyReduced(self): - self.checkSteadyState("SimpleFluxManuallyReduced", "newton") - - def testSimpleFlux(self): - self.checkSteadyState("SimpleFlux", "newton") - - def testVenkatraman2010(self): - self.checkSteadyState("Venkatraman2010", "newton") - - def testBrown2004(self): - self.checkSteadyState("Brown2004", "newton") - - def testBimolecularEnd(self): - self.checkSteadyState("BimolecularEnd", "newton", 4) - - def testBimolecularEndSteadyStateFluxes(self): - self.checkSteadyStateFluxes("BimolecularEnd", "newton") - - - class LineSearchNewtonIterationTests(SteadyStateSolverIntegrationTests): - def testOpenLinearFlux(self): - self.checkSteadyState("OpenLinearFlux", "newton_linesearch") - - def testSimpleFluxManuallyReduced(self): - self.checkSteadyState("SimpleFluxManuallyReduced", "newton_linesearch") - - def testSimpleFlux(self): - self.checkSteadyState("SimpleFlux", "newton_linesearch") - - def testVenkatraman2010(self): - self.checkSteadyState("Venkatraman2010", "newton_linesearch") - - def testBrown2004(self): - self.checkSteadyState("Brown2004", "newton_linesearch") - - def testBimolecularEnd(self): - self.checkSteadyState("BimolecularEnd", "newton_linesearch", 4) - - def testBimolecularEndSteadyStateFluxes(self): - self.checkSteadyStateFluxes("BimolecularEnd", "newton_linesearch", 5) - - - class NLEQ1IntegrationTests(SteadyStateSolverIntegrationTests): - def testOpenLinearFlux(self): - self.checkSteadyState("OpenLinearFlux", "nleq1") - - def testSimpleFluxManuallyReduced(self): - self.checkSteadyState("SimpleFluxManuallyReduced", "nleq1") - - def testSimpleFlux(self): - self.checkSteadyState("SimpleFlux", "nleq1") - - def testVenkatraman2010(self): - self.checkSteadyState("Venkatraman2010", "nleq1") - - def testBrown2004(self): - self.checkSteadyState("Brown2004", "nleq1") - - def testBimolecularEnd(self): - self.checkSteadyState("BimolecularEnd", "nleq1", 4) - - def testBimolecularEndSteadyStateFluxes(self): - self.checkSteadyStateFluxes("BimolecularEnd", "nleq1", 5) - - - class NLEQ2IntegrationTests(SteadyStateSolverIntegrationTests): - def testOpenLinearFlux(self): - self.checkSteadyState("OpenLinearFlux", "nleq2") - - def testSimpleFluxManuallyReduced(self): - self.checkSteadyState("SimpleFluxManuallyReduced", "nleq2") - - def testSimpleFlux(self): - self.checkSteadyState("SimpleFlux", "nleq2") - - def testVenkatraman2010(self): - self.checkSteadyState("Venkatraman2010", "nleq2") - - def testBrown2004(self): - self.checkSteadyState("Brown2004", "nleq2") - - def testBimolecularEnd(self): - self.checkSteadyState("BimolecularEnd", "nleq2", 4) - - def testBimolecularEndSteadyStateFluxes(self): - self.checkSteadyStateFluxes("BimolecularEnd", "nleq2", 5) - - - - if __name__ == "__main__": - unittest.main() +from roadrunner.tests.TestModelFactory import TestModelFactory +import roadrunner.tests.TestModelFactory as tmf + +import unittest + + +class NewtonIterationUnitTests(unittest.TestCase): + + def setUp(self) -> None: + # we choose the easiest model for the unit tests. + # see integration tests for solving other models. + self.testModel = TestModelFactory("SimpleFluxManuallyReduced") + self.rr = RoadRunner(self.testModel.str()) + + def checkResults(self, results): + for i in range(len(results.colnames)): + speciesId = results.colnames[i] + actualResult = results[0][i] + + expected = self.testModel.steadyState()[speciesId] + print("Comparing ", speciesId, "expected result: ", expected, "actual result: ", actualResult) + self.assertAlmostEqual(expected, actualResult) + + def test_newton_iteration_registered(self): + self.assertIn("newton", self.rr.getRegisteredSteadyStateSolverNames()) + + def test_newton_linesearch_registered(self): + self.assertIn("newton_linesearch", self.rr.getRegisteredSteadyStateSolverNames()) + + def test_settings_map_is_dict(self): + solver = BasicNewtonIteration(self.rr.getModel()) + settings = solver.getSettingsMap() + self.assertIsInstance(settings, dict) + + def test_solve_using_newton_iteration_directly(self): + solver = BasicNewtonIteration(self.rr.getModel()) + solver.allow_presimulation = True + solver.solve() + self.checkResults(self.rr.getFloatingSpeciesConcentrationsNamedArray()) + + def test_change_then_reset_settings(self): + solver = BasicNewtonIteration(self.rr.getModel()) + solver.presimulation_maximum_steps = 400 + # ensure we've actually changed something + self.assertEqual(400, solver.presimulation_maximum_steps) + solver.resetSettings() + self.assertEqual(500, solver.presimulation_maximum_steps) + + def test_regenerate_model_before_creating_solver(self): + self.rr.regenerateModel() + solver = BasicNewtonIteration(self.rr.getModel()) + solver.solve() + self.checkResults(self.rr.getFloatingSpeciesConcentrationsNamedArray()) + + def test_regenerate_model_after_creating_solver(self): + solver = BasicNewtonIteration(self.rr.getModel()) + self.rr.regenerateModel() + # after regeneration, the pointer to the model is different so we must sync with model before solving. + solver.syncWithModel(self.rr.getModel()) + solver.solve() + self.checkResults(self.rr.getFloatingSpeciesConcentrationsNamedArray()) + + def test_presimulation_times(self): + solver = BasicNewtonIteration(self.rr.getModel()) + self.assertIsInstance(solver.presimulation_times, list) + self.assertListEqual([0.1, 1.0, 10.0, 100.0, 1000.0, 10000.0], solver.presimulation_times) + + +class SteadyStateSolverIntegrationTests(unittest.TestCase): + # defined by subclasses + strategy = None + + def setUp(self) -> None: + pass + + def tearDown(self) -> None: + pass + + def checkValidTestModelName(self, model_name: str): + if model_name not in tmf.getAvailableTestModels(): + raise ValueError(f"The requested test model_name \"{model_name}\"" + f"is not one of the available test models: {tmf.getAvailableTestModels()}") + + def checkValidTestModelType(self, test_model : tmf.TestModel): + if not issubclass(type(test_model), tmf.SteadyStateResult): + raise ValueError("This test model does not implement the " + "SteadyStateResult interface") + + def checkSteadyState(self, model_name: str, solver_name: str, places:int=5): + # grab the test model + self.checkValidTestModelName(model_name) + + test_model = TestModelFactory(model_name) + + self.checkValidTestModelType(test_model) + + # load it into roadrunner + rr = RoadRunner(test_model.str()) + + # collect reference results + expected_results = test_model.steadyState() + + # set the steady state solver + rr.setSteadyStateSolver(solver_name) + + # get settings for this problem + settings = test_model.steadyStateSettings() + + # apply settings + for setting, value in settings.items(): + if setting == "moiety_conservation": + rr.conservedMoietyAnalysis = True + else: + try: + rr.getSteadyStateSolver().setValue(setting, value) + except Exception: + # its okay for a solver to not have a particular options + continue + + # do steady state calculation + rr.steadyState() + + actual_results = rr.getFloatingSpeciesConcentrationsNamedArray() + for species_name, expected_ss_val in expected_results.items(): + actual = actual_results[species_name][0] + print("Comparing reference value : ", expected_ss_val, "with actual value: ", actual) + self.assertAlmostEqual(expected_ss_val, actual, places=places) + + def checkSteadyStateFluxes(self, model_name: str, solver_name: str, places=5): + self.checkValidTestModelName(model_name) + + test_model = TestModelFactory(model_name) + + self.checkValidTestModelType(test_model) + + # load it into roadrunner + rr = RoadRunner(test_model.str()) + + # collect reference results + expected_results = test_model.steadyStateFluxes() + + # set the steady state solver + rr.setSteadyStateSolver(solver_name) + + # get settings for this problem + settings = test_model.steadyStateSettings() + + # apply settings + for setting, value in settings.items(): + if setting == "moiety_conservation": + rr.conservedMoietyAnalysis = True + else: + try: + rr.getSteadyStateSolver().setValue(setting, value) + except Exception: + # its okay for a solver to not have a particular options + continue + + # do steady state calculation + rr.steadyState() + + for reactionId, expectedSteadyStateFlux in expected_results.items(): + actualSteadyStateFlux = rr.getModel().getValue(reactionId) + print("Comparing reference value : ", expectedSteadyStateFlux, "with actual value: ", actualSteadyStateFlux) + self.assertAlmostEqual(expectedSteadyStateFlux, actualSteadyStateFlux, places=places) + + +class SundialsNewtonIterationTests(SteadyStateSolverIntegrationTests): + + def testOpenLinearFlux(self): + self.checkSteadyState("OpenLinearFlux", "newton") + + def testSimpleFluxManuallyReduced(self): + self.checkSteadyState("SimpleFluxManuallyReduced", "newton") + + def testSimpleFlux(self): + self.checkSteadyState("SimpleFlux", "newton") + + def testVenkatraman2010(self): + self.checkSteadyState("Venkatraman2010", "newton") + + def testBrown2004(self): + self.checkSteadyState("Brown2004", "newton") + + def testBimolecularEnd(self): + self.checkSteadyState("BimolecularEnd", "newton", 4) + + def testBimolecularEndSteadyStateFluxes(self): + self.checkSteadyStateFluxes("BimolecularEnd", "newton") + + +class LineSearchNewtonIterationTests(SteadyStateSolverIntegrationTests): + def testOpenLinearFlux(self): + self.checkSteadyState("OpenLinearFlux", "newton_linesearch") + + def testSimpleFluxManuallyReduced(self): + self.checkSteadyState("SimpleFluxManuallyReduced", "newton_linesearch") + + def testSimpleFlux(self): + self.checkSteadyState("SimpleFlux", "newton_linesearch") + + def testVenkatraman2010(self): + self.checkSteadyState("Venkatraman2010", "newton_linesearch") + + def testBrown2004(self): + self.checkSteadyState("Brown2004", "newton_linesearch") + + def testBimolecularEnd(self): + self.checkSteadyState("BimolecularEnd", "newton_linesearch", 4) + + def testBimolecularEndSteadyStateFluxes(self): + self.checkSteadyStateFluxes("BimolecularEnd", "newton_linesearch", 5) + + +class NLEQ1IntegrationTests(SteadyStateSolverIntegrationTests): + def testOpenLinearFlux(self): + self.checkSteadyState("OpenLinearFlux", "nleq1") + + def testSimpleFluxManuallyReduced(self): + self.checkSteadyState("SimpleFluxManuallyReduced", "nleq1") + + def testSimpleFlux(self): + self.checkSteadyState("SimpleFlux", "nleq1") + + def testVenkatraman2010(self): + self.checkSteadyState("Venkatraman2010", "nleq1") + + def testBrown2004(self): + self.checkSteadyState("Brown2004", "nleq1") + + def testBimolecularEnd(self): + self.checkSteadyState("BimolecularEnd", "nleq1", 4) + + def testBimolecularEndSteadyStateFluxes(self): + self.checkSteadyStateFluxes("BimolecularEnd", "nleq1", 5) + + +class NLEQ2IntegrationTests(SteadyStateSolverIntegrationTests): + def testOpenLinearFlux(self): + self.checkSteadyState("OpenLinearFlux", "nleq2") + + def testSimpleFluxManuallyReduced(self): + self.checkSteadyState("SimpleFluxManuallyReduced", "nleq2") + + def testSimpleFlux(self): + self.checkSteadyState("SimpleFlux", "nleq2") + + def testVenkatraman2010(self): + self.checkSteadyState("Venkatraman2010", "nleq2") + + def testBrown2004(self): + self.checkSteadyState("Brown2004", "nleq2") + + def testBimolecularEnd(self): + self.checkSteadyState("BimolecularEnd", "nleq2", 4) + + def testBimolecularEndSteadyStateFluxes(self): + self.checkSteadyStateFluxes("BimolecularEnd", "nleq2", 5) + + + +if __name__ == "__main__": + unittest.main() diff --git a/test/python/test_structuralAnalysis.py b/test/python/test_structuralAnalysis.py index cb342258a3..bfc2fe3c3d 100644 --- a/test/python/test_structuralAnalysis.py +++ b/test/python/test_structuralAnalysis.py @@ -24,129 +24,126 @@ ) import roadrunner -import platform -if platform.system() != "Darwin": - - try: - from roadrunner.tests import TestModelFactory as tmf - from roadrunner.tests.RoadRunnerTest import RoadRunnerTest - except: - import TestModelFactory as tmf - from RoadRunnerTest import RoadRunnerTest - - - class StructuralAnalysisTests(RoadRunnerTest): - - def setUp(self) -> None: - pass - - def tearDown(self) -> None: - pass - - def loadTestModel(self, modelName: str): - """Instantiate instance of TestModel called modelName""" - self.checkValidTestModelName(modelName) - testModel = tmf.TestModelFactory(modelName) - self.checkTestModelImplements(testModel, tmf.StructuralProperties) - return testModel - - def checkLinkMatrix(self, modelName: str): - testModel = self.loadTestModel(modelName) - expected = testModel.linkMatrix() - rr = RoadRunner(testModel.str()) - actual = rr.getLinkMatrix() - self.checkMatricesEqual(expected, actual) - - def checkNrMatrix(self, modelName: str): - testModel = self.loadTestModel(modelName) - expected = testModel.NrMatrix() - rr = RoadRunner(testModel.str()) - rr.setConservedMoietyAnalysis = True - actual = rr.getNrMatrix() - self.checkMatricesEqual(expected, actual) - - def checkKMatrix(self, modelName: str): - testModel = self.loadTestModel(modelName) - expected = testModel.KMatrix() - rr = RoadRunner(testModel.str()) - actual = rr.getKMatrix() - for i in range(expected.shape[0]): - for j in range(expected.shape[1]): - self.assertAlmostEqual(expected[i][j], actual[i][j], 7) - - def checkReducedStoicMatrix(self, modelName: str): - testModel = self.loadTestModel(modelName) - expected = testModel.reducedStoicMatrix() - rr = RoadRunner(testModel.str()) - rr.setConservedMoietyAnalysis = True - actual = rr.getReducedStoichiometryMatrix() - self.checkMatricesEqual(expected, actual) - - def checkFullStoicMatrix(self, modelName: str): - testModel = self.loadTestModel(modelName) - expected = testModel.fullStoicMatrix() - rr = RoadRunner(testModel.str()) - # note turn this to False and the test fails. - # is this right? - rr.conservedMoietyAnalysis = True - actual = rr.getFullStoichiometryMatrix() - self.checkMatricesEqual(expected, actual) - - def checkExtendedStoicMatrix(self, modelName: str): - testModel = self.loadTestModel(modelName) - expected = testModel.extendedStoicMatrix() - rr = RoadRunner(testModel.str()) - # moiety conservation breaks the test. - # Theres something more going on here that should be investigated - # rr.setConservedMoietyAnalysis = True - actual = rr.getExtendedStoichiometryMatrix() - self.checkMatricesEqual(expected, actual) - - def checkL0Matrix(self, modelName: str): - testModel = self.loadTestModel(modelName) - expected = testModel.L0Matrix() - rr = RoadRunner(testModel.str()) - actual = rr.getL0Matrix() - self.checkMatricesEqual(expected, actual) - - def checkConservationMatrix(self, modelName: str): - testModel = self.loadTestModel(modelName) - expected = testModel.conservationMatrix() - rr = RoadRunner(testModel.str()) - rr.setConservedMoietyAnalysis = True - actual = rr.getConservationMatrix() - self.checkMatricesEqual(expected, actual) - - def test_BimolecularEnd_LinkMatrix(self): - self.checkLinkMatrix("BimolecularEnd") - - def test_BimolecularEnd_NrMatrix(self): - self.checkNrMatrix("BimolecularEnd") - - def test_BimolecularEnd_KMatrix(self): - self.checkKMatrix("BimolecularEnd") - - def test_BimolecularEnd_ReducedStoicMatrix(self): - self.checkReducedStoicMatrix("BimolecularEnd") - - def test_BimolecularEnd_FullStoicMatrix(self): - self.checkFullStoicMatrix("BimolecularEnd") - - def test_BimolecularEnd_ExtendedStoicMatrix(self): - self.checkExtendedStoicMatrix("BimolecularEnd") - - @unittest.skip("L0 matrix is empty for this model. Currently there is a " - "bug in RoadRunner's swig interface when porting an " - "empty Matrix to empty Python np array") - def test_BimolecularEnd_L0Matrix(self): - self.checkL0Matrix("BimolecularEnd") - - @unittest.skip("Conservation matrix is empty for this model. Currently there is a " - "bug in RoadRunner's swig interface when porting an " - "empty Matrix to empty Python np array") - def test_BimolecularEnd_ConservationMatrix(self): - self.checkConservationMatrix("BimolecularEnd") - - if __name__ == "__main__": - unittest.main() - +try: + from roadrunner.tests import TestModelFactory as tmf + from roadrunner.tests.RoadRunnerTest import RoadRunnerTest +except: + import TestModelFactory as tmf + from RoadRunnerTest import RoadRunnerTest + + +class StructuralAnalysisTests(RoadRunnerTest): + + def setUp(self) -> None: + pass + + def tearDown(self) -> None: + pass + + def loadTestModel(self, modelName: str): + """Instantiate instance of TestModel called modelName""" + self.checkValidTestModelName(modelName) + testModel = tmf.TestModelFactory(modelName) + self.checkTestModelImplements(testModel, tmf.StructuralProperties) + return testModel + + def checkLinkMatrix(self, modelName: str): + testModel = self.loadTestModel(modelName) + expected = testModel.linkMatrix() + rr = RoadRunner(testModel.str()) + actual = rr.getLinkMatrix() + self.checkMatricesEqual(expected, actual) + + def checkNrMatrix(self, modelName: str): + testModel = self.loadTestModel(modelName) + expected = testModel.NrMatrix() + rr = RoadRunner(testModel.str()) + rr.setConservedMoietyAnalysis = True + actual = rr.getNrMatrix() + self.checkMatricesEqual(expected, actual) + + def checkKMatrix(self, modelName: str): + testModel = self.loadTestModel(modelName) + expected = testModel.KMatrix() + rr = RoadRunner(testModel.str()) + actual = rr.getKMatrix() + for i in range(expected.shape[0]): + for j in range(expected.shape[1]): + self.assertAlmostEqual(expected[i][j], actual[i][j], 7) + + def checkReducedStoicMatrix(self, modelName: str): + testModel = self.loadTestModel(modelName) + expected = testModel.reducedStoicMatrix() + rr = RoadRunner(testModel.str()) + rr.setConservedMoietyAnalysis = True + actual = rr.getReducedStoichiometryMatrix() + self.checkMatricesEqual(expected, actual) + + def checkFullStoicMatrix(self, modelName: str): + testModel = self.loadTestModel(modelName) + expected = testModel.fullStoicMatrix() + rr = RoadRunner(testModel.str()) + # note turn this to False and the test fails. + # is this right? + rr.conservedMoietyAnalysis = True + actual = rr.getFullStoichiometryMatrix() + self.checkMatricesEqual(expected, actual) + + def checkExtendedStoicMatrix(self, modelName: str): + testModel = self.loadTestModel(modelName) + expected = testModel.extendedStoicMatrix() + rr = RoadRunner(testModel.str()) + # moiety conservation breaks the test. + # Theres something more going on here that should be investigated + # rr.setConservedMoietyAnalysis = True + actual = rr.getExtendedStoichiometryMatrix() + self.checkMatricesEqual(expected, actual) + + def checkL0Matrix(self, modelName: str): + testModel = self.loadTestModel(modelName) + expected = testModel.L0Matrix() + rr = RoadRunner(testModel.str()) + actual = rr.getL0Matrix() + self.checkMatricesEqual(expected, actual) + + def checkConservationMatrix(self, modelName: str): + testModel = self.loadTestModel(modelName) + expected = testModel.conservationMatrix() + rr = RoadRunner(testModel.str()) + rr.setConservedMoietyAnalysis = True + actual = rr.getConservationMatrix() + self.checkMatricesEqual(expected, actual) + + def test_BimolecularEnd_LinkMatrix(self): + self.checkLinkMatrix("BimolecularEnd") + + def test_BimolecularEnd_NrMatrix(self): + self.checkNrMatrix("BimolecularEnd") + + def test_BimolecularEnd_KMatrix(self): + self.checkKMatrix("BimolecularEnd") + + def test_BimolecularEnd_ReducedStoicMatrix(self): + self.checkReducedStoicMatrix("BimolecularEnd") + + def test_BimolecularEnd_FullStoicMatrix(self): + self.checkFullStoicMatrix("BimolecularEnd") + + def test_BimolecularEnd_ExtendedStoicMatrix(self): + self.checkExtendedStoicMatrix("BimolecularEnd") + + @unittest.skip("L0 matrix is empty for this model. Currently there is a " + "bug in RoadRunner's swig interface when porting an " + "empty Matrix to empty Python np array") + def test_BimolecularEnd_L0Matrix(self): + self.checkL0Matrix("BimolecularEnd") + + @unittest.skip("Conservation matrix is empty for this model. Currently there is a " + "bug in RoadRunner's swig interface when porting an " + "empty Matrix to empty Python np array") + def test_BimolecularEnd_ConservationMatrix(self): + self.checkConservationMatrix("BimolecularEnd") + +if __name__ == "__main__": + unittest.main() + diff --git a/test/python/test_testModelFactory.py b/test/python/test_testModelFactory.py index 3deacf37b0..6a54c99f09 100644 --- a/test/python/test_testModelFactory.py +++ b/test/python/test_testModelFactory.py @@ -18,278 +18,274 @@ rr_site_packages, ] import roadrunner +import roadrunner.tests.TestModelFactory as tmf -import platform -if platform.system() != "Darwin": - - import roadrunner.tests.TestModelFactory as tmf - - - class TestModelFactoryTests(unittest.TestCase): - - def setUp(self) -> None: - pass - - def tearDown(self) -> None: - pass - - def testDoublePair(self): - x = tmf._testDoublePair(3.4, 5.6) - self.assertIsInstance(x, tuple) - self.assertEqual(x[0], 3.4) - - def testUseVariant(self): - x = tmf._testVariant() - self.assertIsInstance(x, float) - - def testVariantMap(self): - x = tmf._testVariantMap() - self.assertIsInstance(x, dict) - self.assertIsInstance(list(x.keys())[0], str) - self.assertIsInstance(list(x.values())[0], int) - - def testResultMap(self): - x = tmf._testResultMap() - self.assertIsInstance(x, dict) - - def testGetSettings(self): - open_linear_flux = tmf.OpenLinearFlux() - expected = {'allow_presimulation': False, - 'auto_moiety_analysis': False, - 'moiety_conservation': False, - 'presimulation_time': 5} - self.assertEqual(expected, open_linear_flux.steadyStateSettings()) - - def testSimpleFluxStr(self): - sf = tmf.SimpleFlux() - self.assertTrue(sf.str().startswith(r" None: + pass + + def tearDown(self) -> None: + pass + + def testDoublePair(self): + x = tmf._testDoublePair(3.4, 5.6) + self.assertIsInstance(x, tuple) + self.assertEqual(x[0], 3.4) + + def testUseVariant(self): + x = tmf._testVariant() + self.assertIsInstance(x, float) + + def testVariantMap(self): + x = tmf._testVariantMap() + self.assertIsInstance(x, dict) + self.assertIsInstance(list(x.keys())[0], str) + self.assertIsInstance(list(x.values())[0], int) + + def testResultMap(self): + x = tmf._testResultMap() + self.assertIsInstance(x, dict) + + def testGetSettings(self): + open_linear_flux = tmf.OpenLinearFlux() + expected = {'allow_presimulation': False, + 'auto_moiety_analysis': False, + 'moiety_conservation': False, + 'presimulation_time': 5} + self.assertEqual(expected, open_linear_flux.steadyStateSettings()) + + def testSimpleFluxStr(self): + sf = tmf.SimpleFlux() + self.assertTrue(sf.str().startswith(r" Date: Thu, 16 Mar 2023 16:52:35 -0700 Subject: [PATCH 11/28] Add comment. --- test/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt index b24b4724bd..755abf7e13 100644 --- a/test/CMakeLists.txt +++ b/test/CMakeLists.txt @@ -318,7 +318,7 @@ if (BUILD_PYTHON AND BUILD_TESTS) set(PyTestTests ${PyTestTests} ${TestName}) endmacro() - + #For some reason, the new build of llvm makes importing TestModelFactory fail on MacOS (and causes Python to crash entirely!) if (NOT APPLE) add_pytest_to_ctest(python_tests_AutomaticMoietyConservationAnalysisTests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_automaticMoietyConservationAnalysis.py") add_pytest_to_ctest(python_tests_ForwardSensitivitySolverTests "${RR_PYTHON_TESTING_BUILD_PREFIX}/test_forwardSensitivitySolver.py") From 1ca8fc29b15d112f8047f6e914e56af8e93a7ee1 Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Mon, 10 Apr 2023 10:27:37 -0700 Subject: [PATCH 12/28] First pass at setting absolute tolerances differently. --- source/CVODEIntegrator.cpp | 355 ++++++++----------------------------- source/CVODEIntegrator.h | 30 ++-- 2 files changed, 86 insertions(+), 299 deletions(-) diff --git a/source/CVODEIntegrator.cpp b/source/CVODEIntegrator.cpp index 976158f0d8..124bd31792 100644 --- a/source/CVODEIntegrator.cpp +++ b/source/CVODEIntegrator.cpp @@ -377,230 +377,6 @@ namespace rr { } - void CVODEIntegrator::setConcentrationTolerance(Setting value) { - uint ncomp = mModel->getNumCompartments(); - - double *volumes = (double *) calloc(ncomp, sizeof(double)); - mModel->getCompartmentVolumes(ncomp, 0, volumes); - - // the tolerance std::vector that will be stored - std::vector v; - - switch (value.type()) { - - // all cases below could be convert to a double type - case Setting::INT32: - case Setting::INT64: - case Setting::UINT32: - case Setting::UINT64: - case Setting::FLOAT: - case Setting::DOUBLE: { - // scalar concentration tolerance - // need to be converted to std::vector tolerance since speices might have various compartment sizes - double abstol = value.get(); - int index; - for (int i = 0; i < mModel->getNumIndFloatingSpecies(); i++) { - // get the compartment volume of each species - index = mModel->getCompartmentIndexForFloatingSpecies(i); - if (volumes[index] == 0) { - // when the compartment volume is 0, simply set the amount tolerance as the volume tolerance - // since the tolerance cannot be 0 (ILLEGAL_INPUT) - v.push_back(abstol); - } else { - // compare the concentration tolerance with the adjusted amount tolerace - // store whichever is smaller - v.push_back((std::min)(abstol, abstol * volumes[index])); - } - } - - std::vector symbols = mModel->getRateRuleSymbols(); - for (int i = 0; i < mModel->getNumRateRules(); i++) { - int speciesIndex = mModel->getFloatingSpeciesIndex(symbols[i]); - if (speciesIndex > -1) { - // the symbol defined by the rate rule is a species - index = mModel->getCompartmentIndexForFloatingSpecies(i); - if (volumes[index] == 0) { - // when the compartment volume is 0, simply set the amount tolerance as the volume tolerance - // since the tolerance cannot be 0 (ILLEGAL_INPUT) - v.push_back(abstol); - } else { - // compare the concentration tolerance with the adjusted amount tolerace - // store whichever is smaller - v.push_back((std::min)(abstol, abstol * volumes[index])); - } - } else { - // not a species, no need to multiply compartment volume - v.push_back(abstol); - } - } - - - break; - } - - case Setting::DOUBLEVECTOR: { - // std::vector concentration tolerance - - // [0, numIndFloatingSpecies) stores tolerances for independent floating species - // [numIndFloatingSpecies, numIndFloatingSpecies+numRateRule) stores tolerances for variables that have rate rule - - v = value.get >(); - - checkVectorSize(mModel->getNumIndFloatingSpecies() + mModel->getNumRateRules(), v.size()); - - int index; - for (int i = 0; i < mModel->getNumIndFloatingSpecies(); i++) { - // get the compartment volume of each species - index = mModel->getCompartmentIndexForFloatingSpecies(i); - if (volumes[index] > 0) { - // compare the concentration tolerance with the adjusted amount tolerace - // store whichever is smaller - v[i] = (std::min)(v[i], v[i] * volumes[index]); - } - } - - std::vector symbols = mModel->getRateRuleSymbols(); - for (int i = mModel->getNumIndFloatingSpecies(); - i < mModel->getNumRateRules() + mModel->getNumIndFloatingSpecies(); i++) { - std::string symbol = symbols[i]; - int speciesIndex = mModel->getFloatingSpeciesIndex(symbol); - if (speciesIndex > -1) { - // the symbol defined by the rate rule is a species - index = mModel->getCompartmentIndexForFloatingSpecies(i); - if (volumes[index] > 0) { - // compare the concentration tolerance with the adjusted amount tolerace - // store whichever is smaller - v[i] = (std::min)(v[i], v[i] * volumes[index]); - } - } - } - - break; - } - - default: - throw std::runtime_error( - "CVODEIntegrator::setIndividualTolerance failed, double or double std::vector expected"); - break; - } - - free(volumes); - // update the tolerance - CVODEIntegrator::setValue("absolute_tolerance", Setting(v)); - } - - std::vector CVODEIntegrator::getConcentrationTolerance() { - uint ncomp = mModel->getNumCompartments(); - - double *volumes = (double *) calloc(ncomp, sizeof(double)); - mModel->getCompartmentVolumes(ncomp, 0, volumes); - - // the tolerance std::vector - std::vector v; - - switch (getType("absolute_tolerance")) { - - // all cases below could be convert to a double type - case Setting::INT32: - case Setting::INT64: - case Setting::UINT32: - case Setting::UINT64: - case Setting::FLOAT: - case Setting::DOUBLE: { - // scalar tolerance - double abstol = CVODEIntegrator::getValue("absolute_tolerance"); - int index; - for (int i = 0; i < mModel->getNumIndFloatingSpecies(); i++) { - // get the compartment volume of each species - index = mModel->getCompartmentIndexForFloatingSpecies(i); - if (volumes[index] == 0) { - // when the compartment volume is 0, simply set the amount tolerance as the volume tolerance - // since the tolerance cannot be 0 (ILLEGAL_INPUT) - v.push_back(abstol); - } else { - // convert the amount tolerance to concentration - v.push_back(abstol / volumes[index]); - } - } - - - std::vector symbols = mModel->getRateRuleSymbols(); - for (int i = 0; i < mModel->getNumRateRules(); i++) { - int speciesIndex = mModel->getFloatingSpeciesIndex(symbols[i]); - if (speciesIndex > -1) { - // the symbol defined by the rate rule is a species - index = mModel->getCompartmentIndexForFloatingSpecies(i); - if (volumes[index] == 0) { - v.push_back(abstol); - } else { - v.push_back(abstol / volumes[index]); - } - } else { - speciesIndex = mModel->getBoundarySpeciesIndex(symbols[i]); - if (speciesIndex > -1) { - // the symbol defined by the rate rule is a species - index = mModel->getCompartmentIndexForBoundarySpecies(i); - if (volumes[index] == 0) { - v.push_back(abstol); - } - else { - v.push_back(abstol / volumes[index]); - } - } - else { - // not a species, no need to divide by compartment volume - v.push_back(abstol); - } - } - } - break; - } - - - case Setting::DOUBLEVECTOR: { - // std::vector concentration tolerance - - // [0, numIndFloatingSpecies) stores tolerances for independent floating species - // [numIndFloatingSpecies, numIndFloatingSpecies+numRateRule) stores tolerances for variables that have rate rule - - v = CVODEIntegrator::getValue("absolute_tolerance").get>(); - - int index; - for (int i = 0; i < mModel->getNumIndFloatingSpecies(); i++) { - // get the compartment volume of each species - index = mModel->getCompartmentIndexForFloatingSpecies(i); - if (volumes[index] > 0) { - // compare the concentration tolerance with the adjusted amount tolerace - // store whichever is smaller - v[i] = v[i] / volumes[index]; - } - } - - - std::vector symbols = mModel->getRateRuleSymbols(); - for (int i = mModel->getNumIndFloatingSpecies(); - i < mModel->getNumRateRules() + mModel->getNumIndFloatingSpecies(); i++) { - std::string symbol = symbols[i]; - int speciesIndex = mModel->getFloatingSpeciesIndex(symbol); - if (speciesIndex > -1) { - // the symbol defined by the rate rule is a species - index = mModel->getCompartmentIndexForFloatingSpecies(i); - if (volumes[index] > 0) { - v[i] = v[i] / volumes[index]; - } - } - } - - break; - - } - - default: - break; - } - free(volumes); - return v; - } void CVODEIntegrator::setMaxOrder(int newValue) { auto oldOrderValue = getValue("maximum_adams_order"); @@ -647,7 +423,6 @@ namespace rr { } else if (key == "maximum_num_steps") { CVodeSetMaxNumSteps(mCVODE_Memory, (int) getValue("maximum_num_steps")); } else if (key == "absolute_tolerance" || key == "relative_tolerance") { - CVodeSetMaxNumSteps(mCVODE_Memory, (double) getValue("maximum_num_steps")); setCVODETolerances(); } @@ -1059,18 +834,16 @@ namespace rr { } } - void CVODEIntegrator::setCVODETolerances() { - if (mStateVector == nullptr || mModel == nullptr) { - return; - } + vector CVODEIntegrator::getAbsoluteToleranceVector() + { + int species = mModel->getNumIndFloatingSpecies(); + int rrs = mModel->getNumRateRules(); + vector amount_tolerances; - // If we have a model with only events, cvode still needs a state std::vector of length 1 to integrate. - if (!haveVariables() && mModel->getNumEvents() > 0) { - SetVector(mStateVector, 0, 1.0); - } + uint ncomp = mModel->getNumCompartments(); + double* volumes = (double*)calloc(ncomp, sizeof(double)); + mModel->getCompartmentVolumes(ncomp, 0, volumes); - int err; - // switch on different cases that the absolute tolerance is scalar or std::vector switch (getType("absolute_tolerance")) { // all cases below could be convert to a double type @@ -1080,72 +853,84 @@ namespace rr { case Setting::UINT64: case Setting::FLOAT: case Setting::DOUBLE: + { // scalar tolerance - err = CVodeSStolerances(mCVODE_Memory, (double) getValue("relative_tolerance"), - (double) getValue("absolute_tolerance")); + double abs = (double)getValue("absolute_tolerance"); + for (int n = 0; n < species + rrs; n++) { + amount_tolerances.push_back(abs); + } break; - - + } case Setting::DOUBLEVECTOR: { // std::vector tolerance - // convert a double std::vector to a n_vector? - std::vector v = getValue("absolute_tolerance").get>(); - double *arr = new double[v.size()]; - for (int i = 0; i < v.size(); i++) - arr[i] = v[i]; - N_Vector nv = N_VMake_Serial(static_cast(v.size()), arr); - - - err = CVodeSVtolerances(mCVODE_Memory, (double) getValue("relative_tolerance"), nv); - // need to destroy - - N_VDestroy_Serial(nv); - delete[] arr; + amount_tolerances = getValue("absolute_tolerance").get>(); break; } default: - err = CV_ILL_INPUT; - break; + handleCVODEError(CV_ILL_INPUT); } + vector csizes; + for (int s = 0; s < species; s++) { + int comp = mModel->getCompartmentIndexForFloatingSpecies(s); + double csize = volumes[comp]; + if (csize == 0) { + csize = 1; + } + csizes.push_back(pow(10, round(log(abs(csize))))); + } + std::vector symbols = mModel->getRateRuleSymbols(); + for (int i = 0; i < rrs; i++) { + std::string symbol = symbols[i]; + int speciesIndex = mModel->getFloatingSpeciesIndex(symbol); + if (speciesIndex > -1) { + // the symbol defined by the rate rule is a species + int comp = mModel->getCompartmentIndexForFloatingSpecies(i); + double csize = volumes[comp]; + if (csize == 0) { + csize = 1; + } + csizes.push_back(pow(10, round(log(abs(csize))))); + } + else { + csizes.push_back(1.0); + } + } + //Need to *not* adjust species that are amount-only. LS TODO + assert(csizes.size() == amount_tolerances.size()); + for (size_t mAt = 0; mAt < amount_tolerances.size(); mAt++) { + amount_tolerances[mAt] = amount_tolerances[mAt] * csizes[mAt]; + } + free(volumes); + return amount_tolerances; + } - - if (err != CV_SUCCESS) { - handleCVODEError(err); + void CVODEIntegrator::setCVODETolerances() { + if (mStateVector == nullptr || mModel == nullptr) { + return; } - switch (getType("absolute_tolerance")) { - // scalar tolerance - // all cases below could be convert to a double type - case Setting::INT32: - case Setting::INT64: - case Setting::UINT32: - case Setting::UINT64: - case Setting::FLOAT: - case Setting::DOUBLE: - rrLog(Logger::LOG_INFORMATION) << "Set tolerance to abs: " << std::setprecision(16) - << (double) getValue("absolute_tolerance") << ", rel: " - << (double) getValue("relative_tolerance") << std::endl; - break; + // If we have a model with only events, cvode still needs a state std::vector of length 1 to integrate. + if (!haveVariables() && mModel->getNumEvents() > 0) { + SetVector(mStateVector, 0, 1.0); + } - // std::vector tolerance - case Setting::DOUBLEVECTOR: { - rrLog(Logger::LOG_INFORMATION) << "Set tolerance to abs: " << std::setprecision(16) << "["; - std::vector v = getValue("absolute_tolerance").get>(); - for (int i = 0; i < v.size(); i++) { - if (i != 0) { - rrLog(Logger::LOG_INFORMATION) << ", "; - } - rrLog(Logger::LOG_INFORMATION) << v[i]; - } - rrLog(Logger::LOG_INFORMATION) << "], rel: " << (double) getValue("relative_tolerance") << std::endl; + vector amount_tolerances = getAbsoluteToleranceVector(); - break; + int err; + N_Vector nv = N_VMake_Serial(static_cast(amount_tolerances.size()), amount_tolerances.data()); + err = CVodeSVtolerances(mCVODE_Memory, (double)getValue("relative_tolerance"), nv); + rrLog(Logger::LOG_INFORMATION) << "Tolerances used: abs=[" << std::setprecision(16); + for (int i = 0; i < amount_tolerances.size(); i++) { + if (i != 0) { + rrLog(Logger::LOG_INFORMATION) << ", "; } + rrLog(Logger::LOG_INFORMATION) << amount_tolerances[i]; + } + rrLog(Logger::LOG_INFORMATION) << "]; rel=" << (double)getValue("relative_tolerance") << std::endl; - - default: - break; + if (err != CV_SUCCESS) { + handleCVODEError(err); } } diff --git a/source/CVODEIntegrator.h b/source/CVODEIntegrator.h index b4ba70fb12..5241ad575e 100644 --- a/source/CVODEIntegrator.h +++ b/source/CVODEIntegrator.h @@ -144,20 +144,20 @@ namespace rr { */ void setIndividualTolerance(std::string sid, double value) override; - /** - * @author FY - * @brief Sets tolerance based on concentration of species - * @details First converts the concentration tolerances to amount tolerances - * by multiplying the compartment volume of species. Whichever is smaller - * will be stored as absolute_tolerance and used in the integration process. - */ - void setConcentrationTolerance(Setting value) override; - - /** - * @author FY - * @brief Gets tolerance based on concentration of species - */ - std::vector getConcentrationTolerance() override; + ///** + // * @author FY + // * @brief Sets tolerance based on concentration of species + // * @details First converts the concentration tolerances to amount tolerances + // * by multiplying the compartment volume of species. Whichever is smaller + // * will be stored as absolute_tolerance and used in the integration process. + // */ + //void setConcentrationTolerance(Setting value) override; + + ///** + // * @author FY + // * @brief Gets tolerance based on concentration of species + // */ + //std::vector getConcentrationTolerance() override; /** * @author JKM @@ -279,6 +279,8 @@ namespace rr { void assignResultsToModel() const; + std::vector getAbsoluteToleranceVector(); + /** * @author WBC, ETS, JKM * @brief Propagates changes in the "absolute_tolerance" and From 6796debeb02c5998cc29d3804d21b365ca8f5d63 Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Mon, 10 Apr 2023 11:47:51 -0700 Subject: [PATCH 13/28] Update minor version number. The major version number should probably be changed, as this technically significantly changes behavior, but I'd like to save rr 3.0 to include some other larger changes as well. --- CMakeLists.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index ff9ee86bd8..a0bdca4c38 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -8,8 +8,8 @@ cmake_minimum_required(VERSION 3.16) # Version information and include modules set(ROADRUNNER_VERSION_MAJOR 2) -set(ROADRUNNER_VERSION_MINOR 3) -set(ROADRUNNER_VERSION_PATCH 3) +set(ROADRUNNER_VERSION_MINOR 4) +set(ROADRUNNER_VERSION_PATCH 0) set(ROADRUNNER_VERSION "${ROADRUNNER_VERSION_MAJOR}.${ROADRUNNER_VERSION_MINOR}.${ROADRUNNER_VERSION_PATCH}") From c0f844a73966213530b10e5787fddd517ea7b7e5 Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Mon, 10 Apr 2023 17:40:17 -0700 Subject: [PATCH 14/28] Change rules and add tests. Change to how COPASI does things: a single absolute tolerance value is multiplied by the values of the elements, and hence scaled to amounts when appropriate. Remove the 'concentration tolerance' functions, as hopefully their removal will twig anyone who was using them to the new system. --- source/CVODEIntegrator.cpp | 110 +++++++--------- source/CVODEIntegrator.h | 24 ++-- source/Integrator.cpp | 10 +- source/Integrator.h | 15 +-- test/model_editing/model_editing.cpp | 16 +-- test/serialization/state_saving.cpp | 8 +- .../CvodeIntegrationTest.cpp | 117 +++++++++++++++--- .../CVODEIntegratorTests/CvodeUnitTest.cpp | 95 ++++++-------- wrappers/C/rrc_api.cpp | 19 --- wrappers/C/rrc_api.h | 21 ---- 10 files changed, 213 insertions(+), 222 deletions(-) diff --git a/source/CVODEIntegrator.cpp b/source/CVODEIntegrator.cpp index 124bd31792..1f8781ee6e 100644 --- a/source/CVODEIntegrator.cpp +++ b/source/CVODEIntegrator.cpp @@ -317,13 +317,13 @@ namespace rr { // the tolerance std::vector that will be stored // [0, numIndFloatingSpecies) stores tolerances for independent floating species // [numIndFloatingSpecies, numIndFloatingSpecies+numRateRule) stores tolerances for variables that have rate rule - std::vector v; + std::vector v = getAbsoluteToleranceVector(); int speciesIndex = mModel->getFloatingSpeciesIndex(sid); std::ptrdiff_t index; if (speciesIndex > -1 && speciesIndex < mModel->getNumIndFloatingSpecies()) { // sid is an independent floating species - index = speciesIndex; + v[speciesIndex] = value; } else { // sid might has a rate rule std::vector symbols = mModel->getRateRuleSymbols(); @@ -331,47 +331,13 @@ namespace rr { if (it != symbols.end()) { // found it index = mModel->getNumIndFloatingSpecies() + std::distance(symbols.begin(), it); - + v[index] = value; } else { throw std::invalid_argument("CVODEIntegrator::setIndividualTolerance failed, given sid " + sid + " is neither a floating species nor has a rate rule."); } } - switch (getType("absolute_tolerance")) { - - // all cases below could be convert to a double type - case Setting::INT32: - case Setting::INT64: - case Setting::UINT32: - case Setting::UINT64: - case Setting::FLOAT: - case Setting::DOUBLE: { - // scalar tolerance - // need to be converted to std::vector tolerance since tolerance of individual variables is set - - double abstol = (double) CVODEIntegrator::getValue("absolute_tolerance"); - for (int i = 0; i < mModel->getNumFloatingSpecies(); i++) - v.push_back(i == index ? value : abstol); - } - - case Setting::DOUBLEVECTOR: { - // std::vector tolerance - Setting absTolSetting = CVODEIntegrator::getValue("absolute_tolerance"); - if (auto vec = absTolSetting.get_if>()) { - v = *vec; - } - // only need to update the corresponding index - v[index] = value; - break; - } - - default: - throw std::runtime_error( - "CVODEIntegrator::setIndividualTolerance failed, double or double std::vector expected"); - break; - } - // update the tolerance CVODEIntegrator::setValue("absolute_tolerance", Setting(v)); } @@ -840,10 +806,6 @@ namespace rr { int rrs = mModel->getNumRateRules(); vector amount_tolerances; - uint ncomp = mModel->getNumCompartments(); - double* volumes = (double*)calloc(ncomp, sizeof(double)); - mModel->getCompartmentVolumes(ncomp, 0, volumes); - switch (getType("absolute_tolerance")) { // all cases below could be convert to a double type @@ -863,45 +825,56 @@ namespace rr { } case Setting::DOUBLEVECTOR: { // std::vector tolerance - amount_tolerances = getValue("absolute_tolerance").get>(); - break; + return getValue("absolute_tolerance").get>(); } default: handleCVODEError(CV_ILL_INPUT); } - vector csizes; + uint ncomp = mModel->getNumCompartments(); + double* volumes = (double*)calloc(ncomp, sizeof(double)); + mModel->getCompartmentVolumes(ncomp, 0, volumes); + + double* initSpecies = (double*)calloc(species, sizeof(double)); + mModel->getFloatingSpeciesAmounts(species, 0, initSpecies); + + double* initRRs = (double*)calloc(rrs, sizeof(double)); + mModel->getRateRuleValues(initRRs); + for (int s = 0; s < species; s++) { - int comp = mModel->getCompartmentIndexForFloatingSpecies(s); - double csize = volumes[comp]; - if (csize == 0) { - csize = 1; + if (initSpecies[s] == 0) { + int comp = mModel->getCompartmentIndexForFloatingSpecies(s); + if (volumes[comp] != 0.0) { + amount_tolerances[s] = amount_tolerances[s] * abs(volumes[comp]); + } + } + else { + amount_tolerances[s] = amount_tolerances[s] * abs(initSpecies[s]); } - csizes.push_back(pow(10, round(log(abs(csize))))); } + std::vector symbols = mModel->getRateRuleSymbols(); - for (int i = 0; i < rrs; i++) { - std::string symbol = symbols[i]; - int speciesIndex = mModel->getFloatingSpeciesIndex(symbol); - if (speciesIndex > -1) { - // the symbol defined by the rate rule is a species - int comp = mModel->getCompartmentIndexForFloatingSpecies(i); - double csize = volumes[comp]; - if (csize == 0) { - csize = 1; + for (int rr = 0; rr < rrs; rr++) { + if (initRRs[rr] == 0.0) { + std::string symbol = symbols[rr]; + int speciesIndex = mModel->getFloatingSpeciesIndex(symbol); + if (speciesIndex > -1) { + // the symbol defined by the rate rule is a species + int comp = mModel->getCompartmentIndexForFloatingSpecies(speciesIndex); + if (volumes[comp] != 0.0) { + amount_tolerances[species + rr] = amount_tolerances[species + rr] * abs(volumes[comp]); + } } - csizes.push_back(pow(10, round(log(abs(csize))))); + //Otherwise just leave amount_tolerances as it is. } else { - csizes.push_back(1.0); + amount_tolerances[species + rr] = amount_tolerances[species + rr] * abs(initRRs[rr]); } } - //Need to *not* adjust species that are amount-only. LS TODO - assert(csizes.size() == amount_tolerances.size()); - for (size_t mAt = 0; mAt < amount_tolerances.size(); mAt++) { - amount_tolerances[mAt] = amount_tolerances[mAt] * csizes[mAt]; - } + free(volumes); + free(initSpecies); + free(initRRs); return amount_tolerances; } @@ -910,12 +883,17 @@ namespace rr { return; } + vector amount_tolerances = getAbsoluteToleranceVector(); + if (amount_tolerances.size() == 0) { + amount_tolerances.push_back(1.0); + } + // If we have a model with only events, cvode still needs a state std::vector of length 1 to integrate. if (!haveVariables() && mModel->getNumEvents() > 0) { SetVector(mStateVector, 0, 1.0); } - vector amount_tolerances = getAbsoluteToleranceVector(); + int err; N_Vector nv = N_VMake_Serial(static_cast(amount_tolerances.size()), amount_tolerances.data()); diff --git a/source/CVODEIntegrator.h b/source/CVODEIntegrator.h index 5241ad575e..10740c6536 100644 --- a/source/CVODEIntegrator.h +++ b/source/CVODEIntegrator.h @@ -144,21 +144,6 @@ namespace rr { */ void setIndividualTolerance(std::string sid, double value) override; - ///** - // * @author FY - // * @brief Sets tolerance based on concentration of species - // * @details First converts the concentration tolerances to amount tolerances - // * by multiplying the compartment volume of species. Whichever is smaller - // * will be stored as absolute_tolerance and used in the integration process. - // */ - //void setConcentrationTolerance(Setting value) override; - - ///** - // * @author FY - // * @brief Gets tolerance based on concentration of species - // */ - //std::vector getConcentrationTolerance() override; - /** * @author JKM * @brief Reset all integrator settings to their respective default values @@ -253,6 +238,14 @@ namespace rr { */ void *getCvodeMemory() const; + /** + * @brief Get the absolute tolerance vector for the solver. + * + * The absolute tolerance vector is either set directly by the user as a vector, or is generated from the single absolute tolerance value (either default or set by the user) multiplied by the initial value of every element in the state vector (independent floating species, and elements controlled by rate rules). If the initial value is zero, the corresponding element of the absolute tolerance vector is the single value multiplied by the compartment volume for species, or by one for all other values. + */ + virtual std::vector getAbsoluteToleranceVector(); + + private: // defaults directly from CVODE docs static const int mDefaultMaxNumSteps; @@ -279,7 +272,6 @@ namespace rr { void assignResultsToModel() const; - std::vector getAbsoluteToleranceVector(); /** * @author WBC, ETS, JKM diff --git a/source/Integrator.cpp b/source/Integrator.cpp index a1514b42d7..eb87937780 100644 --- a/source/Integrator.cpp +++ b/source/Integrator.cpp @@ -77,12 +77,10 @@ namespace rr // the functions below will not be implemented here void Integrator::setIndividualTolerance(std::string sid, double value) {} - void Integrator::setConcentrationTolerance(Setting value) {} - - std::vector Integrator::getConcentrationTolerance() { - std::vector v; - return v; - } + std::vector Integrator::getAbsoluteToleranceVector() + { + return std::vector(); + } void Integrator::setIntegrationStartTime(double time) { diff --git a/source/Integrator.h b/source/Integrator.h index 5d3324617f..7956e48f28 100644 --- a/source/Integrator.h +++ b/source/Integrator.h @@ -117,16 +117,11 @@ namespace rr { /** - * @author FY - * @brief Set tolerance based on concentration of species, will only be used in CVODEIntegrator - */ - virtual void setConcentrationTolerance(Setting value); - - /** - * @author FY - * @brief Get tolerance based on concentration of species, will only be used in CVODEIntegrator - */ - virtual std::vector getConcentrationTolerance(); + * @brief Get the absolute tolerance vector for the solver. + * + * Most solvers do not have absolute tolerances; this retrieves the vector for the ones (like CVODE) that do. + */ + virtual std::vector getAbsoluteToleranceVector(); /* CARRYOVER METHODS */ diff --git a/test/model_editing/model_editing.cpp b/test/model_editing/model_editing.cpp index 42e5017482..9477bd8ed5 100644 --- a/test/model_editing/model_editing.cpp +++ b/test/model_editing/model_editing.cpp @@ -1435,12 +1435,12 @@ TEST_F(ModelEditingTests, RETAIN_ABSOLUTE_TOLERANCES_1) { rri->getIntegrator()->setIndividualTolerance("S1", 5.0); rri->getIntegrator()->setIndividualTolerance("S2", 3.0); rri->removeSpecies("S2"); - EXPECT_TRUE(rri->getIntegrator()->getConcentrationTolerance().size() == 1) - << "RETAIN_ABSOLUTE_TOLERANCES_1 failed, rri->getIntegrator()->getConcentrationTolerance().size() != 1" + EXPECT_TRUE(rri->getIntegrator()->getAbsoluteToleranceVector().size() == 1) + << "RETAIN_ABSOLUTE_TOLERANCES_1 failed, rri->getIntegrator()->getAbsoluteToleranceVector().size() != 1" << endl; - EXPECT_TRUE(rri->getIntegrator()->getConcentrationTolerance()[0] == 5.0) - << "RETAIN_ABSOLUTE_TOLERANCES_1 failed, rri->getIntegrator()->getConcentrationTolerance()[0] == 5.0" + EXPECT_TRUE(rri->getIntegrator()->getAbsoluteToleranceVector()[0] == 5.0) + << "RETAIN_ABSOLUTE_TOLERANCES_1 failed, rri->getIntegrator()->getAbsoluteToleranceVector()[0] == 5.0" << endl; delete rri; } @@ -1450,12 +1450,12 @@ TEST_F(ModelEditingTests, RETAIN_ABSOLUTE_TOLERANCES_2) { rri->getIntegrator()->setIndividualTolerance("S1", 5.0); rri->getIntegrator()->setIndividualTolerance("S2", 3.0); rri->removeSpecies("S1"); - EXPECT_TRUE(rri->getIntegrator()->getConcentrationTolerance().size() == 1) - << "RETAIN_ABSOLUTE_TOLERANCES_2 failed, rri->getIntegrator()->getConcentrationTolerance().size() != 1" + EXPECT_TRUE(rri->getIntegrator()->getAbsoluteToleranceVector().size() == 1) + << "RETAIN_ABSOLUTE_TOLERANCES_2 failed, rri->getIntegrator()->getAbsoluteToleranceVector().size() != 1" << endl; - EXPECT_TRUE(rri->getIntegrator()->getConcentrationTolerance()[0] == 3.0) - << "RETAIN_ABSOLUTE_TOLERANCES_2 failed, rri->getIntegrator()->getConcentrationTolerance()[0] == 3.0" + EXPECT_TRUE(rri->getIntegrator()->getAbsoluteToleranceVector()[0] == 3.0) + << "RETAIN_ABSOLUTE_TOLERANCES_2 failed, rri->getIntegrator()->getAbsoluteToleranceVector()[0] == 3.0" << endl; delete rri; } diff --git a/test/serialization/state_saving.cpp b/test/serialization/state_saving.cpp index a094745ff4..eaf1a79ab1 100644 --- a/test/serialization/state_saving.cpp +++ b/test/serialization/state_saving.cpp @@ -460,8 +460,8 @@ TEST_F(StateSavingTests, COPY_RR_WITH_ASSIGNMENT) { RoadRunner rri2(3, 1); rri2 = rri; EXPECT_TRUE(rri.getInstanceID() != rri2.getInstanceID()); - EXPECT_EQ(rri2.getIntegrator()->getConcentrationTolerance()[0], 5.0); - EXPECT_EQ(rri2.getIntegrator()->getConcentrationTolerance()[1], 3.0); + EXPECT_EQ(rri2.getIntegrator()->getAbsoluteToleranceVector()[0], 5.0); + EXPECT_EQ(rri2.getIntegrator()->getAbsoluteToleranceVector()[1], 3.0); } TEST_F(StateSavingTests, COPY_RR_TWICE) { @@ -737,8 +737,8 @@ TEST_F(StateSavingTests, RETAIN_ABSOLUTE_TOLERANCES_1) { rri.saveState(stateFname.string()); RoadRunner rri2; rri2.loadState(stateFname.string()); - EXPECT_EQ(rri2.getIntegrator()->getConcentrationTolerance()[0], 5.0); - EXPECT_EQ(rri2.getIntegrator()->getConcentrationTolerance()[1], 3.0); + EXPECT_EQ(rri2.getIntegrator()->getAbsoluteToleranceVector()[0], 5.0); + EXPECT_EQ(rri2.getIntegrator()->getAbsoluteToleranceVector()[1], 3.0); if (fs::exists(stateFname)){ fs::remove(stateFname); } diff --git a/test/sundials-tests/CVODEIntegratorTests/CvodeIntegrationTest.cpp b/test/sundials-tests/CVODEIntegratorTests/CvodeIntegrationTest.cpp index 9359cbe626..85f4ff30f4 100644 --- a/test/sundials-tests/CVODEIntegratorTests/CvodeIntegrationTest.cpp +++ b/test/sundials-tests/CVODEIntegratorTests/CvodeIntegrationTest.cpp @@ -85,25 +85,108 @@ TEST_F(CVODEIntegratorTests, OneEvent10Triggers) { } +TEST_F(CVODEIntegratorTests, CheckAbsToleranceDefaults) { + TestModel* testModelPtr = TestModelFactory("SimpleFlux"); + + // load model + RoadRunner r(testModelPtr->str()); + std::vector atols = r.getIntegrator()->getAbsoluteToleranceVector(); + ASSERT_EQ(atols.size(), 2); + EXPECT_NEAR(atols[0], 1e-11, 1e-16); + EXPECT_NEAR(atols[1], 1e-12, 1e-16); + + r.setValue("init(default_compartment)", 1e-10); + r.setValue("init([S1])", 10.0); + r.setValue("init([S2])", 1.0); + atols = r.getIntegrator()->getAbsoluteToleranceVector(); + ASSERT_EQ(atols.size(), 2); + EXPECT_NEAR(atols[0], 1e-21, 1e-26); + EXPECT_NEAR(atols[1], 1e-22, 1e-26); + + r.setValue("default_compartment", 1e-15); + r.setValue("[S1]", 10.0); + r.setValue("[S2]", 1.0); + atols = r.getIntegrator()->getAbsoluteToleranceVector(); + ASSERT_EQ(atols.size(), 2); + EXPECT_NEAR(atols[0], 1e-26, 1e-31); + EXPECT_NEAR(atols[1], 1e-27, 1e-31); + + r.setValue("S1", 1e100); + r.setValue("S2", 1e-100); + atols = r.getIntegrator()->getAbsoluteToleranceVector(); + ASSERT_EQ(atols.size(), 2); + EXPECT_NEAR(atols[0], 1e88, 1e80); + EXPECT_NEAR(atols[1], 1e-112, 1e-120); +} +TEST_F(CVODEIntegratorTests, CheckAbsToleranceNegValues) { + TestModel* testModelPtr = TestModelFactory("SimpleFlux"); + // load model + RoadRunner r(testModelPtr->str()); + r.setValue("default_compartment", -1e-15); + r.setValue("[S1]", -10.0); + r.setValue("[S2]", -1.0); + std::vector atols = r.getIntegrator()->getAbsoluteToleranceVector(); + ASSERT_EQ(atols.size(), 2); + EXPECT_NEAR(atols[0], 1e-26, 1e-31); + EXPECT_NEAR(atols[1], 1e-27, 1e-31); +} +TEST_F(CVODEIntegratorTests, CheckAbsToleranceSetDouble) { + TestModel* testModelPtr = TestModelFactory("SimpleFlux"); + + // load model + RoadRunner r(testModelPtr->str()); + r.getIntegrator()->setValue("absolute_tolerance", 1e-15); + std::vector atols = r.getIntegrator()->getAbsoluteToleranceVector(); + ASSERT_EQ(atols.size(), 2); + EXPECT_NEAR(atols[0], 1e-14, 1e-19); + EXPECT_NEAR(atols[1], 1e-15, 1e-19); + + r.setValue("init(default_compartment)", 1e-10); + r.setValue("init([S1])", 10.0); + r.setValue("init([S2])", 1.0); + atols = r.getIntegrator()->getAbsoluteToleranceVector(); + ASSERT_EQ(atols.size(), 2); + EXPECT_NEAR(atols[0], 1e-24, 1e-29); + EXPECT_NEAR(atols[1], 1e-25, 1e-29); + + r.setValue("default_compartment", 1e-15); + r.setValue("[S1]", 10.0); + r.setValue("[S2]", 1.0); + atols = r.getIntegrator()->getAbsoluteToleranceVector(); + ASSERT_EQ(atols.size(), 2); + EXPECT_NEAR(atols[0], 1e-29, 1e-34); + EXPECT_NEAR(atols[1], 1e-30, 1e-34); +} - - - - - - - - - - - - - - - - - +TEST_F(CVODEIntegratorTests, CheckAbsToleranceSetVector) { + TestModel* testModelPtr = TestModelFactory("SimpleFlux"); + + // load model + RoadRunner r(testModelPtr->str()); + std::vector orig = r.getIntegrator()->getAbsoluteToleranceVector(); + r.getIntegrator()->setValue("absolute_tolerance", orig); + std::vector atols = r.getIntegrator()->getAbsoluteToleranceVector(); + ASSERT_EQ(atols.size(), 2); + EXPECT_NEAR(atols[0], 1e-11, 1e-16); + EXPECT_NEAR(atols[1], 1e-12, 1e-16); + + orig[0] = 1e10; + orig[1] = 1e-10; + r.getIntegrator()->setValue("absolute_tolerance", orig); + atols = r.getIntegrator()->getAbsoluteToleranceVector(); + ASSERT_EQ(atols.size(), 2); + EXPECT_NEAR(atols[0], 1e10, 1.0); + EXPECT_NEAR(atols[1], 1e-10, 1e-20); + + //Setting the values of S1 and S2 will no longer change the tolerance vector. + r.setValue("S1", 1e100); + r.setValue("S2", 1e-100); + atols = r.getIntegrator()->getAbsoluteToleranceVector(); + ASSERT_EQ(atols.size(), 2); + EXPECT_NEAR(atols[0], 1e10, 1.0); + EXPECT_NEAR(atols[1], 1e-10, 1e-20); +} diff --git a/test/sundials-tests/CVODEIntegratorTests/CvodeUnitTest.cpp b/test/sundials-tests/CVODEIntegratorTests/CvodeUnitTest.cpp index a68e7a7530..6d30de027f 100644 --- a/test/sundials-tests/CVODEIntegratorTests/CvodeUnitTest.cpp +++ b/test/sundials-tests/CVODEIntegratorTests/CvodeUnitTest.cpp @@ -31,46 +31,46 @@ class CVODEIntegratorUnitTests : public ::testing::Test { }; -TEST_F(CVODEIntegratorUnitTests, SetConcentrationToleranceFromScalar1) { - EXPECT_CALL(mockExecutableModel, getNumCompartments).WillRepeatedly(Return(1)); - EXPECT_CALL(mockExecutableModel, getCompartmentVolumes) - .Times(2); // once in get and once in set - EXPECT_CALL(mockExecutableModel, getNumIndFloatingSpecies).WillRepeatedly(Return(2)); - EXPECT_CALL(mockExecutableModel, getCompartmentIndexForFloatingSpecies).WillRepeatedly(Return(0)); - CVODEIntegrator cvodeIntegrator(&mockExecutableModel); - cvodeIntegrator.setConcentrationTolerance(0.1234); - auto x = cvodeIntegrator.getConcentrationTolerance(); - for (auto i: x) { - ASSERT_NEAR(i, 0.1234, 1e-7); - } -} - -TEST_F(CVODEIntegratorUnitTests, SetConcentrationToleranceFromScalarSmallValue) { - EXPECT_CALL(mockExecutableModel, getNumCompartments).WillRepeatedly(Return(1)); - EXPECT_CALL(mockExecutableModel, getCompartmentVolumes) - .Times(2); // once in get and once in set - EXPECT_CALL(mockExecutableModel, getNumIndFloatingSpecies).WillRepeatedly(Return(2)); - EXPECT_CALL(mockExecutableModel, getCompartmentIndexForFloatingSpecies).WillRepeatedly(Return(0)); - CVODEIntegrator cvodeIntegrator(&mockExecutableModel); - cvodeIntegrator.setConcentrationTolerance(1e-16); - auto x = cvodeIntegrator.getConcentrationTolerance(); - for (auto i: x) { - ASSERT_NEAR(i, 1e-16, 1e-7); - } -} - -TEST_F(CVODEIntegratorUnitTests, SetConcentrationToleranceFromVector) { - EXPECT_CALL(mockExecutableModel, getNumCompartments).WillRepeatedly(Return(1)); - EXPECT_CALL(mockExecutableModel, getCompartmentVolumes) - .Times(2); // once in get and once in set - EXPECT_CALL(mockExecutableModel, getNumIndFloatingSpecies).WillRepeatedly(Return(2)); - EXPECT_CALL(mockExecutableModel, getCompartmentIndexForFloatingSpecies).WillRepeatedly(Return(0)); - CVODEIntegrator cvodeIntegrator(&mockExecutableModel); - cvodeIntegrator.setConcentrationTolerance(std::vector({0.1234, 1.5678})); - auto x = cvodeIntegrator.getConcentrationTolerance(); - ASSERT_EQ(x, std::vector({0.1234, 1.5678})); -} - +//TEST_F(CVODEIntegratorUnitTests, SetConcentrationToleranceFromScalar1) { +// EXPECT_CALL(mockExecutableModel, getNumCompartments).WillRepeatedly(Return(1)); +// EXPECT_CALL(mockExecutableModel, getCompartmentVolumes) +// .Times(2); // once in get and once in set +// EXPECT_CALL(mockExecutableModel, getNumIndFloatingSpecies).WillRepeatedly(Return(2)); +// EXPECT_CALL(mockExecutableModel, getCompartmentIndexForFloatingSpecies).WillRepeatedly(Return(0)); +// CVODEIntegrator cvodeIntegrator(&mockExecutableModel); +// cvodeIntegrator.setConcentrationTolerance(0.1234); +// auto x = cvodeIntegrator.getAbsoluteToleranceVector(); +// for (auto i: x) { +// ASSERT_NEAR(i, 0.1234, 1e-7); +// } +//} +// +//TEST_F(CVODEIntegratorUnitTests, SetConcentrationToleranceFromScalarSmallValue) { +// EXPECT_CALL(mockExecutableModel, getNumCompartments).WillRepeatedly(Return(1)); +// EXPECT_CALL(mockExecutableModel, getCompartmentVolumes) +// .Times(2); // once in get and once in set +// EXPECT_CALL(mockExecutableModel, getNumIndFloatingSpecies).WillRepeatedly(Return(2)); +// EXPECT_CALL(mockExecutableModel, getCompartmentIndexForFloatingSpecies).WillRepeatedly(Return(0)); +// CVODEIntegrator cvodeIntegrator(&mockExecutableModel); +// cvodeIntegrator.setConcentrationTolerance(1e-16); +// auto x = cvodeIntegrator.getAbsoluteToleranceVector(); +// for (auto i: x) { +// ASSERT_NEAR(i, 1e-16, 1e-7); +// } +//} +// +//TEST_F(CVODEIntegratorUnitTests, SetConcentrationToleranceFromVector) { +// EXPECT_CALL(mockExecutableModel, getNumCompartments).WillRepeatedly(Return(1)); +// EXPECT_CALL(mockExecutableModel, getCompartmentVolumes) +// .Times(2); // once in get and once in set +// EXPECT_CALL(mockExecutableModel, getNumIndFloatingSpecies).WillRepeatedly(Return(2)); +// EXPECT_CALL(mockExecutableModel, getCompartmentIndexForFloatingSpecies).WillRepeatedly(Return(0)); +// CVODEIntegrator cvodeIntegrator(&mockExecutableModel); +// cvodeIntegrator.setConcentrationTolerance(std::vector({0.1234, 1.5678})); +// auto x = cvodeIntegrator.getAbsoluteToleranceVector(); +// ASSERT_EQ(x, std::vector({0.1234, 1.5678})); +//} +// /** * The only time loadConfigSettings is actually used is * inside CVODEIntegrator::resetSettings, so I can only @@ -99,21 +99,6 @@ TEST_F(CVODEIntegratorUnitTests, setValue) { ASSERT_NEAR(1e-14, (float) absval, 1e-7); } -TEST_F(CVODEIntegratorUnitTests, DISABLED_setIndividualTolerance) { - EXPECT_CALL(mockExecutableModel, getNumFloatingSpecies) - .WillRepeatedly(Return(2)); - EXPECT_CALL(mockExecutableModel, getFloatingSpeciesIndex) - .WillRepeatedly(Return(0)); // we say that S1 is idx 0 - EXPECT_CALL(mockExecutableModel, getNumIndFloatingSpecies) - .WillRepeatedly(Return(2)); // assume this model has 2 species - CVODEIntegrator cvodeIntegrator(&mockExecutableModel); - cvodeIntegrator.setIndividualTolerance("S1", 1e-14); - //Cannot perform this test because there are no compartments, so the compartment - // volumes are undefined. - //auto x = cvodeIntegrator.getConcentrationTolerance(); - //ASSERT_EQ(x, std::vector({1e-14, 1e-12})); -} - TEST_F(CVODEIntegratorUnitTests, resetSettings) { CVODEIntegrator cvodeIntegrator(&mockExecutableModel); diff --git a/wrappers/C/rrc_api.cpp b/wrappers/C/rrc_api.cpp index 6abe85849d..831df0c844 100644 --- a/wrappers/C/rrc_api.cpp +++ b/wrappers/C/rrc_api.cpp @@ -2535,25 +2535,6 @@ int rrcCallConv setCurrentIntegratorParameterDoubleArray(RRHandle handle, const catch_int_macro } -int rrcCallConv setCurrentIntegratorScalarConcentrationTolerance(RRHandle handle, double value) -{ - start_try - RoadRunner* rri = castToRoadRunner(handle); - rri->getIntegrator()->setConcentrationTolerance(Setting(value)); - return true; - catch_int_macro -} - -int rrcCallConv setCurrentIntegratorVectorConcentrationTolerance(RRHandle handle, double* value, int len) -{ - start_try - RoadRunner* rri = castToRoadRunner(handle); - vector v(value, value + len); - rri->getIntegrator()->setConcentrationTolerance(Setting(v)); - return true; - catch_int_macro -} - int rrcCallConv setCurrentIntegratorIndividualTolerance(RRHandle handle, const char* sid, double value) { start_try diff --git a/wrappers/C/rrc_api.h b/wrappers/C/rrc_api.h index 0d93bfd5c8..e64114e8bf 100644 --- a/wrappers/C/rrc_api.h +++ b/wrappers/C/rrc_api.h @@ -1474,27 +1474,6 @@ C_DECL_SPEC int rrcCallConv getCurrentIntegratorParameterDoubleArray (RRHandle h C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterDoubleArray(RRHandle handle, const char *parameterName, double* value, int len); -/*! -\brief Set the scalar tolerance based on concentration for the current integrator. -\param[in] handle Handle to a RoadRunner instance. -\param[in] value The double value for the integrator setting. -\return Returns True if successful. -\ingroup simopts -*/ -C_DECL_SPEC int rrcCallConv setCurrentIntegratorScalarConcentrationTolerance(RRHandle handle, double value); - - -/*! -\brief Set the vector tolerance based on concentration for the current integrator. -\param[in] handle Handle to a RoadRunner instance. -\param[in] value The double array value for the integrator setting. -\param[in] len The length of given soubld array. -\return Returns True if successful. -\ingroup simopts -*/ -C_DECL_SPEC int rrcCallConv setCurrentIntegratorVectorConcentrationTolerance(RRHandle handle, double* value, int len); - - /*! \brief Set the double array value for a specific integrator setting. Should only used for absoluate tolerace. \param[in] handle Handle to a RoadRunner instance. From c473af32c431c4691f529a655fceea6b3d99836d Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Mon, 10 Apr 2023 17:43:06 -0700 Subject: [PATCH 15/28] Fix azure-pipelines typo. --- azure-pipelines.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 482db52549..fcd28f69d7 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -842,7 +842,7 @@ stages: echo "g++ $(g++ --version)" sudo add-apt-repository ppa:ubuntu-toolchain-r/test sudo apt-get update - sudo apt-get install -y gcc-10 g++-10 doxygen dvipng texlive texlive-font-utils textlive-latex-extra + sudo apt-get install -y gcc-10 g++-10 doxygen dvipng texlive texlive-font-utils texlive-latex-extra sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-10 1 displayName: Install g++10 and doxygen - script: | From 8cdf00f5040dccbfacd4e88ee2bbf11835096de0 Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Mon, 10 Apr 2023 17:44:40 -0700 Subject: [PATCH 16/28] Fix Euler docs, as an aside. --- source/EulerIntegrator.h | 14 +++----------- 1 file changed, 3 insertions(+), 11 deletions(-) diff --git a/source/EulerIntegrator.h b/source/EulerIntegrator.h index c3c21b7dba..7c90ea9bdd 100644 --- a/source/EulerIntegrator.h +++ b/source/EulerIntegrator.h @@ -31,23 +31,15 @@ namespace rr { * forward Euler algorithm is highly unstable and will seldomly * yield numerically correct values. * - * This class also has two dummy variables, exampleParameter1 and - * exampleParameter2. These serve as examples of how to use the Dictionary - * interface to get/set various tuning paramters that an Integrator - * might have. These values will be displayed when the toString method - * is called, typically by Python. - * - * An example of calling simulate in Python, and the results of specifying - * the parameters as keyword arguments is + * An example of calling simulate in Python is * * @code - * rr.simulate(integrator='euler', exampleParameter1=123456, exampleParameter2='some value'); + * rr.setIntegrator('euler') + * rr.simulate(); * * print(rr.integrator) * < roadrunner.EulerIntegrator() * { 'this' : 0x101f28350 - * 'exampleParameter1' : 123456 - * 'exampleParameter2' : some value * }> * @endcode * From 4609365b326263d030447290857b098f1093989a Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Tue, 11 Apr 2023 10:06:39 -0700 Subject: [PATCH 17/28] Fix docs to match. Also, we no longer have the ability to set integrator things with integrator.setting, so change all of that example code. --- .../PythonAPIReference/cls_Integrator.rst | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/docs/source/PythonAPIReference/cls_Integrator.rst b/docs/source/PythonAPIReference/cls_Integrator.rst index 22240c865a..6d5ef8a5a0 100644 --- a/docs/source/PythonAPIReference/cls_Integrator.rst +++ b/docs/source/PythonAPIReference/cls_Integrator.rst @@ -81,23 +81,27 @@ CVODE .. attribute:: Integrator.absolute_tolerance - Specifies the scalar or vector absolute tolerance based on amount of species. A potentially different absolute tolerance for each vector component could be set using a double vector. CVODE then calculates a vector of error weights which is used in all error and convergence tests. The weighted RMS norm for the absolute tolerance should not become smaller than this value. Default value is Config::CVODE_MIN_ABSOLUTE. + Specifies the scalar or vector absolute tolerance. As of roadrunner version 2.4.0, if a scalar absolute tolerance is used, it is multiplied by the value of every element in the state vector before being used. If an element of the state vector is zero, the scalar is multiplied by 1.0 for non-species values, and by the size of the species compartment for species values (i.e. the amount of species present if its concentration was 1.0). + + If desired, the full absolute tolerance vector may be used instead of a scalar. In this case, it is assumed that the user has already done any appropriate scaling for individual state vector levels, and no additional scaling is performed: the values are used in Sundials as-is. + + In Sundials, the CVODE algorithm calculates a vector of error weights which is used in all error and convergence tests. The weighted RMS norm for the absolute tolerance should not become smaller than this value. Default value is Config::CVODE_MIN_ABSOLUTE (a scalar). - >>> rr.integrator.absolute_tolerance = 1 - >>> rr.integrator.absolute_tolerance = [1, 0.1, 0.01, 0.001] // setting vairous tolerance for each species + >>> rr.integrator.setValue("absolute_tolerance", 1) + >>> rr.integrator.setValue("absolute_tolerance", [1, 0.1, 0.01, 0.001] // setting various tolerances for each species. .. attribute:: Integrator.initial_time_step Specifies the initial time step size. If inappropriate, CVODE will attempt to estimate a better initial time step. Default value is 0.0 - >>> rr.integrator.initial_time_step = 1 + >>> rr.integrator.setValue("initial_time_step", 1) .. attribute:: Integrator.maximum_adams_order Specifies the maximum order for Adams-Moulton intergration. This integration method is used for non-stiff problems. Default value is 12. - >>> rr.integrator.maximum_adams_order = 20 + >>> rr.integrator.setValue("maximum_adams_order", 20) .. attribute:: Integrator.maximum_bdf_order @@ -123,7 +127,7 @@ CVODE Perform a multiple time step simulation. Default value is false. - >>> rr.integrator.multiple_steps = True + >>> rr.integrator.setValue("multiple_steps", True) .. attribute:: Integrator.relative_tolerance @@ -152,7 +156,7 @@ Gillespie Specifies the initial time step size. If inappropriate, CVODE will attempt to estimate a better initial time step. Default value is 0.0 >>> rr.setIntegrator('gillespie') # set integrator first - >>> rr.integrator.initial_time_step = 2 + >>> rr.integrator.setValue("initial_time_step", 2) .. attribute:: Integrator.maximum_time_step From ee6fb45f90d5867134f6bb9456ae32e04db25e9a Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Tue, 11 Apr 2023 15:44:35 -0700 Subject: [PATCH 18/28] Ensure that absolute_tolerance vector is always the right size. There was no way to set the tolerance vector to the right size before changing the model, and when the model was changed, the tolerance vector was wrong. So, just make sure it's right. --- source/CVODEIntegrator.cpp | 11 ++++++++++- source/rrRoadRunner.cpp | 5 ++--- 2 files changed, 12 insertions(+), 4 deletions(-) diff --git a/source/CVODEIntegrator.cpp b/source/CVODEIntegrator.cpp index 1f8781ee6e..ccb5bf75c8 100644 --- a/source/CVODEIntegrator.cpp +++ b/source/CVODEIntegrator.cpp @@ -825,7 +825,16 @@ namespace rr { } case Setting::DOUBLEVECTOR: { // std::vector tolerance - return getValue("absolute_tolerance").get>(); + amount_tolerances = getValue("absolute_tolerance").get>(); + if (amount_tolerances.size() == species + rrs) { + return amount_tolerances; + } + //Otherwise, something might have happened, and the amount tolerances vector is the wrong size. This can happen when the model is being resized, among other situations. + amount_tolerances.clear(); + for (int n = 0; n < species + rrs; n++) { + amount_tolerances.push_back(Config::CVODE_MIN_ABSOLUTE); + } + break; } default: diff --git a/source/rrRoadRunner.cpp b/source/rrRoadRunner.cpp index 33b5003654..fe345327a6 100644 --- a/source/rrRoadRunner.cpp +++ b/source/rrRoadRunner.cpp @@ -6899,13 +6899,12 @@ namespace rr { impl->document.get(), impl->loadOpt.modelGeneratorOpt)); - //Force setIndividualTolerance to construct a std::vector of the correct size - if (absTol.get_if>()) - impl->integrator->setValue("absolute_tolerance", Setting(1.0e-7)); impl->syncAllSolversWithModel(impl->model.get()); if (auto v1 = absTol.get_if>()) { + //Force setIndividualTolerance to construct a std::vector of the correct size + impl->integrator->setValue("absolute_tolerance", Setting(Config::CVODE_MIN_ABSOLUTE)); for (const auto &p: indTolerances) { auto ids = getFloatingSpeciesIds(); if (std::find(ids.begin(), ids.end(), p.first) != ids.end()) From 7cd6649b0f2ef43d24f0861ee23ac3d8e424cf4f Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Tue, 11 Apr 2023 17:01:48 -0700 Subject: [PATCH 19/28] Remove 'concentration tolerance' python tests. --- test/python/test_integrator.py | 3 --- test/python/test_rrtests.py | 28 -------------------- test/rrtest_files/Absolute_Tolerance1.rrtest | 8 ------ 3 files changed, 39 deletions(-) diff --git a/test/python/test_integrator.py b/test/python/test_integrator.py index 4265023983..ead56312db 100644 --- a/test/python/test_integrator.py +++ b/test/python/test_integrator.py @@ -224,9 +224,6 @@ def test_set_max_output_rows(self): self.integrator.setValue("max_output_rows", 50) self.assertEqual(50, self.integrator.getValue("max_output_rows")) - def test_set_concentration_tolerance(self): - self.integrator.setConcentrationTolerance(1e-8) - def test_simulate_sequence_with_times(self): results = self.rr.simulate() self.assertEqual(len(results), 51); diff --git a/test/python/test_rrtests.py b/test/python/test_rrtests.py index f17a8c4440..cbd40cb012 100644 --- a/test/python/test_rrtests.py +++ b/test/python/test_rrtests.py @@ -1448,34 +1448,6 @@ def setVectorAmountAbsoluteTolerance(rrInstance, testId): print(passMsg (errorFlag)) -def setScalarConcentrationAbsoluteTolerance(rrInstance, testId): - errorFlag = False - value = float(readLine()) - rrInstance.getIntegrator().setConcentrationTolerance(value) - tolerance = rrInstance.getIntegrator().getValue("absolute_tolerance") - expected = divide(readLine()) - if not (len(tolerance) == len(expected)): - errorFlag = True - for i in range(len(expected)): - if not (tolerance[i] == float(expected[i])): - errorFlag = True - print(passMsg (errorFlag)) - -def setVectorConcentrationAbsoluteTolerance(rrInstance, testId): - errorFlag = False - value = divide(readLine()) - floatValue = [float(i) for i in value] - rrInstance.getIntegrator().setConcentrationTolerance(floatValue) - tolerance = rrInstance.getIntegrator().getValue("absolute_tolerance") - expected = divide(readLine()) - if not (len(tolerance) == len(expected)): - errorFlag = True - for i in range(len(expected)): - if not (tolerance[i] == float(expected[i])): - errorFlag = True - print(passMsg (errorFlag)) - - def setIndividualTolerance(rrInstance, testId): errorFlag = False value = float(readLine()) diff --git a/test/rrtest_files/Absolute_Tolerance1.rrtest b/test/rrtest_files/Absolute_Tolerance1.rrtest index 7c08c1b7fe..2f1e816590 100644 --- a/test/rrtest_files/Absolute_Tolerance1.rrtest +++ b/test/rrtest_files/Absolute_Tolerance1.rrtest @@ -71,11 +71,3 @@ [Set Vector Amount Absolute Tolerance] 0.000000000000001 0.0000000000000001 0.000000000000001 0.0000000000000001 - -[Set Scalar Concentration Absolute Tolerance] -0.0000000000000001 -0.000000000000000001 0.000000000000000001 - -[Set Vector Concentration Absolute Tolerance] -0.000000000000001 0.0000000000000001 -0.00000000000000001 0.000000000000000001 From d79cf144a838b6dbd142af7e884f5fc998ba6378 Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Tue, 11 Apr 2023 19:26:07 -0700 Subject: [PATCH 20/28] Remove 'concentration tolerance' python tests. --- test/python/test_rrtests.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/test/python/test_rrtests.py b/test/python/test_rrtests.py index cbd40cb012..f8089958c9 100644 --- a/test/python/test_rrtests.py +++ b/test/python/test_rrtests.py @@ -1550,8 +1550,6 @@ def setIndividualTolerance(rrInstance, testId): '[Set Steady State Selection List 2]': checkSetSteadyStateSelectionList, '[Set Time Course Selection List]': checkSetTimeCourseSelectionList, '[Set Vector Amount Absolute Tolerance]': setVectorAmountAbsoluteTolerance, - '[Set Scalar Concentration Absolute Tolerance]': setScalarConcentrationAbsoluteTolerance, - '[Set Vector Concentration Absolute Tolerance]': setVectorConcentrationAbsoluteTolerance, '[Set Individual Tolerance]': setIndividualTolerance, '[Species Concentrations]': checkSpeciesConcentrations, '[Species Initial Concentration Ids]': checkFloatingSpeciesInitialConcentrationIds, From 900eb2fa2ad1b8c518974c0301ecc049cdf0a7bb Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Tue, 11 Apr 2023 22:16:44 -0700 Subject: [PATCH 21/28] Fix values. The new tolerances make the algorithm slightly different. But why would it ever have this many digits of precision? Why would it ever work? It mystifies me, but anyway, let's see what happens. --- test/python/test_python_api.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/test/python/test_python_api.py b/test/python/test_python_api.py index 36e787f20a..e31613e750 100644 --- a/test/python/test_python_api.py +++ b/test/python/test_python_api.py @@ -747,19 +747,19 @@ def test_items(self): ('ec(_J1, S2)', 0.9999999999999998), ('ec(_J1, kf)', 0.0), ('ec(_J1, kb)', 1.0000000000000053), - ('ucc(_J0, kf)', 0.09090905110435235), + ('ucc(_J0, kf)', 0.09090905110436161), ('ucc(_J0, kb)', 9.090909090511781), ('ucc(_J1, kf)', 0.09090905110435235), ('ucc(_J1, kb)', 9.090909090511735), - ('ucc(S1, kf)', -9.09090511043516), + ('ucc(S1, kf)', -9.090905110435088), ('ucc(S1, kb)', 90.90909090511799), ('ucc(S2, kf)', 9.090905110435088), ('ucc(S2, kb)', -90.90909090512392), - ('cc(_J0, kf)', 0.009090905110435235), + ('cc(_J0, kf)', 0.009090905110436162), ('cc(_J0, kb)', 0.09090909090511781), ('cc(_J1, kf)', 0.9090905110435236), ('cc(_J1, kb)', 9.090909090511735), - ('cc(S1, kf)', -0.09090905110435162), + ('cc(S1, kf)', -0.09090905110435088), ('cc(S1, kb)', 0.09090909090511799), ('cc(S2, kf)', 0.9090905110435088), ('cc(S2, kb)', -0.9090909090512392), From c8a75fc2ab616b21634918a1dcbe038ed68b0d9c Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Wed, 12 Apr 2023 10:55:19 -0700 Subject: [PATCH 22/28] More output for stochastic tests on Python. --- azure-pipelines.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index fcd28f69d7..19273b02e7 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -1089,7 +1089,7 @@ stages: echo "cd'ing to build dir $(BUILD_DIR)" cd $(BUILD_DIR) - ctest --tests-regex python_tests_RunStochasticTestSuite . + ctest --extra-verbose --output-on-failure --tests-regex python_tests_RunStochasticTestSuite . displayName: Run Stochastic test suite - script: | From b040e177ce3fa81f03e3a0b5ee3e5e40d37fe486 Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Wed, 12 Apr 2023 10:56:38 -0700 Subject: [PATCH 23/28] Update docs for C bindings. I don't know why these are here and not in docs/. Maybe they're in both places? Anyway, no-longer-existing-functions now expunged. --- wrappers/C/html/globals_func_s.html | 6 -- wrappers/C/html/globals_s.html | 6 -- wrappers/C/html/group__simopts.html | 76 ------------------------- wrappers/C/html/rrc__api_8cpp.html | 6 -- wrappers/C/html/rrc__api_8h.html | 6 -- wrappers/C/html/rrc__api_8h_source.html | 8 --- wrappers/C/html/search/all_10.js | 2 - wrappers/C/html/search/functions_d.js | 2 - 8 files changed, 112 deletions(-) diff --git a/wrappers/C/html/globals_func_s.html b/wrappers/C/html/globals_func_s.html index 72ad47092d..9ec138f6f5 100644 --- a/wrappers/C/html/globals_func_s.html +++ b/wrappers/C/html/globals_func_s.html @@ -139,12 +139,6 @@

