Merge branch 'update_ogstools' into 'master'

Update ogstools version See merge request ogs/ogs!5136
ufz · Dec 10, 2024 · abe67b2 · abe67b2
2 parents ed33460 + d8a166a
commit abe67b2
Show file tree

Hide file tree

Showing 94 changed files with 14,171 additions and 20,217 deletions.
diff --git a/.codespellrc b/.codespellrc
@@ -1,5 +1,5 @@
 [codespell]
 skip = *.bib,*.css,*.pdf,*.yaml,*.yml,*/.vale,./.git,./GeoLib/IO/XmlIO/OpenGeoSysSTN.xsd,./Tests/Data,./web/content/imprint.md,./web/node_modules,./web/public/imprint/index.html,./web/resources,CITATION.cff,
-ignore-words-list = ba,bu,ket,nd,pris,strat,sur,theis,
+ignore-words-list = ba,bu,ket,nd,pris,strat,sur,theis,ot,Jupyter,testrunner
 exclude-file = .codespellexclude
 uri-ignore-words-list = *
diff --git a/Documentation/.vale/Vocab/ogs/ignore.txt b/Documentation/.vale/Vocab/ogs/ignore.txt
@@ -63,3 +63,4 @@ cmake
 ctest
 illite
 dissoluted
+testrunner
diff --git a/ProcessLib/ComponentTransport/Tests.cmake b/ProcessLib/ComponentTransport/Tests.cmake
@@ -949,14 +949,18 @@ AddTest(
 )
 
 if(NOT OGS_USE_PETSC)
-    NotebookTest(NOTEBOOKFILE Parabolic/LiquidFlow/AxiSymTheis/axisym_theis.ipynb RUNTIME 10)
-    NotebookTest(NOTEBOOKFILE Parabolic/ComponentTransport/ReactiveTransport/DecayChain/DecayChain.ipynb RUNTIME 160)
-    NotebookTest(NOTEBOOKFILE Parabolic/ComponentTransport/ReactiveTransport/RadionuclidesMigration/RadionuclidesMigration.ipynb RUNTIME 55)
-    NotebookTest(NOTEBOOKFILE Parabolic/ComponentTransport/ReactiveTransport/CO2Injection/CO2Injection.md RUNTIME 5)
-    NotebookTest(NOTEBOOKFILE Parabolic/ComponentTransport/MultiLayerDiffusion/MultiLayerDiffusion.ipynb RUNTIME 25)
-    NotebookTest(NOTEBOOKFILE Parabolic/ComponentTransport/DiffusionSorptionDecay/DiffusionSorptionDecay.ipynb RUNTIME 16)
+    NotebookTest(NOTEBOOKFILE Parabolic/LiquidFlow/AxiSymTheis/axisym_theis.py RUNTIME 10)
+    NotebookTest(NOTEBOOKFILE Parabolic/ComponentTransport/ReactiveTransport/RadionuclidesMigration/RadionuclidesMigration.py RUNTIME 55)
+    NotebookTest(NOTEBOOKFILE Parabolic/ComponentTransport/ReactiveTransport/CO2Injection/CO2Injection.py RUNTIME 5)
+    NotebookTest(NOTEBOOKFILE Parabolic/ComponentTransport/MultiLayerDiffusion/MultiLayerDiffusion.py RUNTIME 25)
+    NotebookTest(NOTEBOOKFILE Parabolic/ComponentTransport/DiffusionSorptionDecay/DiffusionSorptionDecay.py RUNTIME 16)
     NotebookTest(NOTEBOOKFILE Parabolic/ComponentTransport/elder_jupyter/elder_jupyter.py RUNTIME 25)
-    NotebookTest(NOTEBOOKFILE Parabolic/ThermalTwoPhaseFlowPP/HeatPipe/heatpipe.ipynb RUNTIME 10)
+    NotebookTest(NOTEBOOKFILE Parabolic/ThermalTwoPhaseFlowPP/HeatPipe/heatpipe.py RUNTIME 10)
+
+endif()
+
+if(OGS_USE_PETS)
+    NotebookTest(NOTEBOOKFILE Parabolic/ComponentTransport/ReactiveTransport/DecayChain/DecayChain.py RUNTIME 160)
 endif()
 
