replace nose with pytest and attempt to re-add coverage.

Still needs further work on test_algebra.py

Added running of coverage to GHA and also upload to coveralls.io.

Author: KrisThielemans

.coveragerc-Gadgetron

@@ -0,0 +1,9 @@
+[run]
+data_file = .coverage-Gadgetron
+relative_files = True
+source = sirf.Gadgetron
+[paths]
+source =
+    src/xGadgetron/pGadgetron/
+    /home/sirfuser/devel/install/python/sirf
+    /home/runner/install/python/sirf

.coveragerc-Reg

@@ -0,0 +1,9 @@
+[run]
+data_file = .coverage-Reg
+relative_files = True
+source = sirf.Reg
+[paths]
+source =
+    src/Registration/pReg
+    /home/sirfuser/devel/install/python/sirf
+    /home/runner/install/python/sirf

.coveragerc-STIR

@@ -0,0 +1,10 @@
+[run]
+data_file = .coverage-STIR
+relative_files = True
+source = sirf.STIR
+[paths]
+source =
+    src/xSTIR/pSTIR
+    /home/sirfuser/devel/install/python/sirf
+    /home/runner/install/python/sirf
+    

.github/workflows/build-test.yml

@@ -115,5 +115,28 @@ jobs:
           cmake --build . -j 2;
     - name: tests
       shell: bash
-      run: |
+      run:
           bash -ev ${GITHUB_WORKSPACE}/SIRF-SuperBuild/docker/ctest_sirf.sh
+
+    - name: Coverage
+      shell: bash
+      run: |
+          pwd
+          source ~/virtualenv/bin/activate
+          coverage combine .coverage-*
+          coverage report
+    - name: Coveralls
+      uses: AndreMiras/coveralls-python-action@develop
+      with:
+        parallel: true
+        flag-name: python test
+        debug: true
+
+  coveralls_finish:
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+    - name: Coveralls Finished
+      uses: AndreMiras/coveralls-python-action@develop
+      with:
+        parallel-finished: true        

.gitignore

@@ -270,6 +270,7 @@ errr.txt
 output.txt
 
 .coverage
+.coverage-*
 coverage.xml
 
 *_out.txt

requirements.txt

@@ -3,6 +3,7 @@ scipy --only-binary=scipy
 matplotlib --only-binary=matplotlib
 docopt
 psutil
-nose
+pytest
+pytest-cov
 deprecation
 nibabel  # optional

src/Registration/pReg/tests/CMakeLists.txt

@@ -1,6 +1,5 @@
 #========================================================================
-# Author: Richard Brown
-# Copyright 2016-2020 University College London
+# Copyright 2016-2022 University College London
 #
 #  Licensed under the Apache License, Version 2.0 (the "License");
 #  you may not use this file except in compliance with the License.
@@ -15,15 +14,6 @@
 #  limitations under the License.
 #
 #=========================================================================
-if (SPM_BOOL_STR EQUAL "0")
-  set (exclude_tests "--ignore-files=\"test_algebra\"" "--exclude=TestDataContainerAlgebra")
-else()
-  set (exclude_tests "--ignore-files=\"test_algebra\"" "--exclude=TestDataContainerAlgebra")
-endif()
-# Make into test
 ADD_TEST(NAME REG_TESTS_PYTHON
-  COMMAND ${Python_EXECUTABLE} -m nose --with-coverage --cover-package=sirf.Reg --cover-erase -d -v ${CMAKE_SOURCE_DIR}/src/Registration/pReg ${exclude_tests})
-
-add_test(NAME REG_PYTHON_ALGEBRA
-  COMMAND ${Python_EXECUTABLE} -m unittest test_algebra
-  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+  COMMAND ${Python_EXECUTABLE} -m pytest --cov=sirf.Reg --cov-config=.coveragerc-Reg src/Registration/pReg
+  WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})

src/common/Utilities.py

@@ -7,6 +7,7 @@
 import sirf.pyiutilities as pyiutil
 import re
 from deprecation import deprecated
+import pytest
 