- s -

  • setCurrentIntegratorParameterUInt() : rrc_api.h
    • -
  • setCurrentIntegratorScalarConcentrationTolerance() -: rrc_api.h -
    • -
  • setCurrentIntegratorVectorConcentrationTolerance() -: rrc_api.h -
  • setCurrentSteadyStateSolver() : rrc_api.h
    • diff --git a/wrappers/C/html/globals_s.html b/wrappers/C/html/globals_s.html index 695bd9bc57..a2ae1c5939 100644 --- a/wrappers/C/html/globals_s.html +++ b/wrappers/C/html/globals_s.html @@ -139,12 +139,6 @@

    - s -

    • setCurrentIntegratorParameterUInt() : rrc_api.h
      • -
    • setCurrentIntegratorScalarConcentrationTolerance() -: rrc_api.h -
      • -
    • setCurrentIntegratorVectorConcentrationTolerance() -: rrc_api.h -
    • setCurrentSteadyStateSolver() : rrc_api.h
      • diff --git a/wrappers/C/html/group__simopts.html b/wrappers/C/html/group__simopts.html index dac19586e2..b8f7c1e407 100644 --- a/wrappers/C/html/group__simopts.html +++ b/wrappers/C/html/group__simopts.html @@ -169,12 +169,6 @@ C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterDoubleArray (RRHandle handle, char *parameterName, double *value, int len)  Set the double array value for a specific integrator setting. Should only used for absoluate tolerace. More...
        -C_DECL_SPEC int rrcCallConv setCurrentIntegratorScalarConcentrationTolerance (RRHandle handle, double value) - Set the scalar tolerance based on concentration for the current integrator. More...
      -  -C_DECL_SPEC int rrcCallConv setCurrentIntegratorVectorConcentrationTolerance (RRHandle handle, double *value, int len) - Set the vector tolerance based on concentration for the current integrator. More...
      -  C_DECL_SPEC int rrcCallConv setCurrentIntegratorIndividualTolerance (RRHandle handle, char *sid, double value)  Set the double array value for a specific integrator setting. Should only used for absoluate tolerace. More...
        @@ -2216,76 +2210,6 @@

      -

      ◆ setCurrentIntegratorScalarConcentrationTolerance()

      - -
      -
      - - - - - - - - - - - - - - - - - - -
      C_DECL_SPEC int rrcCallConv setCurrentIntegratorScalarConcentrationTolerance (RRHandle handle,
      double value 
      )
      -
      - -

      Set the scalar tolerance based on concentration for the current integrator.

      -
      Parameters
      - - - -
      [in]handleHandle to a RoadRunner instance.
      [in]valueThe double value for the integrator setting.
      -
      -
      -
      Returns
      Returns True if successful.
      - -
      -
      - -

      ◆ setCurrentIntegratorVectorConcentrationTolerance()

      - -
      -
      - - - - - - - - - - - - - - - - - - - - - - - - -
      C_DECL_SPEC int rrcCallConv setCurrentIntegratorVectorConcentrationTolerance (RRHandle handle,
      double * value,
      int len 
      )
      -
      -

      Set the vector tolerance based on concentration for the current integrator.