 OgsTest(PROJECTFILE Parabolic/ComponentTransport/MassFlux/only_grad_c.prj RUNTIME 1)

diff --git a/ProcessLib/HeatConduction/Tests.cmake b/ProcessLib/HeatConduction/Tests.cmake
@@ -635,5 +635,5 @@ AddTest(
 
 if(NOT OGS_USE_PETSC)
     # Both tests above are executed in this notebook (without diff check). Maybe remove regular tests later?
-    NotebookTest(NOTEBOOKFILE Parabolic/T/3D_line_source_term_tests/3D_line_source_term_in_cylinder/heatconduction-line_source_term.md RUNTIME 10)
+    NotebookTest(NOTEBOOKFILE Parabolic/T/3D_line_source_term_tests/3D_line_source_term_in_cylinder/heatconduction-line_source_term.py RUNTIME 10)
 endif()
diff --git a/ProcessLib/HeatTransportBHE/Tests.cmake b/ProcessLib/HeatTransportBHE/Tests.cmake
@@ -430,5 +430,5 @@ AddTest(
 )
 
 if(NOT OGS_USE_PETSC)
-    NotebookTest(NOTEBOOKFILE Parabolic/T/BHE_1P/pipe_flow_ebhe.md RUNTIME 200)
+    NotebookTest(NOTEBOOKFILE Parabolic/T/BHE_1P/pipe_flow_ebhe.py RUNTIME 200)
 endif()
diff --git a/ProcessLib/HydroMechanics/Tests.cmake b/ProcessLib/HydroMechanics/Tests.cmake
@@ -706,7 +706,7 @@ AddTest(
     reference_results_MandelCryerStaggered_ts_1_t_0.010000.vtu results_MandelCryerStaggered_ts_1_t_0.010000.vtu sigma sigma 1e-1 0
 )
 if(NOT OGS_USE_MPI)
-    NotebookTest(NOTEBOOKFILE HydroMechanics/StaggeredScheme/MandelCryer/mandelcryer.md
+    NotebookTest(NOTEBOOKFILE HydroMechanics/StaggeredScheme/MandelCryer/mandelcryer.py
                  RUNTIME 800)
 endif()
 
@@ -921,5 +921,5 @@ AddTest(
 )
 
 if(NOT WIN32 AND NOT OGS_USE_MPI)
-    NotebookTest(NOTEBOOKFILE HydroMechanics/SeabedResponse/Stationary_waves.ipynb RUNTIME 65)
+    NotebookTest(NOTEBOOKFILE HydroMechanics/SeabedResponse/Stationary_waves.py RUNTIME 65)
 endif()
diff --git a/ProcessLib/LargeDeformation/Tests.cmake b/ProcessLib/LargeDeformation/Tests.cmake
@@ -1,8 +1,8 @@
 if (NOT OGS_USE_MPI)
     OgsTest(PROJECTFILE LargeDeformation/RigidBody/square_1e0.prj RUNTIME 1)
     if(OGS_BUILD_PROCESS_SmallDeformation)
-        NotebookTest(NOTEBOOKFILE LargeDeformation/RigidBody/RigidBody.md RUNTIME 15)
+        NotebookTest(NOTEBOOKFILE LargeDeformation/RigidBody/RigidBody.py RUNTIME 15)
     endif()
     OgsTest(PROJECTFILE LargeDeformation/Torsion/bar1to6_torsion.prj RUNTIME 5)
-    NotebookTest(NOTEBOOKFILE LargeDeformation/Torsion/Torsion_robustness.md RUNTIME 15)
+    NotebookTest(NOTEBOOKFILE LargeDeformation/Torsion/Torsion_robustness.py RUNTIME 15)
 endif()
diff --git a/ProcessLib/LiquidFlow/Tests.cmake b/ProcessLib/LiquidFlow/Tests.cmake
@@ -632,7 +632,7 @@ if(NOT OGS_USE_MPI)
     OgsTest(PROJECTFILE Parabolic/LiquidFlow/SimpleSynthetics/PrimaryVariableConstraintDirichletBC/cuboid_1x1x1_hex_1000_Dirichlet_Dirichlet_3.prj)
     OgsTest(PROJECTFILE Parabolic/LiquidFlow/SimpleSynthetics/FunctionParameterTest.prj)
     OgsTest(PROJECTFILE Parabolic/LiquidFlow/BlockingConductingFracture/block_conduct_frac.prj)
-    NotebookTest(NOTEBOOKFILE Parabolic/LiquidFlow/BlockingConductingFracture/BlockingConductingFracture.ipynb RUNTIME 6)
+    NotebookTest(NOTEBOOKFILE Parabolic/LiquidFlow/BlockingConductingFracture/BlockingConductingFracture.py RUNTIME 6)
 endif()
 