 __licence__ = """SyneRBI Synergistic Image Reconstruction Framework (SIRF)
 Copyright 2015 - 2021 Rutherford Appleton Laboratory STFC
@@ -594,7 +595,7 @@ def is_operator_adjoint(operator, num_tests = 5, max_err = 10e-5, verbose = True
                 print("Pass, with a with normalized error of " + str(norm_err) + " (max: " + str(max_err) + ")")
     return True
 
-
+@pytest.mark.skip(reason="This is a base-class for the actual tests")
 class TestDataContainerAlgebra(object):
 
     '''A base class for unit test of DataContainer algebra.'''

src/xGadgetron/pGadgetron/tests/CMakeLists.txt

@@ -1,6 +1,6 @@
 #========================================================================
 # Copyright 2017 - 2021 Science Technology Facilities Council
-# Copyright 2017 - 2021 University College London
+# Copyright 2017 - 2022 University College London
 #
 # This file is part of the SyneRBI Synergistic Image Reconstruction Framework (SIRF) SuperBuild.
 #
@@ -17,16 +17,12 @@
 # limitations under the License.
 #
 #=========================================================================
-set (exclude_tests "--ignore-files=\"test_algebra\"" "--exclude=TestDataContainerAlgebra")
 add_test(NAME MR_TESTS_PYTHON
-  COMMAND ${Python_EXECUTABLE} -m nose --with-coverage --cover-package=sirf.Gadgetron src/xGadgetron/pGadgetron/ ${exclude_tests}
+  COMMAND ${Python_EXECUTABLE} -m pytest --cov=sirf.Gadgetron --cov-config=.coveragerc-Gadgetron src/xGadgetron/pGadgetron/
   WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})
 add_test(NAME MR_DEMOS_PYTHON
   COMMAND ${Python_EXECUTABLE} run_all.py --non-interactive
   WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}/examples/Python/MR")
 add_test(NAME MR_GADGETRON_DEMOS_PYTHON
   COMMAND ${Python_EXECUTABLE} run_all.py --non-interactive
   WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}/examples/Python/MR/Gadgetron")
-add_test(NAME MR_PYTHON_ALGEBRA
-  COMMAND ${Python_EXECUTABLE} -m unittest test_algebra
-  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})

src/xGadgetron/pGadgetron/tests/pytest.ini

@@ -0,0 +1,2 @@
+[pytest]
+python_files = test*.py

src/xSTIR/pSTIR/tests/CMakeLists.txt

@@ -1,5 +1,5 @@
 #========================================================================
-# Copyright 2017 - 2021 University College London
+# Copyright 2017 - 2022 University College London
 # Copyright 2017 - 2021 Science Technology Facilities Council
 #
 # This file is part of the SyneRBI Synergistic Image Reconstruction Framework (SIRF) SuperBuild.
@@ -17,22 +17,10 @@
 # limitations under the License.
 #
 #=========================================================================
-set (exclude_tests "--ignore-files=\"test_algebra\"" "--exclude=TestDataContainerAlgebra")
-# If not NiftyPET projector, dont test that
-if (NiftyPET_BOOL_STR EQUAL "0")
-	set(exclude_tests "--ignore-files=\"test_algebra|tests_NiftyPET\"" "--exclude=TestDataContainerAlgebra")
-endif()
 
 add_test(NAME PET_TESTS_PYTHON
-  COMMAND ${Python_EXECUTABLE} -m nose --with-coverage --cover-package=sirf.STIR src/xSTIR/pSTIR ${exclude_tests}
+  COMMAND ${Python_EXECUTABLE} -m pytest --cov=sirf.STIR --cov-config=.coveragerc-STIR src/xSTIR/pSTIR
   WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})
 #add_test(NAME PET_DEMOS_PYTHON
 #  COMMAND ${PYTHON_EXECUTABLE} run_all.py --non-interactive
 #  WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}/examples/Python/PET")
-add_test(NAME PET_PYTHON_ALGEBRA
-  COMMAND ${Python_EXECUTABLE} -m unittest test_algebra
-  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
-
-add_test(NAME PET_PYTHON_OBJFUN
-  COMMAND ${Python_EXECUTABLE} -m unittest test_ObjectiveFunction
-  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})

src/xSTIR/pSTIR/tests/pytest.ini

@@ -0,0 +1,2 @@
+[pytest]
+python_files = test*.py