      Parameters
      diff --git a/wrappers/C/html/rrc__api_8cpp.html b/wrappers/C/html/rrc__api_8cpp.html index 3a60baae1a..e66a005e2f 100644 --- a/wrappers/C/html/rrc__api_8cpp.html +++ b/wrappers/C/html/rrc__api_8cpp.html @@ -730,12 +730,6 @@ - - - - diff --git a/wrappers/C/html/rrc__api_8h.html b/wrappers/C/html/rrc__api_8h.html index a3e747001e..0953352bca 100644 --- a/wrappers/C/html/rrc__api_8h.html +++ b/wrappers/C/html/rrc__api_8h.html @@ -487,12 +487,6 @@ - - - - - - diff --git a/wrappers/C/html/rrc__api_8h_source.html b/wrappers/C/html/rrc__api_8h_source.html index fb88a24a4a..5233e6473e 100644 --- a/wrappers/C/html/rrc__api_8h_source.html +++ b/wrappers/C/html/rrc__api_8h_source.html @@ -395,12 +395,6 @@
      1423 C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterDoubleArray(RRHandle handle, char *parameterName, double* value, int len);
      1424 
      1425 
      -
      1433 C_DECL_SPEC int rrcCallConv setCurrentIntegratorScalarConcentrationTolerance(RRHandle handle, double value);
      -
      1434 
      -
      1435 
      -
      1444 C_DECL_SPEC int rrcCallConv setCurrentIntegratorVectorConcentrationTolerance(RRHandle handle, double* value, int len);
      -
      1445 
      -
      1446 
      1456 C_DECL_SPEC int rrcCallConv setCurrentIntegratorIndividualTolerance(RRHandle handle, char* sid, double value);
      1457 
      1458 
      @@ -956,9 +950,7 @@
      solverTypeToString
      C_DECL_SPEC const char *rrcCallConv solverTypeToString(int code)
      Get a string description of the type [STATIC MEMORY - DO NOT FREE] \description Can call on return va...
      getCurrentSteadyStateSolverParameterString
      C_DECL_SPEC char *rrcCallConv getCurrentSteadyStateSolverParameterString(RRHandle handle, char *parameterName)
      Get the string value for a specific steady state solver setting.
      getCurrentIntegratorParameterInt
      C_DECL_SPEC int rrcCallConv getCurrentIntegratorParameterInt(RRHandle handle, char *parameterName)
      Get the integer value for a specific integrator setting.
      -
      setCurrentIntegratorScalarConcentrationTolerance
      C_DECL_SPEC int rrcCallConv setCurrentIntegratorScalarConcentrationTolerance(RRHandle handle, double value)
      Set the scalar tolerance based on concentration for the current integrator.
      getCurrentSteadyStateSolverParameterDouble
      C_DECL_SPEC double rrcCallConv getCurrentSteadyStateSolverParameterDouble(RRHandle handle, char *parameterName)
      Get the double value for a specific steady state solver setting.
      -
      setCurrentIntegratorVectorConcentrationTolerance
      C_DECL_SPEC int rrcCallConv setCurrentIntegratorVectorConcentrationTolerance(RRHandle handle, double *value, int len)
      Set the vector tolerance based on concentration for the current integrator.
      setCurrentSteadyStateSolverParameterDouble
      C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolverParameterDouble(RRHandle handle, char *parameterName, double value)
      Set the double value for a specific steady state solver setting.
      getCurrentSteadyStateSolverNthParameterType
      C_DECL_SPEC int rrcCallConv getCurrentSteadyStateSolverNthParameterType(RRHandle handle, int n)
      Get the type of a parameter of the current steady state solver.
      getRegisteredIntegratorDescription
      C_DECL_SPEC char *rrcCallConv getRegisteredIntegratorDescription(int n)
      Get the description of a registered integrator (e.g. cvode etc.)
      diff --git a/wrappers/C/html/search/all_10.js b/wrappers/C/html/search/all_10.js index d945d8e164..0047e590c3 100644 --- a/wrappers/C/html/search/all_10.js +++ b/wrappers/C/html/search/all_10.js @@ -25,8 +25,6 @@ var searchData= ['setcurrentintegratorparameterint_390',['setCurrentIntegratorParameterInt',['../group__simopts.html#ga25d21c24c1eb4d1d29788ec580606a77',1,'rrc_api.h']]], ['setcurrentintegratorparameterstring_391',['setCurrentIntegratorParameterString',['../group__simopts.html#gafeac5c5521cb5b7d4b802e74a93442f5',1,'rrc_api.h']]], ['setcurrentintegratorparameteruint_392',['setCurrentIntegratorParameterUInt',['../group__simopts.html#ga71301c1d8fde82ebbe0c191346995dd7',1,'rrc_api.h']]], - ['setcurrentintegratorscalarconcentrationtolerance_393',['setCurrentIntegratorScalarConcentrationTolerance',['../group__simopts.html#ga5ea249ef0760354eb2bffa0e98596c26',1,'rrc_api.h']]], - ['setcurrentintegratorvectorconcentrationtolerance_394',['setCurrentIntegratorVectorConcentrationTolerance',['../group__simopts.html#ga68ffbd48262e343aa1c451141d6a0dc5',1,'rrc_api.h']]], ['setcurrentsteadystatesolver_395',['setCurrentSteadyStateSolver',['../group__simopts.html#ga95a0ded174b2cc08d1d3201fd02c3f1f',1,'rrc_api.h']]], ['setcurrentsteadystatesolverparameterboolean_396',['setCurrentSteadyStateSolverParameterBoolean',['../group__simopts.html#gaadbc5f4c7bfede9a3ca5ae76d4b85896',1,'rrc_api.h']]], ['setcurrentsteadystatesolverparameterdouble_397',['setCurrentSteadyStateSolverParameterDouble',['../group__simopts.html#ga698d05810c3fa5f94c50d43b90638239',1,'rrc_api.h']]], diff --git a/wrappers/C/html/search/functions_d.js b/wrappers/C/html/search/functions_d.js index 3b40564a3a..5cff48e227 100644 --- a/wrappers/C/html/search/functions_d.js +++ b/wrappers/C/html/search/functions_d.js @@ -25,8 +25,6 @@ var searchData= ['setcurrentintegratorparameterint_779',['setCurrentIntegratorParameterInt',['../group__simopts.html#ga25d21c24c1eb4d1d29788ec580606a77',1,'rrc_api.h']]], ['setcurrentintegratorparameterstring_780',['setCurrentIntegratorParameterString',['../group__simopts.html#gafeac5c5521cb5b7d4b802e74a93442f5',1,'rrc_api.h']]], ['setcurrentintegratorparameteruint_781',['setCurrentIntegratorParameterUInt',['../group__simopts.html#ga71301c1d8fde82ebbe0c191346995dd7',1,'rrc_api.h']]], - ['setcurrentintegratorscalarconcentrationtolerance_782',['setCurrentIntegratorScalarConcentrationTolerance',['../group__simopts.html#ga5ea249ef0760354eb2bffa0e98596c26',1,'rrc_api.h']]], - ['setcurrentintegratorvectorconcentrationtolerance_783',['setCurrentIntegratorVectorConcentrationTolerance',['../group__simopts.html#ga68ffbd48262e343aa1c451141d6a0dc5',1,'rrc_api.h']]], ['setcurrentsteadystatesolver_784',['setCurrentSteadyStateSolver',['../group__simopts.html#ga95a0ded174b2cc08d1d3201fd02c3f1f',1,'rrc_api.h']]], ['setcurrentsteadystatesolverparameterboolean_785',['setCurrentSteadyStateSolverParameterBoolean',['../group__simopts.html#gaadbc5f4c7bfede9a3ca5ae76d4b85896',1,'rrc_api.h']]], ['setcurrentsteadystatesolverparameterdouble_786',['setCurrentSteadyStateSolverParameterDouble',['../group__simopts.html#ga698d05810c3fa5f94c50d43b90638239',1,'rrc_api.h']]], From 9886a5620f51d1a4b56cc6f3217976eb49a33f23 Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Wed, 12 Apr 2023 13:33:54 -0700 Subject: [PATCH 24/28] Try adding -s to pytest command. --- test/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt index 755abf7e13..47b0141997 100644 --- a/test/CMakeLists.txt +++ b/test/CMakeLists.txt @@ -311,7 +311,7 @@ if (BUILD_PYTHON AND BUILD_TESTS) # run pytest with -rP to always capture stdout regardless of pass/fail add_test( NAME ${TestName} - COMMAND Python::Interpreter -m pytest -rP ${TestSourceFile} + COMMAND Python::Interpreter -m pytest -rPs ${TestSourceFile} WORKING_DIRECTORY "${RR_PYTHON_TESTING_BUILD_PREFIX}" ) set_tests_properties(${TestName} PROPERTIES ENVIRONMENT "PYTHONPATH=${PYTHON_PACKAGE_SITE_DIR_BUILD_TREE}:$PYTHONPATH") From c0d0185ded6ab56f18cd20f9fcbc2eaf66858532 Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Wed, 12 Apr 2023 14:30:35 -0700 Subject: [PATCH 25/28] Try reducing the absolute tolerance, in case it's a speed thing. --- test/python/test_runStochasticTestSuite.py | 1 + 1 file changed, 1 insertion(+) diff --git a/test/python/test_runStochasticTestSuite.py b/test/python/test_runStochasticTestSuite.py index 6b1a2b3f31..866752b435 100644 --- a/test/python/test_runStochasticTestSuite.py +++ b/test/python/test_runStochasticTestSuite.py @@ -209,6 +209,7 @@ def simulateFile(self, fname, tnum, expected_results): sim = rr.simulate(self.start, self.duration, self.steps + 1) elif self.testType == "StatisticalDistribution": rr.setIntegrator('cvode') + rr.getIntegrator().setValue("absolute_tolerance", 1e-9) sim = rr.simulate(self.start, self.duration, self.steps + 1) else: self.fail("Unknown stochastic test type " + self.testType + " in test " + tnum + ".") From 970deffe95c5165012a5abd684b9573c173cc47f Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Thu, 13 Apr 2023 14:26:28 -0700 Subject: [PATCH 26/28] Destroy the N_Vector after creating it! --- source/CVODEIntegrator.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/source/CVODEIntegrator.cpp b/source/CVODEIntegrator.cpp index ccb5bf75c8..75cda11d5d 100644 --- a/source/CVODEIntegrator.cpp +++ b/source/CVODEIntegrator.cpp @@ -915,6 +915,7 @@ namespace rr { rrLog(Logger::LOG_INFORMATION) << amount_tolerances[i]; } rrLog(Logger::LOG_INFORMATION) << "]; rel=" << (double)getValue("relative_tolerance") << std::endl; + N_VDestroy_Serial(nv); if (err != CV_SUCCESS) { handleCVODEError(err); From 2405abb1c0157a55377618476a93006604168899 Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Fri, 14 Apr 2023 08:35:42 -0700 Subject: [PATCH 27/28] Cleanup the docs. --- .../PythonAPIReference/cls_Integrator.rst | 26 ++++++--------- .../cls_SteadyStateSolver.rst | 32 +++++++------------ docs/source/tutorial/solvers.rst | 6 ++-- source/CVODEIntegrator.cpp | 4 +-- source/CVODEIntegrator.h | 2 +- 5 files changed, 27 insertions(+), 43 deletions(-) diff --git a/docs/source/PythonAPIReference/cls_Integrator.rst b/docs/source/PythonAPIReference/cls_Integrator.rst index 6d5ef8a5a0..a7da94f227 100644 --- a/docs/source/PythonAPIReference/cls_Integrator.rst +++ b/docs/source/PythonAPIReference/cls_Integrator.rst @@ -59,20 +59,6 @@ ________________ :param double value: tolerance value to set -.. method:: Integrator.setConcentrationTolerance(value) - - Sets the tolerance based on concentration of species. Only used for CVODE Integrator. - First converts the concentration tolerances to amount tolerances by multiplying the compartment volume of species. Whichever is smaller will be stored in absolute_tolerance and used in the integration process. - Note that if a double list is given, the size of list must be equal to numIndFloatingSpecies+numRateRule, including tolerances for each independent floating species that doesn't have a rate rule followed by tolerances for each variable(including dependent floating species) that has a rate rule. The order of independent floating species and variables is the same as the order how they were defined in species list and rate rule list. - - :param double/double list value: tolerance value to set - -.. method:: Integrator.getConcentrationTolerance() - - Gets the tolerance vector based on concentration of species. Only used for CVODE Integrator. - The vector includes tolerances for each independent floating species that doesn't have a rate rule followed by tolerances for each variable(including dependent floating species) that has a rate rule. The order of independent floating species and variables is the same as the order how they were defined in species list and rate rule list. - - CVODE ----- @@ -83,12 +69,15 @@ CVODE Specifies the scalar or vector absolute tolerance. As of roadrunner version 2.4.0, if a scalar absolute tolerance is used, it is multiplied by the value of every element in the state vector before being used. If an element of the state vector is zero, the scalar is multiplied by 1.0 for non-species values, and by the size of the species compartment for species values (i.e. the amount of species present if its concentration was 1.0). - If desired, the full absolute tolerance vector may be used instead of a scalar. In this case, it is assumed that the user has already done any appropriate scaling for individual state vector levels, and no additional scaling is performed: the values are used in Sundials as-is. + If desired, the full absolute tolerance vector may be used instead of a scalar. In this case, it is assumed that the user has already done any appropriate scaling for individual state vector levels, and no additional scaling is performed: the values are used in Sundials as-is. Calling 'getValue('absolute_tolerance') will return the scalar or vector set by the user, or the default Config::CVODE_MIN_ABSOLUTE value. To obtain the full vector obtained from the scalar, use 'getAbsoluteToleranceVector'. In Sundials, the CVODE algorithm calculates a vector of error weights which is used in all error and convergence tests. The weighted RMS norm for the absolute tolerance should not become smaller than this value. Default value is Config::CVODE_MIN_ABSOLUTE (a scalar). - >>> rr.integrator.setValue("absolute_tolerance", 1) + >>> rr.integrator.setValue("absolute_tolerance", 1e-10) >>> rr.integrator.setValue("absolute_tolerance", [1, 0.1, 0.01, 0.001] // setting various tolerances for each species. + + >>> rr.integrator.getValue("absolute_tolerance") //Gets the scalar or vector absolute tolerance, as set by the user or the default value. + >>> rr.integrator.getAbsoluteToleranceVector() //Gets the absolute tolerance vector, as derived from the scalar value, or as set by the user directly. .. attribute:: Integrator.initial_time_step @@ -96,12 +85,14 @@ CVODE Specifies the initial time step size. If inappropriate, CVODE will attempt to estimate a better initial time step. Default value is 0.0 >>> rr.integrator.setValue("initial_time_step", 1) + >>> rr.integrator.getValue("initial_time_step") .. attribute:: Integrator.maximum_adams_order Specifies the maximum order for Adams-Moulton intergration. This integration method is used for non-stiff problems. Default value is 12. >>> rr.integrator.setValue("maximum_adams_order", 20) + >>> rr.integrator.getValue("maximum_adams_order") .. attribute:: Integrator.maximum_bdf_order @@ -128,6 +119,7 @@ CVODE Perform a multiple time step simulation. Default value is false. >>> rr.integrator.setValue("multiple_steps", True) + >>> rr.integrator.getValue("multiple_steps") .. attribute:: Integrator.relative_tolerance @@ -214,7 +206,7 @@ RK45 Specifies the maximum error tolerance allowed. Default value is 1e-12. >>> rr.setIntegrator('rk45') # set integrator first - >>> rr.integrator.epsilon = 1e-10 + >>> rr.integrator.setValue("epsilon", 1e-10) .. attribute:: Integrator.maximum_time_step diff --git a/docs/source/PythonAPIReference/cls_SteadyStateSolver.rst b/docs/source/PythonAPIReference/cls_SteadyStateSolver.rst index fddf80ba24..d4017061b5 100644 --- a/docs/source/PythonAPIReference/cls_SteadyStateSolver.rst +++ b/docs/source/PythonAPIReference/cls_SteadyStateSolver.rst @@ -17,29 +17,21 @@ NLEQ2 To enable, type: - >>> rr.getSteadyStateSolver().allow_presimulation = True - - -.. attribute:: SteadyStateSolver.presimulation_tolerance - - - Tolerance for presimulation before steady state analysis. Absolute tolerance used by presimulation routine. Only used when allow_presimulation is True. Default value is 1e-3. - - >>> rr.getSteadyStateSolver().presimulation_tolerance = 1e-2 + >>> rr.getSteadyStateSolver().setValue("allow_presimulation", True) .. attribute:: SteadyStateSolver.presimulation_maximum_steps Maximum number of steps that can be taken for presimulation before steady state analysis. Takes priority over presimulation_time. Only used when allow_presimulation is True. Default value is 100. - >>> rr.getSteadyStateSolver().presimulation_maximum_steps = 50 + >>> rr.getSteadyStateSolver().setValue("presimulation_maximum_steps", 50) .. attribute:: SteadyStateSolver.presimulation_time End time for presimulation steady state analysis. Only used when allow_presimulation is True. Default value is 100. - >>> rr.getSteadyStateSolver().presimulation_time = 50 + >>> rr.getSteadyStateSolver().setValue("presimulation_time", 50) .. attribute:: SteadyStateSolver.allow_approx @@ -48,28 +40,28 @@ NLEQ2 To disable, type: - >>> rr.getSteadyStateSolver().allow_approx = False + >>> rr.getSteadyStateSolver().setValue("allow_approx", False) .. attribute:: SteadyStateSolver.approx_tolerance Tolerance for steady state approximation routine. Absolute tolerance used by steady state approximation routine. Only used when steady state approximation routine is used. Default value is 1e-12. - >>> rr.getSteadyStateSolver().approx_tolerance = 1e-6 + >>> rr.getSteadyStateSolver().setValue("approx_tolerance", 1e-6) .. attribute:: SteadyStateSolver.approx_maximum_steps Maximum number of steps that can be taken for steady state approximation routine. Takes priority over approx_time. Only used when steady state approximation routine is used. Default value is 10000. - >>> rr.getSteadyStateSolver().approx_maximum_steps = 5000 + >>> rr.getSteadyStateSolver().setValue("approx_maximum_steps", 5000) .. attribute:: SteadyStateSolver.approx_time End time for steady state approximation routine. approx_maximum_steps takes priority. Only used when steady state approximation routine is used. Default value is 10000. - >>> rr.getSteadyStateSolver().approx_time = 5000 + >>> rr.getSteadyStateSolver().setValue("approx_time", 5000) .. attribute:: SteadyStateSolver.broyden_method @@ -78,35 +70,35 @@ NLEQ2 To enable, type: - >>> rr.getSteadyStateSolver().broyden_method = 1 + >>> rr.getSteadyStateSolver().setValue("broyden_method", 1) .. attribute:: SteadyStateSolver.linearity Specifies linearity of the problem. 1 is for linear problem and 4 is for extremly nonlinear problem. Default value is 3. - >>> rr.getSteadyStateSolver().linearity = 1 + >>> rr.getSteadyStateSolver().setValue("linearity", 1) .. attribute:: SteadyStateSolver.maximum_iterations The maximum number of iterations the solver is allowed to use. Iteration caps off at the maximum, regardless of whether a solution has been reached. Default value is 100. - >>> rr.getSteadyStateSolver().maximum_iterations = 50 + >>> rr.getSteadyStateSolver().setValue("maximum_iterations", 50) .. attribute:: SteadyStateSolver.minimum_damping The minimum damping factor used by the algorithm. Default value is 1e-4. - >>> rr.getSteadyStateSolver().minimum_damping = 1e-20 + >>> rr.getSteadyStateSolver().setValue("minimum_damping", 1e-20) .. attribute:: SteadyStateSolver.relative_tolerance Specifies the relative tolerance used by the solver. Default value is 1e-16. - >>> rr.getSteadyStateSolver().relative_tolerance = 1e-15 + >>> rr.getSteadyStateSolver().setValue("relative_tolerance", 1e-15) .. method:: SteadyStateSolver.solve() diff --git a/docs/source/tutorial/solvers.rst b/docs/source/tutorial/solvers.rst index 9301da142d..43dec14184 100644 --- a/docs/source/tutorial/solvers.rst +++ b/docs/source/tutorial/solvers.rst @@ -39,10 +39,10 @@ To see a list of these settings, use :meth:`~roadrunner.Solver.getSettings()` on 'multiple_steps', 'variable_step_size') -To set a parameter, you can use both methods described below: +To set or get a parameter, you can use the methods described below: - >>> rr.getIntegrator().relative_tolerance = 1e-10 >>> rr.getIntegrator().setValue('relative_tolerance', 1e-10) + >>> rr.getIntegrator().getValue('initial_time_step') Be sure to set the parameter to the correct type, which can be obtained from the parameter's hint or description: @@ -60,7 +60,7 @@ Parameters also have a display name: If you prefer to change settings on integrators without switching the current integrator, you can use :meth:`~RoadRunner.getIntegratorByName()` as follows: - >>> rr.getIntegratorByName('gillespie').seed = 12345 + >>> rr.getIntegratorByName('gillespie').setValue("seed", 12345) Also, if you find yourself switching back and forth between integrators a lot, you can use :meth:`~RoadRunner.setIntegratorSetting()`. diff --git a/source/CVODEIntegrator.cpp b/source/CVODEIntegrator.cpp index 75cda11d5d..de36bc284f 100644 --- a/source/CVODEIntegrator.cpp +++ b/source/CVODEIntegrator.cpp @@ -160,8 +160,8 @@ namespace rr { "Specifies the scalar relative tolerance (double).", "(double) CVODE calculates a std::vector of error weights which is used in all error and convergence tests. The weighted RMS norm for the relative tolerance should not become smaller than this value."); addSetting("absolute_tolerance", Setting(Config::getDouble(Config::CVODE_MIN_ABSOLUTE)), "Absolute Tolerance", - "Specifies the scalar or std::vector absolute tolerance based on amounts (double or double std::vector).", - "(double or double std::vector) CVODE calculates a std::vector of error weights which is used in all error and convergence tests. The weighted RMS norm for the absolute tolerance should not become smaller than this value."); + "Specifies the scalar or std::vector absolute tolerance (double or double std::vector).", + "(double or double std::vector) CVODE calculates a std::vector of error weights which is used in all error and convergence tests. If a single value is set, that vector is the single value multiplied by the value of the elements of the state vector (floating species, and elements set by rate rules). If the value of the element is zero, the absolute tolerance value is either multiplied by the species' compartment volume, or, if the element is not a species, the absolute tolerance value is used directly. Note that the state vector uses species amounts, so if the vector is being set, the values need to be scaled to the amounts of the species, not their concentrations. (When setting a single value, this will be taken care of automatically.) The vector being used by the solver can be obtained by calling 'getAbsoluteToleranceVector' on the CVODE integrator. The weighted RMS norm for the absolute tolerance should not become smaller than this value."); addSetting("stiff", Setting(true), "Stiff", "Specifies whether the integrator attempts to solve stiff equations. (bool)", "(bool) Specifies whether the integrator attempts to solve stiff equations. Ensure the integrator can solver stiff differential equations by setting this value to true."); diff --git a/source/CVODEIntegrator.h b/source/CVODEIntegrator.h index 10740c6536..304c3e7cfb 100644 --- a/source/CVODEIntegrator.h +++ b/source/CVODEIntegrator.h @@ -241,7 +241,7 @@ namespace rr { /** * @brief Get the absolute tolerance vector for the solver. * - * The absolute tolerance vector is either set directly by the user as a vector, or is generated from the single absolute tolerance value (either default or set by the user) multiplied by the initial value of every element in the state vector (independent floating species, and elements controlled by rate rules). If the initial value is zero, the corresponding element of the absolute tolerance vector is the single value multiplied by the compartment volume for species, or by one for all other values. + * The absolute tolerance vector is either set directly by the user as a vector, or is generated from the single absolute tolerance value (either default or set by the user) multiplied by the initial value of every element in the state vector (independent floating species, and elements controlled by rate rules). If that initial value is zero, the corresponding element of the absolute tolerance vector is the single value multiplied by the compartment volume for species, or by one for all other values. */ virtual std::vector getAbsoluteToleranceVector(); From 50bca1bab68a680f2fb9e8b9132b9341d0322d47 Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Fri, 14 Apr 2023 11:49:00 -0700 Subject: [PATCH 28/28] Add newly-built docs. --- docs/docs-build/.buildinfo | 2 +- .../C++APIReference/CVODEIntegrator.html | 9 +- .../C++APIReference/Dictionary.html | 9 +- .../C++APIReference/EulerIntegrator.html | 12 +- .../ExecutableModelFactory.html | 3 +- .../C++APIReference/GillespieIntegrator.html | 9 +- .../C++APIReference/Integrator.html | 3 +- .../IntegratorRegistration.html | 3 +- .../C++APIReference/NLEQ1Solver.html | 11 +- .../C++APIReference/NLEQ2Solver.html | 11 +- .../C++APIReference/RK45Integrator.html | 9 +- .../C++APIReference/RK4Integrator.html | 9 +- .../C++APIReference/RoadRunnerMap.html | 15 +- 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docs/docs-build/_sources/rrplugins/rrplugins_monte_carlo_plugin.rst.txt create mode 100644 docs/docs-build/_sources/rrplugins/rrplugins_testmodel_plugin.rst.txt delete mode 100644 docs/docs-build/_static/jquery-3.6.0.js create mode 100644 docs/docs-build/_static/sphinx_highlight.js delete mode 100644 docs/docs-build/_static/underscore-1.13.1.js delete mode 100644 docs/docs-build/_static/underscore.js create mode 100644 docs/docs-build/rrplugins/introduction.html create mode 100644 docs/docs-build/rrplugins/rrplugins_LM_plugin.html create mode 100644 docs/docs-build/rrplugins/rrplugins_NM_plugin.html create mode 100644 docs/docs-build/rrplugins/rrplugins_add_noise_plugin.html create mode 100644 docs/docs-build/rrplugins/rrplugins_architecture.html create mode 100644 docs/docs-build/rrplugins/rrplugins_auto_plugin.html create mode 100644 docs/docs-build/rrplugins/rrplugins_chisquare_plugin.html create mode 100644 docs/docs-build/rrplugins/rrplugins_monte_carlo_plugin.html create mode 100644 docs/docs-build/rrplugins/rrplugins_testmodel_plugin.html diff --git a/docs/docs-build/.buildinfo b/docs/docs-build/.buildinfo index 3a4d3c9c36..1d57357fed 100644 --- a/docs/docs-build/.buildinfo +++ b/docs/docs-build/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 4fdea462f19561a75feef109d8a885cd +config: eeeea70bbadf2ed570191302c1060714 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/docs-build/C++APIReference/CVODEIntegrator.html b/docs/docs-build/C++APIReference/CVODEIntegrator.html index ec4f3fc908..d8b1ede2f2 100644 --- a/docs/docs-build/C++APIReference/CVODEIntegrator.html +++ b/docs/docs-build/C++APIReference/CVODEIntegrator.html @@ -12,10 +12,9 @@ - - + @@ -215,7 +214,7 @@

      CVODEIntegrator

      Note

      -

      Delegates to getName

      +

      Delegates to getName

      @@ -230,7 +229,7 @@

      CVODEIntegrator

      Note

      -

      Delegates to getDescription

      +

      Delegates to getDescription

      @@ -245,7 +244,7 @@

      CVODEIntegrator

      Note

      -

      Delegates to getHint

      +

      Delegates to getHint

      diff --git a/docs/docs-build/C++APIReference/Dictionary.html b/docs/docs-build/C++APIReference/Dictionary.html index 761af29b50..aad42ec13a 100644 --- a/docs/docs-build/C++APIReference/Dictionary.html +++ b/docs/docs-build/C++APIReference/Dictionary.html @@ -12,10 +12,9 @@ - - + @@ -151,13 +150,12 @@

      Dictionaryvirtual void setItem(const std::string &key, const rr::Setting &value) = 0

      Set the value for an arbitrary key.

      The Setting object has a large number of creation operators so you only have to give the value as native C++ object i.e.

      -

      Dictionary*d = (...);
+
      Dictionary*d = (...);
 d->setItem("someIntKey", 1);
 d->setItem("someStrKey", std::string("some std::string"));
 d->setItem("someFloatVal, 0.123);
 
      
 
      
-
      @@ -166,13 +164,12 @@

      Dictionary
      Dictionary* d = ...;
+
      Dictionary* d = ...;
 int a = d->getItem("someIntKey");
 std::string s = d->getItem("someStrVal");
 double val = d->getItem("someDoubleVal");
 
      
 
      
-

      diff --git a/docs/docs-build/C++APIReference/EulerIntegrator.html b/docs/docs-build/C++APIReference/EulerIntegrator.html index 716a1cd9c7..db1d57e521 100644 --- a/docs/docs-build/C++APIReference/EulerIntegrator.html +++ b/docs/docs-build/C++APIReference/EulerIntegrator.html @@ -12,10 +12,9 @@ - - + @@ -146,7 +145,7 @@

      EulerIntegratorDictionary interface to get/set various tuning paramters that an Integrator might have. These values will be displayed when the toString method is called, typically by Python.

      An example of calling simulate in Python, and the results of specifying the parameters as keyword arguments is

      -

      r.simulate(integrator='euler', exampleParameter1=123456, exampleParameter2='some value');
+
      r.simulate(integrator='euler', exampleParameter1=123456, exampleParameter2='some value');
 
 print(r.integrator)
 < roadrunner.EulerIntegrator()
@@ -156,7 +155,6 @@ 
      EulerIntegrator}>
 
      
 
      
- 
      
 
      
 
      Public Functions
      
 
      
@@ -220,7 +218,7 @@ 
      EulerIntegrator
 
      
 inline virtual std::string toString() const override
      
-
      get a description of this object, compatable with python str 
      
+
      get a description of this object, compatable with python str
      
 
      
 
 
      
@@ -246,7 +244,7 @@ 
      EulerIntegrator
 
      Note
      
-
      Delegates to getDescription 
      
+
      Delegates to getDescription

      @@ -261,7 +259,7 @@

      EulerIntegrator

      Note

      -

      Delegates to getHint

      +

      Delegates to getHint

      diff --git a/docs/docs-build/C++APIReference/ExecutableModelFactory.html b/docs/docs-build/C++APIReference/ExecutableModelFactory.html index d2396739b0..e26976a2d5 100644 --- a/docs/docs-build/C++APIReference/ExecutableModelFactory.html +++ b/docs/docs-build/C++APIReference/ExecutableModelFactory.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/GillespieIntegrator.html b/docs/docs-build/C++APIReference/GillespieIntegrator.html index 832f297949..63da846cd8 100644 --- a/docs/docs-build/C++APIReference/GillespieIntegrator.html +++ b/docs/docs-build/C++APIReference/GillespieIntegrator.html @@ -12,10 +12,9 @@ - - + @@ -181,7 +180,7 @@

      GillespieIntegrator

      Note

      -

      Delegates to getName

      +

      Delegates to getName

      @@ -196,7 +195,7 @@

      GillespieIntegrator

      Note

      -

      Delegates to getDescription

      +

      Delegates to getDescription

      @@ -211,7 +210,7 @@

      GillespieIntegrator

      Note

      -

      Delegates to getHint

      +

      Delegates to getHint

      diff --git a/docs/docs-build/C++APIReference/Integrator.html b/docs/docs-build/C++APIReference/Integrator.html index 1dfdd7d7b3..c0baae2c3e 100644 --- a/docs/docs-build/C++APIReference/Integrator.html +++ b/docs/docs-build/C++APIReference/Integrator.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/IntegratorRegistration.html b/docs/docs-build/C++APIReference/IntegratorRegistration.html index f3445975ff..47e781846f 100644 --- a/docs/docs-build/C++APIReference/IntegratorRegistration.html +++ b/docs/docs-build/C++APIReference/IntegratorRegistration.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/NLEQ1Solver.html b/docs/docs-build/C++APIReference/NLEQ1Solver.html index 7a8555a24f..0a2d1ff3e3 100644 --- a/docs/docs-build/C++APIReference/NLEQ1Solver.html +++ b/docs/docs-build/C++APIReference/NLEQ1Solver.html @@ -12,10 +12,9 @@ - - + @@ -159,7 +158,7 @@

      NLEQ1Solver

      Note

      -

      Delegates to getName

      +

      Delegates to getName

      @@ -174,7 +173,7 @@

      NLEQ1Solver

      Note

      -

      Delegates to getDescription

      +

      Delegates to getDescription

      @@ -189,14 +188,14 @@

      NLEQ1Solver

      Note

      -

      Delegates to getHint

      +

      Delegates to getHint

      virtual Solver *construct(ExecutableModel *executableModel) const override
      -

      construct an instance of NLEQ1Solver

      +

      construct an instance of NLEQ1Solver

      Caller is responsible for deleting memory associated with returned Solver*.

      diff --git a/docs/docs-build/C++APIReference/NLEQ2Solver.html b/docs/docs-build/C++APIReference/NLEQ2Solver.html index d006239b7b..9371cc7fa5 100644 --- a/docs/docs-build/C++APIReference/NLEQ2Solver.html +++ b/docs/docs-build/C++APIReference/NLEQ2Solver.html @@ -12,10 +12,9 @@ - - + @@ -154,7 +153,7 @@

      NLEQ2Solver

      Note

      -

      Delegates to getName

      +

      Delegates to getName

      @@ -169,7 +168,7 @@

      NLEQ2Solver

      Note

      -

      Delegates to getDescription

      +

      Delegates to getDescription

      @@ -184,7 +183,7 @@

      NLEQ2Solver

      Note

      -

      Delegates to getHint

      +

      Delegates to getHint

      @@ -196,7 +195,7 @@

      NLEQ2Solver
      virtual Solver *construct(ExecutableModel *executableModel) const override
      -

      construct an instance of NLEQ2Solver

      +

      construct an instance of NLEQ2Solver

      Caller is responsible for deleting memory associated with returned Solver*.

      diff --git a/docs/docs-build/C++APIReference/RK45Integrator.html b/docs/docs-build/C++APIReference/RK45Integrator.html index b2c8114828..8687d71126 100644 --- a/docs/docs-build/C++APIReference/RK45Integrator.html +++ b/docs/docs-build/C++APIReference/RK45Integrator.html @@ -12,10 +12,9 @@ - - + @@ -213,7 +212,7 @@

      RK45Integrator

      Note

      -

      Delegates to getName

      +

      Delegates to getName

      @@ -228,7 +227,7 @@

      RK45Integrator

      Note

      -

      Delegates to getDescription

      +

      Delegates to getDescription

      @@ -243,7 +242,7 @@

      RK45Integrator

      Note

      -

      Delegates to getHint

      +

      Delegates to getHint

      diff --git a/docs/docs-build/C++APIReference/RK4Integrator.html b/docs/docs-build/C++APIReference/RK4Integrator.html index 25aac0eb18..8285e254e2 100644 --- a/docs/docs-build/C++APIReference/RK4Integrator.html +++ b/docs/docs-build/C++APIReference/RK4Integrator.html @@ -12,10 +12,9 @@ - - + @@ -204,7 +203,7 @@

      RK4Integrator

      Note

      -

      Delegates to getName

      +

      Delegates to getName

      @@ -219,7 +218,7 @@

      RK4Integrator

      Note

      -

      Delegates to getDescription

      +

      Delegates to getDescription

      @@ -234,7 +233,7 @@

      RK4Integrator

      Note

      -

      Delegates to getHint

      +

      Delegates to getHint

      diff --git a/docs/docs-build/C++APIReference/RoadRunnerMap.html b/docs/docs-build/C++APIReference/RoadRunnerMap.html index 5fe5a24eb6..ddce293fc9 100644 --- a/docs/docs-build/C++APIReference/RoadRunnerMap.html +++ b/docs/docs-build/C++APIReference/RoadRunnerMap.html @@ -12,10 +12,9 @@ - - + @@ -291,19 +290,18 @@

      RoadRunnerMap ThreadSafeUnorderedMap::iterator begin()

      map iterator

      -

      for (auto&[modelName, rr]: rrm) {
+
      for (auto&[modelName, rr]: rrm) {
    ...
 }
 
      
 
      
-
      
 
      or 
      for (auto& [modelName, rr] : rrm) {
     actual[i] = rr->getInstanceID();
     i++;
 }
 
      
 
      
- 
      
+
      @@ -314,13 +312,12 @@

      RoadRunnerMap
      ThreadSafeUnorderedMap::iterator end()
      -

       for (auto it = rrm.begin(); it != rrm.end(); ++it) {
+
       for (auto it = rrm.begin(); it != rrm.end(); ++it) {
     auto&[modelName, rr] = *it;
     i++;
 }
 
      
 
      
-

      @@ -463,11 +460,11 @@

      RoadRunnerMap

      See also

      -

      RoadRunnerMap::setNumThreads

      +

      RoadRunnerMap::setNumThreads

      See also

      -

      RoadRunnerMap::getNumThreads

      +

      RoadRunnerMap::getNumThreads

      diff --git a/docs/docs-build/C++APIReference/SBMLValidator.html b/docs/docs-build/C++APIReference/SBMLValidator.html index d3ba82608d..b22517b3b6 100644 --- a/docs/docs-build/C++APIReference/SBMLValidator.html +++ b/docs/docs-build/C++APIReference/SBMLValidator.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/Solver.html b/docs/docs-build/C++APIReference/Solver.html index b26a77e761..6abc3fc6c4 100644 --- a/docs/docs-build/C++APIReference/Solver.html +++ b/docs/docs-build/C++APIReference/Solver.html @@ -12,10 +12,9 @@ - - + @@ -222,7 +221,7 @@

      Solver

      get settings for this solver

      See also

      -

      getSettings

      +

      getSettings

      @@ -437,7 +436,7 @@

      Solver
      virtual ExecutableModel *getModel() const
      -

      returns the pointer to the ExecutableModel

      +

      returns the pointer to the ExecutableModel

      diff --git a/docs/docs-build/C++APIReference/SolverRegistration.html b/docs/docs-build/C++APIReference/SolverRegistration.html index 3a44b73bd8..81d0e7eb14 100644 --- a/docs/docs-build/C++APIReference/SolverRegistration.html +++ b/docs/docs-build/C++APIReference/SolverRegistration.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/SteadyStateSolver.html b/docs/docs-build/C++APIReference/SteadyStateSolver.html index 14e842f281..48f423c64f 100644 --- a/docs/docs-build/C++APIReference/SteadyStateSolver.html +++ b/docs/docs-build/C++APIReference/SteadyStateSolver.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/Variant.html b/docs/docs-build/C++APIReference/Variant.html index dae2689d5f..0c859393d5 100644 --- a/docs/docs-build/C++APIReference/Variant.html +++ b/docs/docs-build/C++APIReference/Variant.html @@ -12,10 +12,9 @@ - - + @@ -156,7 +155,7 @@

      Variant
      Variant v = getSomeVariant();
+
      Variant v = getSomeVariant();
 
 // to convert to integer:
 int i = v.convert<int>();
@@ -165,7 +164,6 @@ 
      Variantstd::string s = v.convert<std::string>();
 
      
 
      
-
      
 
      Rationale: C++ does not have a built in variant type. Other variant types exist such as boost::any and Poco dynamic var. However including the one of these as part of our public wrappers would forever tie us to that particular library, and would impose yet another dependency.
      
 
      Only very basic variant type support is needed and this class exposes the absolute minimum possible wrappers to support such features, and provides just two methods of getting and storing native C++ types in it.
      
 
      This is currently implemented by Poco but the implementation is fully opaque and may change in the future. 
      
@@ -261,7 +259,7 @@ 
      VariantVariant v = std::string("a std::string");
      -

      +

      @@ -299,7 +297,7 @@

      Variantconst std::type_info &typeInfo() const

      get the type id of the stored data type.

      This will let you check what kind of data is strored in this variant.

      -

      // to check if this is an integer:
+
      // to check if this is an integer:
 Variant v = ...
 if (v.type() == typeid(int))
     std::cout << "its an int";
@@ -309,7 +307,6 @@ 
      Variantstd::cout << "ints a std::string";
 
      
 
      
-

      @@ -317,11 +314,10 @@

      Varianttemplate<typename T>
      inline       T convert() const

      Convert this variant to a supported data type.

      This method will try to perform type coercion, i.e. if this variant contains a std::string, and it is asked to convert to a int, the std::string will be parsed as an int. Similary, doubles will be rounded to int, so forth.

      -

      // convert to int:
+
      // convert to int:
 int i = v.convert<int>();
 
      
 
      
-

      @@ -447,7 +443,7 @@

      VariantVariant from a file or create a new one from a std::string: 
      Variant v = Variant::parse("0.123");
      -

      +

      diff --git a/docs/docs-build/C++APIReference/index.html b/docs/docs-build/C++APIReference/index.html index c401386409..d6387e7e43 100644 --- a/docs/docs-build/C++APIReference/index.html +++ b/docs/docs-build/C++APIReference/index.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/ASTNodeCodeGen.html b/docs/docs-build/C++APIReference/llvm/ASTNodeCodeGen.html index 4c83d53654..c626d365ed 100644 --- a/docs/docs-build/C++APIReference/llvm/ASTNodeCodeGen.html +++ b/docs/docs-build/C++APIReference/llvm/ASTNodeCodeGen.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/ASTNodeFactory.html b/docs/docs-build/C++APIReference/llvm/ASTNodeFactory.html index d695544fec..5432260d3d 100644 --- a/docs/docs-build/C++APIReference/llvm/ASTNodeFactory.html +++ b/docs/docs-build/C++APIReference/llvm/ASTNodeFactory.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/AssignmentRuleEvaluator.html b/docs/docs-build/C++APIReference/llvm/AssignmentRuleEvaluator.html index 0fce7dea27..ce24b6696c 100644 --- a/docs/docs-build/C++APIReference/llvm/AssignmentRuleEvaluator.html +++ b/docs/docs-build/C++APIReference/llvm/AssignmentRuleEvaluator.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/CodeGen.html b/docs/docs-build/C++APIReference/llvm/CodeGen.html index 20dcf76f03..48792df125 100644 --- a/docs/docs-build/C++APIReference/llvm/CodeGen.html +++ b/docs/docs-build/C++APIReference/llvm/CodeGen.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/CodeGenBase.html b/docs/docs-build/C++APIReference/llvm/CodeGenBase.html index dacd5f9132..25d4b3ba15 100644 --- a/docs/docs-build/C++APIReference/llvm/CodeGenBase.html +++ b/docs/docs-build/C++APIReference/llvm/CodeGenBase.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/EvalConversionFactorCodeGen.html b/docs/docs-build/C++APIReference/llvm/EvalConversionFactorCodeGen.html index 24e790a4d5..5fd6e6c29d 100644 --- a/docs/docs-build/C++APIReference/llvm/EvalConversionFactorCodeGen.html +++ b/docs/docs-build/C++APIReference/llvm/EvalConversionFactorCodeGen.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/EvalInitialConditionsCodeGen.html b/docs/docs-build/C++APIReference/llvm/EvalInitialConditionsCodeGen.html index 1b797ecb7f..5a3d9bbc77 100644 --- a/docs/docs-build/C++APIReference/llvm/EvalInitialConditionsCodeGen.html +++ b/docs/docs-build/C++APIReference/llvm/EvalInitialConditionsCodeGen.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/EvalRateRuleRatesCodeGen.html b/docs/docs-build/C++APIReference/llvm/EvalRateRuleRatesCodeGen.html index bfd07af6b3..3d33e23eca 100644 --- a/docs/docs-build/C++APIReference/llvm/EvalRateRuleRatesCodeGen.html +++ b/docs/docs-build/C++APIReference/llvm/EvalRateRuleRatesCodeGen.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/EvalReactionRatesCodeGen.html b/docs/docs-build/C++APIReference/llvm/EvalReactionRatesCodeGen.html index 73e0da3b29..c8dd8ae182 100644 --- a/docs/docs-build/C++APIReference/llvm/EvalReactionRatesCodeGen.html +++ b/docs/docs-build/C++APIReference/llvm/EvalReactionRatesCodeGen.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/EvalVolatileStoichCodeGen.html b/docs/docs-build/C++APIReference/llvm/EvalVolatileStoichCodeGen.html index 76002de3b0..8d868c6953 100644 --- a/docs/docs-build/C++APIReference/llvm/EvalVolatileStoichCodeGen.html +++ b/docs/docs-build/C++APIReference/llvm/EvalVolatileStoichCodeGen.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/EventAssignCodeGen.html b/docs/docs-build/C++APIReference/llvm/EventAssignCodeGen.html index c171dacfaa..76adaee878 100644 --- a/docs/docs-build/C++APIReference/llvm/EventAssignCodeGen.html +++ b/docs/docs-build/C++APIReference/llvm/EventAssignCodeGen.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/EventCodeGenBase.html b/docs/docs-build/C++APIReference/llvm/EventCodeGenBase.html index 483f680773..0032cbe8df 100644 --- a/docs/docs-build/C++APIReference/llvm/EventCodeGenBase.html +++ b/docs/docs-build/C++APIReference/llvm/EventCodeGenBase.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/EventQueue.html b/docs/docs-build/C++APIReference/llvm/EventQueue.html index 931b4dd6b2..507314b2c5 100644 --- a/docs/docs-build/C++APIReference/llvm/EventQueue.html +++ b/docs/docs-build/C++APIReference/llvm/EventQueue.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/EventTriggerCodeGen.html b/docs/docs-build/C++APIReference/llvm/EventTriggerCodeGen.html index 23cb9c1814..0e6b93a953 100644 --- a/docs/docs-build/C++APIReference/llvm/EventTriggerCodeGen.html +++ b/docs/docs-build/C++APIReference/llvm/EventTriggerCodeGen.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/FunctionResolver.html b/docs/docs-build/C++APIReference/llvm/FunctionResolver.html index 7ac03a988c..c9faf5f6ca 100644 --- a/docs/docs-build/C++APIReference/llvm/FunctionResolver.html +++ b/docs/docs-build/C++APIReference/llvm/FunctionResolver.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/KineticLawParameterResolver.html b/docs/docs-build/C++APIReference/llvm/KineticLawParameterResolver.html index 0a02daefdc..302661d4de 100644 --- a/docs/docs-build/C++APIReference/llvm/KineticLawParameterResolver.html +++ b/docs/docs-build/C++APIReference/llvm/KineticLawParameterResolver.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/LLVMCompiler.html b/docs/docs-build/C++APIReference/llvm/LLVMCompiler.html index e5440b195b..70bb6c2d3b 100644 --- a/docs/docs-build/C++APIReference/llvm/LLVMCompiler.html +++ b/docs/docs-build/C++APIReference/llvm/LLVMCompiler.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/LLVMException.html b/docs/docs-build/C++APIReference/llvm/LLVMException.html index 0cf195ddfc..690e59fb3b 100644 --- a/docs/docs-build/C++APIReference/llvm/LLVMException.html +++ b/docs/docs-build/C++APIReference/llvm/LLVMException.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/LLVMExecutableModel.html b/docs/docs-build/C++APIReference/llvm/LLVMExecutableModel.html index 56a1f03cad..f8ff8b182e 100644 --- a/docs/docs-build/C++APIReference/llvm/LLVMExecutableModel.html +++ b/docs/docs-build/C++APIReference/llvm/LLVMExecutableModel.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/LLVMModelData.html b/docs/docs-build/C++APIReference/llvm/LLVMModelData.html index 3f0a3e7d94..c312620c80 100644 --- a/docs/docs-build/C++APIReference/llvm/LLVMModelData.html +++ b/docs/docs-build/C++APIReference/llvm/LLVMModelData.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/LLVMModelDataSymbols.html b/docs/docs-build/C++APIReference/llvm/LLVMModelDataSymbols.html index f7c701638a..0a327cc515 100644 --- a/docs/docs-build/C++APIReference/llvm/LLVMModelDataSymbols.html +++ b/docs/docs-build/C++APIReference/llvm/LLVMModelDataSymbols.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/LLVMModelGenerator.html b/docs/docs-build/C++APIReference/llvm/LLVMModelGenerator.html index 6f94763d8e..7f03dab9f4 100644 --- a/docs/docs-build/C++APIReference/llvm/LLVMModelGenerator.html +++ b/docs/docs-build/C++APIReference/llvm/LLVMModelGenerator.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/LLVMModelSymbols.html b/docs/docs-build/C++APIReference/llvm/LLVMModelSymbols.html index 64f7044517..d9e9eeeb9d 100644 --- a/docs/docs-build/C++APIReference/llvm/LLVMModelSymbols.html +++ b/docs/docs-build/C++APIReference/llvm/LLVMModelSymbols.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/LoadSymbolResolverBase.html b/docs/docs-build/C++APIReference/llvm/LoadSymbolResolverBase.html index c22b967a14..cdfcb8bd22 100644 --- a/docs/docs-build/C++APIReference/llvm/LoadSymbolResolverBase.html +++ b/docs/docs-build/C++APIReference/llvm/LoadSymbolResolverBase.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/ModelDataIRBuilder.html b/docs/docs-build/C++APIReference/llvm/ModelDataIRBuilder.html index 542c5f9fc6..7ee18e5bb1 100644 --- a/docs/docs-build/C++APIReference/llvm/ModelDataIRBuilder.html +++ b/docs/docs-build/C++APIReference/llvm/ModelDataIRBuilder.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/ModelDataSymbolResolver.html b/docs/docs-build/C++APIReference/llvm/ModelDataSymbolResolver.html index 211c7cbd75..51af6202b6 100644 --- a/docs/docs-build/C++APIReference/llvm/ModelDataSymbolResolver.html +++ b/docs/docs-build/C++APIReference/llvm/ModelDataSymbolResolver.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/ModelGeneratorContext.html b/docs/docs-build/C++APIReference/llvm/ModelGeneratorContext.html index 2dee1a3eec..74ab88f4ad 100644 --- a/docs/docs-build/C++APIReference/llvm/ModelGeneratorContext.html +++ b/docs/docs-build/C++APIReference/llvm/ModelGeneratorContext.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/ModelInitialValueSymbolResolver.html b/docs/docs-build/C++APIReference/llvm/ModelInitialValueSymbolResolver.html index b01ad9c3cc..92df79cb99 100644 --- a/docs/docs-build/C++APIReference/llvm/ModelInitialValueSymbolResolver.html +++ b/docs/docs-build/C++APIReference/llvm/ModelInitialValueSymbolResolver.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/ModelResources.html b/docs/docs-build/C++APIReference/llvm/ModelResources.html index a10b6a9370..f3fde3a280 100644 --- a/docs/docs-build/C++APIReference/llvm/ModelResources.html +++ b/docs/docs-build/C++APIReference/llvm/ModelResources.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/Random.html b/docs/docs-build/C++APIReference/llvm/Random.html index 739d03dc2a..a336c35ff8 100644 --- a/docs/docs-build/C++APIReference/llvm/Random.html +++ b/docs/docs-build/C++APIReference/llvm/Random.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/SBMLInitialValueSymbolResolver.html b/docs/docs-build/C++APIReference/llvm/SBMLInitialValueSymbolResolver.html index ae43858185..b9256e8ec8 100644 --- a/docs/docs-build/C++APIReference/llvm/SBMLInitialValueSymbolResolver.html +++ b/docs/docs-build/C++APIReference/llvm/SBMLInitialValueSymbolResolver.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/SetInitialValueCodeGenBase.html b/docs/docs-build/C++APIReference/llvm/SetInitialValueCodeGenBase.html index a9a1eb7fa1..1e73fa5d57 100644 --- a/docs/docs-build/C++APIReference/llvm/SetInitialValueCodeGenBase.html +++ b/docs/docs-build/C++APIReference/llvm/SetInitialValueCodeGenBase.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/SetInitialValuesCodeGen.html b/docs/docs-build/C++APIReference/llvm/SetInitialValuesCodeGen.html index f9af1f2ff8..7c2c53ba28 100644 --- a/docs/docs-build/C++APIReference/llvm/SetInitialValuesCodeGen.html +++ b/docs/docs-build/C++APIReference/llvm/SetInitialValuesCodeGen.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/SetValueCodeGenBase.html b/docs/docs-build/C++APIReference/llvm/SetValueCodeGenBase.html index 5a147f07ef..3cabd60e61 100644 --- a/docs/docs-build/C++APIReference/llvm/SetValueCodeGenBase.html +++ b/docs/docs-build/C++APIReference/llvm/SetValueCodeGenBase.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/SetValuesCodeGen.html b/docs/docs-build/C++APIReference/llvm/SetValuesCodeGen.html index 51cc89259f..3809a7f1fb 100644 --- a/docs/docs-build/C++APIReference/llvm/SetValuesCodeGen.html +++ b/docs/docs-build/C++APIReference/llvm/SetValuesCodeGen.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/SymbolForest.html b/docs/docs-build/C++APIReference/llvm/SymbolForest.html index e495789762..a4c0a98844 100644 --- a/docs/docs-build/C++APIReference/llvm/SymbolForest.html +++ b/docs/docs-build/C++APIReference/llvm/SymbolForest.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/llvm/index.html b/docs/docs-build/C++APIReference/llvm/index.html index 80a8d08b34..49932cc56e 100644 --- a/docs/docs-build/C++APIReference/llvm/index.html +++ b/docs/docs-build/C++APIReference/llvm/index.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/rrCompiler.html b/docs/docs-build/C++APIReference/rrCompiler.html index 2fd18915cf..8807ba9558 100644 --- a/docs/docs-build/C++APIReference/rrCompiler.html +++ b/docs/docs-build/C++APIReference/rrCompiler.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/rrConfig.html b/docs/docs-build/C++APIReference/rrConfig.html index 9233c224bd..96049a37fa 100644 --- a/docs/docs-build/C++APIReference/rrConfig.html +++ b/docs/docs-build/C++APIReference/rrConfig.html @@ -12,10 +12,9 @@ - - + @@ -243,13 +242,13 @@

      rrConfig enumerator SIMULATEOPTIONS_STEPS

      The number of steps at which the output is sampled.