 # inclined mesh

diff --git a/ProcessLib/PhaseField/Tests.cmake b/ProcessLib/PhaseField/Tests.cmake
@@ -160,10 +160,10 @@ AddTest(
 )
 
 if(OGS_USE_PETSC)
-    NotebookTest(NOTEBOOKFILE PhaseField/surfing_jupyter_notebook/surfing_pyvista.ipynb RUNTIME 25)
-    NotebookTest(NOTEBOOKFILE PhaseField/beam_jupyter_notebook/beam.ipynb RUNTIME 1200 PROPERTIES PROCESSORS 3)
-    NotebookTest(NOTEBOOKFILE PhaseField/tpb_jupyter_notebook/TPB.ipynb RUNTIME 110 PROPERTIES PROCESSORS 4)
-    NotebookTest(NOTEBOOKFILE PhaseField/kregime_jupyter_notebook/Kregime_Static_jupyter.ipynb RUNTIME 40)
-    NotebookTest(NOTEBOOKFILE PhaseField/PForthotropy_jupyter_notebook/sen_shear.ipynb RUNTIME 500 PROPERTIES PROCESSORS 4)
-    NotebookTest(NOTEBOOKFILE PhaseField/Kregime_Propagating_jupyter_notebook/Kregime_Propagating_jupyter.ipynb RUNTIME 550)
+    NotebookTest(NOTEBOOKFILE PhaseField/surfing_jupyter_notebook/surfing_pyvista.py RUNTIME 25)
+    NotebookTest(NOTEBOOKFILE PhaseField/beam_jupyter_notebook/beam.py RUNTIME 1200 PROPERTIES PROCESSORS 3)
+    NotebookTest(NOTEBOOKFILE PhaseField/tpb_jupyter_notebook/TPB.py RUNTIME 110 PROPERTIES PROCESSORS 4)
+    NotebookTest(NOTEBOOKFILE PhaseField/kregime_jupyter_notebook/Kregime_Static_jupyter.py RUNTIME 40)
+    NotebookTest(NOTEBOOKFILE PhaseField/PForthotropy_jupyter_notebook/sen_shear.py RUNTIME 500 PROPERTIES PROCESSORS 4)
+    NotebookTest(NOTEBOOKFILE PhaseField/Kregime_Propagating_jupyter_notebook/Kregime_Propagating_jupyter.py RUNTIME 550)
 endif()
diff --git a/ProcessLib/SmallDeformation/Tests.cmake b/ProcessLib/SmallDeformation/Tests.cmake
@@ -352,16 +352,16 @@ AddTest(
 
