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Merge branch 'update_ogstools' into 'master'
Update ogstools version See merge request ogs/ogs!5136
2 parents ed33460 + d8a166a commit abe67b2

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‎.codespellrc

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
[codespell]
22
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,
3-
ignore-words-list = ba,bu,ket,nd,pris,strat,sur,theis,
3+
ignore-words-list = ba,bu,ket,nd,pris,strat,sur,theis,ot,Jupyter,testrunner
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exclude-file = .codespellexclude
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uri-ignore-words-list = *

‎Documentation/.vale/Vocab/ogs/ignore.txt

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -63,3 +63,4 @@ cmake
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ctest
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illite
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dissoluted
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testrunner

‎ProcessLib/ComponentTransport/Tests.cmake

Lines changed: 11 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -949,14 +949,18 @@ AddTest(
949949
)
950950

951951
if(NOT OGS_USE_PETSC)
952-
NotebookTest(NOTEBOOKFILE Parabolic/LiquidFlow/AxiSymTheis/axisym_theis.ipynb RUNTIME 10)
953-
NotebookTest(NOTEBOOKFILE Parabolic/ComponentTransport/ReactiveTransport/DecayChain/DecayChain.ipynb RUNTIME 160)
954-
NotebookTest(NOTEBOOKFILE Parabolic/ComponentTransport/ReactiveTransport/RadionuclidesMigration/RadionuclidesMigration.ipynb RUNTIME 55)
955-
NotebookTest(NOTEBOOKFILE Parabolic/ComponentTransport/ReactiveTransport/CO2Injection/CO2Injection.md RUNTIME 5)
956-
NotebookTest(NOTEBOOKFILE Parabolic/ComponentTransport/MultiLayerDiffusion/MultiLayerDiffusion.ipynb RUNTIME 25)
957-
NotebookTest(NOTEBOOKFILE Parabolic/ComponentTransport/DiffusionSorptionDecay/DiffusionSorptionDecay.ipynb RUNTIME 16)
952+
NotebookTest(NOTEBOOKFILE Parabolic/LiquidFlow/AxiSymTheis/axisym_theis.py RUNTIME 10)
953+
NotebookTest(NOTEBOOKFILE Parabolic/ComponentTransport/ReactiveTransport/RadionuclidesMigration/RadionuclidesMigration.py RUNTIME 55)
954+
NotebookTest(NOTEBOOKFILE Parabolic/ComponentTransport/ReactiveTransport/CO2Injection/CO2Injection.py RUNTIME 5)
955+
NotebookTest(NOTEBOOKFILE Parabolic/ComponentTransport/MultiLayerDiffusion/MultiLayerDiffusion.py RUNTIME 25)
956+
NotebookTest(NOTEBOOKFILE Parabolic/ComponentTransport/DiffusionSorptionDecay/DiffusionSorptionDecay.py RUNTIME 16)
958957
NotebookTest(NOTEBOOKFILE Parabolic/ComponentTransport/elder_jupyter/elder_jupyter.py RUNTIME 25)
959-
NotebookTest(NOTEBOOKFILE Parabolic/ThermalTwoPhaseFlowPP/HeatPipe/heatpipe.ipynb RUNTIME 10)
958+
NotebookTest(NOTEBOOKFILE Parabolic/ThermalTwoPhaseFlowPP/HeatPipe/heatpipe.py RUNTIME 10)
959+
960+
endif()
961+
962+
if(OGS_USE_PETS)
963+
NotebookTest(NOTEBOOKFILE Parabolic/ComponentTransport/ReactiveTransport/DecayChain/DecayChain.py RUNTIME 160)
960964
endif()
961965

962966
OgsTest(PROJECTFILE Parabolic/ComponentTransport/MassFlux/only_grad_c.prj RUNTIME 1)

‎ProcessLib/HeatConduction/Tests.cmake

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -635,5 +635,5 @@ AddTest(
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636636
if(NOT OGS_USE_PETSC)
637637
# Both tests above are executed in this notebook (without diff check). Maybe remove regular tests later?
638-
NotebookTest(NOTEBOOKFILE Parabolic/T/3D_line_source_term_tests/3D_line_source_term_in_cylinder/heatconduction-line_source_term.md RUNTIME 10)
638+
NotebookTest(NOTEBOOKFILE Parabolic/T/3D_line_source_term_tests/3D_line_source_term_in_cylinder/heatconduction-line_source_term.py RUNTIME 10)
639639
endif()

‎ProcessLib/HeatTransportBHE/Tests.cmake

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Original file line numberDiff line numberDiff line change
@@ -430,5 +430,5 @@ AddTest(
430430
)
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432432
if(NOT OGS_USE_PETSC)
433-
NotebookTest(NOTEBOOKFILE Parabolic/T/BHE_1P/pipe_flow_ebhe.md RUNTIME 200)
433+
NotebookTest(NOTEBOOKFILE Parabolic/T/BHE_1P/pipe_flow_ebhe.py RUNTIME 200)
434434
endif()

‎ProcessLib/HydroMechanics/Tests.cmake

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -706,7 +706,7 @@ AddTest(
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reference_results_MandelCryerStaggered_ts_1_t_0.010000.vtu results_MandelCryerStaggered_ts_1_t_0.010000.vtu sigma sigma 1e-1 0
707707
)
708708
if(NOT OGS_USE_MPI)
709-
NotebookTest(NOTEBOOKFILE HydroMechanics/StaggeredScheme/MandelCryer/mandelcryer.md
709+
NotebookTest(NOTEBOOKFILE HydroMechanics/StaggeredScheme/MandelCryer/mandelcryer.py
710710
RUNTIME 800)
711711
endif()
712712