      -

      The samples are evenly spaced. When a simulation system calculates the data points to record, it will typically divide the duration by the number of time steps. Thus, for X steps, the output will have X+1 data rows. see SimulateOptions::steps

      +

      The samples are evenly spaced. When a simulation system calculates the data points to record, it will typically divide the duration by the number of time steps. Thus, for X steps, the output will have X+1 data rows. see SimulateOptions::steps

      enumerator SIMULATEOPTIONS_DURATION
      -

      see SimulateOptions::duration

      +

      see SimulateOptions::duration

      diff --git a/docs/docs-build/C++APIReference/rrException.html b/docs/docs-build/C++APIReference/rrException.html index 0f69ba14b1..62593c5cf8 100644 --- a/docs/docs-build/C++APIReference/rrException.html +++ b/docs/docs-build/C++APIReference/rrException.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/rrExecutableModel.html b/docs/docs-build/C++APIReference/rrExecutableModel.html index bbb1415e76..8bb92c056e 100644 --- a/docs/docs-build/C++APIReference/rrExecutableModel.html +++ b/docs/docs-build/C++APIReference/rrExecutableModel.html @@ -12,10 +12,9 @@ - - + @@ -539,7 +538,7 @@

      rrExecutableModelParameters:

      diff --git a/docs/docs-build/C++APIReference/rrFileName.html b/docs/docs-build/C++APIReference/rrFileName.html index b405695be0..983d305cd9 100644 --- a/docs/docs-build/C++APIReference/rrFileName.html +++ b/docs/docs-build/C++APIReference/rrFileName.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/rrIniFile.html b/docs/docs-build/C++APIReference/rrIniFile.html index 44f0ce95c7..172749e58a 100644 --- a/docs/docs-build/C++APIReference/rrIniFile.html +++ b/docs/docs-build/C++APIReference/rrIniFile.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/rrIniKey.html b/docs/docs-build/C++APIReference/rrIniKey.html index 6972a40c79..d37bae4243 100644 --- a/docs/docs-build/C++APIReference/rrIniKey.html +++ b/docs/docs-build/C++APIReference/rrIniKey.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/rrIniSection.html b/docs/docs-build/C++APIReference/rrIniSection.html index 8392baca52..bf8c5599cc 100644 --- a/docs/docs-build/C++APIReference/rrIniSection.html +++ b/docs/docs-build/C++APIReference/rrIniSection.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/rrLogger.html b/docs/docs-build/C++APIReference/rrLogger.html index fb951ca97a..31cdc73448 100644 --- a/docs/docs-build/C++APIReference/rrLogger.html +++ b/docs/docs-build/C++APIReference/rrLogger.html @@ -12,10 +12,9 @@ - - + @@ -205,7 +204,7 @@

      rrLogger
      static void setLevel(int level = LOG_CURRENT)
      -

      sets the logging level to one a value from Logger::Level

      +

      sets the logging level to one a value from Logger::Level

      @@ -324,7 +323,7 @@

      rrLogger
      static Level stringToLevel(const std::string &str)
      -

      parses a std::string and returns a Logger::Level

      +

      parses a std::string and returns a Logger::Level

      diff --git a/docs/docs-build/C++APIReference/rrNLEQ1Interface.html b/docs/docs-build/C++APIReference/rrNLEQ1Interface.html index f39bad8cb5..ab6f124a65 100644 --- a/docs/docs-build/C++APIReference/rrNLEQ1Interface.html +++ b/docs/docs-build/C++APIReference/rrNLEQ1Interface.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/rrNLEQ2Interface.html b/docs/docs-build/C++APIReference/rrNLEQ2Interface.html index 1cd6f2e330..d05e3493b7 100644 --- a/docs/docs-build/C++APIReference/rrNLEQ2Interface.html +++ b/docs/docs-build/C++APIReference/rrNLEQ2Interface.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/rrRoadRunner.html b/docs/docs-build/C++APIReference/rrRoadRunner.html index 8eff3f33af..a8cd48fe63 100644 --- a/docs/docs-build/C++APIReference/rrRoadRunner.html +++ b/docs/docs-build/C++APIReference/rrRoadRunner.html @@ -12,10 +12,9 @@ - - + @@ -358,7 +357,7 @@

      rrRoadRunner
      bool steadyStateSolverExists(const std::string &name)
      -

      returns true if SteadyStateSolver

      +

      returns true if SteadyStateSolver

      Parameters:

      name – exists.

      @@ -369,7 +368,7 @@

      rrRoadRunner
      bool sensitivitySolverExists(const std::string &name)
      -

      returns true if SensitivitySolver

      +

      returns true if SensitivitySolver

      Parameters:

      name – exists.

      @@ -551,11 +550,11 @@

      rrRoadRunner

      See also

      -

      RoadRunner::saveStateS

      +

      RoadRunner::saveStateS

      See also

      -

      RoadRunner::loadState

      +

      RoadRunner::loadState

      @@ -571,11 +570,11 @@

      rrRoadRunner

      See also

      -

      RoadRunner::loadStateS

      +

      RoadRunner::loadStateS

      See also

      -

      RoadRunner::saveState

      +

      RoadRunner::saveState

      @@ -594,11 +593,11 @@

      rrRoadRunner

      See also

      -

      RoadRunner::loadStateS

      +

      RoadRunner::loadStateS

      See also

      -

      RoadRunner::saveState

      +

      RoadRunner::saveState

      @@ -1669,7 +1668,7 @@

      rrRoadRunner double getGlobalParameterByIndex(const int &index)

      Alias for this function on the child model object.

      -

      use ExecutableModel::getGlobalParameterValues

      +

      use ExecutableModel::getGlobalParameterValues

      @@ -1886,7 +1885,7 @@

      rrRoadRunner std::vector<double> getGlobalParameterValues()

      Alias for this function on the child model object.

      -

      use ExecutableModel::getGlobalParameterValues

      +

      use ExecutableModel::getGlobalParameterValues

      @@ -1904,14 +1903,14 @@

      rrRoadRunner std::vector<double> getReactionRates()

      Alias for this function on the child model object.

      -

      use ExecutableModel::getReactionRates

      +

      use ExecutableModel::getReactionRates

      std::vector<std::string> getReactionIds()

      Alias for this function on the child model object.

      -

      returns a list of reaction ids obtained from ExecutableModel::getReactionId

      +

      returns a list of reaction ids obtained from ExecutableModel::getReactionId

      diff --git a/docs/docs-build/C++APIReference/rrRoadRunnerData.html b/docs/docs-build/C++APIReference/rrRoadRunnerData.html index 144e3a37b5..8712d05910 100644 --- a/docs/docs-build/C++APIReference/rrRoadRunnerData.html +++ b/docs/docs-build/C++APIReference/rrRoadRunnerData.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/rrRoadRunnerOptions.html b/docs/docs-build/C++APIReference/rrRoadRunnerOptions.html index 7fd3d77883..2780c4c350 100644 --- a/docs/docs-build/C++APIReference/rrRoadRunnerOptions.html +++ b/docs/docs-build/C++APIReference/rrRoadRunnerOptions.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/rrSBMLModelSimulation.html b/docs/docs-build/C++APIReference/rrSBMLModelSimulation.html index fd050b03a8..df899a7d41 100644 --- a/docs/docs-build/C++APIReference/rrSBMLModelSimulation.html +++ b/docs/docs-build/C++APIReference/rrSBMLModelSimulation.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/rrSBMLReader.html b/docs/docs-build/C++APIReference/rrSBMLReader.html index c87b8f3e4d..4674fbafff 100644 --- a/docs/docs-build/C++APIReference/rrSBMLReader.html +++ b/docs/docs-build/C++APIReference/rrSBMLReader.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/rrSelectionRecord.html b/docs/docs-build/C++APIReference/rrSelectionRecord.html index d5ae63ce02..baaf2cb7ec 100644 --- a/docs/docs-build/C++APIReference/rrSelectionRecord.html +++ b/docs/docs-build/C++APIReference/rrSelectionRecord.html @@ -12,10 +12,9 @@ - - + @@ -583,7 +582,7 @@

      rrSelectionRecord
      std::string to_repr() const
      -

      gets a longer description of this selection, this is intended to called as a python repr

      +

      gets a longer description of this selection, this is intended to called as a python repr

      diff --git a/docs/docs-build/C++APIReference/rrSparse.html b/docs/docs-build/C++APIReference/rrSparse.html index c7f4a2a96a..8a59af3eb7 100644 --- a/docs/docs-build/C++APIReference/rrSparse.html +++ b/docs/docs-build/C++APIReference/rrSparse.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/C++APIReference/rrSteadyStateSolver.html b/docs/docs-build/C++APIReference/rrSteadyStateSolver.html index 5072bb05f2..b9d1c3d619 100644 --- a/docs/docs-build/C++APIReference/rrSteadyStateSolver.html +++ b/docs/docs-build/C++APIReference/rrSteadyStateSolver.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/Installation/installation.html b/docs/docs-build/Installation/installation.html index b8a17a1925..7fa0f1ac7e 100644 --- a/docs/docs-build/Installation/installation.html +++ b/docs/docs-build/Installation/installation.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/Installation/llvm_dependency.html b/docs/docs-build/Installation/llvm_dependency.html index bde8ffaedd..4b0abef351 100644 --- a/docs/docs-build/Installation/llvm_dependency.html +++ b/docs/docs-build/Installation/llvm_dependency.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/Installation/troubleshooting_the_build.html b/docs/docs-build/Installation/troubleshooting_the_build.html index 2be923dab1..155b4e6fb6 100644 --- a/docs/docs-build/Installation/troubleshooting_the_build.html +++ b/docs/docs-build/Installation/troubleshooting_the_build.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/Installation/windows_warning.html b/docs/docs-build/Installation/windows_warning.html index 6a6e10442f..6c7a733866 100644 --- a/docs/docs-build/Installation/windows_warning.html +++ b/docs/docs-build/Installation/windows_warning.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/PythonAPIReference/api_reference.html b/docs/docs-build/PythonAPIReference/api_reference.html index 586df1b344..ad6661b6a3 100644 --- a/docs/docs-build/PythonAPIReference/api_reference.html +++ b/docs/docs-build/PythonAPIReference/api_reference.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/PythonAPIReference/cls_Compiler.html b/docs/docs-build/PythonAPIReference/cls_Compiler.html index cb9e47f27c..33c1c1dd7d 100644 --- a/docs/docs-build/PythonAPIReference/cls_Compiler.html +++ b/docs/docs-build/PythonAPIReference/cls_Compiler.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/PythonAPIReference/cls_Config.html b/docs/docs-build/PythonAPIReference/cls_Config.html index 51ed502b95..c37a713421 100644 --- a/docs/docs-build/PythonAPIReference/cls_Config.html +++ b/docs/docs-build/PythonAPIReference/cls_Config.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/PythonAPIReference/cls_ExecutableModel.html b/docs/docs-build/PythonAPIReference/cls_ExecutableModel.html index b9f99a304f..7b07846d03 100644 --- a/docs/docs-build/PythonAPIReference/cls_ExecutableModel.html +++ b/docs/docs-build/PythonAPIReference/cls_ExecutableModel.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/PythonAPIReference/cls_Integrator.html b/docs/docs-build/PythonAPIReference/cls_Integrator.html index fd96f2304f..67f1714119 100644 --- a/docs/docs-build/PythonAPIReference/cls_Integrator.html +++ b/docs/docs-build/PythonAPIReference/cls_Integrator.html @@ -12,10 +12,9 @@ - - + @@ -77,8 +76,6 @@
    • Integrator.setListener()
    • Integrator.tweakTolerances()
    • Integrator.setIndividualTolerance()
      • -
    • Integrator.setConcentrationTolerance()
      • -
    • Integrator.getConcentrationTolerance()
    • CVODE
      • Integrator.absolute_tolerance
      • Integrator.initial_time_step
        • @@ -242,26 +239,6 @@

        Integrator Class -
        -Integrator.setConcentrationTolerance(value)
        -

        Sets the tolerance based on concentration of species. Only used for CVODE Integrator. -First converts the concentration tolerances to amount tolerances by multiplying the compartment volume of species. Whichever is smaller will be stored in absolute_tolerance and used in the integration process. -Note that if a double list is given, the size of list must be equal to numIndFloatingSpecies+numRateRule, including tolerances for each independent floating species that doesn’t have a rate rule followed by tolerances for each variable(including dependent floating species) that has a rate rule. The order of independent floating species and variables is the same as the order how they were defined in species list and rate rule list.

        -
        -
        Parameters:
        -

        value (double/double list) – tolerance value to set

        -
        -
        -

      • - -
      -
      -Integrator.getConcentrationTolerance()
      -

      Gets the tolerance vector based on concentration of species. Only used for CVODE Integrator. -The vector includes tolerances for each independent floating species that doesn’t have a rate rule followed by tolerances for each variable(including dependent floating species) that has a rate rule. The order of independent floating species and variables is the same as the order how they were defined in species list and rate rule list.

      -
      -

      CVODE

      @@ -270,9 +247,15 @@

      CVODE
      Integrator.absolute_tolerance
      -

      Specifies the scalar or vector absolute tolerance based on amount of species. A potentially different absolute tolerance for each vector component could be set using a double vector. CVODE then calculates a vector of error weights which is used in all error and convergence tests. The weighted RMS norm for the absolute tolerance should not become smaller than this value. Default value is Config::CVODE_MIN_ABSOLUTE.

      -
      >>> rr.integrator.absolute_tolerance = 1
->>> rr.integrator.absolute_tolerance = [1, 0.1, 0.01, 0.001] // setting vairous tolerance for each species
+
      Specifies the scalar or vector absolute tolerance. As of roadrunner version 2.4.0, if a scalar absolute tolerance is used, it is multiplied by the value of every element in the state vector before being used.  If an element of the state vector is zero, the scalar is multiplied by 1.0 for non-species values, and by the size of the species compartment for species values (i.e. the amount of species present if its concentration was 1.0).
      
+
      If desired, the full absolute tolerance vector may be used instead of a scalar.  In this case, it is assumed that the user has already done any appropriate scaling for individual state vector levels, and no additional scaling is performed: the values are used in Sundials as-is.  Calling ‘getValue(‘absolute_tolerance’) will return the scalar or vector set by the user, or the default Config::CVODE_MIN_ABSOLUTE value.  To obtain the full vector obtained from the scalar, use ‘getAbsoluteToleranceVector’.
      
+
      In Sundials, the CVODE algorithm calculates a vector of error weights which is used in all error and convergence tests. The weighted RMS norm for the absolute tolerance should not become smaller than this value. Default value is Config::CVODE_MIN_ABSOLUTE (a scalar).
      
+
      >>> rr.integrator.setValue("absolute_tolerance", 1e-10)
+>>> rr.integrator.setValue("absolute_tolerance", [1, 0.1, 0.01, 0.001] // setting various tolerances for each species.
+
      
+
      
+
      >>> rr.integrator.getValue("absolute_tolerance") //Gets the scalar or vector absolute tolerance, as set by the user or the default value.
+>>> rr.integrator.getAbsoluteToleranceVector()   //Gets the absolute tolerance vector, as derived from the scalar value, or as set by the user directly.
      @@ -281,7 +264,8 @@

      CVODE
      Integrator.initial_time_step

      Specifies the initial time step size. If inappropriate, CVODE will attempt to estimate a better initial time step. Default value is 0.0

      -
      >>> rr.integrator.initial_time_step = 1
+
      >>> rr.integrator.setValue("initial_time_step", 1)
+>>> rr.integrator.getValue("initial_time_step")
      @@ -290,7 +274,8 @@

      CVODE
      Integrator.maximum_adams_order

      Specifies the maximum order for Adams-Moulton intergration. This integration method is used for non-stiff problems. Default value is 12.

      -
      >>> rr.integrator.maximum_adams_order = 20
+
      >>> rr.integrator.setValue("maximum_adams_order", 20)
+>>> rr.integrator.getValue("maximum_adams_order")
      @@ -323,7 +308,8 @@

      CVODE
      Integrator.multiple_steps

      Perform a multiple time step simulation. Default value is false.

      -
      >>> rr.integrator.multiple_steps = True
+
      >>> rr.integrator.setValue("multiple_steps", True)
+>>> rr.integrator.getValue("multiple_steps")
      @@ -358,7 +344,7 @@

      GillespieIntegrator.initial_time_step

      Specifies the initial time step size. If inappropriate, CVODE will attempt to estimate a better initial time step. Default value is 0.0

      >>> rr.setIntegrator('gillespie') # set integrator first
->>> rr.integrator.initial_time_step = 2
+>>> rr.integrator.setValue("initial_time_step", 2)
      @@ -428,7 +414,7 @@

      RK45Integrator.epsilon

      Specifies the maximum error tolerance allowed. Default value is 1e-12.

      >>> rr.setIntegrator('rk45') # set integrator first
->>> rr.integrator.epsilon = 1e-10
+>>> rr.integrator.setValue("epsilon", 1e-10)
      diff --git a/docs/docs-build/PythonAPIReference/cls_LoadSBMLOptions.html b/docs/docs-build/PythonAPIReference/cls_LoadSBMLOptions.html index ce7f721b20..8a9ebb7364 100644 --- a/docs/docs-build/PythonAPIReference/cls_LoadSBMLOptions.html +++ b/docs/docs-build/PythonAPIReference/cls_LoadSBMLOptions.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/PythonAPIReference/cls_Logger.html b/docs/docs-build/PythonAPIReference/cls_Logger.html index 0bbd8b6c5e..e03923eb28 100644 --- a/docs/docs-build/PythonAPIReference/cls_Logger.html +++ b/docs/docs-build/PythonAPIReference/cls_Logger.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/PythonAPIReference/cls_Misc.html b/docs/docs-build/PythonAPIReference/cls_Misc.html index 5352789385..25c0ab918a 100644 --- a/docs/docs-build/PythonAPIReference/cls_Misc.html +++ b/docs/docs-build/PythonAPIReference/cls_Misc.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/PythonAPIReference/cls_PyConservedMoietyConverter.html b/docs/docs-build/PythonAPIReference/cls_PyConservedMoietyConverter.html index c78b2576c2..f060e209be 100644 --- a/docs/docs-build/PythonAPIReference/cls_PyConservedMoietyConverter.html +++ b/docs/docs-build/PythonAPIReference/cls_PyConservedMoietyConverter.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/PythonAPIReference/cls_RoadRunner.html b/docs/docs-build/PythonAPIReference/cls_RoadRunner.html index 920d4ca0f0..87b7c1e6f9 100644 --- a/docs/docs-build/PythonAPIReference/cls_RoadRunner.html +++ b/docs/docs-build/PythonAPIReference/cls_RoadRunner.html @@ -12,10 +12,9 @@ - - + @@ -1750,8 +1749,8 @@

      Stoichiometric Analysis
      RoadRunner.getConservationMatrix()
      -

      Returns a conservation matrix \Gamma which is a c \times m matrix -where c is the number of conservation laws and m the number of species.

      +

      Returns a conservation matrix \Gamma which is a c \times m matrix +where c is the number of conservation laws and m the number of species.

      @@ -1782,8 +1781,8 @@

      Stoichiometric Analysis
      RoadRunner.getNrMatrix()
      -

      Returns the reduced stoichiometry matrix, N_R, which will have only r rows where r is the rank of -the full stoichiometry matrix. The matrix will be reordered such that the rows of N_R are independent.

      +

      Returns the reduced stoichiometry matrix, N_R, which will have only r rows where r is the rank of +the full stoichiometry matrix. The matrix will be reordered such that the rows of N_R are independent.

      Return type:

      numpy.ndarray

      @@ -1794,8 +1793,8 @@

      Stoichiometric Analysis
      RoadRunner.getKMatrix()
      -

      Returns the K matrix, ker(N_R), (right nullspace of Nr) -The K matrix has the structure, [I K0]'

      +

      Returns the K matrix, ker(N_R), (right nullspace of Nr) +The K matrix has the structure, [I K0]'

      Return type:

      numpy.ndarray

      diff --git a/docs/docs-build/PythonAPIReference/cls_SelectionRecord.html b/docs/docs-build/PythonAPIReference/cls_SelectionRecord.html index a17bfc66fe..985e7edc74 100644 --- a/docs/docs-build/PythonAPIReference/cls_SelectionRecord.html +++ b/docs/docs-build/PythonAPIReference/cls_SelectionRecord.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/PythonAPIReference/cls_Solver.html b/docs/docs-build/PythonAPIReference/cls_Solver.html index 730e88e212..9eab63520a 100644 --- a/docs/docs-build/PythonAPIReference/cls_Solver.html +++ b/docs/docs-build/PythonAPIReference/cls_Solver.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/PythonAPIReference/cls_SteadyStateSolver.html b/docs/docs-build/PythonAPIReference/cls_SteadyStateSolver.html index b02e09b9e4..2e99c8ab8d 100644 --- a/docs/docs-build/PythonAPIReference/cls_SteadyStateSolver.html +++ b/docs/docs-build/PythonAPIReference/cls_SteadyStateSolver.html @@ -12,10 +12,9 @@ - - + @@ -72,7 +71,6 @@
    • roadrunner.SteadyStateSolver
    • NLEQ2
      • - -
      -
      -SteadyStateSolver.presimulation_tolerance
      -

      Tolerance for presimulation before steady state analysis. Absolute tolerance used by presimulation routine. Only used when allow_presimulation is True. Default value is 1e-3.

      -
      >>> rr.getSteadyStateSolver().presimulation_tolerance = 1e-2
+
      >>> rr.getSteadyStateSolver().setValue("allow_presimulation", True)
      @@ -163,7 +152,7 @@

      NLEQ2
      SteadyStateSolver.presimulation_maximum_steps

      Maximum number of steps that can be taken for presimulation before steady state analysis. Takes priority over presimulation_time. Only used when allow_presimulation is True. Default value is 100.

      -
      >>> rr.getSteadyStateSolver().presimulation_maximum_steps = 50
+
      >>> rr.getSteadyStateSolver().setValue("presimulation_maximum_steps", 50)

      @@ -172,7 +161,7 @@

      NLEQ2
      SteadyStateSolver.presimulation_time

      End time for presimulation steady state analysis. Only used when allow_presimulation is True. Default value is 100.

      -
      >>> rr.getSteadyStateSolver().presimulation_time = 50
+
      >>> rr.getSteadyStateSolver().setValue("presimulation_time", 50)

      @@ -182,7 +171,7 @@

      NLEQ2 SteadyStateSolver.allow_approx

      Flag for using steady state approximation routine when steady state solver fails. Approximation routine will run only when the default solver fails to fine a solution. This flag does not affect usage of approximation routine for pre-simulation. Default is True.

      To disable, type:

      -
      >>> rr.getSteadyStateSolver().allow_approx = False
+
      >>> rr.getSteadyStateSolver().setValue("allow_approx", False)
      @@ -191,7 +180,7 @@

      NLEQ2
      SteadyStateSolver.approx_tolerance

      Tolerance for steady state approximation routine. Absolute tolerance used by steady state approximation routine. Only used when steady state approximation routine is used. Default value is 1e-12.

      -
      >>> rr.getSteadyStateSolver().approx_tolerance = 1e-6
+
      >>> rr.getSteadyStateSolver().setValue("approx_tolerance", 1e-6)
      @@ -200,7 +189,7 @@

      NLEQ2
      SteadyStateSolver.approx_maximum_steps

      Maximum number of steps that can be taken for steady state approximation routine. Takes priority over approx_time. Only used when steady state approximation routine is used. Default value is 10000.

      -
      >>> rr.getSteadyStateSolver().approx_maximum_steps = 5000
+
      >>> rr.getSteadyStateSolver().setValue("approx_maximum_steps", 5000)
      @@ -209,7 +198,7 @@

      NLEQ2
      SteadyStateSolver.approx_time

      End time for steady state approximation routine. approx_maximum_steps takes priority. Only used when steady state approximation routine is used. Default value is 10000.

      -
      >>> rr.getSteadyStateSolver().approx_time = 5000
+
      >>> rr.getSteadyStateSolver().setValue("approx_time", 5000)
      @@ -221,7 +210,7 @@

      NLEQ2

      Switches on Broyden method, which is a quasi-Newton approximation for rank-1 updates. Default value is 0.

      To enable, type:

      -
      >>> rr.getSteadyStateSolver().broyden_method = 1
+
      >>> rr.getSteadyStateSolver().setValue("broyden_method", 1)
 
      
 
      
 
@@ -230,7 +219,7 @@ 
      NLEQ2
 
      
 SteadyStateSolver.linearity
      
 
      Specifies linearity of the problem. 1 is for linear problem and 4 is for extremly nonlinear problem. Default value is 3.
      
-
      >>> rr.getSteadyStateSolver().linearity = 1
+
      >>> rr.getSteadyStateSolver().setValue("linearity", 1)
 
      
 
      
 
      
@@ -239,7 +228,7 @@ 
      NLEQ2
 
      
 SteadyStateSolver.maximum_iterations
      
 
      The maximum number of iterations the solver is allowed to use. Iteration caps off at the maximum, regardless of whether a solution has been reached. Default value is 100.
      
-
      >>> rr.getSteadyStateSolver().maximum_iterations = 50
+
      >>> rr.getSteadyStateSolver().setValue("maximum_iterations", 50)
 
      
 
      
 
      
@@ -248,7 +237,7 @@ 
      NLEQ2
 
      
 SteadyStateSolver.minimum_damping
      
 
      The minimum damping factor used by the algorithm. Default value is 1e-4.
      
-
      >>> rr.getSteadyStateSolver().minimum_damping = 1e-20
+
      >>> rr.getSteadyStateSolver().setValue("minimum_damping", 1e-20)
 
      
 
      
 
      
@@ -257,7 +246,7 @@ 
      NLEQ2
 
      
 SteadyStateSolver.relative_tolerance
      
 
      Specifies the relative tolerance used by the solver. Default value is 1e-16.
      
-
      >>> rr.getSteadyStateSolver().relative_tolerance = 1e-15
+
      >>> rr.getSteadyStateSolver().setValue("relative_tolerance", 1e-15)
 
      
 
      
 
      
diff --git a/docs/docs-build/UsingRoadRunnerFromCxx/using_roadrunner_from_cxx.html b/docs/docs-build/UsingRoadRunnerFromCxx/using_roadrunner_from_cxx.html
index 40b5f5b755..41b02cd459 100644
--- a/docs/docs-build/UsingRoadRunnerFromCxx/using_roadrunner_from_cxx.html
+++ b/docs/docs-build/UsingRoadRunnerFromCxx/using_roadrunner_from_cxx.html
@@ -12,10 +12,9 @@
     
   
   
-        
         
-        
         
+        
         
         
     
diff --git a/docs/docs-build/_images/AddNoise.png b/docs/docs-build/_images/AddNoise.png
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       or other required elements. - thead: [ 1, "
       
      int rrcCallConv rrc::setCurrentIntegratorParameterDoubleArray (RRHandle handle, char *parameterName, double *value, int len)
       
      -int rrcCallConv rrc::setCurrentIntegratorScalarConcentrationTolerance (RRHandle handle, double value)
       
      -int rrcCallConv rrc::setCurrentIntegratorVectorConcentrationTolerance (RRHandle handle, double *value, int len)
       
      int rrcCallConv rrc::setCurrentIntegratorIndividualTolerance (RRHandle handle, char *sid, double value)
      C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterDoubleArray (RRHandle handle, char *parameterName, double *value, int len)
       Set the double array value for a specific integrator setting. Should only used for absoluate tolerace. More...
       
      C_DECL_SPEC int rrcCallConv setCurrentIntegratorScalarConcentrationTolerance (RRHandle handle, double value)
       Set the scalar tolerance based on concentration for the current integrator. More...
       
      C_DECL_SPEC int rrcCallConv setCurrentIntegratorVectorConcentrationTolerance (RRHandle handle, double *value, int len)
       Set the vector tolerance based on concentration for the current integrator. More...
       
      C_DECL_SPEC int rrcCallConv setCurrentIntegratorIndividualTolerance (RRHandle handle, char *sid, double value)
       Set the double array value for a specific integrator setting. Should only used for absoluate tolerace. More...
       