 if(NOT OGS_USE_PETSC)
     NotebookTest(NOTEBOOKFILE Mechanics/CooksMembrane/CooksMembraneBbar.py RUNTIME 1)
-    NotebookTest(NOTEBOOKFILE Mechanics/Linear/SimpleMechanics.ipynb RUNTIME 5)
+    NotebookTest(NOTEBOOKFILE Mechanics/Linear/SimpleMechanics.py RUNTIME 5)
     NotebookTest(NOTEBOOKFILE Mechanics/EvaluatingBbarWithSimpleExamples/evaluating_bbbar_with_simple_examples.py RUNTIME 5)
-    NotebookTest(NOTEBOOKFILE Mechanics/Linear/DiscWithHole/Linear_Disc_with_hole.md RUNTIME 15)
+    NotebookTest(NOTEBOOKFILE Mechanics/Linear/DiscWithHole/Linear_Disc_with_hole.py RUNTIME 15)
     if(NOT WIN32)
-        NotebookTest(NOTEBOOKFILE Mechanics/Linear/DiscWithHole/Linear_Disc_with_hole_convergence_analysis.ipynb RUNTIME 40)
+        NotebookTest(NOTEBOOKFILE Mechanics/Linear/DiscWithHole/Linear_Disc_with_hole_convergence_analysis.py RUNTIME 40)
     endif()
     if (OGS_USE_MFRONT)
-        NotebookTest(NOTEBOOKFILE Mechanics/PLLC/PLLC.ipynb RUNTIME 7)
+        NotebookTest(NOTEBOOKFILE Mechanics/PLLC/PLLC.py RUNTIME 7)
         if(TFEL_WITH_PYTHON)
-            NotebookTest(NOTEBOOKFILE Mechanics/HoekBrown/HoekBrownYieldCriterion.md RUNTIME 20)
+            NotebookTest(NOTEBOOKFILE Mechanics/HoekBrown/HoekBrownYieldCriterion.py RUNTIME 20)
         endif()
     endif()
 endif()

diff --git a/ProcessLib/SteadyStateDiffusion/Tests.cmake b/ProcessLib/SteadyStateDiffusion/Tests.cmake
@@ -1048,7 +1048,7 @@ AddTest(
 )
 
 if(OGS_USE_MPI)
-    NotebookTest(NOTEBOOKFILE Notebooks/SimplePETSc.ipynb RUNTIME 10)
+    NotebookTest(NOTEBOOKFILE Notebooks/SimplePETSc.py RUNTIME 10)
 else()
     NotebookTest(
         NOTEBOOKFILE Elliptic/cube_1x1x1_SteadyStateDiffusion/ssd-cube.ipynb