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-} - -// Support: IE <=9 only -// Accessing document.activeElement can throw unexpectedly -// https://bugs.jquery.com/ticket/13393 -function safeActiveElement() { - try { - return document.activeElement; - } catch ( err ) { } -} - -function on( elem, types, selector, data, fn, one ) { - var origFn, type; - - // Types can be a map of types/handlers - if ( typeof types === "object" ) { - - // ( types-Object, selector, data ) - if ( typeof selector !== "string" ) { - - // ( types-Object, data ) - data = data || selector; - selector = undefined; - } - for ( type in types ) { - on( elem, type, selector, data, types[ type ], one ); - } - return elem; - } - - if ( data == null && fn == null ) { - - // ( types, fn ) - fn = selector; - data = selector = undefined; - } else if ( fn == null ) { - if ( typeof selector === "string" ) { - - // ( types, selector, fn ) - fn = data; - data = undefined; - } else { - - // ( types, data, fn ) - fn = data; - data = selector; - selector = undefined; - } - } - if ( fn === false ) { - fn = returnFalse; - } else if ( !fn ) { - return elem; - } - - if ( one === 1 ) { - origFn = fn; - fn = function( event ) { - - // Can use an empty set, since event contains the info - jQuery().off( event ); - return origFn.apply( this, arguments ); - }; - - // Use same guid so caller can remove using origFn - fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ ); - } - return elem.each( function() { - jQuery.event.add( this, types, fn, data, selector ); - } ); -} - -/* - * Helper functions for managing events -- not part of the public interface. - * Props to Dean Edwards' addEvent library for many of the ideas. - */ -jQuery.event = { - - global: {}, - - add: function( elem, types, handler, data, selector ) { - - var handleObjIn, eventHandle, tmp, - events, t, handleObj, - special, handlers, type, namespaces, origType, - elemData = dataPriv.get( elem ); - - // Only attach events to objects that accept data - if ( !acceptData( elem ) ) { - return; - } - - // Caller can pass in an object of custom data in lieu of the handler - if ( handler.handler ) { - handleObjIn = handler; - handler = handleObjIn.handler; - selector = handleObjIn.selector; - } - - // Ensure that invalid selectors throw exceptions at attach time - // Evaluate against documentElement in case elem is a non-element node (e.g., document) - if ( selector ) { - jQuery.find.matchesSelector( documentElement, selector ); - } - - // Make sure that the handler has a unique ID, used to find/remove it later - if ( !handler.guid ) { - handler.guid = jQuery.guid++; - } - - // Init the element's event structure and main handler, if this is the first - if ( !( events = elemData.events ) ) { - events = elemData.events = Object.create( null ); - } - if ( !( eventHandle = elemData.handle ) ) { - eventHandle = elemData.handle = function( e ) { - - // Discard the second event of a jQuery.event.trigger() and - // when an event is called after a page has unloaded - return typeof jQuery !== "undefined" && jQuery.event.triggered !== e.type ? - jQuery.event.dispatch.apply( elem, arguments ) : undefined; - }; - } - - // Handle multiple events separated by a space - types = ( types || "" ).match( rnothtmlwhite ) || [ "" ]; - t = types.length; - while ( t-- ) { - tmp = rtypenamespace.exec( types[ t ] ) || []; - type = origType = tmp[ 1 ]; - namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort(); - - // There *must* be a type, no attaching namespace-only handlers - if ( !type ) { - continue; - } - - // If event changes its type, use the special event handlers for the changed type - special = jQuery.event.special[ type ] || {}; - - // If selector defined, determine special event api type, otherwise given type - type = ( selector ? special.delegateType : special.bindType ) || type; - - // Update special based on newly reset type - special = jQuery.event.special[ type ] || {}; - - // handleObj is passed to all event handlers - handleObj = jQuery.extend( { - type: type, - origType: origType, - data: data, - handler: handler, - guid: handler.guid, - selector: selector, - needsContext: selector && jQuery.expr.match.needsContext.test( selector ), - namespace: namespaces.join( "." ) - }, handleObjIn ); - - // Init the event handler queue if we're the first - if ( !( handlers = events[ type ] ) ) { - handlers = events[ type ] = []; - handlers.delegateCount = 0; - - // Only use addEventListener if the special events handler returns false - if ( !special.setup || - special.setup.call( elem, data, namespaces, eventHandle ) === false ) { - - if ( elem.addEventListener ) { - elem.addEventListener( type, eventHandle ); - } - } - } - - if ( special.add ) { - special.add.call( elem, handleObj ); - - if ( !handleObj.handler.guid ) { - handleObj.handler.guid = handler.guid; - } - } - - // Add to the element's handler list, delegates in front - if ( selector ) { - handlers.splice( handlers.delegateCount++, 0, handleObj ); - } else { - handlers.push( handleObj ); - } - - // Keep track of which events have ever been used, for event optimization - jQuery.event.global[ type ] = true; - } - - }, - - // Detach an event or set of events from an element - remove: function( elem, types, handler, selector, mappedTypes ) { - - var j, origCount, tmp, - events, t, handleObj, - special, handlers, type, namespaces, origType, - elemData = dataPriv.hasData( elem ) && dataPriv.get( elem ); - - if ( !elemData || !( events = elemData.events ) ) { - return; - } - - // Once for each type.namespace in types; type may be omitted - types = ( types || "" ).match( rnothtmlwhite ) || [ "" ]; - t = types.length; - while ( t-- ) { - tmp = rtypenamespace.exec( types[ t ] ) || []; - type = origType = tmp[ 1 ]; - namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort(); - - // Unbind all events (on this namespace, if provided) for the element - if ( !type ) { - for ( type in events ) { - jQuery.event.remove( elem, type + types[ t ], handler, selector, true ); - } - continue; - } - - special = jQuery.event.special[ type ] || {}; - type = ( selector ? special.delegateType : special.bindType ) || type; - handlers = events[ type ] || []; - tmp = tmp[ 2 ] && - new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" ); - - // Remove matching events - origCount = j = handlers.length; - while ( j-- ) { - handleObj = handlers[ j ]; - - if ( ( mappedTypes || origType === handleObj.origType ) && - ( !handler || handler.guid === handleObj.guid ) && - ( !tmp || tmp.test( handleObj.namespace ) ) && - ( !selector || selector === handleObj.selector || - selector === "**" && handleObj.selector ) ) { - handlers.splice( j, 1 ); - - if ( handleObj.selector ) { - handlers.delegateCount--; - } - if ( special.remove ) { - special.remove.call( elem, handleObj ); - } - } - } - - // Remove generic event handler if we removed something and no more handlers exist - // (avoids potential for endless recursion during removal of special event handlers) - if ( origCount && !handlers.length ) { - if ( !special.teardown || - special.teardown.call( elem, namespaces, elemData.handle ) === false ) { - - jQuery.removeEvent( elem, type, elemData.handle ); - } - - delete events[ type ]; - } - } - - // Remove data and the expando if it's no longer used - if ( jQuery.isEmptyObject( events ) ) { - dataPriv.remove( elem, "handle events" ); - } - }, - - dispatch: function( nativeEvent ) { - - var i, j, ret, matched, handleObj, handlerQueue, - args = new Array( arguments.length ), - - // Make a writable jQuery.Event from the native event object - event = jQuery.event.fix( nativeEvent ), - - handlers = ( - dataPriv.get( this, "events" ) || Object.create( null ) - )[ event.type ] || [], - special = jQuery.event.special[ event.type ] || {}; - - // Use the fix-ed jQuery.Event rather than the (read-only) native event - args[ 0 ] = event; - - for ( i = 1; i < arguments.length; i++ ) { - args[ i ] = arguments[ i ]; - } - - event.delegateTarget = this; - - // Call the preDispatch hook for the mapped type, and let it bail if desired - if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) { - return; - } - - // Determine handlers - handlerQueue = jQuery.event.handlers.call( this, event, handlers ); - - // Run delegates first; they may want to stop propagation beneath us - i = 0; - while ( ( matched = handlerQueue[ i++ ] ) && !event.isPropagationStopped() ) { - event.currentTarget = matched.elem; - - j = 0; - while ( ( handleObj = matched.handlers[ j++ ] ) && - !event.isImmediatePropagationStopped() ) { - - // If the event is namespaced, then each handler is only invoked if it is - // specially universal or its namespaces are a superset of the event's. - if ( !event.rnamespace || handleObj.namespace === false || - event.rnamespace.test( handleObj.namespace ) ) { - - event.handleObj = handleObj; - event.data = handleObj.data; - - ret = ( ( jQuery.event.special[ handleObj.origType ] || {} ).handle || - handleObj.handler ).apply( matched.elem, args ); - - if ( ret !== undefined ) { - if ( ( event.result = ret ) === false ) { - event.preventDefault(); - event.stopPropagation(); - } - } - } - } - } - - // Call the postDispatch hook for the mapped type - if ( special.postDispatch ) { - special.postDispatch.call( this, event ); - } - - return event.result; - }, - - handlers: function( event, handlers ) { - var i, handleObj, sel, matchedHandlers, matchedSelectors, - handlerQueue = [], - delegateCount = handlers.delegateCount, - cur = event.target; - - // Find delegate handlers - if ( delegateCount && - - // Support: IE <=9 - // Black-hole SVG instance trees (trac-13180) - cur.nodeType && - - // Support: Firefox <=42 - // Suppress spec-violating clicks indicating a non-primary pointer button (trac-3861) - // https://www.w3.org/TR/DOM-Level-3-Events/#event-type-click - // Support: IE 11 only - // ...but not arrow key "clicks" of radio inputs, which can have `button` -1 (gh-2343) - !( event.type === "click" && event.button >= 1 ) ) { - - for ( ; cur !== this; cur = cur.parentNode || this ) { - - // Don't check non-elements (#13208) - // Don't process clicks on disabled elements (#6911, #8165, #11382, #11764) - if ( cur.nodeType === 1 && !( event.type === "click" && cur.disabled === true ) ) { - matchedHandlers = []; - matchedSelectors = {}; - for ( i = 0; i < delegateCount; i++ ) { - handleObj = handlers[ i ]; - - // Don't conflict with Object.prototype properties (#13203) - sel = handleObj.selector + " "; - - if ( matchedSelectors[ sel ] === undefined ) { - matchedSelectors[ sel ] = handleObj.needsContext ? - jQuery( sel, this ).index( cur ) > -1 : - jQuery.find( sel, this, null, [ cur ] ).length; - } - if ( matchedSelectors[ sel ] ) { - matchedHandlers.push( handleObj ); - } - } - if ( matchedHandlers.length ) { - handlerQueue.push( { elem: cur, handlers: matchedHandlers } ); - } - } - } - } - - // Add the remaining (directly-bound) handlers - cur = this; - if ( delegateCount < handlers.length ) { - handlerQueue.push( { elem: cur, handlers: handlers.slice( delegateCount ) } ); - } - - return handlerQueue; - }, - - addProp: function( name, hook ) { - Object.defineProperty( jQuery.Event.prototype, name, { - enumerable: true, - configurable: true, - - get: isFunction( hook ) ? - function() { - if ( this.originalEvent ) { - return hook( this.originalEvent ); - } - } : - function() { - if ( this.originalEvent ) { - return this.originalEvent[ name ]; - } - }, - - set: function( value ) { - Object.defineProperty( this, name, { - enumerable: true, - configurable: true, - writable: true, - value: value - } ); - } - } ); - }, - - fix: function( originalEvent ) { - return originalEvent[ jQuery.expando ] ? - originalEvent : - new jQuery.Event( originalEvent ); - }, - - special: { - load: { - - // Prevent triggered image.load events from bubbling to window.load - noBubble: true - }, - click: { - - // Utilize native event to ensure correct state for checkable inputs - setup: function( data ) { - - // For mutual compressibility with _default, replace `this` access with a local var. - // `|| data` is dead code meant only to preserve the variable through minification. - var el = this || data; - - // Claim the first handler - if ( rcheckableType.test( el.type ) && - el.click && nodeName( el, "input" ) ) { - - // dataPriv.set( el, "click", ... ) - leverageNative( el, "click", returnTrue ); - } - - // Return false to allow normal processing in the caller - return false; - }, - trigger: function( data ) { - - // For mutual compressibility with _default, replace `this` access with a local var. - // `|| data` is dead code meant only to preserve the variable through minification. - var el = this || data; - - // Force setup before triggering a click - if ( rcheckableType.test( el.type ) && - el.click && nodeName( el, "input" ) ) { - - leverageNative( el, "click" ); - } - - // Return non-false to allow normal event-path propagation - return true; - }, - - // For cross-browser consistency, suppress native .click() on links - // Also prevent it if we're currently inside a leveraged native-event stack - _default: function( event ) { - var target = event.target; - return rcheckableType.test( target.type ) && - target.click && nodeName( target, "input" ) && - dataPriv.get( target, "click" ) || - nodeName( target, "a" ); - } - }, - - beforeunload: { - postDispatch: function( event ) { - - // Support: Firefox 20+ - // Firefox doesn't alert if the returnValue field is not set. - if ( event.result !== undefined && event.originalEvent ) { - event.originalEvent.returnValue = event.result; - } - } - } - } -}; - -// Ensure the presence of an event listener that handles manually-triggered -// synthetic events by interrupting progress until reinvoked in response to -// *native* events that it fires directly, ensuring that state changes have -// already occurred before other listeners are invoked. -function leverageNative( el, type, expectSync ) { - - // Missing expectSync indicates a trigger call, which must force setup through jQuery.event.add - if ( !expectSync ) { - if ( dataPriv.get( el, type ) === undefined ) { - jQuery.event.add( el, type, returnTrue ); - } - return; - } - - // Register the controller as a special universal handler for all event namespaces - dataPriv.set( el, type, false ); - jQuery.event.add( el, type, { - namespace: false, - handler: function( event ) { - var notAsync, result, - saved = dataPriv.get( this, type ); - - if ( ( event.isTrigger & 1 ) && this[ type ] ) { - - // Interrupt processing of the outer synthetic .trigger()ed event - // Saved data should be false in such cases, but might be a leftover capture object - // from an async native handler (gh-4350) - if ( !saved.length ) { - - // Store arguments for use when handling the inner native event - // There will always be at least one argument (an event object), so this array - // will not be confused with a leftover capture object. - saved = slice.call( arguments ); - dataPriv.set( this, type, saved ); - - // Trigger the native event and capture its result - // Support: IE <=9 - 11+ - // focus() and blur() are asynchronous - notAsync = expectSync( this, type ); - this[ type ](); - result = dataPriv.get( this, type ); - if ( saved !== result || notAsync ) { - dataPriv.set( this, type, false ); - } else { - result = {}; - } - if ( saved !== result ) { - - // Cancel the outer synthetic event - event.stopImmediatePropagation(); - event.preventDefault(); - - // Support: Chrome 86+ - // In Chrome, if an element having a focusout handler is blurred by - // clicking outside of it, it invokes the handler synchronously. If - // that handler calls `.remove()` on the element, the data is cleared, - // leaving `result` undefined. We need to guard against this. - return result && result.value; - } - - // If this is an inner synthetic event for an event with a bubbling surrogate - // (focus or blur), assume that the surrogate already propagated from triggering the - // native event and prevent that from happening again here. - // This technically gets the ordering wrong w.r.t. to `.trigger()` (in which the - // bubbling surrogate propagates *after* the non-bubbling base), but that seems - // less bad than duplication. - } else if ( ( jQuery.event.special[ type ] || {} ).delegateType ) { - event.stopPropagation(); - } - - // If this is a native event triggered above, everything is now in order - // Fire an inner synthetic event with the original arguments - } else if ( saved.length ) { - - // ...and capture the result - dataPriv.set( this, type, { - value: jQuery.event.trigger( - - // Support: IE <=9 - 11+ - // Extend with the prototype to reset the above stopImmediatePropagation() - jQuery.extend( saved[ 0 ], jQuery.Event.prototype ), - saved.slice( 1 ), - this - ) - } ); - - // Abort handling of the native event - event.stopImmediatePropagation(); - } - } - } ); -} - -jQuery.removeEvent = function( elem, type, handle ) { - - // This "if" is needed for plain objects - if ( elem.removeEventListener ) { - elem.removeEventListener( type, handle ); - } -}; - -jQuery.Event = function( src, props ) { - - // Allow instantiation without the 'new' keyword - if ( !( this instanceof jQuery.Event ) ) { - return new jQuery.Event( src, props ); - } - - // Event object - if ( src && src.type ) { - this.originalEvent = src; - this.type = src.type; - - // Events bubbling up the document may have been marked as prevented - // by a handler lower down the tree; reflect the correct value. - this.isDefaultPrevented = src.defaultPrevented || - src.defaultPrevented === undefined && - - // Support: Android <=2.3 only - src.returnValue === false ? - returnTrue : - returnFalse; - - // Create target properties - // Support: Safari <=6 - 7 only - // Target should not be a text node (#504, #13143) - this.target = ( src.target && src.target.nodeType === 3 ) ? - src.target.parentNode : - src.target; - - this.currentTarget = src.currentTarget; - this.relatedTarget = src.relatedTarget; - - // Event type - } else { - this.type = src; - } - - // Put explicitly provided properties onto the event object - if ( props ) { - jQuery.extend( this, props ); - } - - // Create a timestamp if incoming event doesn't have one - this.timeStamp = src && src.timeStamp || Date.now(); - - // Mark it as fixed - this[ jQuery.expando ] = true; -}; - -// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding -// https://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html -jQuery.Event.prototype = { - constructor: jQuery.Event, - isDefaultPrevented: returnFalse, - isPropagationStopped: returnFalse, - isImmediatePropagationStopped: returnFalse, - isSimulated: false, - - preventDefault: function() { - var e = this.originalEvent; - - this.isDefaultPrevented = returnTrue; - - if ( e && !this.isSimulated ) { - e.preventDefault(); - } - }, - stopPropagation: function() { - var e = this.originalEvent; - - this.isPropagationStopped = returnTrue; - - if ( e && !this.isSimulated ) { - e.stopPropagation(); - } - }, - stopImmediatePropagation: function() { - var e = this.originalEvent; - - this.isImmediatePropagationStopped = returnTrue; - - if ( e && !this.isSimulated ) { - e.stopImmediatePropagation(); - } - - this.stopPropagation(); - } -}; - -// Includes all common event props including KeyEvent and MouseEvent specific props -jQuery.each( { - altKey: true, - bubbles: true, - cancelable: true, - changedTouches: true, - ctrlKey: true, - detail: true, - eventPhase: true, - metaKey: true, - pageX: true, - pageY: true, - shiftKey: true, - view: true, - "char": true, - code: true, - charCode: true, - key: true, - keyCode: true, - button: true, - buttons: true, - clientX: true, - clientY: true, - offsetX: true, - offsetY: true, - pointerId: true, - pointerType: true, - screenX: true, - screenY: true, - targetTouches: true, - toElement: true, - touches: true, - which: true -}, jQuery.event.addProp ); - -jQuery.each( { focus: "focusin", blur: "focusout" }, function( type, delegateType ) { - jQuery.event.special[ type ] = { - - // Utilize native event if possible so blur/focus sequence is correct - setup: function() { - - // Claim the first handler - // dataPriv.set( this, "focus", ... ) - // dataPriv.set( this, "blur", ... ) - leverageNative( this, type, expectSync ); - - // Return false to allow normal processing in the caller - return false; - }, - trigger: function() { - - // Force setup before trigger - leverageNative( this, type ); - - // Return non-false to allow normal event-path propagation - return true; - }, - - // Suppress native focus or blur as it's already being fired - // in leverageNative. - _default: function() { - return true; - }, - - delegateType: delegateType - }; -} ); - -// Create mouseenter/leave events using mouseover/out and event-time checks -// so that event delegation works in jQuery. -// Do the same for pointerenter/pointerleave and pointerover/pointerout -// -// Support: Safari 7 only -// Safari sends mouseenter too often; see: -// https://bugs.chromium.org/p/chromium/issues/detail?id=470258 -// for the description of the bug (it existed in older Chrome versions as well). -jQuery.each( { - mouseenter: "mouseover", - mouseleave: "mouseout", - pointerenter: "pointerover", - pointerleave: "pointerout" -}, function( orig, fix ) { - jQuery.event.special[ orig ] = { - delegateType: fix, - bindType: fix, - - handle: function( event ) { - var ret, - target = this, - related = event.relatedTarget, - handleObj = event.handleObj; - - // For mouseenter/leave call the handler if related is outside the target. - // NB: No relatedTarget if the mouse left/entered the browser window - if ( !related || ( related !== target && !jQuery.contains( target, related ) ) ) { - event.type = handleObj.origType; - ret = handleObj.handler.apply( this, arguments ); - event.type = fix; - } - return ret; - } - }; -} ); - -jQuery.fn.extend( { - - on: function( types, selector, data, fn ) { - return on( this, types, selector, data, fn ); - }, - one: function( types, selector, data, fn ) { - return on( this, types, selector, data, fn, 1 ); - }, - off: function( types, selector, fn ) { - var handleObj, type; - if ( types && types.preventDefault && types.handleObj ) { - - // ( event ) dispatched jQuery.Event - handleObj = types.handleObj; - jQuery( types.delegateTarget ).off( - handleObj.namespace ? - handleObj.origType + "." + handleObj.namespace : - handleObj.origType, - handleObj.selector, - handleObj.handler - ); - return this; - } - if ( typeof types === "object" ) { - - // ( types-object [, selector] ) - for ( type in types ) { - this.off( type, selector, types[ type ] ); - } - return this; - } - if ( selector === false || typeof selector === "function" ) { - - // ( types [, fn] ) - fn = selector; - selector = undefined; - } - if ( fn === false ) { - fn = returnFalse; - } - return this.each( function() { - jQuery.event.remove( this, types, fn, selector ); - } ); - } -} ); - - -var - - // Support: IE <=10 - 11, Edge 12 - 13 only - // In IE/Edge using regex groups here causes severe slowdowns. - // See https://connect.microsoft.com/IE/feedback/details/1736512/ - rnoInnerhtml = /\s*$/g; - -// Prefer a tbody over its parent table for containing new rows -function manipulationTarget( elem, content ) { - if ( nodeName( elem, "table" ) && - nodeName( content.nodeType !== 11 ? content : content.firstChild, "tr" ) ) { - - return jQuery( elem ).children( "tbody" )[ 0 ] || elem; - } - - return elem; -} - -// Replace/restore the type attribute of script elements for safe DOM manipulation -function disableScript( elem ) { - elem.type = ( elem.getAttribute( "type" ) !== null ) + "/" + elem.type; - return elem; -} -function restoreScript( elem ) { - if ( ( elem.type || "" ).slice( 0, 5 ) === "true/" ) { - elem.type = elem.type.slice( 5 ); - } else { - elem.removeAttribute( "type" ); - } - - return elem; -} - -function cloneCopyEvent( src, dest ) { - var i, l, type, pdataOld, udataOld, udataCur, events; - - if ( dest.nodeType !== 1 ) { - return; - } - - // 1. Copy private data: events, handlers, etc. - if ( dataPriv.hasData( src ) ) { - pdataOld = dataPriv.get( src ); - events = pdataOld.events; - - if ( events ) { - dataPriv.remove( dest, "handle events" ); - - for ( type in events ) { - for ( i = 0, l = events[ type ].length; i < l; i++ ) { - jQuery.event.add( dest, type, events[ type ][ i ] ); - } - } - } - } - - // 2. Copy user data - if ( dataUser.hasData( src ) ) { - udataOld = dataUser.access( src ); - udataCur = jQuery.extend( {}, udataOld ); - - dataUser.set( dest, udataCur ); - } -} - -// Fix IE bugs, see support tests -function fixInput( src, dest ) { - var nodeName = dest.nodeName.toLowerCase(); - - // Fails to persist the checked state of a cloned checkbox or radio button. - if ( nodeName === "input" && rcheckableType.test( src.type ) ) { - dest.checked = src.checked; - - // Fails to return the selected option to the default selected state when cloning options - } else if ( nodeName === "input" || nodeName === "textarea" ) { - dest.defaultValue = src.defaultValue; - } -} - -function domManip( collection, args, callback, ignored ) { - - // Flatten any nested arrays - args = flat( args ); - - var fragment, first, scripts, hasScripts, node, doc, - i = 0, - l = collection.length, - iNoClone = l - 1, - value = args[ 0 ], - valueIsFunction = isFunction( value ); - - // We can't cloneNode fragments that contain checked, in WebKit - if ( valueIsFunction || - ( l > 1 && typeof value === "string" && - !support.checkClone && rchecked.test( value ) ) ) { - return collection.each( function( index ) { - var self = collection.eq( index ); - if ( valueIsFunction ) { - args[ 0 ] = value.call( this, index, self.html() ); - } - domManip( self, args, callback, ignored ); - } ); - } - - if ( l ) { - fragment = buildFragment( args, collection[ 0 ].ownerDocument, false, collection, ignored ); - first = fragment.firstChild; - - if ( fragment.childNodes.length === 1 ) { - fragment = first; - } - - // Require either new content or an interest in ignored elements to invoke the callback - if ( first || ignored ) { - scripts = jQuery.map( getAll( fragment, "script" ), disableScript ); - hasScripts = scripts.length; - - // Use the original fragment for the last item - // instead of the first because it can end up - // being emptied incorrectly in certain situations (#8070). - for ( ; i < l; i++ ) { - node = fragment; - - if ( i !== iNoClone ) { - node = jQuery.clone( node, true, true ); - - // Keep references to cloned scripts for later restoration - if ( hasScripts ) { - - // Support: Android <=4.0 only, PhantomJS 1 only - // push.apply(_, arraylike) throws on ancient WebKit - jQuery.merge( scripts, getAll( node, "script" ) ); - } - } - - callback.call( collection[ i ], node, i ); - } - - if ( hasScripts ) { - doc = scripts[ scripts.length - 1 ].ownerDocument; - - // Reenable scripts - jQuery.map( scripts, restoreScript ); - - // Evaluate executable scripts on first document insertion - for ( i = 0; i < hasScripts; i++ ) { - node = scripts[ i ]; - if ( rscriptType.test( node.type || "" ) && - !dataPriv.access( node, "globalEval" ) && - jQuery.contains( doc, node ) ) { - - if ( node.src && ( node.type || "" ).toLowerCase() !== "module" ) { - - // Optional AJAX dependency, but won't run scripts if not present - if ( jQuery._evalUrl && !node.noModule ) { - jQuery._evalUrl( node.src, { - nonce: node.nonce || node.getAttribute( "nonce" ) - }, doc ); - } - } else { - DOMEval( node.textContent.replace( rcleanScript, "" ), node, doc ); - } - } - } - } - } - } - - return collection; -} - -function remove( elem, selector, keepData ) { - var node, - nodes = selector ? jQuery.filter( selector, elem ) : elem, - i = 0; - - for ( ; ( node = nodes[ i ] ) != null; i++ ) { - if ( !keepData && node.nodeType === 1 ) { - jQuery.cleanData( getAll( node ) ); - } - - if ( node.parentNode ) { - if ( keepData && isAttached( node ) ) { - setGlobalEval( getAll( node, "script" ) ); - } - node.parentNode.removeChild( node ); - } - } - - return elem; -} - -jQuery.extend( { - htmlPrefilter: function( html ) { - return html; - }, - - clone: function( elem, dataAndEvents, deepDataAndEvents ) { - var i, l, srcElements, destElements, - clone = elem.cloneNode( true ), - inPage = isAttached( elem ); - - // Fix IE cloning issues - if ( !support.noCloneChecked && ( elem.nodeType === 1 || elem.nodeType === 11 ) && - !jQuery.isXMLDoc( elem ) ) { - - // We eschew Sizzle here for performance reasons: https://jsperf.com/getall-vs-sizzle/2 - destElements = getAll( clone ); - srcElements = getAll( elem ); - - for ( i = 0, l = srcElements.length; i < l; i++ ) { - fixInput( srcElements[ i ], destElements[ i ] ); - } - } - - // Copy the events from the original to the clone - if ( dataAndEvents ) { - if ( deepDataAndEvents ) { - srcElements = srcElements || getAll( elem ); - destElements = destElements || getAll( clone ); - - for ( i = 0, l = srcElements.length; i < l; i++ ) { - cloneCopyEvent( srcElements[ i ], destElements[ i ] ); - } - } else { - cloneCopyEvent( elem, clone ); - } - } - - // Preserve script evaluation history - destElements = getAll( clone, "script" ); - if ( destElements.length > 0 ) { - setGlobalEval( destElements, !inPage && getAll( elem, "script" ) ); - } - - // Return the cloned set - return clone; - }, - - cleanData: function( elems ) { - var data, elem, type, - special = jQuery.event.special, - i = 0; - - for ( ; ( elem = elems[ i ] ) !== undefined; i++ ) { - if ( acceptData( elem ) ) { - if ( ( data = elem[ dataPriv.expando ] ) ) { - if ( data.events ) { - for ( type in data.events ) { - if ( special[ type ] ) { - jQuery.event.remove( elem, type ); - - // This is a shortcut to avoid jQuery.event.remove's overhead - } else { - jQuery.removeEvent( elem, type, data.handle ); - } - } - } - - // Support: Chrome <=35 - 45+ - // Assign undefined instead of using delete, see Data#remove - elem[ dataPriv.expando ] = undefined; - } - if ( elem[ dataUser.expando ] ) { - - // Support: Chrome <=35 - 45+ - // Assign undefined instead of using delete, see Data#remove - elem[ dataUser.expando ] = undefined; - } - } - } - } -} ); - -jQuery.fn.extend( { - detach: function( selector ) { - return remove( this, selector, true ); - }, - - remove: function( selector ) { - return remove( this, selector ); - }, - - text: function( value ) { - return access( this, function( value ) { - return value === undefined ? - jQuery.text( this ) : - this.empty().each( function() { - if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { - this.textContent = value; - } - } ); - }, null, value, arguments.length ); - }, - - append: function() { - return domManip( this, arguments, function( elem ) { - if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { - var target = manipulationTarget( this, elem ); - target.appendChild( elem ); - } - } ); - }, - - prepend: function() { - return domManip( this, arguments, function( elem ) { - if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { - var target = manipulationTarget( this, elem ); - target.insertBefore( elem, target.firstChild ); - } - } ); - }, - - before: function() { - return domManip( this, arguments, function( elem ) { - if ( this.parentNode ) { - this.parentNode.insertBefore( elem, this ); - } - } ); - }, - - after: function() { - return domManip( this, arguments, function( elem ) { - if ( this.parentNode ) { - this.parentNode.insertBefore( elem, this.nextSibling ); - } - } ); - }, - - empty: function() { - var elem, - i = 0; - - for ( ; ( elem = this[ i ] ) != null; i++ ) { - if ( elem.nodeType === 1 ) { - - // Prevent memory leaks - jQuery.cleanData( getAll( elem, false ) ); - - // Remove any remaining nodes - elem.textContent = ""; - } - } - - return this; - }, - - clone: function( dataAndEvents, deepDataAndEvents ) { - dataAndEvents = dataAndEvents == null ? false : dataAndEvents; - deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents; - - return this.map( function() { - return jQuery.clone( this, dataAndEvents, deepDataAndEvents ); - } ); - }, - - html: function( value ) { - return access( this, function( value ) { - var elem = this[ 0 ] || {}, - i = 0, - l = this.length; - - if ( value === undefined && elem.nodeType === 1 ) { - return elem.innerHTML; - } - - // See if we can take a shortcut and just use innerHTML - if ( typeof value === "string" && !rnoInnerhtml.test( value ) && - !wrapMap[ ( rtagName.exec( value ) || [ "", "" ] )[ 1 ].toLowerCase() ] ) { - - value = jQuery.htmlPrefilter( value ); - - try { - for ( ; i < l; i++ ) { - elem = this[ i ] || {}; - - // Remove element nodes and prevent memory leaks - if ( elem.nodeType === 1 ) { - jQuery.cleanData( getAll( elem, false ) ); - elem.innerHTML = value; - } - } - - elem = 0; - - // If using innerHTML throws an exception, use the fallback method - } catch ( e ) {} - } - - if ( elem ) { - this.empty().append( value ); - } - }, null, value, arguments.length ); - }, - - replaceWith: function() { - var ignored = []; - - // Make the changes, replacing each non-ignored context element with the new content - return domManip( this, arguments, function( elem ) { - var parent = this.parentNode; - - if ( jQuery.inArray( this, ignored ) < 0 ) { - jQuery.cleanData( getAll( this ) ); - if ( parent ) { - parent.replaceChild( elem, this ); - } - } - - // Force callback invocation - }, ignored ); - } -} ); - -jQuery.each( { - appendTo: "append", - prependTo: "prepend", - insertBefore: "before", - insertAfter: "after", - replaceAll: "replaceWith" -}, function( name, original ) { - jQuery.fn[ name ] = function( selector ) { - var elems, - ret = [], - insert = jQuery( selector ), - last = insert.length - 1, - i = 0; - - for ( ; i <= last; i++ ) { - elems = i === last ? this : this.clone( true ); - jQuery( insert[ i ] )[ original ]( elems ); - - // Support: Android <=4.0 only, PhantomJS 1 only - // .get() because push.apply(_, arraylike) throws on ancient WebKit - push.apply( ret, elems.get() ); - } - - return this.pushStack( ret ); - }; -} ); -var rnumnonpx = new RegExp( "^(" + pnum + ")(?!px)[a-z%]+$", "i" ); - -var getStyles = function( elem ) { - - // Support: IE <=11 only, Firefox <=30 (#15098, #14150) - // IE throws on elements created in popups - // FF meanwhile throws on frame elements through "defaultView.getComputedStyle" - var view = elem.ownerDocument.defaultView; - - if ( !view || !view.opener ) { - view = window; - } - - return view.getComputedStyle( elem ); - }; - -var swap = function( elem, options, callback ) { - var ret, name, - old = {}; - - // Remember the old values, and insert the new ones - for ( name in options ) { - old[ name ] = elem.style[ name ]; - elem.style[ name ] = options[ name ]; - } - - ret = callback.call( elem ); - - // Revert the old values - for ( name in options ) { - elem.style[ name ] = old[ name ]; - } - - return ret; -}; - - -var rboxStyle = new RegExp( cssExpand.join( "|" ), "i" ); - - - -( function() { - - // Executing both pixelPosition & boxSizingReliable tests require only one layout - // so they're executed at the same time to save the second computation. - function computeStyleTests() { - - // This is a singleton, we need to execute it only once - if ( !div ) { - return; - } - - container.style.cssText = "position:absolute;left:-11111px;width:60px;" + - "margin-top:1px;padding:0;border:0"; - div.style.cssText = - "position:relative;display:block;box-sizing:border-box;overflow:scroll;" + - "margin:auto;border:1px;padding:1px;" + - "width:60%;top:1%"; - documentElement.appendChild( container ).appendChild( div ); - - var divStyle = window.getComputedStyle( div ); - pixelPositionVal = divStyle.top !== "1%"; - - // Support: Android 4.0 - 4.3 only, Firefox <=3 - 44 - reliableMarginLeftVal = roundPixelMeasures( divStyle.marginLeft ) === 12; - - // Support: Android 4.0 - 4.3 only, Safari <=9.1 - 10.1, iOS <=7.0 - 9.3 - // Some styles come back with percentage values, even though they shouldn't - div.style.right = "60%"; - pixelBoxStylesVal = roundPixelMeasures( divStyle.right ) === 36; - - // Support: IE 9 - 11 only - // Detect misreporting of content dimensions for box-sizing:border-box elements - boxSizingReliableVal = roundPixelMeasures( divStyle.width ) === 36; - - // Support: IE 9 only - // Detect overflow:scroll screwiness (gh-3699) - // Support: Chrome <=64 - // Don't get tricked when zoom affects offsetWidth (gh-4029) - div.style.position = "absolute"; - scrollboxSizeVal = roundPixelMeasures( div.offsetWidth / 3 ) === 12; - - documentElement.removeChild( container ); - - // Nullify the div so it wouldn't be stored in the memory and - // it will also be a sign that checks already performed - div = null; - } - - function roundPixelMeasures( measure ) { - return Math.round( parseFloat( measure ) ); - } - - var pixelPositionVal, boxSizingReliableVal, scrollboxSizeVal, pixelBoxStylesVal, - reliableTrDimensionsVal, reliableMarginLeftVal, - container = document.createElement( "div" ), - div = document.createElement( "div" ); - - // Finish early in limited (non-browser) environments - if ( !div.style ) { - return; - } - - // Support: IE <=9 - 11 only - // Style of cloned element affects source element cloned (#8908) - div.style.backgroundClip = "content-box"; - div.cloneNode( true ).style.backgroundClip = ""; - support.clearCloneStyle = div.style.backgroundClip === "content-box"; - - jQuery.extend( support, { - boxSizingReliable: function() { - computeStyleTests(); - return boxSizingReliableVal; - }, - pixelBoxStyles: function() { - computeStyleTests(); - return pixelBoxStylesVal; - }, - pixelPosition: function() { - computeStyleTests(); - return pixelPositionVal; - }, - reliableMarginLeft: function() { - computeStyleTests(); - return reliableMarginLeftVal; - }, - scrollboxSize: function() { - computeStyleTests(); - return scrollboxSizeVal; - }, - - // Support: IE 9 - 11+, Edge 15 - 18+ - // IE/Edge misreport `getComputedStyle` of table rows with width/height - // set in CSS while `offset*` properties report correct values. - // Behavior in IE 9 is more subtle than in newer versions & it passes - // some versions of this test; make sure not to make it pass there! - // - // Support: Firefox 70+ - // Only Firefox includes border widths - // in computed dimensions. (gh-4529) - reliableTrDimensions: function() { - var table, tr, trChild, trStyle; - if ( reliableTrDimensionsVal == null ) { - table = document.createElement( "table" ); - tr = document.createElement( "tr" ); - trChild = document.createElement( "div" ); - - table.style.cssText = "position:absolute;left:-11111px;border-collapse:separate"; - tr.style.cssText = "border:1px solid"; - - // Support: Chrome 86+ - // Height set through cssText does not get applied. - // Computed height then comes back as 0. - tr.style.height = "1px"; - trChild.style.height = "9px"; - - // Support: Android 8 Chrome 86+ - // In our bodyBackground.html iframe, - // display for all div elements is set to "inline", - // which causes a problem only in Android 8 Chrome 86. - // Ensuring the div is display: block - // gets around this issue. - trChild.style.display = "block"; - - documentElement - .appendChild( table ) - .appendChild( tr ) - .appendChild( trChild ); - - trStyle = window.getComputedStyle( tr ); - reliableTrDimensionsVal = ( parseInt( trStyle.height, 10 ) + - parseInt( trStyle.borderTopWidth, 10 ) + - parseInt( trStyle.borderBottomWidth, 10 ) ) === tr.offsetHeight; - - documentElement.removeChild( table ); - } - return reliableTrDimensionsVal; - } - } ); -} )(); - - -function curCSS( elem, name, computed ) { - var width, minWidth, maxWidth, ret, - - // Support: Firefox 51+ - // Retrieving style before computed somehow - // fixes an issue with getting wrong values - // on detached elements - style = elem.style; - - computed = computed || getStyles( elem ); - - // getPropertyValue is needed for: - // .css('filter') (IE 9 only, #12537) - // .css('--customProperty) (#3144) - if ( computed ) { - ret = computed.getPropertyValue( name ) || computed[ name ]; - - if ( ret === "" && !isAttached( elem ) ) { - ret = jQuery.style( elem, name ); - } - - // A tribute to the "awesome hack by Dean Edwards" - // Android Browser returns percentage for some values, - // but width seems to be reliably pixels. - // This is against the CSSOM draft spec: - // https://drafts.csswg.org/cssom/#resolved-values - if ( !support.pixelBoxStyles() && rnumnonpx.test( ret ) && rboxStyle.test( name ) ) { - - // Remember the original values - width = style.width; - minWidth = style.minWidth; - maxWidth = style.maxWidth; - - // Put in the new values to get a computed value out - style.minWidth = style.maxWidth = style.width = ret; - ret = computed.width; - - // Revert the changed values - style.width = width; - style.minWidth = minWidth; - style.maxWidth = maxWidth; - } - } - - return ret !== undefined ? - - // Support: IE <=9 - 11 only - // IE returns zIndex value as an integer. - ret + "" : - ret; -} - - -function addGetHookIf( conditionFn, hookFn ) { - - // Define the hook, we'll check on the first run if it's really needed. - return { - get: function() { - if ( conditionFn() ) { - - // Hook not needed (or it's not possible to use it due - // to missing dependency), remove it. - delete this.get; - return; - } - - // Hook needed; redefine it so that the support test is not executed again. - return ( this.get = hookFn ).apply( this, arguments ); - } - }; -} - - -var cssPrefixes = [ "Webkit", "Moz", "ms" ], - emptyStyle = document.createElement( "div" ).style, - vendorProps = {}; - -// Return a vendor-prefixed property or undefined -function vendorPropName( name ) { - - // Check for vendor prefixed names - var capName = name[ 0 ].toUpperCase() + name.slice( 1 ), - i = cssPrefixes.length; - - while ( i-- ) { - name = cssPrefixes[ i ] + capName; - if ( name in emptyStyle ) { - return name; - } - } -} - -// Return a potentially-mapped jQuery.cssProps or vendor prefixed property -function finalPropName( name ) { - var final = jQuery.cssProps[ name ] || vendorProps[ name ]; - - if ( final ) { - return final; - } - if ( name in emptyStyle ) { - return name; - } - return vendorProps[ name ] = vendorPropName( name ) || name; -} - - -var - - // Swappable if display is none or starts with table - // except "table", "table-cell", or "table-caption" - // See here for display values: https://developer.mozilla.org/en-US/docs/CSS/display - rdisplayswap = /^(none|table(?!-c[ea]).+)/, - rcustomProp = /^--/, - cssShow = { position: "absolute", visibility: "hidden", display: "block" }, - cssNormalTransform = { - letterSpacing: "0", - fontWeight: "400" - }; - -function setPositiveNumber( _elem, value, subtract ) { - - // Any relative (+/-) values have already been - // normalized at this point - var matches = rcssNum.exec( value ); - return matches ? - - // Guard against undefined "subtract", e.g., when used as in cssHooks - Math.max( 0, matches[ 2 ] - ( subtract || 0 ) ) + ( matches[ 3 ] || "px" ) : - value; -} - -function boxModelAdjustment( elem, dimension, box, isBorderBox, styles, computedVal ) { - var i = dimension === "width" ? 1 : 0, - extra = 0, - delta = 0; - - // Adjustment may not be necessary - if ( box === ( isBorderBox ? "border" : "content" ) ) { - return 0; - } - - for ( ; i < 4; i += 2 ) { - - // Both box models exclude margin - if ( box === "margin" ) { - delta += jQuery.css( elem, box + cssExpand[ i ], true, styles ); - } - - // If we get here with a content-box, we're seeking "padding" or "border" or "margin" - if ( !isBorderBox ) { - - // Add padding - delta += jQuery.css( elem, "padding" + cssExpand[ i ], true, styles ); - - // For "border" or "margin", add border - if ( box !== "padding" ) { - delta += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); - - // But still keep track of it otherwise - } else { - extra += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); - } - - // If we get here with a border-box (content + padding + border), we're seeking "content" or - // "padding" or "margin" - } else { - - // For "content", subtract padding - if ( box === "content" ) { - delta -= jQuery.css( elem, "padding" + cssExpand[ i ], true, styles ); - } - - // For "content" or "padding", subtract border - if ( box !== "margin" ) { - delta -= jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); - } - } - } - - // Account for positive content-box scroll gutter when requested by providing computedVal - if ( !isBorderBox && computedVal >= 0 ) { - - // offsetWidth/offsetHeight is a rounded sum of content, padding, scroll gutter, and border - // Assuming integer scroll gutter, subtract the rest and round down - delta += Math.max( 0, Math.ceil( - elem[ "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ) ] - - computedVal - - delta - - extra - - 0.5 - - // If offsetWidth/offsetHeight is unknown, then we can't determine content-box scroll gutter - // Use an explicit zero to avoid NaN (gh-3964) - ) ) || 0; - } - - return delta; -} - -function getWidthOrHeight( elem, dimension, extra ) { - - // Start with computed style - var styles = getStyles( elem ), - - // To avoid forcing a reflow, only fetch boxSizing if we need it (gh-4322). - // Fake content-box until we know it's needed to know the true value. - boxSizingNeeded = !support.boxSizingReliable() || extra, - isBorderBox = boxSizingNeeded && - jQuery.css( elem, "boxSizing", false, styles ) === "border-box", - valueIsBorderBox = isBorderBox, - - val = curCSS( elem, dimension, styles ), - offsetProp = "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ); - - // Support: Firefox <=54 - // Return a confounding non-pixel value or feign ignorance, as appropriate. - if ( rnumnonpx.test( val ) ) { - if ( !extra ) { - return val; - } - val = "auto"; - } - - - // Support: IE 9 - 11 only - // Use offsetWidth/offsetHeight for when box sizing is unreliable. - // In those cases, the computed value can be trusted to be border-box. - if ( ( !support.boxSizingReliable() && isBorderBox || - - // Support: IE 10 - 11+, Edge 15 - 18+ - // IE/Edge misreport `getComputedStyle` of table rows with width/height - // set in CSS while `offset*` properties report correct values. - // Interestingly, in some cases IE 9 doesn't suffer from this issue. - !support.reliableTrDimensions() && nodeName( elem, "tr" ) || - - // Fall back to offsetWidth/offsetHeight when value is "auto" - // This happens for inline elements with no explicit setting (gh-3571) - val === "auto" || - - // Support: Android <=4.1 - 4.3 only - // Also use offsetWidth/offsetHeight for misreported inline dimensions (gh-3602) - !parseFloat( val ) && jQuery.css( elem, "display", false, styles ) === "inline" ) && - - // Make sure the element is visible & connected - elem.getClientRects().length ) { - - isBorderBox = jQuery.css( elem, "boxSizing", false, styles ) === "border-box"; - - // Where available, offsetWidth/offsetHeight approximate border box dimensions. - // Where not available (e.g., SVG), assume unreliable box-sizing and interpret the - // retrieved value as a content box dimension. - valueIsBorderBox = offsetProp in elem; - if ( valueIsBorderBox ) { - val = elem[ offsetProp ]; - } - } - - // Normalize "" and auto - val = parseFloat( val ) || 0; - - // Adjust for the element's box model - return ( val + - boxModelAdjustment( - elem, - dimension, - extra || ( isBorderBox ? "border" : "content" ), - valueIsBorderBox, - styles, - - // Provide the current computed size to request scroll gutter calculation (gh-3589) - val - ) - ) + "px"; -} - -jQuery.extend( { - - // Add in style property hooks for overriding the default - // behavior of getting and setting a style property - cssHooks: { - opacity: { - get: function( elem, computed ) { - if ( computed ) { - - // We should always get a number back from opacity - var ret = curCSS( elem, "opacity" ); - return ret === "" ? "1" : ret; - } - } - } - }, - - // Don't automatically add "px" to these possibly-unitless properties - cssNumber: { - "animationIterationCount": true, - "columnCount": true, - "fillOpacity": true, - "flexGrow": true, - "flexShrink": true, - "fontWeight": true, - "gridArea": true, - "gridColumn": true, - "gridColumnEnd": true, - "gridColumnStart": true, - "gridRow": true, - "gridRowEnd": true, - "gridRowStart": true, - "lineHeight": true, - "opacity": true, - "order": true, - "orphans": true, - "widows": true, - "zIndex": true, - "zoom": true - }, - - // Add in properties whose names you wish to fix before - // setting or getting the value - cssProps: {}, - - // Get and set the style property on a DOM Node - style: function( elem, name, value, extra ) { - - // Don't set styles on text and comment nodes - if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) { - return; - } - - // Make sure that we're working with the right name - var ret, type, hooks, - origName = camelCase( name ), - isCustomProp = rcustomProp.test( name ), - style = elem.style; - - // Make sure that we're working with the right name. We don't - // want to query the value if it is a CSS custom property - // since they are user-defined. - if ( !isCustomProp ) { - name = finalPropName( origName ); - } - - // Gets hook for the prefixed version, then unprefixed version - hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ]; - - // Check if we're setting a value - if ( value !== undefined ) { - type = typeof value; - - // Convert "+=" or "-=" to relative numbers (#7345) - if ( type === "string" && ( ret = rcssNum.exec( value ) ) && ret[ 1 ] ) { - value = adjustCSS( elem, name, ret ); - - // Fixes bug #9237 - type = "number"; - } - - // Make sure that null and NaN values aren't set (#7116) - if ( value == null || value !== value ) { - return; - } - - // If a number was passed in, add the unit (except for certain CSS properties) - // The isCustomProp check can be removed in jQuery 4.0 when we only auto-append - // "px" to a few hardcoded values. - if ( type === "number" && !isCustomProp ) { - value += ret && ret[ 3 ] || ( jQuery.cssNumber[ origName ] ? "" : "px" ); - } - - // background-* props affect original clone's values - if ( !support.clearCloneStyle && value === "" && name.indexOf( "background" ) === 0 ) { - style[ name ] = "inherit"; - } - - // If a hook was provided, use that value, otherwise just set the specified value - if ( !hooks || !( "set" in hooks ) || - ( value = hooks.set( elem, value, extra ) ) !== undefined ) { - - if ( isCustomProp ) { - style.setProperty( name, value ); - } else { - style[ name ] = value; - } - } - - } else { - - // If a hook was provided get the non-computed value from there - if ( hooks && "get" in hooks && - ( ret = hooks.get( elem, false, extra ) ) !== undefined ) { - - return ret; - } - - // Otherwise just get the value from the style object - return style[ name ]; - } - }, - - css: function( elem, name, extra, styles ) { - var val, num, hooks, - origName = camelCase( name ), - isCustomProp = rcustomProp.test( name ); - - // Make sure that we're working with the right name. We don't - // want to modify the value if it is a CSS custom property - // since they are user-defined. - if ( !isCustomProp ) { - name = finalPropName( origName ); - } - - // Try prefixed name followed by the unprefixed name - hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ]; - - // If a hook was provided get the computed value from there - if ( hooks && "get" in hooks ) { - val = hooks.get( elem, true, extra ); - } - - // Otherwise, if a way to get the computed value exists, use that - if ( val === undefined ) { - val = curCSS( elem, name, styles ); - } - - // Convert "normal" to computed value - if ( val === "normal" && name in cssNormalTransform ) { - val = cssNormalTransform[ name ]; - } - - // Make numeric if forced or a qualifier was provided and val looks numeric - if ( extra === "" || extra ) { - num = parseFloat( val ); - return extra === true || isFinite( num ) ? num || 0 : val; - } - - return val; - } -} ); - -jQuery.each( [ "height", "width" ], function( _i, dimension ) { - jQuery.cssHooks[ dimension ] = { - get: function( elem, computed, extra ) { - if ( computed ) { - - // Certain elements can have dimension info if we invisibly show them - // but it must have a current display style that would benefit - return rdisplayswap.test( jQuery.css( elem, "display" ) ) && - - // Support: Safari 8+ - // Table columns in Safari have non-zero offsetWidth & zero - // getBoundingClientRect().width unless display is changed. - // Support: IE <=11 only - // Running getBoundingClientRect on a disconnected node - // in IE throws an error. - ( !elem.getClientRects().length || !elem.getBoundingClientRect().width ) ? - swap( elem, cssShow, function() { - return getWidthOrHeight( elem, dimension, extra ); - } ) : - getWidthOrHeight( elem, dimension, extra ); - } - }, - - set: function( elem, value, extra ) { - var matches, - styles = getStyles( elem ), - - // Only read styles.position if the test has a chance to fail - // to avoid forcing a reflow. - scrollboxSizeBuggy = !support.scrollboxSize() && - styles.position === "absolute", - - // To avoid forcing a reflow, only fetch boxSizing if we need it (gh-3991) - boxSizingNeeded = scrollboxSizeBuggy || extra, - isBorderBox = boxSizingNeeded && - jQuery.css( elem, "boxSizing", false, styles ) === "border-box", - subtract = extra ? - boxModelAdjustment( - elem, - dimension, - extra, - isBorderBox, - styles - ) : - 0; - - // Account for unreliable border-box dimensions by comparing offset* to computed and - // faking a content-box to get border and padding (gh-3699) - if ( isBorderBox && scrollboxSizeBuggy ) { - subtract -= Math.ceil( - elem[ "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ) ] - - parseFloat( styles[ dimension ] ) - - boxModelAdjustment( elem, dimension, "border", false, styles ) - - 0.5 - ); - } - - // Convert to pixels if value adjustment is needed - if ( subtract && ( matches = rcssNum.exec( value ) ) && - ( matches[ 3 ] || "px" ) !== "px" ) { - - elem.style[ dimension ] = value; - value = jQuery.css( elem, dimension ); - } - - return setPositiveNumber( elem, value, subtract ); - } - }; -} ); - -jQuery.cssHooks.marginLeft = addGetHookIf( support.reliableMarginLeft, - function( elem, computed ) { - if ( computed ) { - return ( parseFloat( curCSS( elem, "marginLeft" ) ) || - elem.getBoundingClientRect().left - - swap( elem, { marginLeft: 0 }, function() { - return elem.getBoundingClientRect().left; - } ) - ) + "px"; - } - } -); - -// These hooks are used by animate to expand properties -jQuery.each( { - margin: "", - padding: "", - border: "Width" -}, function( prefix, suffix ) { - jQuery.cssHooks[ prefix + suffix ] = { - expand: function( value ) { - var i = 0, - expanded = {}, - - // Assumes a single number if not a string - parts = typeof value === "string" ? value.split( " " ) : [ value ]; - - for ( ; i < 4; i++ ) { - expanded[ prefix + cssExpand[ i ] + suffix ] = - parts[ i ] || parts[ i - 2 ] || parts[ 0 ]; - } - - return expanded; - } - }; - - if ( prefix !== "margin" ) { - jQuery.cssHooks[ prefix + suffix ].set = setPositiveNumber; - } -} ); - -jQuery.fn.extend( { - css: function( name, value ) { - return access( this, function( elem, name, value ) { - var styles, len, - map = {}, - i = 0; - - if ( Array.isArray( name ) ) { - styles = getStyles( elem ); - len = name.length; - - for ( ; i < len; i++ ) { - map[ name[ i ] ] = jQuery.css( elem, name[ i ], false, styles ); - } - - return map; - } - - return value !== undefined ? - jQuery.style( elem, name, value ) : - jQuery.css( elem, name ); - }, name, value, arguments.length > 1 ); - } -} ); - - -function Tween( elem, options, prop, end, easing ) { - return new Tween.prototype.init( elem, options, prop, end, easing ); -} -jQuery.Tween = Tween; - -Tween.prototype = { - constructor: Tween, - init: function( elem, options, prop, end, easing, unit ) { - this.elem = elem; - this.prop = prop; - this.easing = easing || jQuery.easing._default; - this.options = options; - this.start = this.now = this.cur(); - this.end = end; - this.unit = unit || ( jQuery.cssNumber[ prop ] ? "" : "px" ); - }, - cur: function() { - var hooks = Tween.propHooks[ this.prop ]; - - return hooks && hooks.get ? - hooks.get( this ) : - Tween.propHooks._default.get( this ); - }, - run: function( percent ) { - var eased, - hooks = Tween.propHooks[ this.prop ]; - - if ( this.options.duration ) { - this.pos = eased = jQuery.easing[ this.easing ]( - percent, this.options.duration * percent, 0, 1, this.options.duration - ); - } else { - this.pos = eased = percent; - } - this.now = ( this.end - this.start ) * eased + this.start; - - if ( this.options.step ) { - this.options.step.call( this.elem, this.now, this ); - } - - if ( hooks && hooks.set ) { - hooks.set( this ); - } else { - Tween.propHooks._default.set( this ); - } - return this; - } -}; - -Tween.prototype.init.prototype = Tween.prototype; - -Tween.propHooks = { - _default: { - get: function( tween ) { - var result; - - // Use a property on the element directly when it is not a DOM element, - // or when there is no matching style property that exists. - if ( tween.elem.nodeType !== 1 || - tween.elem[ tween.prop ] != null && tween.elem.style[ tween.prop ] == null ) { - return tween.elem[ tween.prop ]; - } - - // Passing an empty string as a 3rd parameter to .css will automatically - // attempt a parseFloat and fallback to a string if the parse fails. - // Simple values such as "10px" are parsed to Float; - // complex values such as "rotate(1rad)" are returned as-is. - result = jQuery.css( tween.elem, tween.prop, "" ); - - // Empty strings, null, undefined and "auto" are converted to 0. - return !result || result === "auto" ? 0 : result; - }, - set: function( tween ) { - - // Use step hook for back compat. - // Use cssHook if its there. - // Use .style if available and use plain properties where available. - if ( jQuery.fx.step[ tween.prop ] ) { - jQuery.fx.step[ tween.prop ]( tween ); - } else if ( tween.elem.nodeType === 1 && ( - jQuery.cssHooks[ tween.prop ] || - tween.elem.style[ finalPropName( tween.prop ) ] != null ) ) { - jQuery.style( tween.elem, tween.prop, tween.now + tween.unit ); - } else { - tween.elem[ tween.prop ] = tween.now; - } - } - } -}; - -// Support: IE <=9 only -// Panic based approach to setting things on disconnected nodes -Tween.propHooks.scrollTop = Tween.propHooks.scrollLeft = { - set: function( tween ) { - if ( tween.elem.nodeType && tween.elem.parentNode ) { - tween.elem[ tween.prop ] = tween.now; - } - } -}; - -jQuery.easing = { - linear: function( p ) { - return p; - }, - swing: function( p ) { - return 0.5 - Math.cos( p * Math.PI ) / 2; - }, - _default: "swing" -}; - -jQuery.fx = Tween.prototype.init; - -// Back compat <1.8 extension point -jQuery.fx.step = {}; - - - - -var - fxNow, inProgress, - rfxtypes = /^(?:toggle|show|hide)$/, - rrun = /queueHooks$/; - -function schedule() { - if ( inProgress ) { - if ( document.hidden === false && window.requestAnimationFrame ) { - window.requestAnimationFrame( schedule ); - } else { - window.setTimeout( schedule, jQuery.fx.interval ); - } - - jQuery.fx.tick(); - } -} - -// Animations created synchronously will run synchronously -function createFxNow() { - window.setTimeout( function() { - fxNow = undefined; - } ); - return ( fxNow = Date.now() ); -} - -// Generate parameters to create a standard animation -function genFx( type, includeWidth ) { - var which, - i = 0, - attrs = { height: type }; - - // If we include width, step value is 1 to do all cssExpand values, - // otherwise step value is 2 to skip over Left and Right - includeWidth = includeWidth ? 1 : 0; - for ( ; i < 4; i += 2 - includeWidth ) { - which = cssExpand[ i ]; - attrs[ "margin" + which ] = attrs[ "padding" + which ] = type; - } - - if ( includeWidth ) { - attrs.opacity = attrs.width = type; - } - - return attrs; -} - -function createTween( value, prop, animation ) { - var tween, - collection = ( Animation.tweeners[ prop ] || [] ).concat( Animation.tweeners[ "*" ] ), - index = 0, - length = collection.length; - for ( ; index < length; index++ ) { - if ( ( tween = collection[ index ].call( animation, prop, value ) ) ) { - - // We're done with this property - return tween; - } - } -} - -function defaultPrefilter( elem, props, opts ) { - var prop, value, toggle, hooks, oldfire, propTween, restoreDisplay, display, - isBox = "width" in props || "height" in props, - anim = this, - orig = {}, - style = elem.style, - hidden = elem.nodeType && isHiddenWithinTree( elem ), - dataShow = dataPriv.get( elem, "fxshow" ); - - // Queue-skipping animations hijack the fx hooks - if ( !opts.queue ) { - hooks = jQuery._queueHooks( elem, "fx" ); - if ( hooks.unqueued == null ) { - hooks.unqueued = 0; - oldfire = hooks.empty.fire; - hooks.empty.fire = function() { - if ( !hooks.unqueued ) { - oldfire(); - } - }; - } - hooks.unqueued++; - - anim.always( function() { - - // Ensure the complete handler is called before this completes - anim.always( function() { - hooks.unqueued--; - if ( !jQuery.queue( elem, "fx" ).length ) { - hooks.empty.fire(); - } - } ); - } ); - } - - // Detect show/hide animations - for ( prop in props ) { - value = props[ prop ]; - if ( rfxtypes.test( value ) ) { - delete props[ prop ]; - toggle = toggle || value === "toggle"; - if ( value === ( hidden ? "hide" : "show" ) ) { - - // Pretend to be hidden if this is a "show" and - // there is still data from a stopped show/hide - if ( value === "show" && dataShow && dataShow[ prop ] !== undefined ) { - hidden = true; - - // Ignore all other no-op show/hide data - } else { - continue; - } - } - orig[ prop ] = dataShow && dataShow[ prop ] || jQuery.style( elem, prop ); - } - } - - // Bail out if this is a no-op like .hide().hide() - propTween = !jQuery.isEmptyObject( props ); - if ( !propTween && jQuery.isEmptyObject( orig ) ) { - return; - } - - // Restrict "overflow" and "display" styles during box animations - if ( isBox && elem.nodeType === 1 ) { - - // Support: IE <=9 - 11, Edge 12 - 15 - // Record all 3 overflow attributes because IE does not infer the shorthand - // from identically-valued overflowX and overflowY and Edge just mirrors - // the overflowX value there. - opts.overflow = [ style.overflow, style.overflowX, style.overflowY ]; - - // Identify a display type, preferring old show/hide data over the CSS cascade - restoreDisplay = dataShow && dataShow.display; - if ( restoreDisplay == null ) { - restoreDisplay = dataPriv.get( elem, "display" ); - } - display = jQuery.css( elem, "display" ); - if ( display === "none" ) { - if ( restoreDisplay ) { - display = restoreDisplay; - } else { - - // Get nonempty value(s) by temporarily forcing visibility - showHide( [ elem ], true ); - restoreDisplay = elem.style.display || restoreDisplay; - display = jQuery.css( elem, "display" ); - showHide( [ elem ] ); - } - } - - // Animate inline elements as inline-block - if ( display === "inline" || display === "inline-block" && restoreDisplay != null ) { - if ( jQuery.css( elem, "float" ) === "none" ) { - - // Restore the original display value at the end of pure show/hide animations - if ( !propTween ) { - anim.done( function() { - style.display = restoreDisplay; - } ); - if ( restoreDisplay == null ) { - display = style.display; - restoreDisplay = display === "none" ? "" : display; - } - } - style.display = "inline-block"; - } - } - } - - if ( opts.overflow ) { - style.overflow = "hidden"; - anim.always( function() { - style.overflow = opts.overflow[ 0 ]; - style.overflowX = opts.overflow[ 1 ]; - style.overflowY = opts.overflow[ 2 ]; - } ); - } - - // Implement show/hide animations - propTween = false; - for ( prop in orig ) { - - // General show/hide setup for this element animation - if ( !propTween ) { - if ( dataShow ) { - if ( "hidden" in dataShow ) { - hidden = dataShow.hidden; - } - } else { - dataShow = dataPriv.access( elem, "fxshow", { display: restoreDisplay } ); - } - - // Store hidden/visible for toggle so `.stop().toggle()` "reverses" - if ( toggle ) { - dataShow.hidden = !hidden; - } - - // Show elements before animating them - if ( hidden ) { - showHide( [ elem ], true ); - } - - /* eslint-disable no-loop-func */ - - anim.done( function() { - - /* eslint-enable no-loop-func */ - - // The final step of a "hide" animation is actually hiding the element - if ( !hidden ) { - showHide( [ elem ] ); - } - dataPriv.remove( elem, "fxshow" ); - for ( prop in orig ) { - jQuery.style( elem, prop, orig[ prop ] ); - } - } ); - } - - // Per-property setup - propTween = createTween( hidden ? dataShow[ prop ] : 0, prop, anim ); - if ( !( prop in dataShow ) ) { - dataShow[ prop ] = propTween.start; - if ( hidden ) { - propTween.end = propTween.start; - propTween.start = 0; - } - } - } -} - -function propFilter( props, specialEasing ) { - var index, name, easing, value, hooks; - - // camelCase, specialEasing and expand cssHook pass - for ( index in props ) { - name = camelCase( index ); - easing = specialEasing[ name ]; - value = props[ index ]; - if ( Array.isArray( value ) ) { - easing = value[ 1 ]; - value = props[ index ] = value[ 0 ]; - } - - if ( index !== name ) { - props[ name ] = value; - delete props[ index ]; - } - - hooks = jQuery.cssHooks[ name ]; - if ( hooks && "expand" in hooks ) { - value = hooks.expand( value ); - delete props[ name ]; - - // Not quite $.extend, this won't overwrite existing keys. - // Reusing 'index' because we have the correct "name" - for ( index in value ) { - if ( !( index in props ) ) { - props[ index ] = value[ index ]; - specialEasing[ index ] = easing; - } - } - } else { - specialEasing[ name ] = easing; - } - } -} - -function Animation( elem, properties, options ) { - var result, - stopped, - index = 0, - length = Animation.prefilters.length, - deferred = jQuery.Deferred().always( function() { - - // Don't match elem in the :animated selector - delete tick.elem; - } ), - tick = function() { - if ( stopped ) { - return false; - } - var currentTime = fxNow || createFxNow(), - remaining = Math.max( 0, animation.startTime + animation.duration - currentTime ), - - // Support: Android 2.3 only - // Archaic crash bug won't allow us to use `1 - ( 0.5 || 0 )` (#12497) - temp = remaining / animation.duration || 0, - percent = 1 - temp, - index = 0, - length = animation.tweens.length; - - for ( ; index < length; index++ ) { - animation.tweens[ index ].run( percent ); - } - - deferred.notifyWith( elem, [ animation, percent, remaining ] ); - - // If there's more to do, yield - if ( percent < 1 && length ) { - return remaining; - } - - // If this was an empty animation, synthesize a final progress notification - if ( !length ) { - deferred.notifyWith( elem, [ animation, 1, 0 ] ); - } - - // Resolve the animation and report its conclusion - deferred.resolveWith( elem, [ animation ] ); - return false; - }, - animation = deferred.promise( { - elem: elem, - props: jQuery.extend( {}, properties ), - opts: jQuery.extend( true, { - specialEasing: {}, - easing: jQuery.easing._default - }, options ), - originalProperties: properties, - originalOptions: options, - startTime: fxNow || createFxNow(), - duration: options.duration, - tweens: [], - createTween: function( prop, end ) { - var tween = jQuery.Tween( elem, animation.opts, prop, end, - animation.opts.specialEasing[ prop ] || animation.opts.easing ); - animation.tweens.push( tween ); - return tween; - }, - stop: function( gotoEnd ) { - var index = 0, - - // If we are going to the end, we want to run all the tweens - // otherwise we skip this part - length = gotoEnd ? animation.tweens.length : 0; - if ( stopped ) { - return this; - } - stopped = true; - for ( ; index < length; index++ ) { - animation.tweens[ index ].run( 1 ); - } - - // Resolve when we played the last frame; otherwise, reject - if ( gotoEnd ) { - deferred.notifyWith( elem, [ animation, 1, 0 ] ); - deferred.resolveWith( elem, [ animation, gotoEnd ] ); - } else { - deferred.rejectWith( elem, [ animation, gotoEnd ] ); - } - return this; - } - } ), - props = animation.props; - - propFilter( props, animation.opts.specialEasing ); - - for ( ; index < length; index++ ) { - result = Animation.prefilters[ index ].call( animation, elem, props, animation.opts ); - if ( result ) { - if ( isFunction( result.stop ) ) { - jQuery._queueHooks( animation.elem, animation.opts.queue ).stop = - result.stop.bind( result ); - } - return result; - } - } - - jQuery.map( props, createTween, animation ); - - if ( isFunction( animation.opts.start ) ) { - animation.opts.start.call( elem, animation ); - } - - // Attach callbacks from options - animation - .progress( animation.opts.progress ) - .done( animation.opts.done, animation.opts.complete ) - .fail( animation.opts.fail ) - .always( animation.opts.always ); - - jQuery.fx.timer( - jQuery.extend( tick, { - elem: elem, - anim: animation, - queue: animation.opts.queue - } ) - ); - - return animation; -} - -jQuery.Animation = jQuery.extend( Animation, { - - tweeners: { - "*": [ function( prop, value ) { - var tween = this.createTween( prop, value ); - adjustCSS( tween.elem, prop, rcssNum.exec( value ), tween ); - return tween; - } ] - }, - - tweener: function( props, callback ) { - if ( isFunction( props ) ) { - callback = props; - props = [ "*" ]; - } else { - props = props.match( rnothtmlwhite ); - } - - var prop, - index = 0, - length = props.length; - - for ( ; index < length; index++ ) { - prop = props[ index ]; - Animation.tweeners[ prop ] = Animation.tweeners[ prop ] || []; - Animation.tweeners[ prop ].unshift( callback ); - } - }, - - prefilters: [ defaultPrefilter ], - - prefilter: function( callback, prepend ) { - if ( prepend ) { - Animation.prefilters.unshift( callback ); - } else { - Animation.prefilters.push( callback ); - } - } -} ); - -jQuery.speed = function( speed, easing, fn ) { - var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : { - complete: fn || !fn && easing || - isFunction( speed ) && speed, - duration: speed, - easing: fn && easing || easing && !isFunction( easing ) && easing - }; - - // Go to the end state if fx are off - if ( jQuery.fx.off ) { - opt.duration = 0; - - } else { - if ( typeof opt.duration !== "number" ) { - if ( opt.duration in jQuery.fx.speeds ) { - opt.duration = jQuery.fx.speeds[ opt.duration ]; - - } else { - opt.duration = jQuery.fx.speeds._default; - } - } - } - - // Normalize opt.queue - true/undefined/null -> "fx" - if ( opt.queue == null || opt.queue === true ) { - opt.queue = "fx"; - } - - // Queueing - opt.old = opt.complete; - - opt.complete = function() { - if ( isFunction( opt.old ) ) { - opt.old.call( this ); - } - - if ( opt.queue ) { - jQuery.dequeue( this, opt.queue ); - } - }; - - return opt; -}; - -jQuery.fn.extend( { - fadeTo: function( speed, to, easing, callback ) { - - // Show any hidden elements after setting opacity to 0 - return this.filter( isHiddenWithinTree ).css( "opacity", 0 ).show() - - // Animate to the value specified - .end().animate( { opacity: to }, speed, easing, callback ); - }, - animate: function( prop, speed, easing, callback ) { - var empty = jQuery.isEmptyObject( prop ), - optall = jQuery.speed( speed, easing, callback ), - doAnimation = function() { - - // Operate on a copy of prop so per-property easing won't be lost - var anim = Animation( this, jQuery.extend( {}, prop ), optall ); - - // Empty animations, or finishing resolves immediately - if ( empty || dataPriv.get( this, "finish" ) ) { - anim.stop( true ); - } - }; - - doAnimation.finish = doAnimation; - - return empty || optall.queue === false ? - this.each( doAnimation ) : - this.queue( optall.queue, doAnimation ); - }, - stop: function( type, clearQueue, gotoEnd ) { - var stopQueue = function( hooks ) { - var stop = hooks.stop; - delete hooks.stop; - stop( gotoEnd ); - }; - - if ( typeof type !== "string" ) { - gotoEnd = clearQueue; - clearQueue = type; - type = undefined; - } - if ( clearQueue ) { - this.queue( type || "fx", [] ); - } - - return this.each( function() { - var dequeue = true, - index = type != null && type + "queueHooks", - timers = jQuery.timers, - data = dataPriv.get( this ); - - if ( index ) { - if ( data[ index ] && data[ index ].stop ) { - stopQueue( data[ index ] ); - } - } else { - for ( index in data ) { - if ( data[ index ] && data[ index ].stop && rrun.test( index ) ) { - stopQueue( data[ index ] ); - } - } - } - - for ( index = timers.length; index--; ) { - if ( timers[ index ].elem === this && - ( type == null || timers[ index ].queue === type ) ) { - - timers[ index ].anim.stop( gotoEnd ); - dequeue = false; - timers.splice( index, 1 ); - } - } - - // Start the next in the queue if the last step wasn't forced. - // Timers currently will call their complete callbacks, which - // will dequeue but only if they were gotoEnd. - if ( dequeue || !gotoEnd ) { - jQuery.dequeue( this, type ); - } - } ); - }, - finish: function( type ) { - if ( type !== false ) { - type = type || "fx"; - } - return this.each( function() { - var index, - data = dataPriv.get( this ), - queue = data[ type + "queue" ], - hooks = data[ type + "queueHooks" ], - timers = jQuery.timers, - length = queue ? queue.length : 0; - - // Enable finishing flag on private data - data.finish = true; - - // Empty the queue first - jQuery.queue( this, type, [] ); - - if ( hooks && hooks.stop ) { - hooks.stop.call( this, true ); - } - - // Look for any active animations, and finish them - for ( index = timers.length; index--; ) { - if ( timers[ index ].elem === this && timers[ index ].queue === type ) { - timers[ index ].anim.stop( true ); - timers.splice( index, 1 ); - } - } - - // Look for any animations in the old queue and finish them - for ( index = 0; index < length; index++ ) { - if ( queue[ index ] && queue[ index ].finish ) { - queue[ index ].finish.call( this ); - } - } - - // Turn off finishing flag - delete data.finish; - } ); - } -} ); - -jQuery.each( [ "toggle", "show", "hide" ], function( _i, name ) { - var cssFn = jQuery.fn[ name ]; - jQuery.fn[ name ] = function( speed, easing, callback ) { - return speed == null || typeof speed === "boolean" ? - cssFn.apply( this, arguments ) : - this.animate( genFx( name, true ), speed, easing, callback ); - }; -} ); - -// Generate shortcuts for custom animations -jQuery.each( { - slideDown: genFx( "show" ), - slideUp: genFx( "hide" ), - slideToggle: genFx( "toggle" ), - fadeIn: { opacity: "show" }, - fadeOut: { opacity: "hide" }, - fadeToggle: { opacity: "toggle" } -}, function( name, props ) { - jQuery.fn[ name ] = function( speed, easing, callback ) { - return this.animate( props, speed, easing, callback ); - }; -} ); - -jQuery.timers = []; -jQuery.fx.tick = function() { - var timer, - i = 0, - timers = jQuery.timers; - - fxNow = Date.now(); - - for ( ; i < timers.length; i++ ) { - timer = timers[ i ]; - - // Run the timer and safely remove it when done (allowing for external removal) - if ( !timer() && timers[ i ] === timer ) { - timers.splice( i--, 1 ); - } - } - - if ( !timers.length ) { - jQuery.fx.stop(); - } - fxNow = undefined; -}; - -jQuery.fx.timer = function( timer ) { - jQuery.timers.push( timer ); - jQuery.fx.start(); -}; - -jQuery.fx.interval = 13; -jQuery.fx.start = function() { - if ( inProgress ) { - return; - } - - inProgress = true; - schedule(); -}; - -jQuery.fx.stop = function() { - inProgress = null; -}; - -jQuery.fx.speeds = { - slow: 600, - fast: 200, - - // Default speed - _default: 400 -}; - - -// Based off of the plugin by Clint Helfers, with permission. -// https://web.archive.org/web/20100324014747/http://blindsignals.com/index.php/2009/07/jquery-delay/ -jQuery.fn.delay = function( time, type ) { - time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time; - type = type || "fx"; - - return this.queue( type, function( next, hooks ) { - var timeout = window.setTimeout( next, time ); - hooks.stop = function() { - window.clearTimeout( timeout ); - }; - } ); -}; - - -( function() { - var input = document.createElement( "input" ), - select = document.createElement( "select" ), - opt = select.appendChild( document.createElement( "option" ) ); - - input.type = "checkbox"; - - // Support: Android <=4.3 only - // Default value for a checkbox should be "on" - support.checkOn = input.value !== ""; - - // Support: IE <=11 only - // Must access selectedIndex to make default options select - support.optSelected = opt.selected; - - // Support: IE <=11 only - // An input loses its value after becoming a radio - input = document.createElement( "input" ); - input.value = "t"; - input.type = "radio"; - support.radioValue = input.value === "t"; -} )(); - - -var boolHook, - attrHandle = jQuery.expr.attrHandle; - -jQuery.fn.extend( { - attr: function( name, value ) { - return access( this, jQuery.attr, name, value, arguments.length > 1 ); - }, - - removeAttr: function( name ) { - return this.each( function() { - jQuery.removeAttr( this, name ); - } ); - } -} ); - -jQuery.extend( { - attr: function( elem, name, value ) { - var ret, hooks, - nType = elem.nodeType; - - // Don't get/set attributes on text, comment and attribute nodes - if ( nType === 3 || nType === 8 || nType === 2 ) { - return; - } - - // Fallback to prop when attributes are not supported - if ( typeof elem.getAttribute === "undefined" ) { - return jQuery.prop( elem, name, value ); - } - - // Attribute hooks are determined by the lowercase version - // Grab necessary hook if one is defined - if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) { - hooks = jQuery.attrHooks[ name.toLowerCase() ] || - ( jQuery.expr.match.bool.test( name ) ? boolHook : undefined ); - } - - if ( value !== undefined ) { - if ( value === null ) { - jQuery.removeAttr( elem, name ); - return; - } - - if ( hooks && "set" in hooks && - ( ret = hooks.set( elem, value, name ) ) !== undefined ) { - return ret; - } - - elem.setAttribute( name, value + "" ); - return value; - } - - if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) { - return ret; - } - - ret = jQuery.find.attr( elem, name ); - - // Non-existent attributes return null, we normalize to undefined - return ret == null ? undefined : ret; - }, - - attrHooks: { - type: { - set: function( elem, value ) { - if ( !support.radioValue && value === "radio" && - nodeName( elem, "input" ) ) { - var val = elem.value; - elem.setAttribute( "type", value ); - if ( val ) { - elem.value = val; - } - return value; - } - } - } - }, - - removeAttr: function( elem, value ) { - var name, - i = 0, - - // Attribute names can contain non-HTML whitespace characters - // https://html.spec.whatwg.org/multipage/syntax.html#attributes-2 - attrNames = value && value.match( rnothtmlwhite ); - - if ( attrNames && elem.nodeType === 1 ) { - while ( ( name = attrNames[ i++ ] ) ) { - elem.removeAttribute( name ); - } - } - } -} ); - -// Hooks for boolean attributes -boolHook = { - set: function( elem, value, name ) { - if ( value === false ) { - - // Remove boolean attributes when set to false - jQuery.removeAttr( elem, name ); - } else { - elem.setAttribute( name, name ); - } - return name; - } -}; - -jQuery.each( jQuery.expr.match.bool.source.match( /\w+/g ), function( _i, name ) { - var getter = attrHandle[ name ] || jQuery.find.attr; - - attrHandle[ name ] = function( elem, name, isXML ) { - var ret, handle, - lowercaseName = name.toLowerCase(); - - if ( !isXML ) { - - // Avoid an infinite loop by temporarily removing this function from the getter - handle = attrHandle[ lowercaseName ]; - attrHandle[ lowercaseName ] = ret; - ret = getter( elem, name, isXML ) != null ? - lowercaseName : - null; - attrHandle[ lowercaseName ] = handle; - } - return ret; - }; -} ); - - - - -var rfocusable = /^(?:input|select|textarea|button)$/i, - rclickable = /^(?:a|area)$/i; - -jQuery.fn.extend( { - prop: function( name, value ) { - return access( this, jQuery.prop, name, value, arguments.length > 1 ); - }, - - removeProp: function( name ) { - return this.each( function() { - delete this[ jQuery.propFix[ name ] || name ]; - } ); - } -} ); - -jQuery.extend( { - prop: function( elem, name, value ) { - var ret, hooks, - nType = elem.nodeType; - - // Don't get/set properties on text, comment and attribute nodes - if ( nType === 3 || nType === 8 || nType === 2 ) { - return; - } - - if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) { - - // Fix name and attach hooks - name = jQuery.propFix[ name ] || name; - hooks = jQuery.propHooks[ name ]; - } - - if ( value !== undefined ) { - if ( hooks && "set" in hooks && - ( ret = hooks.set( elem, value, name ) ) !== undefined ) { - return ret; - } - - return ( elem[ name ] = value ); - } - - if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) { - return ret; - } - - return elem[ name ]; - }, - - propHooks: { - tabIndex: { - get: function( elem ) { - - // Support: IE <=9 - 11 only - // elem.tabIndex doesn't always return the - // correct value when it hasn't been explicitly set - // https://web.archive.org/web/20141116233347/http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/ - // Use proper attribute retrieval(#12072) - var tabindex = jQuery.find.attr( elem, "tabindex" ); - - if ( tabindex ) { - return parseInt( tabindex, 10 ); - } - - if ( - rfocusable.test( elem.nodeName ) || - rclickable.test( elem.nodeName ) && - elem.href - ) { - return 0; - } - - return -1; - } - } - }, - - propFix: { - "for": "htmlFor", - "class": "className" - } -} ); - -// Support: IE <=11 only -// Accessing the selectedIndex property -// forces the browser to respect setting selected -// on the option -// The getter ensures a default option is selected -// when in an optgroup -// eslint rule "no-unused-expressions" is disabled for this code -// since it considers such accessions noop -if ( !support.optSelected ) { - jQuery.propHooks.selected = { - get: function( elem ) { - - /* eslint no-unused-expressions: "off" */ - - var parent = elem.parentNode; - if ( parent && parent.parentNode ) { - parent.parentNode.selectedIndex; - } - return null; - }, - set: function( elem ) { - - /* eslint no-unused-expressions: "off" */ - - var parent = elem.parentNode; - if ( parent ) { - parent.selectedIndex; - - if ( parent.parentNode ) { - parent.parentNode.selectedIndex; - } - } - } - }; -} - -jQuery.each( [ - "tabIndex", - "readOnly", - "maxLength", - "cellSpacing", - "cellPadding", - "rowSpan", - "colSpan", - "useMap", - "frameBorder", - "contentEditable" -], function() { - jQuery.propFix[ this.toLowerCase() ] = this; -} ); - - - - - // Strip and collapse whitespace according to HTML spec - // https://infra.spec.whatwg.org/#strip-and-collapse-ascii-whitespace - function stripAndCollapse( value ) { - var tokens = value.match( rnothtmlwhite ) || []; - return tokens.join( " " ); - } - - -function getClass( elem ) { - return elem.getAttribute && elem.getAttribute( "class" ) || ""; -} - -function classesToArray( value ) { - if ( Array.isArray( value ) ) { - return value; - } - if ( typeof value === "string" ) { - return value.match( rnothtmlwhite ) || []; - } - return []; -} - -jQuery.fn.extend( { - addClass: function( value ) { - var classes, elem, cur, curValue, clazz, j, finalValue, - i = 0; - - if ( isFunction( value ) ) { - return this.each( function( j ) { - jQuery( this ).addClass( value.call( this, j, getClass( this ) ) ); - } ); - } - - classes = classesToArray( value ); - - if ( classes.length ) { - while ( ( elem = this[ i++ ] ) ) { - curValue = getClass( elem ); - cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " ); - - if ( cur ) { - j = 0; - while ( ( clazz = classes[ j++ ] ) ) { - if ( cur.indexOf( " " + clazz + " " ) < 0 ) { - cur += clazz + " "; - } - } - - // Only assign if different to avoid unneeded rendering. - finalValue = stripAndCollapse( cur ); - if ( curValue !== finalValue ) { - elem.setAttribute( "class", finalValue ); - } - } - } - } - - return this; - }, - - removeClass: function( value ) { - var classes, elem, cur, curValue, clazz, j, finalValue, - i = 0; - - if ( isFunction( value ) ) { - return this.each( function( j ) { - jQuery( this ).removeClass( value.call( this, j, getClass( this ) ) ); - } ); - } - - if ( !arguments.length ) { - return this.attr( "class", "" ); - } - - classes = classesToArray( value ); - - if ( classes.length ) { - while ( ( elem = this[ i++ ] ) ) { - curValue = getClass( elem ); - - // This expression is here for better compressibility (see addClass) - cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " ); - - if ( cur ) { - j = 0; - while ( ( clazz = classes[ j++ ] ) ) { - - // Remove *all* instances - while ( cur.indexOf( " " + clazz + " " ) > -1 ) { - cur = cur.replace( " " + clazz + " ", " " ); - } - } - - // Only assign if different to avoid unneeded rendering. - finalValue = stripAndCollapse( cur ); - if ( curValue !== finalValue ) { - elem.setAttribute( "class", finalValue ); - } - } - } - } - - return this; - }, - - toggleClass: function( value, stateVal ) { - var type = typeof value, - isValidValue = type === "string" || Array.isArray( value ); - - if ( typeof stateVal === "boolean" && isValidValue ) { - return stateVal ? this.addClass( value ) : this.removeClass( value ); - } - - if ( isFunction( value ) ) { - return this.each( function( i ) { - jQuery( this ).toggleClass( - value.call( this, i, getClass( this ), stateVal ), - stateVal - ); - } ); - } - - return this.each( function() { - var className, i, self, classNames; - - if ( isValidValue ) { - - // Toggle individual class names - i = 0; - self = jQuery( this ); - classNames = classesToArray( value ); - - while ( ( className = classNames[ i++ ] ) ) { - - // Check each className given, space separated list - if ( self.hasClass( className ) ) { - self.removeClass( className ); - } else { - self.addClass( className ); - } - } - - // Toggle whole class name - } else if ( value === undefined || type === "boolean" ) { - className = getClass( this ); - if ( className ) { - - // Store className if set - dataPriv.set( this, "__className__", className ); - } - - // If the element has a class name or if we're passed `false`, - // then remove the whole classname (if there was one, the above saved it). - // Otherwise bring back whatever was previously saved (if anything), - // falling back to the empty string if nothing was stored. - if ( this.setAttribute ) { - this.setAttribute( "class", - className || value === false ? - "" : - dataPriv.get( this, "__className__" ) || "" - ); - } - } - } ); - }, - - hasClass: function( selector ) { - var className, elem, - i = 0; - - className = " " + selector + " "; - while ( ( elem = this[ i++ ] ) ) { - if ( elem.nodeType === 1 && - ( " " + stripAndCollapse( getClass( elem ) ) + " " ).indexOf( className ) > -1 ) { - return true; - } - } - - return false; - } -} ); - - - - -var rreturn = /\r/g; - -jQuery.fn.extend( { - val: function( value ) { - var hooks, ret, valueIsFunction, - elem = this[ 0 ]; - - if ( !arguments.length ) { - if ( elem ) { - hooks = jQuery.valHooks[ elem.type ] || - jQuery.valHooks[ elem.nodeName.toLowerCase() ]; - - if ( hooks && - "get" in hooks && - ( ret = hooks.get( elem, "value" ) ) !== undefined - ) { - return ret; - } - - ret = elem.value; - - // Handle most common string cases - if ( typeof ret === "string" ) { - return ret.replace( rreturn, "" ); - } - - // Handle cases where value is null/undef or number - return ret == null ? "" : ret; - } - - return; - } - - valueIsFunction = isFunction( value ); - - return this.each( function( i ) { - var val; - - if ( this.nodeType !== 1 ) { - return; - } - - if ( valueIsFunction ) { - val = value.call( this, i, jQuery( this ).val() ); - } else { - val = value; - } - - // Treat null/undefined as ""; convert numbers to string - if ( val == null ) { - val = ""; - - } else if ( typeof val === "number" ) { - val += ""; - - } else if ( Array.isArray( val ) ) { - val = jQuery.map( val, function( value ) { - return value == null ? "" : value + ""; - } ); - } - - hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ]; - - // If set returns undefined, fall back to normal setting - if ( !hooks || !( "set" in hooks ) || hooks.set( this, val, "value" ) === undefined ) { - this.value = val; - } - } ); - } -} ); - -jQuery.extend( { - valHooks: { - option: { - get: function( elem ) { - - var val = jQuery.find.attr( elem, "value" ); - return val != null ? - val : - - // Support: IE <=10 - 11 only - // option.text throws exceptions (#14686, #14858) - // Strip and collapse whitespace - // https://html.spec.whatwg.org/#strip-and-collapse-whitespace - stripAndCollapse( jQuery.text( elem ) ); - } - }, - select: { - get: function( elem ) { - var value, option, i, - options = elem.options, - index = elem.selectedIndex, - one = elem.type === "select-one", - values = one ? null : [], - max = one ? index + 1 : options.length; - - if ( index < 0 ) { - i = max; - - } else { - i = one ? index : 0; - } - - // Loop through all the selected options - for ( ; i < max; i++ ) { - option = options[ i ]; - - // Support: IE <=9 only - // IE8-9 doesn't update selected after form reset (#2551) - if ( ( option.selected || i === index ) && - - // Don't return options that are disabled or in a disabled optgroup - !option.disabled && - ( !option.parentNode.disabled || - !nodeName( option.parentNode, "optgroup" ) ) ) { - - // Get the specific value for the option - value = jQuery( option ).val(); - - // We don't need an array for one selects - if ( one ) { - return value; - } - - // Multi-Selects return an array - values.push( value ); - } - } - - return values; - }, - - set: function( elem, value ) { - var optionSet, option, - options = elem.options, - values = jQuery.makeArray( value ), - i = options.length; - - while ( i-- ) { - option = options[ i ]; - - /* eslint-disable no-cond-assign */ - - if ( option.selected = - jQuery.inArray( jQuery.valHooks.option.get( option ), values ) > -1 - ) { - optionSet = true; - } - - /* eslint-enable no-cond-assign */ - } - - // Force browsers to behave consistently when non-matching value is set - if ( !optionSet ) { - elem.selectedIndex = -1; - } - return values; - } - } - } -} ); - -// Radios and checkboxes getter/setter -jQuery.each( [ "radio", "checkbox" ], function() { - jQuery.valHooks[ this ] = { - set: function( elem, value ) { - if ( Array.isArray( value ) ) { - return ( elem.checked = jQuery.inArray( jQuery( elem ).val(), value ) > -1 ); - } - } - }; - if ( !support.checkOn ) { - jQuery.valHooks[ this ].get = function( elem ) { - return elem.getAttribute( "value" ) === null ? "on" : elem.value; - }; - } -} ); - - - - -// Return jQuery for attributes-only inclusion - - -support.focusin = "onfocusin" in window; - - -var rfocusMorph = /^(?:focusinfocus|focusoutblur)$/, - stopPropagationCallback = function( e ) { - e.stopPropagation(); - }; - -jQuery.extend( jQuery.event, { - - trigger: function( event, data, elem, onlyHandlers ) { - - var i, cur, tmp, bubbleType, ontype, handle, special, lastElement, - eventPath = [ elem || document ], - type = hasOwn.call( event, "type" ) ? event.type : event, - namespaces = hasOwn.call( event, "namespace" ) ? event.namespace.split( "." ) : []; - - cur = lastElement = tmp = elem = elem || document; - - // Don't do events on text and comment nodes - if ( elem.nodeType === 3 || elem.nodeType === 8 ) { - return; - } - - // focus/blur morphs to focusin/out; ensure we're not firing them right now - if ( rfocusMorph.test( type + jQuery.event.triggered ) ) { - return; - } - - if ( type.indexOf( "." ) > -1 ) { - - // Namespaced trigger; create a regexp to match event type in handle() - namespaces = type.split( "." ); - type = namespaces.shift(); - namespaces.sort(); - } - ontype = type.indexOf( ":" ) < 0 && "on" + type; - - // Caller can pass in a jQuery.Event object, Object, or just an event type string - event = event[ jQuery.expando ] ? - event : - new jQuery.Event( type, typeof event === "object" && event ); - - // Trigger bitmask: & 1 for native handlers; & 2 for jQuery (always true) - event.isTrigger = onlyHandlers ? 2 : 3; - event.namespace = namespaces.join( "." ); - event.rnamespace = event.namespace ? - new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" ) : - null; - - // Clean up the event in case it is being reused - event.result = undefined; - if ( !event.target ) { - event.target = elem; - } - - // Clone any incoming data and prepend the event, creating the handler arg list - data = data == null ? - [ event ] : - jQuery.makeArray( data, [ event ] ); - - // Allow special events to draw outside the lines - special = jQuery.event.special[ type ] || {}; - if ( !onlyHandlers && special.trigger && special.trigger.apply( elem, data ) === false ) { - return; - } - - // Determine event propagation path in advance, per W3C events spec (#9951) - // Bubble up to document, then to window; watch for a global ownerDocument var (#9724) - if ( !onlyHandlers && !special.noBubble && !isWindow( elem ) ) { - - bubbleType = special.delegateType || type; - if ( !rfocusMorph.test( bubbleType + type ) ) { - cur = cur.parentNode; - } - for ( ; cur; cur = cur.parentNode ) { - eventPath.push( cur ); - tmp = cur; - } - - // Only add window if we got to document (e.g., not plain obj or detached DOM) - if ( tmp === ( elem.ownerDocument || document ) ) { - eventPath.push( tmp.defaultView || tmp.parentWindow || window ); - } - } - - // Fire handlers on the event path - i = 0; - while ( ( cur = eventPath[ i++ ] ) && !event.isPropagationStopped() ) { - lastElement = cur; - event.type = i > 1 ? - bubbleType : - special.bindType || type; - - // jQuery handler - handle = ( dataPriv.get( cur, "events" ) || Object.create( null ) )[ event.type ] && - dataPriv.get( cur, "handle" ); - if ( handle ) { - handle.apply( cur, data ); - } - - // Native handler - handle = ontype && cur[ ontype ]; - if ( handle && handle.apply && acceptData( cur ) ) { - event.result = handle.apply( cur, data ); - if ( event.result === false ) { - event.preventDefault(); - } - } - } - event.type = type; - - // If nobody prevented the default action, do it now - if ( !onlyHandlers && !event.isDefaultPrevented() ) { - - if ( ( !special._default || - special._default.apply( eventPath.pop(), data ) === false ) && - acceptData( elem ) ) { - - // Call a native DOM method on the target with the same name as the event. - // Don't do default actions on window, that's where global variables be (#6170) - if ( ontype && isFunction( elem[ type ] ) && !isWindow( elem ) ) { - - // Don't re-trigger an onFOO event when we call its FOO() method - tmp = elem[ ontype ]; - - if ( tmp ) { - elem[ ontype ] = null; - } - - // Prevent re-triggering of the same event, since we already bubbled it above - jQuery.event.triggered = type; - - if ( event.isPropagationStopped() ) { - lastElement.addEventListener( type, stopPropagationCallback ); - } - - elem[ type ](); - - if ( event.isPropagationStopped() ) { - lastElement.removeEventListener( type, stopPropagationCallback ); - } - - jQuery.event.triggered = undefined; - - if ( tmp ) { - elem[ ontype ] = tmp; - } - } - } - } - - return event.result; - }, - - // Piggyback on a donor event to simulate a different one - // Used only for `focus(in | out)` events - simulate: function( type, elem, event ) { - var e = jQuery.extend( - new jQuery.Event(), - event, - { - type: type, - isSimulated: true - } - ); - - jQuery.event.trigger( e, null, elem ); - } - -} ); - -jQuery.fn.extend( { - - trigger: function( type, data ) { - return this.each( function() { - jQuery.event.trigger( type, data, this ); - } ); - }, - triggerHandler: function( type, data ) { - var elem = this[ 0 ]; - if ( elem ) { - return jQuery.event.trigger( type, data, elem, true ); - } - } -} ); - - -// Support: Firefox <=44 -// Firefox doesn't have focus(in | out) events -// Related ticket - https://bugzilla.mozilla.org/show_bug.cgi?id=687787 -// -// Support: Chrome <=48 - 49, Safari <=9.0 - 9.1 -// focus(in | out) events fire after focus & blur events, -// which is spec violation - http://www.w3.org/TR/DOM-Level-3-Events/#events-focusevent-event-order -// Related ticket - https://bugs.chromium.org/p/chromium/issues/detail?id=449857 -if ( !support.focusin ) { - jQuery.each( { focus: "focusin", blur: "focusout" }, function( orig, fix ) { - - // Attach a single capturing handler on the document while someone wants focusin/focusout - var handler = function( event ) { - jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ) ); - }; - - jQuery.event.special[ fix ] = { - setup: function() { - - // Handle: regular nodes (via `this.ownerDocument`), window - // (via `this.document`) & document (via `this`). - var doc = this.ownerDocument || this.document || this, - attaches = dataPriv.access( doc, fix ); - - if ( !attaches ) { - doc.addEventListener( orig, handler, true ); - } - dataPriv.access( doc, fix, ( attaches || 0 ) + 1 ); - }, - teardown: function() { - var doc = this.ownerDocument || this.document || this, - attaches = dataPriv.access( doc, fix ) - 1; - - if ( !attaches ) { - doc.removeEventListener( orig, handler, true ); - dataPriv.remove( doc, fix ); - - } else { - dataPriv.access( doc, fix, attaches ); - } - } - }; - } ); -} -var location = window.location; - -var nonce = { guid: Date.now() }; - -var rquery = ( /\?/ ); - - - -// Cross-browser xml parsing -jQuery.parseXML = function( data ) { - var xml, parserErrorElem; - if ( !data || typeof data !== "string" ) { - return null; - } - - // Support: IE 9 - 11 only - // IE throws on parseFromString with invalid input. - try { - xml = ( new window.DOMParser() ).parseFromString( data, "text/xml" ); - } catch ( e ) {} - - parserErrorElem = xml && xml.getElementsByTagName( "parsererror" )[ 0 ]; - if ( !xml || parserErrorElem ) { - jQuery.error( "Invalid XML: " + ( - parserErrorElem ? - jQuery.map( parserErrorElem.childNodes, function( el ) { - return el.textContent; - } ).join( "\n" ) : - data - ) ); - } - return xml; -}; - - -var - rbracket = /\[\]$/, - rCRLF = /\r?\n/g, - rsubmitterTypes = /^(?:submit|button|image|reset|file)$/i, - rsubmittable = /^(?:input|select|textarea|keygen)/i; - -function buildParams( prefix, obj, traditional, add ) { - var name; - - if ( Array.isArray( obj ) ) { - - // Serialize array item. - jQuery.each( obj, function( i, v ) { - if ( traditional || rbracket.test( prefix ) ) { - - // Treat each array item as a scalar. - add( prefix, v ); - - } else { - - // Item is non-scalar (array or object), encode its numeric index. - buildParams( - prefix + "[" + ( typeof v === "object" && v != null ? i : "" ) + "]", - v, - traditional, - add - ); - } - } ); - - } else if ( !traditional && toType( obj ) === "object" ) { - - // Serialize object item. - for ( name in obj ) { - buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add ); - } - - } else { - - // Serialize scalar item. - add( prefix, obj ); - } -} - -// Serialize an array of form elements or a set of -// key/values into a query string -jQuery.param = function( a, traditional ) { - var prefix, - s = [], - add = function( key, valueOrFunction ) { - - // If value is a function, invoke it and use its return value - var value = isFunction( valueOrFunction ) ? - valueOrFunction() : - valueOrFunction; - - s[ s.length ] = encodeURIComponent( key ) + "=" + - encodeURIComponent( value == null ? "" : value ); - }; - - if ( a == null ) { - return ""; - } - - // If an array was passed in, assume that it is an array of form elements. - if ( Array.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) { - - // Serialize the form elements - jQuery.each( a, function() { - add( this.name, this.value ); - } ); - - } else { - - // If traditional, encode the "old" way (the way 1.3.2 or older - // did it), otherwise encode params recursively. - for ( prefix in a ) { - buildParams( prefix, a[ prefix ], traditional, add ); - } - } - - // Return the resulting serialization - return s.join( "&" ); -}; - -jQuery.fn.extend( { - serialize: function() { - return jQuery.param( this.serializeArray() ); - }, - serializeArray: function() { - return this.map( function() { - - // Can add propHook for "elements" to filter or add form elements - var elements = jQuery.prop( this, "elements" ); - return elements ? jQuery.makeArray( elements ) : this; - } ).filter( function() { - var type = this.type; - - // Use .is( ":disabled" ) so that fieldset[disabled] works - return this.name && !jQuery( this ).is( ":disabled" ) && - rsubmittable.test( this.nodeName ) && !rsubmitterTypes.test( type ) && - ( this.checked || !rcheckableType.test( type ) ); - } ).map( function( _i, elem ) { - var val = jQuery( this ).val(); - - if ( val == null ) { - return null; - } - - if ( Array.isArray( val ) ) { - return jQuery.map( val, function( val ) { - return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) }; - } ); - } - - return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) }; - } ).get(); - } -} ); - - -var - r20 = /%20/g, - rhash = /#.*$/, - rantiCache = /([?&])_=[^&]*/, - rheaders = /^(.*?):[ \t]*([^\r\n]*)$/mg, - - // #7653, #8125, #8152: local protocol detection - rlocalProtocol = /^(?:about|app|app-storage|.+-extension|file|res|widget):$/, - rnoContent = /^(?:GET|HEAD)$/, - rprotocol = /^\/\//, - - /* Prefilters - * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example) - * 2) These are called: - * - BEFORE asking for a transport - * - AFTER param serialization (s.data is a string if s.processData is true) - * 3) key is the dataType - * 4) the catchall symbol "*" can be used - * 5) execution will start with transport dataType and THEN continue down to "*" if needed - */ - prefilters = {}, - - /* Transports bindings - * 1) key is the dataType - * 2) the catchall symbol "*" can be used - * 3) selection will start with transport dataType and THEN go to "*" if needed - */ - transports = {}, - - // Avoid comment-prolog char sequence (#10098); must appease lint and evade compression - allTypes = "*/".concat( "*" ), - - // Anchor tag for parsing the document origin - originAnchor = document.createElement( "a" ); - -originAnchor.href = location.href; - -// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport -function addToPrefiltersOrTransports( structure ) { - - // dataTypeExpression is optional and defaults to "*" - return function( dataTypeExpression, func ) { - - if ( typeof dataTypeExpression !== "string" ) { - func = dataTypeExpression; - dataTypeExpression = "*"; - } - - var dataType, - i = 0, - dataTypes = dataTypeExpression.toLowerCase().match( rnothtmlwhite ) || []; - - if ( isFunction( func ) ) { - - // For each dataType in the dataTypeExpression - while ( ( dataType = dataTypes[ i++ ] ) ) { - - // Prepend if requested - if ( dataType[ 0 ] === "+" ) { - dataType = dataType.slice( 1 ) || "*"; - ( structure[ dataType ] = structure[ dataType ] || [] ).unshift( func ); - - // Otherwise append - } else { - ( structure[ dataType ] = structure[ dataType ] || [] ).push( func ); - } - } - } - }; -} - -// Base inspection function for prefilters and transports -function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR ) { - - var inspected = {}, - seekingTransport = ( structure === transports ); - - function inspect( dataType ) { - var selected; - inspected[ dataType ] = true; - jQuery.each( structure[ dataType ] || [], function( _, prefilterOrFactory ) { - var dataTypeOrTransport = prefilterOrFactory( options, originalOptions, jqXHR ); - if ( typeof dataTypeOrTransport === "string" && - !seekingTransport && !inspected[ dataTypeOrTransport ] ) { - - options.dataTypes.unshift( dataTypeOrTransport ); - inspect( dataTypeOrTransport ); - return false; - } else if ( seekingTransport ) { - return !( selected = dataTypeOrTransport ); - } - } ); - return selected; - } - - return inspect( options.dataTypes[ 0 ] ) || !inspected[ "*" ] && inspect( "*" ); -} - -// A special extend for ajax options -// that takes "flat" options (not to be deep extended) -// Fixes #9887 -function ajaxExtend( target, src ) { - var key, deep, - flatOptions = jQuery.ajaxSettings.flatOptions || {}; - - for ( key in src ) { - if ( src[ key ] !== undefined ) { - ( flatOptions[ key ] ? target : ( deep || ( deep = {} ) ) )[ key ] = src[ key ]; - } - } - if ( deep ) { - jQuery.extend( true, target, deep ); - } - - return target; -} - -/* Handles responses to an ajax request: - * - finds the right dataType (mediates between content-type and expected dataType) - * - returns the corresponding response - */ -function ajaxHandleResponses( s, jqXHR, responses ) { - - var ct, type, finalDataType, firstDataType, - contents = s.contents, - dataTypes = s.dataTypes; - - // Remove auto dataType and get content-type in the process - while ( dataTypes[ 0 ] === "*" ) { - dataTypes.shift(); - if ( ct === undefined ) { - ct = s.mimeType || jqXHR.getResponseHeader( "Content-Type" ); - } - } - - // Check if we're dealing with a known content-type - if ( ct ) { - for ( type in contents ) { - if ( contents[ type ] && contents[ type ].test( ct ) ) { - dataTypes.unshift( type ); - break; - } - } - } - - // Check to see if we have a response for the expected dataType - if ( dataTypes[ 0 ] in responses ) { - finalDataType = dataTypes[ 0 ]; - } else { - - // Try convertible dataTypes - for ( type in responses ) { - if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[ 0 ] ] ) { - finalDataType = type; - break; - } - if ( !firstDataType ) { - firstDataType = type; - } - } - - // Or just use first one - finalDataType = finalDataType || firstDataType; - } - - // If we found a dataType - // We add the dataType to the list if needed - // and return the corresponding response - if ( finalDataType ) { - if ( finalDataType !== dataTypes[ 0 ] ) { - dataTypes.unshift( finalDataType ); - } - return responses[ finalDataType ]; - } -} - -/* Chain conversions given the request and the original response - * Also sets the responseXXX fields on the jqXHR instance - */ -function ajaxConvert( s, response, jqXHR, isSuccess ) { - var conv2, current, conv, tmp, prev, - converters = {}, - - // Work with a copy of dataTypes in case we need to modify it for conversion - dataTypes = s.dataTypes.slice(); - - // Create converters map with lowercased keys - if ( dataTypes[ 1 ] ) { - for ( conv in s.converters ) { - converters[ conv.toLowerCase() ] = s.converters[ conv ]; - } - } - - current = dataTypes.shift(); - - // Convert to each sequential dataType - while ( current ) { - - if ( s.responseFields[ current ] ) { - jqXHR[ s.responseFields[ current ] ] = response; - } - - // Apply the dataFilter if provided - if ( !prev && isSuccess && s.dataFilter ) { - response = s.dataFilter( response, s.dataType ); - } - - prev = current; - current = dataTypes.shift(); - - if ( current ) { - - // There's only work to do if current dataType is non-auto - if ( current === "*" ) { - - current = prev; - - // Convert response if prev dataType is non-auto and differs from current - } else if ( prev !== "*" && prev !== current ) { - - // Seek a direct converter - conv = converters[ prev + " " + current ] || converters[ "* " + current ]; - - // If none found, seek a pair - if ( !conv ) { - for ( conv2 in converters ) { - - // If conv2 outputs current - tmp = conv2.split( " " ); - if ( tmp[ 1 ] === current ) { - - // If prev can be converted to accepted input - conv = converters[ prev + " " + tmp[ 0 ] ] || - converters[ "* " + tmp[ 0 ] ]; - if ( conv ) { - - // Condense equivalence converters - if ( conv === true ) { - conv = converters[ conv2 ]; - - // Otherwise, insert the intermediate dataType - } else if ( converters[ conv2 ] !== true ) { - current = tmp[ 0 ]; - dataTypes.unshift( tmp[ 1 ] ); - } - break; - } - } - } - } - - // Apply converter (if not an equivalence) - if ( conv !== true ) { - - // Unless errors are allowed to bubble, catch and return them - if ( conv && s.throws ) { - response = conv( response ); - } else { - try { - response = conv( response ); - } catch ( e ) { - return { - state: "parsererror", - error: conv ? e : "No conversion from " + prev + " to " + current - }; - } - } - } - } - } - } - - return { state: "success", data: response }; -} - -jQuery.extend( { - - // Counter for holding the number of active queries - active: 0, - - // Last-Modified header cache for next request - lastModified: {}, - etag: {}, - - ajaxSettings: { - url: location.href, - type: "GET", - isLocal: rlocalProtocol.test( location.protocol ), - global: true, - processData: true, - async: true, - contentType: "application/x-www-form-urlencoded; charset=UTF-8", - - /* - timeout: 0, - data: null, - dataType: null, - username: null, - password: null, - cache: null, - throws: false, - traditional: false, - headers: {}, - */ - - accepts: { - "*": allTypes, - text: "text/plain", - html: "text/html", - xml: "application/xml, text/xml", - json: "application/json, text/javascript" - }, - - contents: { - xml: /\bxml\b/, - html: /\bhtml/, - json: /\bjson\b/ - }, - - responseFields: { - xml: "responseXML", - text: "responseText", - json: "responseJSON" - }, - - // Data converters - // Keys separate source (or catchall "*") and destination types with a single space - converters: { - - // Convert anything to text - "* text": String, - - // Text to html (true = no transformation) - "text html": true, - - // Evaluate text as a json expression - "text json": JSON.parse, - - // Parse text as xml - "text xml": jQuery.parseXML - }, - - // For options that shouldn't be deep extended: - // you can add your own custom options here if - // and when you create one that shouldn't be - // deep extended (see ajaxExtend) - flatOptions: { - url: true, - context: true - } - }, - - // Creates a full fledged settings object into target - // with both ajaxSettings and settings fields. - // If target is omitted, writes into ajaxSettings. - ajaxSetup: function( target, settings ) { - return settings ? - - // Building a settings object - ajaxExtend( ajaxExtend( target, jQuery.ajaxSettings ), settings ) : - - // Extending ajaxSettings - ajaxExtend( jQuery.ajaxSettings, target ); - }, - - ajaxPrefilter: addToPrefiltersOrTransports( prefilters ), - ajaxTransport: addToPrefiltersOrTransports( transports ), - - // Main method - ajax: function( url, options ) { - - // If url is an object, simulate pre-1.5 signature - if ( typeof url === "object" ) { - options = url; - url = undefined; - } - - // Force options to be an object - options = options || {}; - - var transport, - - // URL without anti-cache param - cacheURL, - - // Response headers - responseHeadersString, - responseHeaders, - - // timeout handle - timeoutTimer, - - // Url cleanup var - urlAnchor, - - // Request state (becomes false upon send and true upon completion) - completed, - - // To know if global events are to be dispatched - fireGlobals, - - // Loop variable - i, - - // uncached part of the url - uncached, - - // Create the final options object - s = jQuery.ajaxSetup( {}, options ), - - // Callbacks context - callbackContext = s.context || s, - - // Context for global events is callbackContext if it is a DOM node or jQuery collection - globalEventContext = s.context && - ( callbackContext.nodeType || callbackContext.jquery ) ? - jQuery( callbackContext ) : - jQuery.event, - - // Deferreds - deferred = jQuery.Deferred(), - completeDeferred = jQuery.Callbacks( "once memory" ), - - // Status-dependent callbacks - statusCode = s.statusCode || {}, - - // Headers (they are sent all at once) - requestHeaders = {}, - requestHeadersNames = {}, - - // Default abort message - strAbort = "canceled", - - // Fake xhr - jqXHR = { - readyState: 0, - - // Builds headers hashtable if needed - getResponseHeader: function( key ) { - var match; - if ( completed ) { - if ( !responseHeaders ) { - responseHeaders = {}; - while ( ( match = rheaders.exec( responseHeadersString ) ) ) { - responseHeaders[ match[ 1 ].toLowerCase() + " " ] = - ( responseHeaders[ match[ 1 ].toLowerCase() + " " ] || [] ) - .concat( match[ 2 ] ); - } - } - match = responseHeaders[ key.toLowerCase() + " " ]; - } - return match == null ? null : match.join( ", " ); - }, - - // Raw string - getAllResponseHeaders: function() { - return completed ? responseHeadersString : null; - }, - - // Caches the header - setRequestHeader: function( name, value ) { - if ( completed == null ) { - name = requestHeadersNames[ name.toLowerCase() ] = - requestHeadersNames[ name.toLowerCase() ] || name; - requestHeaders[ name ] = value; - } - return this; - }, - - // Overrides response content-type header - overrideMimeType: function( type ) { - if ( completed == null ) { - s.mimeType = type; - } - return this; - }, - - // Status-dependent callbacks - statusCode: function( map ) { - var code; - if ( map ) { - if ( completed ) { - - // Execute the appropriate callbacks - jqXHR.always( map[ jqXHR.status ] ); - } else { - - // Lazy-add the new callbacks in a way that preserves old ones - for ( code in map ) { - statusCode[ code ] = [ statusCode[ code ], map[ code ] ]; - } - } - } - return this; - }, - - // Cancel the request - abort: function( statusText ) { - var finalText = statusText || strAbort; - if ( transport ) { - transport.abort( finalText ); - } - done( 0, finalText ); - return this; - } - }; - - // Attach deferreds - deferred.promise( jqXHR ); - - // Add protocol if not provided (prefilters might expect it) - // Handle falsy url in the settings object (#10093: consistency with old signature) - // We also use the url parameter if available - s.url = ( ( url || s.url || location.href ) + "" ) - .replace( rprotocol, location.protocol + "//" ); - - // Alias method option to type as per ticket #12004 - s.type = options.method || options.type || s.method || s.type; - - // Extract dataTypes list - s.dataTypes = ( s.dataType || "*" ).toLowerCase().match( rnothtmlwhite ) || [ "" ]; - - // A cross-domain request is in order when the origin doesn't match the current origin. - if ( s.crossDomain == null ) { - urlAnchor = document.createElement( "a" ); - - // Support: IE <=8 - 11, Edge 12 - 15 - // IE throws exception on accessing the href property if url is malformed, - // e.g. http://example.com:80x/ - try { - urlAnchor.href = s.url; - - // Support: IE <=8 - 11 only - // Anchor's host property isn't correctly set when s.url is relative - urlAnchor.href = urlAnchor.href; - s.crossDomain = originAnchor.protocol + "//" + originAnchor.host !== - urlAnchor.protocol + "//" + urlAnchor.host; - } catch ( e ) { - - // If there is an error parsing the URL, assume it is crossDomain, - // it can be rejected by the transport if it is invalid - s.crossDomain = true; - } - } - - // Convert data if not already a string - if ( s.data && s.processData && typeof s.data !== "string" ) { - s.data = jQuery.param( s.data, s.traditional ); - } - - // Apply prefilters - inspectPrefiltersOrTransports( prefilters, s, options, jqXHR ); - - // If request was aborted inside a prefilter, stop there - if ( completed ) { - return jqXHR; - } - - // We can fire global events as of now if asked to - // Don't fire events if jQuery.event is undefined in an AMD-usage scenario (#15118) - fireGlobals = jQuery.event && s.global; - - // Watch for a new set of requests - if ( fireGlobals && jQuery.active++ === 0 ) { - jQuery.event.trigger( "ajaxStart" ); - } - - // Uppercase the type - s.type = s.type.toUpperCase(); - - // Determine if request has content - s.hasContent = !rnoContent.test( s.type ); - - // Save the URL in case we're toying with the If-Modified-Since - // and/or If-None-Match header later on - // Remove hash to simplify url manipulation - cacheURL = s.url.replace( rhash, "" ); - - // More options handling for requests with no content - if ( !s.hasContent ) { - - // Remember the hash so we can put it back - uncached = s.url.slice( cacheURL.length ); - - // If data is available and should be processed, append data to url - if ( s.data && ( s.processData || typeof s.data === "string" ) ) { - cacheURL += ( rquery.test( cacheURL ) ? "&" : "?" ) + s.data; - - // #9682: remove data so that it's not used in an eventual retry - delete s.data; - } - - // Add or update anti-cache param if needed - if ( s.cache === false ) { - cacheURL = cacheURL.replace( rantiCache, "$1" ); - uncached = ( rquery.test( cacheURL ) ? "&" : "?" ) + "_=" + ( nonce.guid++ ) + - uncached; - } - - // Put hash and anti-cache on the URL that will be requested (gh-1732) - s.url = cacheURL + uncached; - - // Change '%20' to '+' if this is encoded form body content (gh-2658) - } else if ( s.data && s.processData && - ( s.contentType || "" ).indexOf( "application/x-www-form-urlencoded" ) === 0 ) { - s.data = s.data.replace( r20, "+" ); - } - - // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode. - if ( s.ifModified ) { - if ( jQuery.lastModified[ cacheURL ] ) { - jqXHR.setRequestHeader( "If-Modified-Since", jQuery.lastModified[ cacheURL ] ); - } - if ( jQuery.etag[ cacheURL ] ) { - jqXHR.setRequestHeader( "If-None-Match", jQuery.etag[ cacheURL ] ); - } - } - - // Set the correct header, if data is being sent - if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) { - jqXHR.setRequestHeader( "Content-Type", s.contentType ); - } - - // Set the Accepts header for the server, depending on the dataType - jqXHR.setRequestHeader( - "Accept", - s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[ 0 ] ] ? - s.accepts[ s.dataTypes[ 0 ] ] + - ( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) : - s.accepts[ "*" ] - ); - - // Check for headers option - for ( i in s.headers ) { - jqXHR.setRequestHeader( i, s.headers[ i ] ); - } - - // Allow custom headers/mimetypes and early abort - if ( s.beforeSend && - ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || completed ) ) { - - // Abort if not done already and return - return jqXHR.abort(); - } - - // Aborting is no longer a cancellation - strAbort = "abort"; - - // Install callbacks on deferreds - completeDeferred.add( s.complete ); - jqXHR.done( s.success ); - jqXHR.fail( s.error ); - - // Get transport - transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR ); - - // If no transport, we auto-abort - if ( !transport ) { - done( -1, "No Transport" ); - } else { - jqXHR.readyState = 1; - - // Send global event - if ( fireGlobals ) { - globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] ); - } - - // If request was aborted inside ajaxSend, stop there - if ( completed ) { - return jqXHR; - } - - // Timeout - if ( s.async && s.timeout > 0 ) { - timeoutTimer = window.setTimeout( function() { - jqXHR.abort( "timeout" ); - }, s.timeout ); - } - - try { - completed = false; - transport.send( requestHeaders, done ); - } catch ( e ) { - - // Rethrow post-completion exceptions - if ( completed ) { - throw e; - } - - // Propagate others as results - done( -1, e ); - } - } - - // Callback for when everything is done - function done( status, nativeStatusText, responses, headers ) { - var isSuccess, success, error, response, modified, - statusText = nativeStatusText; - - // Ignore repeat invocations - if ( completed ) { - return; - } - - completed = true; - - // Clear timeout if it exists - if ( timeoutTimer ) { - window.clearTimeout( timeoutTimer ); - } - - // Dereference transport for early garbage collection - // (no matter how long the jqXHR object will be used) - transport = undefined; - - // Cache response headers - responseHeadersString = headers || ""; - - // Set readyState - jqXHR.readyState = status > 0 ? 4 : 0; - - // Determine if successful - isSuccess = status >= 200 && status < 300 || status === 304; - - // Get response data - if ( responses ) { - response = ajaxHandleResponses( s, jqXHR, responses ); - } - - // Use a noop converter for missing script but not if jsonp - if ( !isSuccess && - jQuery.inArray( "script", s.dataTypes ) > -1 && - jQuery.inArray( "json", s.dataTypes ) < 0 ) { - s.converters[ "text script" ] = function() {}; - } - - // Convert no matter what (that way responseXXX fields are always set) - response = ajaxConvert( s, response, jqXHR, isSuccess ); - - // If successful, handle type chaining - if ( isSuccess ) { - - // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode. - if ( s.ifModified ) { - modified = jqXHR.getResponseHeader( "Last-Modified" ); - if ( modified ) { - jQuery.lastModified[ cacheURL ] = modified; - } - modified = jqXHR.getResponseHeader( "etag" ); - if ( modified ) { - jQuery.etag[ cacheURL ] = modified; - } - } - - // if no content - if ( status === 204 || s.type === "HEAD" ) { - statusText = "nocontent"; - - // if not modified - } else if ( status === 304 ) { - statusText = "notmodified"; - - // If we have data, let's convert it - } else { - statusText = response.state; - success = response.data; - error = response.error; - isSuccess = !error; - } - } else { - - // Extract error from statusText and normalize for non-aborts - error = statusText; - if ( status || !statusText ) { - statusText = "error"; - if ( status < 0 ) { - status = 0; - } - } - } - - // Set data for the fake xhr object - jqXHR.status = status; - jqXHR.statusText = ( nativeStatusText || statusText ) + ""; - - // Success/Error - if ( isSuccess ) { - deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] ); - } else { - deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] ); - } - - // Status-dependent callbacks - jqXHR.statusCode( statusCode ); - statusCode = undefined; - - if ( fireGlobals ) { - globalEventContext.trigger( isSuccess ? "ajaxSuccess" : "ajaxError", - [ jqXHR, s, isSuccess ? success : error ] ); - } - - // Complete - completeDeferred.fireWith( callbackContext, [ jqXHR, statusText ] ); - - if ( fireGlobals ) { - globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] ); - - // Handle the global AJAX counter - if ( !( --jQuery.active ) ) { - jQuery.event.trigger( "ajaxStop" ); - } - } - } - - return jqXHR; - }, - - getJSON: function( url, data, callback ) { - return jQuery.get( url, data, callback, "json" ); - }, - - getScript: function( url, callback ) { - return jQuery.get( url, undefined, callback, "script" ); - } -} ); - -jQuery.each( [ "get", "post" ], function( _i, method ) { - jQuery[ method ] = function( url, data, callback, type ) { - - // Shift arguments if data argument was omitted - if ( isFunction( data ) ) { - type = type || callback; - callback = data; - data = undefined; - } - - // The url can be an options object (which then must have .url) - return jQuery.ajax( jQuery.extend( { - url: url, - type: method, - dataType: type, - data: data, - success: callback - }, jQuery.isPlainObject( url ) && url ) ); - }; -} ); - -jQuery.ajaxPrefilter( function( s ) { - var i; - for ( i in s.headers ) { - if ( i.toLowerCase() === "content-type" ) { - s.contentType = s.headers[ i ] || ""; - } - } -} ); - - -jQuery._evalUrl = function( url, options, doc ) { - return jQuery.ajax( { - url: url, - - // Make this explicit, since user can override this through ajaxSetup (#11264) - type: "GET", - dataType: "script", - cache: true, - async: false, - global: false, - - // Only evaluate the response if it is successful (gh-4126) - // dataFilter is not invoked for failure responses, so using it instead - // of the default converter is kludgy but it works. - converters: { - "text script": function() {} - }, - dataFilter: function( response ) { - jQuery.globalEval( response, options, doc ); - } - } ); -}; - - -jQuery.fn.extend( { - wrapAll: function( html ) { - var wrap; - - if ( this[ 0 ] ) { - if ( isFunction( html ) ) { - html = html.call( this[ 0 ] ); - } - - // The elements to wrap the target around - wrap = jQuery( html, this[ 0 ].ownerDocument ).eq( 0 ).clone( true ); - - if ( this[ 0 ].parentNode ) { - wrap.insertBefore( this[ 0 ] ); - } - - wrap.map( function() { - var elem = this; - - while ( elem.firstElementChild ) { - elem = elem.firstElementChild; - } - - return elem; - } ).append( this ); - } - - return this; - }, - - wrapInner: function( html ) { - if ( isFunction( html ) ) { - return this.each( function( i ) { - jQuery( this ).wrapInner( html.call( this, i ) ); - } ); - } - - return this.each( function() { - var self = jQuery( this ), - contents = self.contents(); - - if ( contents.length ) { - contents.wrapAll( html ); - - } else { - self.append( html ); - } - } ); - }, - - wrap: function( html ) { - var htmlIsFunction = isFunction( html ); - - return this.each( function( i ) { - jQuery( this ).wrapAll( htmlIsFunction ? html.call( this, i ) : html ); - } ); - }, - - unwrap: function( selector ) { - this.parent( selector ).not( "body" ).each( function() { - jQuery( this ).replaceWith( this.childNodes ); - } ); - return this; - } -} ); - - -jQuery.expr.pseudos.hidden = function( elem ) { - return !jQuery.expr.pseudos.visible( elem ); -}; -jQuery.expr.pseudos.visible = function( elem ) { - return !!( elem.offsetWidth || elem.offsetHeight || elem.getClientRects().length ); -}; - - - - -jQuery.ajaxSettings.xhr = function() { - try { - return new window.XMLHttpRequest(); - } catch ( e ) {} -}; - -var xhrSuccessStatus = { - - // File protocol always yields status code 0, assume 200 - 0: 200, - - // Support: IE <=9 only - // #1450: sometimes IE returns 1223 when it should be 204 - 1223: 204 - }, - xhrSupported = jQuery.ajaxSettings.xhr(); - -support.cors = !!xhrSupported && ( "withCredentials" in xhrSupported ); -support.ajax = xhrSupported = !!xhrSupported; - -jQuery.ajaxTransport( function( options ) { - var callback, errorCallback; - - // Cross domain only allowed if supported through XMLHttpRequest - if ( support.cors || xhrSupported && !options.crossDomain ) { - return { - send: function( headers, complete ) { - var i, - xhr = options.xhr(); - - xhr.open( - options.type, - options.url, - options.async, - options.username, - options.password - ); - - // Apply custom fields if provided - if ( options.xhrFields ) { - for ( i in options.xhrFields ) { - xhr[ i ] = options.xhrFields[ i ]; - } - } - - // Override mime type if needed - if ( options.mimeType && xhr.overrideMimeType ) { - xhr.overrideMimeType( options.mimeType ); - } - - // X-Requested-With header - // For cross-domain requests, seeing as conditions for a preflight are - // akin to a jigsaw puzzle, we simply never set it to be sure. - // (it can always be set on a per-request basis or even using ajaxSetup) - // For same-domain requests, won't change header if already provided. - if ( !options.crossDomain && !headers[ "X-Requested-With" ] ) { - headers[ "X-Requested-With" ] = "XMLHttpRequest"; - } - - // Set headers - for ( i in headers ) { - xhr.setRequestHeader( i, headers[ i ] ); - } - - // Callback - callback = function( type ) { - return function() { - if ( callback ) { - callback = errorCallback = xhr.onload = - xhr.onerror = xhr.onabort = xhr.ontimeout = - xhr.onreadystatechange = null; - - if ( type === "abort" ) { - xhr.abort(); - } else if ( type === "error" ) { - - // Support: IE <=9 only - // On a manual native abort, IE9 throws - // errors on any property access that is not readyState - if ( typeof xhr.status !== "number" ) { - complete( 0, "error" ); - } else { - complete( - - // File: protocol always yields status 0; see #8605, #14207 - xhr.status, - xhr.statusText - ); - } - } else { - complete( - xhrSuccessStatus[ xhr.status ] || xhr.status, - xhr.statusText, - - // Support: IE <=9 only - // IE9 has no XHR2 but throws on binary (trac-11426) - // For XHR2 non-text, let the caller handle it (gh-2498) - ( xhr.responseType || "text" ) !== "text" || - typeof xhr.responseText !== "string" ? - { binary: xhr.response } : - { text: xhr.responseText }, - xhr.getAllResponseHeaders() - ); - } - } - }; - }; - - // Listen to events - xhr.onload = callback(); - errorCallback = xhr.onerror = xhr.ontimeout = callback( "error" ); - - // Support: IE 9 only - // Use onreadystatechange to replace onabort - // to handle uncaught aborts - if ( xhr.onabort !== undefined ) { - xhr.onabort = errorCallback; - } else { - xhr.onreadystatechange = function() { - - // Check readyState before timeout as it changes - if ( xhr.readyState === 4 ) { - - // Allow onerror to be called first, - // but that will not handle a native abort - // Also, save errorCallback to a variable - // as xhr.onerror cannot be accessed - window.setTimeout( function() { - if ( callback ) { - errorCallback(); - } - } ); - } - }; - } - - // Create the abort callback - callback = callback( "abort" ); - - try { - - // Do send the request (this may raise an exception) - xhr.send( options.hasContent && options.data || null ); - } catch ( e ) { - - // #14683: Only rethrow if this hasn't been notified as an error yet - if ( callback ) { - throw e; - } - } - }, - - abort: function() { - if ( callback ) { - callback(); - } - } - }; - } -} ); - - - - -// Prevent auto-execution of scripts when no explicit dataType was provided (See gh-2432) -jQuery.ajaxPrefilter( function( s ) { - if ( s.crossDomain ) { - s.contents.script = false; - } -} ); - -// Install script dataType -jQuery.ajaxSetup( { - accepts: { - script: "text/javascript, application/javascript, " + - "application/ecmascript, application/x-ecmascript" - }, - contents: { - script: /\b(?:java|ecma)script\b/ - }, - converters: { - "text script": function( text ) { - jQuery.globalEval( text ); - return text; - } - } -} ); - -// Handle cache's special case and crossDomain -jQuery.ajaxPrefilter( "script", function( s ) { - if ( s.cache === undefined ) { - s.cache = false; - } - if ( s.crossDomain ) { - s.type = "GET"; - } -} ); - -// Bind script tag hack transport -jQuery.ajaxTransport( "script", function( s ) { - - // This transport only deals with cross domain or forced-by-attrs requests - if ( s.crossDomain || s.scriptAttrs ) { - var script, callback; - return { - send: function( _, complete ) { - script = jQuery( " - - + diff --git a/docs/docs-build/bifurcation.html b/docs/docs-build/bifurcation.html index 8e3d158905..db6e357ebc 100644 --- a/docs/docs-build/bifurcation.html +++ b/docs/docs-build/bifurcation.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/developers_docs/build_with_python_debug.html b/docs/docs-build/developers_docs/build_with_python_debug.html index ae2133cb98..b97fcb2be7 100644 --- a/docs/docs-build/developers_docs/build_with_python_debug.html +++ b/docs/docs-build/developers_docs/build_with_python_debug.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/developers_docs/building_documentation.html b/docs/docs-build/developers_docs/building_documentation.html index 4b4875516a..984309bd89 100644 --- a/docs/docs-build/developers_docs/building_documentation.html +++ b/docs/docs-build/developers_docs/building_documentation.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/developers_docs/git_workflow.html b/docs/docs-build/developers_docs/git_workflow.html index f2bd78abbd..989ffc23de 100644 --- a/docs/docs-build/developers_docs/git_workflow.html +++ b/docs/docs-build/developers_docs/git_workflow.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/developers_docs/index.html b/docs/docs-build/developers_docs/index.html index 9a40c74c79..b4fbe89a8a 100644 --- a/docs/docs-build/developers_docs/index.html +++ b/docs/docs-build/developers_docs/index.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/developers_docs/making_releases.html b/docs/docs-build/developers_docs/making_releases.html index 3dbd08819f..aaddf5aabd 100644 --- a/docs/docs-build/developers_docs/making_releases.html +++ b/docs/docs-build/developers_docs/making_releases.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/genindex.html b/docs/docs-build/genindex.html index 86952d5c9b..e1bc168d44 100644 --- a/docs/docs-build/genindex.html +++ b/docs/docs-build/genindex.html @@ -11,10 +11,9 @@ - - + @@ -325,8 +324,6 @@