diff --git a/ProcessLib/TH2M/Tests.cmake b/ProcessLib/TH2M/Tests.cmake
@@ -13,7 +13,7 @@ if (NOT OGS_USE_MPI)
     OgsTest(PROJECTFILE TH2M/THM/Confined_Compression/THM_confined_compression_liquid.prj RUNTIME 55)
     OgsTest(PROJECTFILE TH2M/TH/idealGasLaw/compression_gas.prj RUNTIME 1)
     OgsTest(PROJECTFILE TH2M/H2M/Liakopoulos/liakopoulos_TH2M.prj RUNTIME 15)
-    NotebookTest(NOTEBOOKFILE TH2M/H2M/Liakopoulos/ogs-jupyter-lab-h2m-2d-liakopoulos.ipynb RUNTIME 15)
+    NotebookTest(NOTEBOOKFILE TH2M/H2M/Liakopoulos/ogs-jupyter-lab-h2m-2d-liakopoulos.py RUNTIME 15)
     if(NOT ENABLE_ASAN)
         OgsTest(PROJECTFILE TH2M/H2M/Liakopoulos/liakopoulos_newton.xml RUNTIME 5)
     endif()
@@ -25,13 +25,13 @@ if (NOT OGS_USE_MPI)
     OgsTest(PROJECTFILE TH2M/TH2/heatpipe/heat_pipe_strict.prj RUNTIME 80)
     OgsTest(PROJECTFILE TH2M/H2/dissolution_diffusion/continuous_injection.prj RUNTIME 60)
     OgsTest(PROJECTFILE TH2M/H2/dissolution_diffusion/bourgeat.prj RUNTIME 60)
-    NotebookTest(NOTEBOOKFILE TH2M/H2/dissolution_diffusion/phase_appearance.ipynb RUNTIME 60)
-    NotebookTest(NOTEBOOKFILE TH2M/H2/mcWhorter/mcWhorter.ipynb RUNTIME 55)
+    NotebookTest(NOTEBOOKFILE TH2M/H2/dissolution_diffusion/phase_appearance.py RUNTIME 60)
+    NotebookTest(NOTEBOOKFILE TH2M/H2/mcWhorter/mcWhorter.py RUNTIME 55)
     OgsTest(PROJECTFILE TH2M/H/diffusion/diffusion.prj RUNTIME 10)
-    NotebookTest(NOTEBOOKFILE TH2M/H/diffusion/diffusion.ipynb RUNTIME 30)
+    NotebookTest(NOTEBOOKFILE TH2M/H/diffusion/diffusion.py RUNTIME 30)
     OgsTest(PROJECTFILE TH2M/TH/Ogata-Banks/ogata-banks.prj RUNTIME 60)
-    NotebookTest(NOTEBOOKFILE TH2M/TH/Ogata-Banks/Ogata-Banks.ipynb RUNTIME 120)
-    NotebookTest(NOTEBOOKFILE TH2M/TH/idealGasLaw/confined_gas_compression.ipynb RUNTIME 10)
+    NotebookTest(NOTEBOOKFILE TH2M/TH/Ogata-Banks/Ogata-Banks.py RUNTIME 120)
+    NotebookTest(NOTEBOOKFILE TH2M/TH/idealGasLaw/confined_gas_compression.py RUNTIME 10)
     # submesh residuum output
     OgsTest(PROJECTFILE TH2M/submesh_residuum_assembly/T.xml RUNTIME 1)
     OgsTest(PROJECTFILE TH2M/submesh_residuum_assembly/p_G.xml RUNTIME 1)
@@ -454,5 +454,5 @@ AddTest(
 )
 
 if(NOT OGS_USE_PETSC)
-    NotebookTest(NOTEBOOKFILE TH2M/TH2/heatpipe/heatpipe.ipynb RUNTIME 140)
+    NotebookTest(NOTEBOOKFILE TH2M/TH2/heatpipe/heatpipe.py RUNTIME 140)
 endif()
diff --git a/ProcessLib/Tests.cmake b/ProcessLib/Tests.cmake
@@ -6,7 +6,7 @@ if(TARGET ThermoHydroMechanics
 )
     NotebookTest(
         NOTEBOOKFILE
-        ThermoHydroMechanics/Linear/Point_injection/SaturatedPointheatsource.ipynb
+        ThermoHydroMechanics/Linear/Point_injection/SaturatedPointheatsource.py
         RUNTIME 1800
         PROPERTIES PROCESSORS 4
     )

diff --git a/ProcessLib/TwoPhaseFlowWithPrho/Tests.cmake b/ProcessLib/TwoPhaseFlowWithPrho/Tests.cmake
@@ -45,5 +45,5 @@ AddTest(
 )
 
 if(NOT WIN32 AND NOT OGS_USE_MPI)
-    NotebookTest(NOTEBOOKFILE Parabolic/TwoPhaseFlowPrho/MoMaS/MoMaS.ipynb RUNTIME 10)
+    NotebookTest(NOTEBOOKFILE Parabolic/TwoPhaseFlowPrho/MoMaS/MoMaS.py RUNTIME 10)
 endif()
-Original file line number
+Diff line change
@@ Expand Up / @@ -63,3 +63,4 @@ cmake @@
     ctest
     illite
     dissoluted
+    testrunner