      G

  • getCompilerLocation() (RoadRunner.Compiler method) -
    • -
  • getConcentrationTolerance() (Integrator method)
  • getConfigFilePath() (RoadRunner.Config static method)
    • @@ -750,14 +747,12 @@

    P

  • p1 (RoadRunner.SelectionRecord attribute)
  • p2 (RoadRunner.SelectionRecord attribute) -
    • -
  • presimulation_maximum_steps (SteadyStateSolver attribute)
- +
  • setIntegratorSetting() (RoadRunner.RoadRunner method)
  • setKineticLaw() (RoadRunner.RoadRunner method) diff --git a/docs/docs-build/index.html b/docs/docs-build/index.html index 96de427e33..bfed55754f 100644 --- a/docs/docs-build/index.html +++ b/docs/docs-build/index.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/metabolic.html b/docs/docs-build/metabolic.html index fd37537b65..c132e4ee74 100644 --- a/docs/docs-build/metabolic.html +++ b/docs/docs-build/metabolic.html @@ -12,10 +12,9 @@ - - + @@ -104,26 +103,26 @@

    Preliminaries -

    \varepsilon^v_S = \frac{\partial v}{\partial S} \frac{S}{v} = \frac{\partial \ln v}{\partial \ln S}

    -

    Given a reaction rate v_i, the elasticity describes how a given effector of the reaction step affects +

    \varepsilon^v_S = \frac{\partial v}{\partial S} \frac{S}{v} = \frac{\partial \ln v}{\partial \ln S}

    +

    Given a reaction rate v_i, the elasticity describes how a given effector of the reaction step affects the reaction rate. Because the definition is in terms of partial deriviatives, any effector that is perturbed assumes that all other potential effectors are unchanged.

    The system sensitivities are described by the control and response coefficients. These come in two forms, flux and concentration. The flux control coefficients measures how senstive a given flux is to a perturbation in the local rate of a reaction step. Often the local rate is perturbed by changing the enzyme concentration at the step. -In this siutation the flux control coefficicent with respect to enzyme E_i is defined as follow:

    +In this siutation the flux control coefficicent with respect to enzyme E_i is defined as follow:

    -

    C^J_{E_i} = \frac{dJ}{dE_i} \frac{E_1}{J} = \frac{d\ln J}{d\ln E_i}

    +

    C^J_{E_i} = \frac{dJ}{dE_i} \frac{E_1}{J} = \frac{d\ln J}{d\ln E_i}

    Likewise the concentration control coefficient is defined by:

    -

    C^S_{E_i} = \frac{dS}{d E_i} \frac{E_1}{S} = \frac{d\ln S}{d\ln E_i}

    -

    where S is a given species. The response coefficients measure the sensitivity of a flux or species concentration +

    C^S_{E_i} = \frac{dS}{d E_i} \frac{E_1}{S} = \frac{d\ln S}{d\ln E_i}

    +

    where S is a given species. The response coefficients measure the sensitivity of a flux or species concentration to a perturbation in some external effector. These are defined by:

    -

    R^J_{X} = \frac{dJ}{dX} \frac{X}{J} = \frac{d\ln J}{d\ln X}

    +

    R^J_{X} = \frac{dJ}{dX} \frac{X}{J} = \frac{d\ln J}{d\ln X}

    -

    R^S_{X} = \frac{dJ}{dX} \frac{X}{S} = \frac{d\ln S}{d\ln X}

    -

    where X is the external effector.

    +

    R^S_{X} = \frac{dJ}{dX} \frac{X}{S} = \frac{d\ln S}{d\ln X}

    +

    where X is the external effector.

    Methods

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a/docs/docs-build/parallel/multiprocessing/multiprocessing_index.html b/docs/docs-build/parallel/multiprocessing/multiprocessing_index.html index 9cefbbb8d1..7af91477b2 100644 --- a/docs/docs-build/parallel/multiprocessing/multiprocessing_index.html +++ b/docs/docs-build/parallel/multiprocessing/multiprocessing_index.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/parallel/parallel_index.html b/docs/docs-build/parallel/parallel_index.html index 87325ebe8a..e5a8e7740d 100644 --- a/docs/docs-build/parallel/parallel_index.html +++ b/docs/docs-build/parallel/parallel_index.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/parallel/roadrunner_map/roadrunner_map_index.html b/docs/docs-build/parallel/roadrunner_map/roadrunner_map_index.html index e38c1290c4..923a59887e 100644 --- a/docs/docs-build/parallel/roadrunner_map/roadrunner_map_index.html +++ b/docs/docs-build/parallel/roadrunner_map/roadrunner_map_index.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/py-modindex.html b/docs/docs-build/py-modindex.html index ecf9ce24a1..ce2f0ec1a7 100644 --- a/docs/docs-build/py-modindex.html +++ b/docs/docs-build/py-modindex.html @@ -11,10 +11,9 @@ - - + diff --git a/docs/docs-build/read_write_functions.html b/docs/docs-build/read_write_functions.html index 418fda968e..e66dc54dea 100644 --- a/docs/docs-build/read_write_functions.html +++ b/docs/docs-build/read_write_functions.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/rrplugins/introduction.html b/docs/docs-build/rrplugins/introduction.html new file mode 100644 index 0000000000..1e521bff6e --- /dev/null +++ b/docs/docs-build/rrplugins/introduction.html @@ -0,0 +1,283 @@ + + + + + + + rrPlugins — libRoadRunner 1.1.16 documentation + + + + + + + + + + + + + + + + + + +
    + + +
    + +
    +
    +
    + +
    +
    +
    +
    + +
    +

    rrPlugins

    +
    +
    +
    +

    Introduction

    +

    The plugin API allows users to easily access roadrunner plugins. Only three concepts need to be understood:

    +
      +

    1. Loading a plugin

      2. +

    2. Setting and Getting plugin properties

      3. +

    3. Executing the plugin

      4. +
    +

    Before using the plugin system the plugin library must be imported using the line:

    +
    import rrplugins as tel
+
    +
    +

    To load a plugin called “add_noise” use the Python command:

    +
    p = tel.Plugin("tel_add_noise")
+
    +
    +

    The variable p now represents the plugin. Plugins expose a number of properties, these are variables that can be inspected or set. For example the add noise plugin has a property called Sigma. To set this to a particular value we would use:

    +
    p.Sigma = 0.5
+
    +
    +

    Likewise, properties can be inspected:

    +
    print(p.Sigma)
+
    +
    +

    To list all propreties in a plugin use the method listOfProperties. The following uses call together with pprint to make the output more understandable:

    +
    p.listOfProperties()
+[['NoiseType', 'Type of noise (Gaussian = 0).'], ['Sigma', 'Size of applied noise'], ['InputData', 'Data on which noise will be applied to'], ['AssumeTime', "Assume the first column in the input data is time, and don't add noise to it."], ['Progress', 'Indicate progress in (0-100%)'], ['Seed', "Seed to use for each use of 'execute' (0 to ignore)"]]
+
    +
    +

    To run a plugin so that it carries out its function, use the execute method:

    +
    p.execute()
+
    +
    +

    The results from an execute call will either be saved to a file or more likely via properties of the plugin. As a trivial example, consider a plugin called “test” that has three properties, x, y and z. When the execute() method is called the plugin will take the values stored in x and y, add them together and store the result in z. The following script illustrates how the plugin would be used from Python:

    +
    import rrplugins as tel
+p = tel.Plugin("test")
+p.x = 1.2
+p.y = 4.5
+p.execute()
+print(p.z)
+
    +
    +

    The following script illustrates a more substantial example using the add_noise plugin:

    +
    import roadrunner
+import rrplugins as tel
+
+rr = roadrunner.RoadRunner()
+rr.load("path to any model. Eg. some models are provided in source code, like, sbml_test_0001")
+
+data = rr.simulate(0, 10, 50)
+
+noisePlugin = tel.Plugin("tel_add_noise")
+
+d = tel.getDataSeries(data)
+
+noisePlugin.InputData = d
+
+noisePlugin.Sigma = 5.e-6
+
+noisePlugin.execute()
+
+noisePlugin.InputData.plot()
+
    +
    +
    +
    +

    DataSeries

    +

    The plugin system supports a special data type called a Data Series. This is a convenient way to represent rows and colums of data. The data type also has the ability to label columns with a text string and to associate each value in the data series with an additional value called a weight. In practice the data series will usually store experimental data and the weights will represent a measure of undertaintly, perhaps a standard deviation, of the data point. A Data Series can be created using the call:

    +
    import rrplugins as tel
+data = tel.DataSeries()
+
    +
    +

    Data can be entered into a data series either by loading the data from a specially formated file or from a Python NumPy array. For example:

    +
    data.readDataSeries ("mydata.txt")
+
    +
    +

    To read numpy arrays into a data series use the code:

    +
    import numpy as np
+values = np.array([[1,2],{2,5],[3,7]])
+data = tel.DataSeries.fromNumPy (values)
+
    +
    +

    The number of rows and columns in a Data Series can be obtained using:

    +
    print(data.rows)
+print(data.cols)
+
    +
    +

    Currently individual values in a data series can be accessed using the set and get methods:

    +
    p.setElement (1, 2, 4.567)
+print(p.getElement(1, 2))
+
    +
    +

    Data series can be plotted using the plot method:

    +
    data.plot()
+
    +
    +

    The following script is an example of using the add_noise plugin. This plugin takes a data series and add a given amount of Guassian noise to all data except the data in the first column.

    +
    import rrplugins as tel
+p = tel.Plugin ("tel_add_noise")
+p.viewManual()
+pl = p.listOfProperties()
+for item in pl:
+    print(item)
+
+p.Sigma = 0.00005
+series = DataSeries.loadDataSeries("..\\Examples\\testData.dat")
+series.plot()
+p.InputData = series
+p.execute()
+p.InputData.plot()
+
+print("Test Finished")
+
    +
    +
    +
    +

    Plugins

    +

    Plugin objects are instanciated using Plugin class. For example to instanciate a plugin called myplugin, we would use the code:

    +
    p = Plugin("myplugin")
+
    +
    +

    All interactions with plugins are via plugin properties. Values can be set and retrieved via plugin properties. For example, if a plugin has a property sigma, we can assign or access the value using the code:

    +
    p.sigma = 0.1
+print(p.sigma)
+
    +
    +

    Plugins have a single method that can be used to excecute the plugin’s functionality:

    +
    p.execute()
+
    +
    +

    Once a plugin has been executed, any output from the plugin can be retrieved via properties. Let’s suppose for example there is a plugin all “test”, which has three properties called, x, y and result. When executed the plugin will take the values in x and y, compute the sum and assign it to result. The plugin can therefore be used as follows:

    +
    p = Plugin("add")
+p.x = 3.4
+p.y = 5.6
+p.execute()
+print(p.result)
+
    +
    +
    +
    + + +
    +
    +
    + +
    + +
    +

    © Copyright 2013-2021, Andy Somogyi, J Kyle Medley, Kiri Choi, Ciaran Welsh, Lucian Smith, Herbert Sauro.

    +
    + + Built with Sphinx using a + theme + provided by Read the Docs. + + +
    +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/docs/docs-build/rrplugins/rrplugins_LM_plugin.html b/docs/docs-build/rrplugins/rrplugins_LM_plugin.html new file mode 100644 index 0000000000..9a8b2589c6 --- /dev/null +++ b/docs/docs-build/rrplugins/rrplugins_LM_plugin.html @@ -0,0 +1,285 @@ + + + + + + + Levenberg-Marquardt algorithm Plugin — libRoadRunner 1.1.16 documentation + + + + + + + + + + + + + + + + + + +
    + + +
    + +
    +
    +
    + +
    +
    +
    +
    + +
    +

    Levenberg-Marquardt algorithm Plugin

    +
    +

    Introduction

    +

    The Levenberg-Marquardt plugin is used to fit an SBML model’s parameters to experimental data.

    +

    The plugin has numerous properties to allow the user full control over the internal fitting engine, as well as access to generated fitted data after a minimization session. In addition, various statistical properties, such as standardized residuals, Q-Q data, ChiSquare and reduced ChiSquare are made accessible to the user. The resulting parameter values also come with estimated confidence limits.

    +

    The current implementation is based on the lmfit C library by Joachim Wuttke1.

    +
    +
    +

    Plugin Properties

    +

    Available properties in the Levenberg-Marquardt plugin are listed in the table below. +The following properties are used internally by the fitting engine. They are pre-set with default values. Depending on the minimization problem at hand, they may need to be tweaked.

    +
      +

    1. SBML: SBML document as a string. Model to be used in the fitting.

      2. +

    2. ExperimentalData: Input data.

      3. +

    3. FittedData: Output data.

      4. +

    4. InputParameterList: Parameters to fit.

      5. +

    5. OutputParameterList: List of fitted parameters.

      6. +

    6. ExperimentalDataSelectionList: Species selection list for experimental data.

      7. +

    7. FittedDataSelectionList: Selection list for model data.

      8. +

    8. Norm: Norm of fitting. An estimate of goodness of fit.

      9. +

    9. Norms: The norm is calculated throughout a fitting session. Each Norm value is stored in the Norms (read-only) property.

      10. +

    10. ConfidenceLimits: Confidence limits for each fitted parameter. The confidence limits are calculated at a 95% confidence level.

      11. +

    11. Hessian: Hessian matrix. The Hessian is calculated using approximation at a found parameter minimum.

      12. +

    12. CovarianceMatrix: Covariance matrix. Calculated as the inverse of the Hessian.

      13. +

    13. Residuals: Residuals data.

      14. +

    14. StandardizedResiduals: Standardized Residuals.

      15. +

    15. NormalProbabilityOfResiduals: Normal Probability of Residuals.

      16. +

    16. ChiSquare: The ChiSquare at the minimum.

      17. +

    17. ReducedChiSquare: The Reduced ChiSquare at the minimum.

      18. +

    18. StatusMessage: Message from the internal fitting engine, communicating the status of the obtained fit.

      19. +

    19. NrOfIter: Number of iterations.

      20. +

    20. ftol: Relative error desired in the sum of squares.

      21. +

    21. xtol: Relative error between last two approximations.

      22. +

    22. gtol: Orthogonality desired between fvec and its derivs.

      23. +

    23. epsilon: Step used to calculate the Jacobian.

      24. +

    24. stepbound: Initial bound to steps in the outer loop. Default is 100.

      25. +

    25. patience: Used for setting maximum number of iterations, calculated as patience*(nr_of_parameters +1). Default is 100.

      26. +
    +
    +
    +

    Plugin Events

    +

    The Levenberg-Marquardt plugin are using all of a plugins available plugin events, i.e. the PluginStarted, PluginProgress and the PluginFinished events. The available data variables for each event are internally treated as pass through variables, so any data, for any of the events, assigned prior to the plugin’s execute function (in the assignOn() family of functions), can be retrieved unmodified in the corresponding event function.

    +
      +

    1. PluginStarted: Signals to application that the plugin has started applying noise on data. Both parameters are pass through parameters and are unused internally by the plugin.

      2. +

    2. PluginProgress: Communicates progress of noise generation. Both parameters are pass through parameters and are unused internally by the plugin.

      3. +

    3. PluginFinished: Signals to application that execution of the plugin has finished. Both parameters are pass through parameters and are unused internally by the plugin.

      4. +
    +
    +
    +

    The execute Function

    +

    The execute() function will start the Levenberg-Marquardt algorithm. Depending on the problem at hand, the algorithm may run for a long time. +The execute() method supports a boolean argument indicating if the execution of the plugin work will be done in a thread, or not. Threading is fully implemented in the Levenberg-Marquardt plugin. +The inThread argument defaults to false.

    +
    +
    +

    Python examples

    +

    The following Python script illustrates how the plugin can be used.

    +
    from rrplugins import *
+
+# Load Plugins
+chiPlugin       = Plugin("tel_chisquare")
+lm              = Plugin("tel_levenberg_marquardt")
+modelPlugin     = Plugin("tel_test_model")
+addNoisePlugin  = Plugin("tel_add_noise")
+
+try:
+    #========== EVENT FUNCTION SETUP ===========================
+    def myEvent(dummy): #We are not capturing any data from the plugin, so just pass a dummy
+        print('Iteration, Norm = ' + `lm.getProperty("NrOfIter")`  + ', ' + `lm.getProperty("Norm")`)
+
+    #Setup progress event function
+    progressEvent =  NotifyEventEx(myEvent)
+    assignOnProgressEvent(lm.plugin, progressEvent)
+    #============================================================
+
+    #Create model data, with and without noise using the test_model plugin
+    modelPlugin.execute()
+
+    #Setup lmfit properties.
+    lm.SBML             = modelPlugin.Model
+    lm.ExperimentalData = modelPlugin.TestDataWithNoise
+
+    # Add the parameters that we're going to fit and an initial 'start' value
+    lm.setProperty("InputParameterList", ["k1", .3])
+    lm.setProperty("FittedDataSelectionList", "[S1] [S2]")
+    lm.setProperty("ExperimentalDataSelectionList", "[S1] [S2]")
+
+    # Start minimization
+    lm.execute()
+
+    print('Minimization finished. \n==== Result ====')
+    print('Fit engine status: ' + `lm.getProperty('StatusMessage')`)
+
+    print('Hessian Matrix')
+    print(lm.getProperty("Hessian"))
+
+    print('Covariance  Matrix')
+    print(lm.getProperty("CovarianceMatrix"))
+
+    print('ChiSquare = '            + `lm.getProperty("ChiSquare")`)
+    print('Reduced ChiSquare = '    + `lm.getProperty("ReducedChiSquare")`)
+
+    #This is a list of parameters
+    parameters = tpc.getPluginProperty (lm.plugin, "OutputParameterList")
+    confLimits = tpc.getPluginProperty (lm.plugin, "ConfidenceLimits")
+
+    #Iterate trough list of parameters and confidence limits
+    para  = getFirstProperty(parameters)
+    limit = getFirstProperty(confLimits)
+    while para and limit:
+        print(getPropertyName(para) + ' = ' + `getPropertyValue(para)` + ' +/- ' + `getPropertyValue(limit)`)
+        para  = getNextProperty(parameters)
+        limit = getNextProperty(confLimits)
+
+
+    # Get the fitted and residual data
+    fittedData = lm.getProperty ("FittedData").toNumpy
+    residuals  = lm.getProperty ("Residuals").toNumpy
+
+    # Get the experimental data as a numpy array
+    experimentalData = modelPlugin.TestDataWithNoise.toNumpy
+
+    telplugins.plot(fittedData         [:,[0,1]], "blue", "-",    "",    "S1 Fitted")
+    telplugins.plot(fittedData         [:,[0,2]], "blue", "-",    "",    "S2 Fitted")
+    telplugins.plot(residuals          [:,[0,1]], "blue", "None", "x",   "S1 Residual")
+    telplugins.plot(residuals          [:,[0,2]], "red",  "None", "x",   "S2 Residual")
+    telplugins.plot(experimentalData   [:,[0,1]], "red",  "",     "*",   "S1 Data")
+    telplugins.plot(experimentalData   [:,[0,2]], "blue", "",     "*",   "S2 Data")
+    telplugins.plt.show()
+
+except Exception as e:
+    print('Problem.. ' + `e`)
+
    +
    +../_images/Minimization.png +
    +
    + + +
    +
    +
    + +
    + +
    +

    © Copyright 2013-2021, Andy Somogyi, J Kyle Medley, Kiri Choi, Ciaran Welsh, Lucian Smith, Herbert Sauro.

    +
    + + Built with Sphinx using a + theme + provided by Read the Docs. + + +
    +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/docs/docs-build/rrplugins/rrplugins_NM_plugin.html b/docs/docs-build/rrplugins/rrplugins_NM_plugin.html new file mode 100644 index 0000000000..6ba5ed4e9a --- /dev/null +++ b/docs/docs-build/rrplugins/rrplugins_NM_plugin.html @@ -0,0 +1,284 @@ + + + + + + + Nelder-Mead algorithm Plugin — libRoadRunner 1.1.16 documentation + + + + + + + + + + + + + + + + + + +
    + + +
    + +
    +
    +
    + +
    +
    +
    +
    + +
    +

    Nelder-Mead algorithm Plugin

    +
    +

    Introduction

    +

    The Nelder-Mead plugin is used to fit an SBML model’s parameters to experimental data.

    +

    The plugin has numerous properties to allow the user full control over the internal fitting engine, as well as access to generated fitted data after a minimization session. In addition, various statistical properties, such as standardized residuals, Q-Q data, ChiSquare and reduced ChiSquare are made accessible to the user. The resulting parameter values also come with estimated confidence limits.

    +

    The current implementation is based on the Nelder-Mead C implementation by Michael F. Hutt 1.

    +

    1 An implementation of the Nelder-Mead simplex method. Copyright (c) 1997-2011 Michael F. Hutt

    +
    +
    +

    Plugin Properties

    +

    Available properties in the Nelder-Mead plugin are listed in the table below. +The following properties are used internally by the fitting engine. They are pre-set with default values. Depending on the minimization problem at hand, they may need to be tweaked.

    +
      +

    1. SBML: SBML document as a string. Model to be used in the fitting.

      2. +

    2. ExperimentalData: Input data.

      3. +

    3. FittedData: Output data.

      4. +

    4. InputParameterList: Parameters to fit.

      5. +

    5. OutputParameterList: List of fitted parameters.

      6. +

    6. ExperimentalDataSelectionList: Species selection list for experimental data.

      7. +

    7. FittedDataSelectionList: Selection list for model data.

      8. +

    8. Norm: Norm of fitting. An estimate of goodness of fit.

      9. +

    9. Norms: The norm is calculated throughout a fitting session. Each Norm value is stored in the Norms (read-only) property.

      10. +

    10. ConfidenceLimits: Confidence limits for each fitted parameter. The confidence limits are calculated at a 95% confidence level.

      11. +

    11. Hessian: Hessian matrix. The Hessian is calculated using approximation at a found parameter minimum.

      12. +

    12. CovarianceMatrix: Covariance matrix. Calculated as the inverse of the Hessian.

      13. +

    13. Residuals: Residuals data.

      14. +

    14. StandardizedResiduals: Standardized Residuals.

      15. +

    15. NormalProbabilityOfResiduals: Normal Probability of Residuals.

      16. +

    16. ChiSquare: The ChiSquare at the minimum.

      17. +

    17. ReducedChiSquare: The Reduced ChiSquare at the minimum.

      18. +

    18. StatusMessage: Message from the internal fitting engine, communicating the status of the obtained fit (Currently not used).

      19. +

    19. NrOfIter: Number of (internal outer loop) iterations.

      20. +

    20. NrOfFuncIter: Number of objective function iterations.

      21. +

    21. Epsilon: Convergence tolerance. Default is 1e-6.

      22. +

    22. Scale: Scaling of vertices. Default is 1.

      23. +

    23. MaxNrOfIterations: Maximum number of iterations. Default is 1000.

      24. +

    24. Alpha: Reflection coefficient. Default is 1.

      25. +

    25. Beta: Contraction coefficient. Default is 0.5.

      26. +

    26. Gamma: Expansion coefficient. Default is 1.

      27. +
    +
    +
    +

    Plugin Events

    +

    The Nelder-Mead plugin uses all of the available plugin events, i.e. the PluginStarted, PluginProgress and the PluginFinished events. +The available data variables for each event are internally treated as pass through variables, so any data, for any of the events, assigned prior to the plugin’s execute function (in the assignOn() family of functions), can be retrieved unmodified in the corresponding event function.

    +
      +

    1. PluginStarted: Signals to application that the plugin has started applying noise on data. Both parameters are pass through parameters and are unused internally by the plugin.

      2. +

    2. PluginProgress: Communicates progress of noise generation. Both parameters are pass through parameters and are unused internally by the plugin.

      3. +

    3. PluginFinished: Signals to application that execution of the plugin has finished. Both parameters are pass through parameters and are unused internally by the plugin.

      4. +
    +
    +
    +

    Python examples

    +

    The following Python script illustrates how the plugin can be used.

    +
    from rrplugins import *
+
+# Load Plugins
+chiPlugin       = Plugin("tel_chisquare")
+nm              = Plugin("tel_nelder_mead")
+modelPlugin     = Plugin("tel_test_model")
+addNoisePlugin  = Plugin("tel_add_noise")
+
+try:
+    #========== EVENT FUNCTION SETUP ===========================
+    def myEvent(dummy): #We are not capturing any data from the plugin, so just pass a dummy
+        print('Iteration, Norm = ' + `nm.getProperty("NrOfIter")`  + ', ' + `nm.getProperty("Norm")`)
+
+    #Setup progress event function
+    progressEvent =  NotifyEventEx(myEvent)
+    assignOnProgressEvent(nm.plugin, progressEvent)
+    #============================================================
+
+    #Create model data, with and without noise using the test_model plugin
+    modelPlugin.execute()
+
+    #Setup plugin properties.
+    nm.SBML             = modelPlugin.Model
+    nm.ExperimentalData = modelPlugin.TestDataWithNoise
+
+    # Add the parameters that we're going to fit and an initial 'start' value
+    nm.setProperty("InputParameterList", ["k1", .3])
+    nm.setProperty("FittedDataSelectionList", "[S1] [S2]")
+    nm.setProperty("ExperimentalDataSelectionList", "[S1] [S2]")
+
+    # Start minimization
+    nm.execute()
+
+    print('Minimization finished. \n==== Result ====')
+
+    print('Hessian Matrix')
+    print(nm.getProperty("Hessian"))
+
+    print('Covariance  Matrix')
+    print(nm.getProperty("CovarianceMatrix"))
+
+    print('ChiSquare = '            + `nm.getProperty("ChiSquare")`)
+    print('Reduced ChiSquare = '    + `nm.getProperty("ReducedChiSquare")`)
+
+    #This is a list of parameters
+    parameters = tpc.getPluginProperty (nm.plugin, "OutputParameterList")
+    confLimits = tpc.getPluginProperty (nm.plugin, "ConfidenceLimits")
+
+    #Iterate trough list of parameters and confidence limits
+    para  = getFirstProperty(parameters)
+    limit = getFirstProperty(confLimits)
+    while para and limit:
+        print(getPropertyName(para) + ' = ' + `getPropertyValue(para)` + ' +/- ' + `getPropertyValue(limit)`)
+        para  = getNextProperty(parameters)
+        limit = getNextProperty(confLimits)
+
+
+    # Get the fitted and residual data
+    fittedData = nm.getProperty ("FittedData").toNumpy
+    residuals  = nm.getProperty ("Residuals").toNumpy
+
+    # Get the experimental data as a numpy array
+    experimentalData = modelPlugin.TestDataWithNoise.toNumpy
+
+    telplugins.plot(fittedData         [:,[0,1]], "blue", "-",    "",    "S1 Fitted")
+    telplugins.plot(fittedData         [:,[0,2]], "blue", "-",    "",    "S2 Fitted")
+    telplugins.plot(residuals          [:,[0,1]], "blue", "None", "x",   "S1 Residual")
+    telplugins.plot(residuals          [:,[0,2]], "red",  "None", "x",   "S2 Residual")
+    telplugins.plot(experimentalData   [:,[0,1]], "red",  "",     "*",   "S1 Data")
+    telplugins.plot(experimentalData   [:,[0,2]], "blue", "",     "*",   "S2 Data")
+    telplugins.plt.show()
+
+    #Finally, view the manual and version
+    nm.viewManual()
+    print('Plugin version: ' + `nm.getVersion()`)
+
+except Exception as e:
+    print('Problem.. ' + `e`)
+
    +
    +../_images/NelderMeadOutput.png +
    +
    + + +
    +
    +
    + +
    + +
    +

    © Copyright 2013-2021, Andy Somogyi, J Kyle Medley, Kiri Choi, Ciaran Welsh, Lucian Smith, Herbert Sauro.

    +
    + + Built with Sphinx using a + theme + provided by Read the Docs. + + +
    +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/docs/docs-build/rrplugins/rrplugins_add_noise_plugin.html b/docs/docs-build/rrplugins/rrplugins_add_noise_plugin.html new file mode 100644 index 0000000000..5eeea67234 --- /dev/null +++ b/docs/docs-build/rrplugins/rrplugins_add_noise_plugin.html @@ -0,0 +1,261 @@ + + + + + + + Add Noise Plugin — libRoadRunner 1.1.16 documentation + + + + + + + + + + + + + + + + + + +
    + + +
    + +
    +
    +
    + +
    +
    +
    +
    + +
    +

    Add Noise Plugin

    +
    +

    Introduction

    +

    The purpose of the AddNoise plugin is to introduce random noise to Tellurium data.

    +

    Noise generation uses the fact that a Rayleigh-distributed random variable R, with the probability distribution F(R) = 0 if R < 0 and F(R) = 1 - exp(-R^2/2*\sigma^2) if R >= 0, is related to a pair of Gaussian variables C and D through the transformation C = R * cos(\theta) and D = R * sin(\theta), where \theta is a uniformly distributed variable in the interval (0, 2 * \pi)1.

    +

    Currently only Gaussian noise is implemented.

    +

    1 From Contemporary Communication Systems USING MATLAB(R), by John G. Proakis and Masoud Salehi, published by PWS Publishing Company, 1998, pp 49-50.

    +
    +
    +

    Plugin Properties

    +
      +

    1. InputData: Data on which noise will be applied to.

      2. +

    2. Sigma: Size of applied noise. Noise is generated for each single data value, with a probability corresponding to a Gaussian distribution, centered around the value, and with a variance equal to \sigma^{2}.

      3. +

    3. NoiseType: Type of noise applied on data. Only Gaussian noise is currently supported.

      4. +

    4. Progress: The progress property communicates the progress (in percent) of Noise application.

      5. +
    +
    +
    +

    Plugin Events

    +

    The AddNoiseplugin uses all of the available plugin events, i.e. the PluginStarted, PluginProgress and the PluginFinished events. +The available data variables for each event are internally treated as pass trough variables, so any data, for any of the events, assigned prior to the plugin’s execute function (in the assignOn() family of functions), can be retrieved unmodified in the corresponding event function.

    +
      +

    1. PluginStarted: Signals to application that the plugin has started applying noise on data. Both parameters are pass through parameters and are unused internally by the plugin.

      2. +

    2. PluginProgress: Communicates progress of noise generation. Both parameters are pass through parameters and are unused internally by the plugin.

      3. +

    3. PluginFinished: Signals to application that execution of the plugin has finished. Both parameters are pass through parameters and are unused internally by the plugin.

      4. +
    +
    +
    +

    The execute Function

    +

    The execute() function will apply noise to all rows and columns of the assigned data, with one exception. Data not affected are data in the first column, and if, and only if, its column header equals ”time” (case insensitive). +The execute method supports a boolean argument indicating if the execution of the plugin work will be done in a thread, or not. Threading is fully implemented in the AddNoise plugin. +The inThread argument defaults to false.

    +
    +
    +

    Python examples

    +
    +

    Add noise to data acquired from RoadRunner

    +

    The python script below shows how to acquire simulation data from RoadRunner and pass it to the noise plugin. The format of this data, which is obtained from the simulate() function, is not directly compatible with the Noise plugin’s InputData property. This incompatibility is handled by an intermediate data structure in Python, called DataSeries.

    +
    import roadrunner
+import rrplugins as tel
+
+try:
+    # Create a roadrunner instance and create some data
+    rr = roadrunner.RoadRunner()
+    rr.load("sbml_test_0001.xml")
+    data = rr.simulate(0, 10, 511) # Want 512 points
+
+    #Add noise to the data
+    noisePlugin = tel.Plugin("tel_add_noise")
+
+    # Get the dataseries from data returned by roadrunner
+    d = tel.getDataSeries(data)
+
+    # Assign the dataseries to the plugin inputdata
+    noisePlugin.InputData = d
+
+    # Set parameter for the ’size’ of the noise
+    noisePlugin.Sigma = 3.e-6
+
+    # Add the noise
+    noisePlugin.execute()
+
+    # Get the data to plot
+    noisePlugin.InputData.plot()
+
+except Exception as e:
+    print('Problem: ' + `e`)
+
    +
    +../_images/AddNoise.png +
    +
    +

    Visualization of the noise distribution used in the AddNoise plugin

    +

    The Python script below demonstrates how to obtain and visualize the actual distribution (Gaussian) of noise that is applied on data.

    +
    import roadrunner
+import rrplugins as tel
+import matplotlib.pyplot as plt
+import scipy.stats as stats
+
+p = tel.Plugin ("tel_add_noise")
+
+value = 2.34    #This will be the mean
+n = 80000
+inputData  = np.zeros (shape=(1,2))
+inputData[0] = [0, value]
+
+data = tel.DataSeries.fromNumPy (inputData)
+p.Sigma = 0.25
+
+outArray = []
+for i in range(n):
+    p.InputData = data
+    p.execute()
+    outValues = p.InputData.toNumpy
+    outArray.append(outValues[0][1])
+
+plt.hist(outArray, 200, normed=True)
+
+# Overlay analytical solution
+aRange = np.arange(min(outArray), max(outArray), 0.001)
+plt.plot(aRange, stats.norm.pdf(aRange, value, p.Sigma), linestyle=’--’, linewidth=’2’, color=’red’)
+
+plt.show()
+
    +
    +../_images/AddNoise2.png +
    +
    +
    + + +
    +
    +
    + +
    + +
    +

    © Copyright 2013-2021, Andy Somogyi, J Kyle Medley, Kiri Choi, Ciaran Welsh, Lucian Smith, Herbert Sauro.

    +
    + + Built with Sphinx using a + theme + provided by Read the Docs. + + +
    +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/docs/docs-build/rrplugins/rrplugins_architecture.html b/docs/docs-build/rrplugins/rrplugins_architecture.html new file mode 100644 index 0000000000..2edbc47027 --- /dev/null +++ b/docs/docs-build/rrplugins/rrplugins_architecture.html @@ -0,0 +1,186 @@ + + + + + + + rrPlugins Architecture — libRoadRunner 1.1.16 documentation + + + + + + + + + + + + + + + + + + +
    + + +
    + +
    +
    +
    + +
    +
    +
    +
    + +
    +

    rrPlugins Architecture

    +
    +

    The basic philosophy behind the design of the new architecture of rrplugins as compared to the old one

    +

    Let’s first discuss what is the problem with the old architecture of rrplugins . Earlier roadrunner and rrplugins were separate entities. To build rrplugins first we need to build roadrunner then rrplugins using the libraries of libRoadRunner. In short rrplugins is dependent on roadrunner, so any change in roadrunner will need to rebuild the plugins. Also, there are two separate installations. So the primary objective was any change in roadrunner will not affect plugins and any change in plugins will not affect roadrunner.

    +

    To do so instead of using roadrunner libraries directly we used roadrunner C API (Why C API because unless we change C API the user of the API will have no impact on the project). So if we change roadrunner and the API remains the same then we have no need to rebuild rrplugins.

    +

    Let’s dive into the broad implementation details

    +

    Plugins are using the structure which consists of function pointers pointing towards C API functions of the roadrunner. This approach is devised from the mentor Dr. Herbert. We are using this because if we change libRoadRunner then plugins need to be rebuilt. But following this case, there will be no such requirements.

    +

    Every plugin requires certain classes to be used. For example, cpp plugins require this file. Earlier this used to be a part of rrplugins core (plugin loader). Now since plugins need (classes) this and the plugin loader is dependent on roadrunner we can’t use plugin loader as a dependency. So we split the plugin loader into two parts:

    +
      +

    • Core It consists of a minimal plugin loader

      • +

    • Plugin Base Class It has all the base class require for plugins

      • +
    +

    Now plugins are dependent on Base classes only not the part which requires roadrunner as a dependency. So, a change in roadrunner will have no impact on plugins.

    +

    To use roadrunner functionalities, the structure that consists of function pointers pointing towards C API functions of the roadrunner is used. Whenever a plugin loads, the plugin manager passes a pointer to the structure, so that plugin can access the roadrunner functionality using the function pointer.

    +

    A block diagram describing the interaction is given below

    +../_images/rrplugins_block_diagram.png +
    +
    +

    Extending support to C and other languages

    +

    We can currently build plugins in C++ only. We can make plugins in any language which supports interaction with C++, provided we need to make a separate API for them. Let’s consider an example of C language. There is a C API already present so we can use it to make plugins. But here is a catch. Currently, the C API we have is dependent on the roadrunner. This means using that to build plugins will generate plugins that need to be rebuilt if roadrunner is changed. Now the big question is how to overcome this. To overcome this we can make API in such a way that we use only those functions which are not dependent on roadrunner. That is a way to achieve the task.

    +
    +
    +

    How to write a new plugin and use it in Python

    +

    A minimal example to make a plugin is given in this link. And for python consider this python code. This is a minimal example and the complexity can be increased based on the need, but, the functions used here are necessary and need to be used for every plugin.

    +
    +
    +

    Current issues

    +

    We can’t skip the parameters for minimization i.e. if we have 3 parameters S1, S2, and S3 in the model and we need to minimize based on S1 and S3, we can’t do that. It is due to a problem in function.

    +

    So in general if we have parameters S1, S2, S3,…..Sn we can use parameter S1, S2,…Si (prefix) only where 1<=i<=n only.

    +
    +
    +

    Scope of Improvements

    +
      +

    • At present to use any functionality of libRoadRunner we do it with roadrunner C API. But the problem with that is it converts roadrunner data types which are in C++ to C data types and then using pointers we reference that and again convert C to C++. It is a time-consuming process. Instead, we could use void pointers and send and then cast to appropriate data types on the side of the plugin. This will significantly boost the performance.

      • +

    • A very long-term merging rrplugins python wrapper which is in CPython with SWIG. It will be a very tough task. It’s super hard to debug code if something has gone wrong. I tried it but failed to merge and to be honest there is no present need for this and it can be delayed.

      • +
    +
    +
    + + +
    +
    +
    + +
    + +
    +

    © Copyright 2013-2021, Andy Somogyi, J Kyle Medley, Kiri Choi, Ciaran Welsh, Lucian Smith, Herbert Sauro.

    +
    + + Built with Sphinx using a + theme + provided by Read the Docs. + + +
    +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/docs/docs-build/rrplugins/rrplugins_auto_plugin.html b/docs/docs-build/rrplugins/rrplugins_auto_plugin.html new file mode 100644 index 0000000000..73a135de6b --- /dev/null +++ b/docs/docs-build/rrplugins/rrplugins_auto_plugin.html @@ -0,0 +1,275 @@ + + + + + + + AUTO2000 Plugin — libRoadRunner 1.1.16 documentation + + + + + + + + + + + + + + + + + + +
    + + +
    + +
    +
    +
    + +
    +
    +
    +
    + +
    +

    AUTO2000 Plugin

    +
    +

    Introduction

    +

    The AUTO2000 plugin serves as a front-end for the AUTO2000 library, which is a library for continuation and bifurcation problems in ordinary differential equations 1.

    +

    Current limitations: Multiple continuation parameters are not supported, i.e. only one parameter can be selected for any continuation problem.

    +

    Available properties in the auto2000 plugin are documented in the next section.

    +

    1 AUTO2000 by Eusebius J. Doedel , Randy C. Paffenroth, Alan R. Champneys, Thomas F. Fairgrieve, Yuri A. Kuznetsov, Bart E. Oldeman, Bj�rn Sandstede and Xianjun Wang. See http://www.dam.brown.edu/people/sandsted/publications/auto2000.pdf.

    +
    +
    +

    Plugin Properties

    +

    The AUTO library has numerous properties that have been wrapped and made available to a plugin client. Each property is listed below with its data type, default value and a short description. For the exact usage and a more in detail description please consult the main AUTO2000 manual.

    +

    The following properties are used internally by the auto library. Depending on the problem at hand, they may need to be tweaked.

    +
      +

    1. SBML: SBML document as a string. Model to be used by AUTO

      2. +

    2. TempFolder: Folder used by auto and the plugin for saving temporary files. Takes a string

      3. +

    3. KeepTempFiles: Boolean indicating if temporary files should be deleted after an AUTO session or not. Default is ‘False’

      4. +

    4. ScanDirection: Parameter instructing AUTO how to sweep its principal continuation parameter. Either ‘Positive’ or ‘Negative’. Default is ‘Positive’

      5. +

    5. PrincipalContinuationParameter: The principal continuation parameter (PCP) is the first parameter that AUTO will sweep. Currently only one parameter is supported, which by default is the PCP. Takes a string

      6. +

    6. BifurcationPoints: This integer vector holds the exact point number (in the sequence of all output data) for an AUTO solution point. It can be used together with the labels in the bifurcationlabels property to assist in plotting a bifurcation diagram.

      7. +

    7. BifurcationLabels: The string list holds the AUTO designated solution type label for a solution point, as found in the bifurcationpoints property. Consult the AUTO documentation for possible label types and their meaning

      8. +

    8. BifurcationData: The BifurcationData property holds the bifurcation diagram after a session. The first column contains the values of the selected parameter, and successive columns are selected species

      9. +

    9. fort2: Property containing the content of the AUTO temporary file, fort.2. Fort.2 is the input file for AUTO and created by the plugin

      10. +

    10. fort3: Property containing the content of the AUTO temporary file, fort.3. The content of fort.3 file is undocumented in AUTO’s documentation

      11. +

    11. fort6: Property containing the content of the AUTO temporary file, fort.6. The content of fort.6 file is a bifurcation session summary

      12. +

    12. fort7: Property containing the content of the AUTO temporary file, fort.7. The content of fort.7 file is a bifurcation diagram on success

      13. +

    13. fort8: Property containing the content of the AUTO temporary file, fort.8. The content of fort.8 file contain various statistics from the session

      14. +

    14. fort9: Property containing the content of the AUTO temporary file, fort.8. Diagnostic messages, convergence history, eigenvalues, and Floquet multipliers are written in fort.9

      15. +

    15. NDIM: The NDIM property correspond to the dimension of the system of equations

      16. +

    16. IPS: Constant defining the problem type

      17. +

    17. IRS: This constant sets the label of the solution where the computation is to be restarted.

      18. +

    18. ILP: Fold detection; 1=ON, 0=OFF

      19. +

    19. NICP: Property denoting the number of free parameters

      20. +

    20. ICP: Free parameters

      21. +

    21. NTST: The number of mesh intervals

      22. +

    22. NCOL: The number of collocation points per mesh interval

      23. +

    23. IAD: Mesh adaption every IAD steps; 0=OFF

      24. +

    24. ISP: Bifurcation detection; 0=OFF, 1=BP(FP), 3=BP(PO,BVP), 2=all

      25. +

    25. ISW: Branch switching: 1=normal, -1=switch branch (BP, HB, PD), 2=switch to two-parameter continuation (LP, BP, HB, TR) 3=switch to three-parameter continuation (BP)

      26. +

    26. IPLT: This constant allows redefinition of the principal solution measure, which is printed as the second (real) column in the fort.7 output-file. See AUTO manual for possible settings

      27. +

    27. NBC: Number of boundary conditions

      28. +

    28. NINT: Number of integral conditions

      29. +

    29. NMX: Maximum number of steps

      30. +

    30. RL0: The lower bound on the principal continuation parameter

      31. +

    31. RL1: The upper bound on the principal continuation parameter

      32. +

    32. A0: The lower bound on the principal solution measure

      33. +

    33. A1: The upper bound on the principal solution measure

      34. +

    34. NPR: Save the solution in the solution file every NPR continuation steps

      35. +

    35. MXBF: Automatic branch switching for the first MXBF bifurcation points if IPS=0, 1

      36. +

    36. IID: Control diagnostic output; 0=none, 1=little, 2=normal, 4=extensive

      37. +

    37. ITMX: Maximum number of iterations for locating special solutions/points

      38. +

    38. ITNW: Maximum number of correction steps

      39. +

    39. NWTN: Corrector uses full newton for NWTN steps

      40. +

    40. JAC: User defines derivatives; 0=no, 1=yes

      41. +

    41. EPSL: Property setting the convergence criterion for parameters

      42. +

    42. EPSU: Property setting the convergence criterion for solution components

      43. +

    43. EPSS: Property setting the convergence criterion for special points

      44. +

    44. DS: Session start step size

      45. +

    45. DSMIN: Minimum continuation step size

      46. +

    46. DSMAX: Maximum continuation step size

      47. +

    47. IADS: Step size adaption every IADS steps; 0=OFF

      48. +

    48. NTHL: The number of modified parameter weights (for BVP)

      49. +

    49. THL: List of parameter weights

      50. +

    50. NTHU: The number of modified solution component weights (for BVP)

      51. +

    51. THU: List of solution weights

      52. +

    52. NUZR: The number of user output points specified

      53. +

    53. UZR: List of values for user defined output

      54. +
    +
    +
    +

    The execute Function

    +

    The execute() function will start a bifurcation session. Depending on the problem at hand, the algorithm may run for a long time. +The execute() method supports a boolean argument indicating if the execution of the plugin work will be done in a thread, or not. If set to false, i.e. executing execute(false), the function will be a blocking function and will not return until the plugin work is done. If it is set to true, the execute(true) will return immediately and the plugin work will be executed in a thread. The user can use the isPluginDone(plugin) to query the status of the plugin progression. +The inThread argument defaults to false.

    +
    +
    +

    Plugin Events

    +

    The auto2000 plugin uses all of the available plugin events, i.e. the PluginStarted, PluginProgress and the PluginFinished events. +The available data variables for each event are internally treated as pass through variables, so any data, for any of the events, assigned prior to the plugins execute function (in the assignOn() family of functions), can be retrieved unmodified in the corresponding event function.

    +
      +

    1. PluginStarted: Signals to application that the plugin has started applying noise on data. Both parameters are pass through parameters and are unused internally by the plugin.

      2. +

    2. PluginProgress: Communicates progress of noise generation. Both parameters are pass through parameters and are unused internally by the plugin.

      3. +

    3. PluginFinished: Signals to application that execution of the plugin has finished. Both parameters are pass through parameters and are unused internally by the plugin.

      4. +
    +
    +
    +

    Python examples

    +

    The following Python script illustrates how the auto plugin can be invoked, how to set its properties and finally how to plot a bifurcation diagram.

    +
    from rrplugins import *
+
+try:
+    sbmlModel ="BIOMD0000000203.xml"
+    auto = Plugin("tel_auto2000")
+
+    #Setup Auto Propertys
+    auto.setProperty("SBML", readAllText(sbmlModel))
+
+    #Auto specific properties
+    auto.setProperty("ScanDirection", "Positive")
+    auto.setProperty("PrincipalContinuationParameter", "A")
+    auto.setProperty("PCPLowerBound", 10)
+    auto.setProperty("PCPUpperBound", 200)
+
+    #Max numberof points
+    auto.setProperty("NMX", 5000)
+
+    #Execute the plugin
+    auto.execute()
+
+    # Bifurcation summary
+    print("Summary: " + auto.BifurcationSummary)
+
+    #Plot Bifurcation diagram
+    pts     = auto.BifurcationPoints
+    lbls    = auto.BifurcationLabels
+    biData  = auto.BifurcationData
+
+    biData.plotBifurcationDiagram(pts, lbls)
+
+    print("Done")
+
+except Exception as e:
+    print("There was a problem: " + `e`)
+
    +
    +../_images/AutoOutput.png +
    +
    + + +
    +
    +
    + +
    + +
    +

    © Copyright 2013-2021, Andy Somogyi, J Kyle Medley, Kiri Choi, Ciaran Welsh, Lucian Smith, Herbert Sauro.

    +
    + + Built with Sphinx using a + theme + provided by Read the Docs. + + +
    +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/docs/docs-build/rrplugins/rrplugins_chisquare_plugin.html b/docs/docs-build/rrplugins/rrplugins_chisquare_plugin.html new file mode 100644 index 0000000000..0d14dacc53 --- /dev/null +++ b/docs/docs-build/rrplugins/rrplugins_chisquare_plugin.html @@ -0,0 +1,204 @@ + + + + + + + Chi Square Plugin — libRoadRunner 1.1.16 documentation + + + + + + + + + + + + + + + + + + +
    + + +
    + +
    +
    +
    + +
    +
    +
    +
    + +
    +

    Chi Square Plugin

    +
    +

    Introduction

    +

    The purpose of the ChiSquare plugin is to calculate the ChiSquare and the reduced ChiSquare for two sets of data.

    +
    +
    +

    Plugin Properties

    +
      +

    1. ExperimentalData: Data representing Experimental data.

      2. +

    2. ModelData: Data representing Model data.

      3. +

    3. NrOfModelParameters: Number of model parameters used to create the model data.

      4. +

    4. ChiSquare: The calculated ChiSquare.

      5. +

    5. ReducedChiSquare: The calculated reduced ChiSquare.

      6. +
    +
    +
    +

    Plugin Events

    +

    This plugin does not use any plugin events.

    +
    +
    +

    The execute Function

    +

    The execute() function will attempt to calculate the ChiSquare, and the reduced ChiSquare, using data supplied by the user.

    +
    +
    +

    Python examples

    +

    The python script below shows how to use the plugin.

    +
    from rrplugins import *
+
+try:
+    modelPlugin     = Plugin("tel_test_model")
+    noisePlugin     = Plugin("tel_add_noise")
+    chiSquarePlugin = Plugin("tel_chisquare")
+
+    #Generate internal test data
+    modelPlugin.execute()
+    modelData = modelPlugin.TestData
+    expData = modelPlugin.TestDataWithNoise
+
+    chiSquarePlugin.ExperimentalData = expData
+    chiSquarePlugin.ModelData = modelData
+    chiSquarePlugin.NrOfModelParameters = 1
+
+    chiSquarePlugin.execute()
+
+    chi = chiSquarePlugin.ChiSquare
+    reduced_chi = chiSquarePlugin.ReducedChiSquare
+
+    print('ChiSquare is: ' + `chi`)
+    print('Reduced ChiSquare is: ' + `reduced_chi`)
+
+except Exception as e:
+    print('Problem: ' + `e`)
+
    +
    +
    +
    + + +
    +
    +
    + +
    + +
    +

    © Copyright 2013-2021, Andy Somogyi, J Kyle Medley, Kiri Choi, Ciaran Welsh, Lucian Smith, Herbert Sauro.

    +
    + + Built with Sphinx using a + theme + provided by Read the Docs. + + +
    +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/docs/docs-build/rrplugins/rrplugins_monte_carlo_plugin.html b/docs/docs-build/rrplugins/rrplugins_monte_carlo_plugin.html new file mode 100644 index 0000000000..44a6d385f4 --- /dev/null +++ b/docs/docs-build/rrplugins/rrplugins_monte_carlo_plugin.html @@ -0,0 +1,280 @@ + + + + + + + Monte Carlo bootstrap algorithm Plugin — libRoadRunner 1.1.16 documentation + + + + + + + + + + + + + + + + + + +
    + + +
    + +
    +
    +
    + +
    +
    +
    +
    + +
    +

    Monte Carlo bootstrap algorithm Plugin

    +
    +

    Introduction

    +

    The Monte Carlo plugin is used to obtain estimates of the confidence limits for a model’s parameters. This is in the context where experimental data exists and a parameter minimization method, such as Levenberg-Marquardt or Nelder-Mead has already been used in order to find a parameter minimum.

    +

    The Monte Carlo algorithm is used subsequently at this minimum and will give an estimate of parameter confidence limits corresponding to the variance in the original experimental data.

    +

    The plugin has properties such as the size of the Monte Carlo population, minimization algorithm to use (e.g. Nelder-Mead or Levenberg-Marquardt), and on output, confidence limits for each involved parameter.

    +

    Plugin properties are documented in more detail in the next section.

    +
    +
    +

    Plugin Properties

    +

    Available properties in the Monte Carlo plugin are listed in the table below.

    +
      +

    1. SBML: SBML document as a string. Model to be used by the Monte Carlo plugin.

      2. +

    2. ExperimentalData: Input data.

      3. +

    3. InputParameterList: Parameters to estimate confidence limits for.

      4. +

    4. MonteCarloParameters: Parameters obtained from a Monte Carlo session.

      5. +

    5. ConfidenceLimits: Confidence limits for each fitted parameter. The confidence limits are calculated at a 95% confidence level.

      6. +

    6. ExperimentalDataSelectionList: Selection list for experimental data.

      7. +

    7. FittedDataSelectionList: Selection list for model data.

      8. +

    8. NrOfMCRuns: Number of Monte Carlo data sets to generate and use.

      9. +

    9. MinimizerPlugin: Minimizer used by the Monte Carlo Engine, e.g. ”Levenberg_Marquardt”.

      10. +
    +
    +
    +

    Plugin Events

    +

    The Monte Carlo plugin uses all of the available plugin events, i.e. the PluginStarted, PluginProgress and the PluginFinished events. +The available data variables for each event are internally treated as pass through variables, so any data, for any of the events, assigned prior to the plugins execute function (in the assignOn() family of functions), can be retrieved unmodified in the corresponding event function.

    +
      +

    1. PluginStarted: Signals to application that the plugin has started applying noise on data. Both parameters are pass through parameters and are unused internally by the plugin.

      2. +

    2. PluginProgress: Communicates progress of noise generation. Both parameters are pass through parameters and are unused internally by the plugin.

      3. +

    3. PluginFinished: Signals to application that execution of the plugin has finished. Both parameters are pass through parameters and are unused internally by the plugin.

      4. +
    +
    +
    +

    The execute Function

    +

    The execute() function will start the Monte Carlo algorithm. Depending on the problem at hand, the algorithm may run for a long time. +The execute(), method supports a boolean argument indicating if the execution of the plugin work will be done in a thread, or not. Threading is fully implemented in the Monte Carlo plugin. +The inThread argument defaults to false. +Each generated Monte Carlo dataset is available in a file named, MCDataSets.dat (saved in current working directory).

    +
    +
    +

    Python examples

    +

    The following Python script illustrates how the plugin can be used.

    +
    from rrplugins import *
+import matplotlib.pyplot as plt
+
+try:
+    #Load plugins
+    modelP      = Plugin("tel_test_model")
+    nP          = Plugin("tel_add_noise")
+    chiP        = Plugin("tel_chisquare")
+    lmP         = Plugin("tel_levenberg_marquardt")
+    nmP         = Plugin("tel_nelder_mead")
+    mcP         = Plugin("tel_monte_carlo_bs")
+
+    #========== EVENT FUNCTION SETUP ===========================
+    def myEventFunction(ignore):
+        # Get the fitted and residual data
+        experimentalData    = lmP.getProperty ("ExperimentalData").toNumpy
+        fittedData          = lmP.getProperty ("FittedData").toNumpy
+        residuals           = lmP.getProperty ("Residuals").toNumpy
+
+        telplugins.plot(fittedData         [:,[0,1]], "blue", "-",    "",    "S1 Fitted")
+        telplugins.plot(fittedData         [:,[0,2]], "blue", "-",    "",    "S2 Fitted")
+        telplugins.plot(residuals          [:,[0,1]], "blue", "None", "x",   "S1 Residual")
+        telplugins.plot(residuals          [:,[0,2]], "red",  "None", "x",   "S2 Residual")
+        telplugins.plot(experimentalData   [:,[0,1]], "red",  "",     "*",   "S1 Data")
+        telplugins.plot(experimentalData   [:,[0,2]], "blue", "",     "*",   "S2 Data")
+
+        print 'Minimization finished. \n==== Result ===='
+        print getPluginResult(lmP.plugin)
+        telplugins.plt.show()
+
+    #Communicating event
+    myEvent =  NotifyEventEx(myEventFunction)
+
+    #Uncomment the event assignment below to plot each monte carlo data set
+    #assignOnFinishedEvent(lmP.plugin, myEvent, None)
+
+    #This will create test data with noise. We will use that as 'experimental' data
+    modelP.execute()
+
+    #Setup Monte Carlo properties.
+    mcP.SBML                             = modelP.Model
+    mcP.ExperimentalData                 = modelP.TestDataWithNoise
+
+    #Select what minimization plugin to use
+    #mcP.MinimizerPlugin                  = "Nelder-Mead"
+    mcP.MinimizerPlugin                  = "Levenberg-Marquardt"
+    mcP.NrOfMCRuns                       = 100
+    mcP.InputParameterList               = ["k1", 1.5]
+    mcP.FittedDataSelectionList          = "[S1] [S2]"
+    mcP.ExperimentalDataSelectionList    = "[S1] [S2]"
+
+    # Start Monte Carlo
+    mcP.execute()
+
+    print 'Monte Carlo Finished. \n==== Result ===='
+    print mcP.MonteCarloParameters.getColumnHeaders()
+    paras = mcP.MonteCarloParameters.toNumpy
+    print paras
+
+    #Get mean (assuming normal distribution).
+    print "The mean: k1= " + `np.mean(paras)`
+
+
+    PropertyOfTypeListHandle = getPluginProperty(mcP.plugin, "ConfidenceLimits")
+    print `getNamesFromPropertyList(PropertyOfTypeListHandle)`
+    aProperty = getFirstProperty(PropertyOfTypeListHandle)
+    if aProperty:
+        print getPropertyValueAsString(aProperty)
+
+    #Show MOnte Carlo parameters as a histogram
+    plt.hist(paras, 50, normed=True)
+    plt.show()
+
+    #Plot Monte Carlo data sets
+    #dataSeries =  DataSeries.readDataSeries("MCDataSets.dat")
+    #dataSeries.plot()
+
+    #Finally, view the manual and version
+    mcP.viewManual()
+    print 'Plugin version: ' + `mcP.getVersion()`
+
+
+except Exception as e:
+    print 'Problem.. ' + `e`
+
    +
    +../_images/MonteCarloOutput.png +
    +
    + + +
    +
    +
    + +
    + +
    +

    © Copyright 2013-2021, Andy Somogyi, J Kyle Medley, Kiri Choi, Ciaran Welsh, Lucian Smith, Herbert Sauro.

    +
    + + Built with Sphinx using a + theme + provided by Read the Docs. + + +
    +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/docs/docs-build/rrplugins/rrplugins_testmodel_plugin.html b/docs/docs-build/rrplugins/rrplugins_testmodel_plugin.html new file mode 100644 index 0000000000..5b7db10764 --- /dev/null +++ b/docs/docs-build/rrplugins/rrplugins_testmodel_plugin.html @@ -0,0 +1,196 @@ + + + + + + + Test Model Plugin — libRoadRunner 1.1.16 documentation + + + + + + + + + + + + + + + + + + +
    + + +
    + +
    +
    +
    + +
    +
    +
    +
    + +
    +

    Test Model Plugin

    +
    +

    Introduction

    +

    The purpose of the TestModel plugin is to conveniently embed a SBML test model in a plugin. In addition, the plugin provides the user with simulated data, with and without applied artificial Gaussian noise.

    +

    Currently no settings are exposed for the actual simulation of the test model.

    +

    The TestModel plugin depends on the AddNoise plugin.

    +
    +
    +

    Plugin Properties

    +
      +

    1. Model: The actual test model, in XML format.

      2. +

    2. TestData: Simulated data, using the TestModel as input and default RoadRunner Simulation values.

      3. +

    3. TestDataWithNoise: NumberSimulated data, with applied noise.

      4. +
    +
    +
    +

    Plugin Events

    +

    This plugin does not use any plugin events.

    +
    +
    +

    The execute Function

    +

    The execute() function will generate simulated data, and simulated data with noise. The data will be available in the properties, TestData and TestDataWithNoise respectively.

    +
    +
    +

    Python examples

    +

    The python script below shows how to use the plugin.

    +
    import rrplugins as tel
+
+try:
+    modelPlugin = tel.Plugin("tel_test_model")
+
+    #Test model plugin depends on the add_noise plugin
+    noisePlugin = tel.Plugin("tel_add_noise")
+
+    #Generate internal test data
+    modelPlugin.execute()
+    test_data = modelPlugin.TestData
+    test_data_with_noise = modelPlugin.TestDataWithNoise
+
+    test_data.plot()
+    test_data_with_noise.plot()
+
+except Exception as e:
+    print('Problem: ' + `e`)
+
    +
    +
    +
    + + +
    +
    +
    + +
    + +
    +

    © Copyright 2013-2021, Andy Somogyi, J Kyle Medley, Kiri Choi, Ciaran Welsh, Lucian Smith, Herbert Sauro.

    +
    + + Built with Sphinx using a + theme + provided by Read the Docs. + + +
    +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/docs/docs-build/search.html b/docs/docs-build/search.html index 240e31b9dc..bfde5fc2d3 100644 --- a/docs/docs-build/search.html +++ b/docs/docs-build/search.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/searchindex.js b/docs/docs-build/searchindex.js index ee96a6d644..3172f041e9 100644 --- a/docs/docs-build/searchindex.js +++ b/docs/docs-build/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["C++APIReference/CVODEIntegrator", "C++APIReference/Dictionary", "C++APIReference/EulerIntegrator", "C++APIReference/ExecutableModelFactory", "C++APIReference/GillespieIntegrator", "C++APIReference/Integrator", "C++APIReference/IntegratorRegistration", "C++APIReference/NLEQ1Solver", "C++APIReference/NLEQ2Solver", "C++APIReference/RK45Integrator", "C++APIReference/RK4Integrator", "C++APIReference/RoadRunnerMap", "C++APIReference/SBMLValidator", "C++APIReference/Solver", "C++APIReference/SolverRegistration", "C++APIReference/SteadyStateSolver", "C++APIReference/Variant", "C++APIReference/index", "C++APIReference/llvm/ASTNodeCodeGen", "C++APIReference/llvm/ASTNodeFactory", "C++APIReference/llvm/AssignmentRuleEvaluator", "C++APIReference/llvm/CodeGen", "C++APIReference/llvm/CodeGenBase", "C++APIReference/llvm/EvalConversionFactorCodeGen", "C++APIReference/llvm/EvalInitialConditionsCodeGen", "C++APIReference/llvm/EvalRateRuleRatesCodeGen", "C++APIReference/llvm/EvalReactionRatesCodeGen", "C++APIReference/llvm/EvalVolatileStoichCodeGen", "C++APIReference/llvm/EventAssignCodeGen", "C++APIReference/llvm/EventCodeGenBase", "C++APIReference/llvm/EventQueue", "C++APIReference/llvm/EventTriggerCodeGen", "C++APIReference/llvm/FunctionResolver", "C++APIReference/llvm/KineticLawParameterResolver", "C++APIReference/llvm/LLVMCompiler", "C++APIReference/llvm/LLVMException", "C++APIReference/llvm/LLVMExecutableModel", "C++APIReference/llvm/LLVMModelData", "C++APIReference/llvm/LLVMModelDataSymbols", 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"roadrunner.getsimulationdata() (in module roadrunner)": [[87, "RoadRunner.Roadrunner.getSimulationData"]], "__init__() (roadrunner method)": [[87, "RoadRunner.__init__"]], "addassignmentrule() (roadrunner.roadrunner method)": [[87, "RoadRunner.RoadRunner.addAssignmentRule"]], "addcompartment() (roadrunner.roadrunner method)": [[87, "RoadRunner.RoadRunner.addCompartment"]], "adddelay() (roadrunner.roadrunner method)": [[87, "RoadRunner.RoadRunner.addDelay"]], "addevent() (roadrunner.roadrunner method)": [[87, "RoadRunner.RoadRunner.addEvent"]], "addeventassignment() (roadrunner.roadrunner method)": [[87, "RoadRunner.RoadRunner.addEventAssignment"]], "addparameter() (roadrunner.roadrunner method)": [[87, "RoadRunner.RoadRunner.addParameter"]], "addpriority() (roadrunner.roadrunner method)": [[87, "RoadRunner.RoadRunner.addPriority"]], "addraterule() (roadrunner.roadrunner method)": [[87, "RoadRunner.RoadRunner.addRateRule"]], "addreaction() (roadrunner.roadrunner method)": [[87, "RoadRunner.RoadRunner.addReaction"], [87, "id0"]], "addspeciesconcentration() (roadrunner.roadrunner method)": [[87, "RoadRunner.RoadRunner.addSpeciesConcentration"]], "addtrigger() (roadrunner.roadrunner method)": [[87, "RoadRunner.RoadRunner.addTrigger"]], "clearmodel() (roadrunner.roadrunner method)": [[87, "RoadRunner.RoadRunner.clearModel"]], "conservedmoietyanalysis (roadrunner.roadrunner attribute)": [[87, "RoadRunner.RoadRunner.conservedMoietyAnalysis"]], "createselection() (roadrunner method)": [[87, "RoadRunner.createSelection"]], "getavailableintegrators() (roadrunner.roadrunner method)": [[87, "RoadRunner.RoadRunner.getAvailableIntegrators"]], "getcc() (roadrunner.roadrunner method)": [[87, "RoadRunner.RoadRunner.getCC"]], "getcompiler() (roadrunner method)": [[87, "RoadRunner.getCompiler"]], "getconfigurationxml() (roadrunner.roadrunner method)": [[87, "RoadRunner.RoadRunner.getConfigurationXML"]], "getconservationmatrix() (roadrunner.roadrunner method)": [[87, 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"SteadyStateSolver.approx_tolerance"]], "broyden_method (steadystatesolver attribute)": [[90, "SteadyStateSolver.broyden_method"]], "linearity (steadystatesolver attribute)": [[90, "SteadyStateSolver.linearity"]], "maximum_iterations (steadystatesolver attribute)": [[90, "SteadyStateSolver.maximum_iterations"]], "minimum_damping (steadystatesolver attribute)": [[90, "SteadyStateSolver.minimum_damping"]], "presimulation_maximum_steps (steadystatesolver attribute)": [[90, "SteadyStateSolver.presimulation_maximum_steps"]], "presimulation_time (steadystatesolver attribute)": [[90, "SteadyStateSolver.presimulation_time"]], "relative_tolerance (steadystatesolver attribute)": [[90, "SteadyStateSolver.relative_tolerance"]], "roadrunner.steadystatesolver (built-in class)": [[90, "roadrunner.SteadyStateSolver"]], "solve() (steadystatesolver method)": [[90, "SteadyStateSolver.solve"]]}}) \ No newline at end of file diff --git a/docs/docs-build/selecting_values.html b/docs/docs-build/selecting_values.html index 2ef6bb0af6..f22e75e0b3 100644 --- a/docs/docs-build/selecting_values.html +++ b/docs/docs-build/selecting_values.html @@ -12,10 +12,9 @@ - - + @@ -125,7 +124,7 @@

    Selection syntax[] is interpreted as a concentration, i.e. [S1], [S2], etc. The identifier must be a valid SBML species, otherwise an exception is raised.

    -
    Rates of Change: '

    Represents the rate of change, \frac{dy}{dt} of a species amount. Rates of change +

    Rates of Change: '

    Represents the rate of change, \frac{dy}{dt} of a species amount. Rates of change selections follow generally accepted mathematical convention of using the single quote, ' to represent a time derivative. A rate of change selection is any identifier followed by a single quote, i.e. S1', S2', P1', etc. A rates of change selection diff --git a/docs/docs-build/sensitivities/sensitivities_index.html b/docs/docs-build/sensitivities/sensitivities_index.html index e995561179..75de9ea139 100644 --- a/docs/docs-build/sensitivities/sensitivities_index.html +++ b/docs/docs-build/sensitivities/sensitivities_index.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/simulation_and_integration.html b/docs/docs-build/simulation_and_integration.html index 4c4fcee52c..88f0b1497e 100644 --- a/docs/docs-build/simulation_and_integration.html +++ b/docs/docs-build/simulation_and_integration.html @@ -12,10 +12,9 @@ - - + @@ -102,7 +101,7 @@

    Preliminaries -

    y(t) = \int_0^t f(t, y) dt

    +

    y(t) = \int_0^t f(t, y) dt

    where the function :math: f(t) is generated from the SBML document.

    As this is numerically integrated, it is impossible to specify a time step and other integration parameters that are ideal for all functions. As a general rule for numeric stability, if you have a diff --git a/docs/docs-build/stability.html b/docs/docs-build/stability.html index c333abfdc7..d36ef5422a 100644 --- a/docs/docs-build/stability.html +++ b/docs/docs-build/stability.html @@ -12,10 +12,9 @@ - - + @@ -95,12 +94,12 @@

    Stability Analysis

    The stability of a biochemical system is determined by the eigenvalues of the Jacobian matrix. Given -m floating species and n reactions, the Jacobian matrix is defined as follows:

    +m floating species and n reactions, the Jacobian matrix is defined as follows:

    -

    J=\begin{bmatrix} \dfrac{\partial F_1}{\partial S_1} & \cdots & \dfrac{\partial F_1}{\partial S_m} \\ +

    J=\begin{bmatrix} \dfrac{\partial F_1}{\partial S_1} & \cdots & \dfrac{\partial F_1}{\partial S_m} \\ \vdots & \ddots & \vdots \\ \dfrac{\partial F_n}{\partial S_1} & \cdots & \dfrac{\partial F_n}{\partial S_m} -\end{bmatrix}</span></p> -</div><p>where <span class=F_i is the ith differential equation and S_i the ith floating species. From RoadRunner it is easy to obtain the Jacobian matrix using :cpp:rr::RoadRunner::getFullJacobian, i.e.:

    +\end{bmatrix}"/>

    +

    where F_i is the ith differential equation and S_i the ith floating species. From RoadRunner it is easy to obtain the Jacobian matrix using :cpp:rr::RoadRunner::getFullJacobian, i.e.:

    Jac = rr.getFullJacobian()
    diff --git a/docs/docs-build/steady_state.html b/docs/docs-build/steady_state.html index e7044451a6..1ab8631146 100644 --- a/docs/docs-build/steady_state.html +++ b/docs/docs-build/steady_state.html @@ -12,10 +12,9 @@ - - + @@ -96,21 +95,21 @@

    Steady State Analysis

    The dynamics of a biochemical network is described by the system equation

    -

    \frac{d}{dt}\mathbf{s}(t) = \mathbf{N} \mathbf{v}(\mathbf{s}(t),\mathbf{p},t),

    +

    \frac{d}{dt}\mathbf{s}(t) = \mathbf{N} \mathbf{v}(\mathbf{s}(t),\mathbf{p},t),

    where
      -

    • \mathbf{s} is the vector of species concentrations

      • -

    • mathbf{N} is the stoichiometry matrix

      • -

    • \mathbf{p} is a vector of time independent parameters

      • -

    • t is time.

      • -

    • mathbf{v} is a matrix of reaction fluxes dependent on \mathbf{s}(t), \mathbf{p} and time t

      • +

    • \mathbf{s} is the vector of species concentrations

      • +

    • mathbf{N} is the stoichiometry matrix

      • +

    • \mathbf{p} is a vector of time independent parameters

      • +

    • t is time.

      • +

    • mathbf{v} is a matrix of reaction fluxes dependent on \mathbf{s}(t), \mathbf{p} and time t

    The steady state is the solution to the network equations when all the rates of change are zero. That is the concentrations of the floating -species, \mathbf{s} that satisfy:

    +species, \mathbf{s} that satisfy:

    -

    \mathbf{N} \mathbf{v}(\mathbf{s}(t),\mathbf{p},t) = 0

    +

    \mathbf{N} \mathbf{v}(\mathbf{s}(t),\mathbf{p},t) = 0

    The steady state is easily calculated using the steady state method:

    >>> rr.steadyState()
 1.234567E-9
diff --git a/docs/docs-build/stochastic.html b/docs/docs-build/stochastic.html
index 9bb5b75fc4..872f1434a6 100644
--- a/docs/docs-build/stochastic.html
+++ b/docs/docs-build/stochastic.html
@@ -12,10 +12,9 @@
     
   
   
-        
         
-        
         
+        
         
         
     
diff --git a/docs/docs-build/stoichiometric.html b/docs/docs-build/stoichiometric.html
index 636c4ade90..5cb9fe07d6 100644
--- a/docs/docs-build/stoichiometric.html
+++ b/docs/docs-build/stoichiometric.html
@@ -12,10 +12,9 @@
     
   
   
-        
         
-        
         
+        
         
         
     
@@ -101,30 +100,30 @@
 
    Stoichiometric Analysis
    
 
    
 
    Preliminaries
    
-
    A network of m chemical species and n reactions can be described by the
-m by n stochiometry matrix \mathbf{N}. \mathbf{N}_{i,j} is the net number of
-species i produced or consumed in reaction j.  The dynamics of the network are
+
    A network of m chemical species and n reactions can be described by the
+m by n stochiometry matrix \mathbf{N}. \mathbf{N}_{i,j} is the net number of
+species i produced or consumed in reaction j.  The dynamics of the network are
 described by
    
 
    
-
    \frac{d}{dt}\mathbf{s}(t) = \mathbf{N} \mathbf{v}(\mathbf{s}(t),\mathbf{p},t),
    
-
    where \mathbf{s} is the vector of species concentrations, \mathbf{p}
-is a vector of time independent parameters, and t is time.
    
+
    \frac{d}{dt}\mathbf{s}(t) = \mathbf{N} \mathbf{v}(\mathbf{s}(t),\mathbf{p},t),
    
+

    where \mathbf{s} is the vector of species concentrations, \mathbf{p} +is a vector of time independent parameters, and t is time.

    Each structural conservation, or interchangably, conserved sum (e.g. conserved moiety) in -the network coresponds to a lineraly dependent row in the stoichiometry matrix \mathbf{N}.

    -

    If there are conserved sums, then the row rank, r of N is < m, and -the stochiometry matrix N may first be re-ordered such that the first r are linearly -independent, and the remaining m-r rows are linear combinations of the first r -rows. The reduced stochiometry matrix \mathbf{N_R} is then formed from the first -r rows of N. Finally, N may be expressed as a product of the m \times r -link matrix \mathbf{L} and the r \times n \mathbf{N_R} matrix:

    +the network coresponds to a lineraly dependent row in the stoichiometry matrix \mathbf{N}.

    +

    If there are conserved sums, then the row rank, r of N is < m, and +the stochiometry matrix N may first be re-ordered such that the first r are linearly +independent, and the remaining m-r rows are linear combinations of the first r +rows. The reduced stochiometry matrix \mathbf{N_R} is then formed from the first +r rows of N. Finally, N may be expressed as a product of the m \times r +link matrix \mathbf{L} and the r \times n \mathbf{N_R} matrix:

    -

    \mathbf{N} = \mathbf{L}\mathbf{N_R}.

    -

    The link matrix \mathbf{L} has the form

    +

    \mathbf{N} = \mathbf{L}\mathbf{N_R}.

    +

    The link matrix \mathbf{L} has the form

    -

    \mathbf{L} = \left[ \begin{array}{c} +

    \mathbf{L} = \left[ \begin{array}{c} \mathbf{I}_{r} \\ - \mathbf{L}_0 \end{array} \right],</span></p> -</div><p>where <span class=\mathbf{I}_{r} is the r \times r identity matrix and \mathbf{L}_0 is a (m-r) \times r + \mathbf{L}_0 \end{array} \right],"/>

    +

    where \mathbf{I}_{r} is the r \times r identity matrix and \mathbf{L}_0 is a (m-r) \times r matrix.

    diff --git a/docs/docs-build/tutorial/changing_initial_conditions.html b/docs/docs-build/tutorial/changing_initial_conditions.html index 596e0653ff..3ea3238ea4 100644 --- a/docs/docs-build/tutorial/changing_initial_conditions.html +++ b/docs/docs-build/tutorial/changing_initial_conditions.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/tutorial/changing_parameters.html b/docs/docs-build/tutorial/changing_parameters.html index a04a2483d4..c244b87185 100644 --- a/docs/docs-build/tutorial/changing_parameters.html +++ b/docs/docs-build/tutorial/changing_parameters.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/tutorial/import_roadrunner.html b/docs/docs-build/tutorial/import_roadrunner.html index 594956215d..3c6b67055d 100644 --- a/docs/docs-build/tutorial/import_roadrunner.html +++ b/docs/docs-build/tutorial/import_roadrunner.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/tutorial/jit_engines.html b/docs/docs-build/tutorial/jit_engines.html index ddaea584fe..aed134f301 100644 --- a/docs/docs-build/tutorial/jit_engines.html +++ b/docs/docs-build/tutorial/jit_engines.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/tutorial/loading_models.html b/docs/docs-build/tutorial/loading_models.html index 3eabe096d0..84d9ef9276 100644 --- a/docs/docs-build/tutorial/loading_models.html +++ b/docs/docs-build/tutorial/loading_models.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/tutorial/plotting_data.html b/docs/docs-build/tutorial/plotting_data.html index 02dec7a1da..b5e886bf58 100644 --- a/docs/docs-build/tutorial/plotting_data.html +++ b/docs/docs-build/tutorial/plotting_data.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/tutorial/running_simulations.html b/docs/docs-build/tutorial/running_simulations.html index 101a4448e2..3822f9db11 100644 --- a/docs/docs-build/tutorial/running_simulations.html +++ b/docs/docs-build/tutorial/running_simulations.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/tutorial/selecting_output.html b/docs/docs-build/tutorial/selecting_output.html index c5db1cf5c7..9154a7a89d 100644 --- a/docs/docs-build/tutorial/selecting_output.html +++ b/docs/docs-build/tutorial/selecting_output.html @@ -12,10 +12,9 @@ - - + diff --git a/docs/docs-build/tutorial/solvers.html b/docs/docs-build/tutorial/solvers.html index 5c12d0d987..ab764f1e60 100644 --- a/docs/docs-build/tutorial/solvers.html +++ b/docs/docs-build/tutorial/solvers.html @@ -12,10 +12,9 @@ - - + @@ -146,9 +145,9 @@

    Roadrunner Solvers'variable_step_size') -

    To set a parameter, you can use both methods described below:

    -
    >>>  rr.getIntegrator().relative_tolerance = 1e-10
->>>  rr.getIntegrator().setValue('relative_tolerance', 1e-10)
+
    To set or get a parameter, you can use the methods described below:
    
+
    >>>  rr.getIntegrator().setValue('relative_tolerance', 1e-10)
+>>>  rr.getIntegrator().getValue('initial_time_step')
 
    
 
    
 
    Be sure to set the parameter to the correct type, which can be obtained from
@@ -166,7 +165,7 @@ 
    Roadrunner SolversgetIntegratorByName() as follows:
    
-
    >>>  rr.getIntegratorByName('gillespie').seed = 12345
+
    >>>  rr.getIntegratorByName('gillespie').setValue("seed", 12345)
 
    
 
    
 
    Also, if you find yourself switching back and forth between integrators a lot, you can use
diff --git a/docs/docs-build/tutorial/tutorial.html b/docs/docs-build/tutorial/tutorial.html
index 734618432a..268baab73f 100644
--- a/docs/docs-build/tutorial/tutorial.html
+++ b/docs/docs-build/tutorial/tutorial.html
@@ -12,10 +12,9 @@
     
   
   
-        
         
-        
         
+        
         
         
     
diff --git a/docs/docs-build/tutorial/what_is_rr.html b/docs/docs-build/tutorial/what_is_rr.html
index 7b86781740..b2f7d3b316 100644
--- a/docs/docs-build/tutorial/what_is_rr.html
+++ b/docs/docs-build/tutorial/what_is_rr.html
@@ -12,10 +12,9 @@
     
   
   
-        
         
-        
         
+        
         
         
     
diff --git a/docs/docs-build/tutorial/what_is_sbml.html b/docs/docs-build/tutorial/what_is_sbml.html
index 053ec8aeea..b163e10a90 100644
--- a/docs/docs-build/tutorial/what_is_sbml.html
+++ b/docs/docs-build/tutorial/what_is_sbml.html
@@ -12,10 +12,9 @@
     
   
   
-        
         
-        
         
+        
         
         
     
diff --git a/docs/docs-build/utility_functions.html b/docs/docs-build/utility_functions.html
index d8b415dd35..ad413ee5fd 100644
--- a/docs/docs-build/utility_functions.html
+++ b/docs/docs-build/utility_functions.html
@@ -12,10 +12,9 @@
     
   
   
-        
         
-        
         
+