@@ -921,5 +921,5 @@ AddTest(
921921
)
922922

923923
if(NOT WIN32 AND NOT OGS_USE_MPI)
924-
NotebookTest(NOTEBOOKFILE HydroMechanics/SeabedResponse/Stationary_waves.ipynb RUNTIME 65)
924+
NotebookTest(NOTEBOOKFILE HydroMechanics/SeabedResponse/Stationary_waves.py RUNTIME 65)
925925
endif()

‎ProcessLib/LargeDeformation/Tests.cmake

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Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
11
if (NOT OGS_USE_MPI)
22
OgsTest(PROJECTFILE LargeDeformation/RigidBody/square_1e0.prj RUNTIME 1)
33
if(OGS_BUILD_PROCESS_SmallDeformation)
4-
NotebookTest(NOTEBOOKFILE LargeDeformation/RigidBody/RigidBody.md RUNTIME 15)
4+
NotebookTest(NOTEBOOKFILE LargeDeformation/RigidBody/RigidBody.py RUNTIME 15)
55
endif()
66
OgsTest(PROJECTFILE LargeDeformation/Torsion/bar1to6_torsion.prj RUNTIME 5)
7-
NotebookTest(NOTEBOOKFILE LargeDeformation/Torsion/Torsion_robustness.md RUNTIME 15)
7+
NotebookTest(NOTEBOOKFILE LargeDeformation/Torsion/Torsion_robustness.py RUNTIME 15)
88
endif()

‎ProcessLib/LiquidFlow/Tests.cmake

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -632,7 +632,7 @@ if(NOT OGS_USE_MPI)
632632
OgsTest(PROJECTFILE Parabolic/LiquidFlow/SimpleSynthetics/PrimaryVariableConstraintDirichletBC/cuboid_1x1x1_hex_1000_Dirichlet_Dirichlet_3.prj)
633633
OgsTest(PROJECTFILE Parabolic/LiquidFlow/SimpleSynthetics/FunctionParameterTest.prj)
634634
OgsTest(PROJECTFILE Parabolic/LiquidFlow/BlockingConductingFracture/block_conduct_frac.prj)
635-
NotebookTest(NOTEBOOKFILE Parabolic/LiquidFlow/BlockingConductingFracture/BlockingConductingFracture.ipynb RUNTIME 6)
635+
NotebookTest(NOTEBOOKFILE Parabolic/LiquidFlow/BlockingConductingFracture/BlockingConductingFracture.py RUNTIME 6)
636636
endif()
637637

638638
# inclined mesh

‎ProcessLib/PhaseField/Tests.cmake

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@@ -160,10 +160,10 @@ AddTest(
160160
)
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162162
if(OGS_USE_PETSC)
163-
NotebookTest(NOTEBOOKFILE PhaseField/surfing_jupyter_notebook/surfing_pyvista.ipynb RUNTIME 25)
164-
NotebookTest(NOTEBOOKFILE PhaseField/beam_jupyter_notebook/beam.ipynb RUNTIME 1200 PROPERTIES PROCESSORS 3)
165-
NotebookTest(NOTEBOOKFILE PhaseField/tpb_jupyter_notebook/TPB.ipynb RUNTIME 110 PROPERTIES PROCESSORS 4)
166-
NotebookTest(NOTEBOOKFILE PhaseField/kregime_jupyter_notebook/Kregime_Static_jupyter.ipynb RUNTIME 40)
167-
NotebookTest(NOTEBOOKFILE PhaseField/PForthotropy_jupyter_notebook/sen_shear.ipynb RUNTIME 500 PROPERTIES PROCESSORS 4)
168-
NotebookTest(NOTEBOOKFILE PhaseField/Kregime_Propagating_jupyter_notebook/Kregime_Propagating_jupyter.ipynb RUNTIME 550)
163+
NotebookTest(NOTEBOOKFILE PhaseField/surfing_jupyter_notebook/surfing_pyvista.py RUNTIME 25)
164+
NotebookTest(NOTEBOOKFILE PhaseField/beam_jupyter_notebook/beam.py RUNTIME 1200 PROPERTIES PROCESSORS 3)
165+
NotebookTest(NOTEBOOKFILE PhaseField/tpb_jupyter_notebook/TPB.py RUNTIME 110 PROPERTIES PROCESSORS 4)
166+
NotebookTest(NOTEBOOKFILE PhaseField/kregime_jupyter_notebook/Kregime_Static_jupyter.py RUNTIME 40)
167+
NotebookTest(NOTEBOOKFILE PhaseField/PForthotropy_jupyter_notebook/sen_shear.py RUNTIME 500 PROPERTIES PROCESSORS 4)
168+
NotebookTest(NOTEBOOKFILE PhaseField/Kregime_Propagating_jupyter_notebook/Kregime_Propagating_jupyter.py RUNTIME 550)
169169
endif()

‎ProcessLib/SmallDeformation/Tests.cmake

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@@ -352,16 +352,16 @@ AddTest(
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353353
if(NOT OGS_USE_PETSC)
354354
NotebookTest(NOTEBOOKFILE Mechanics/CooksMembrane/CooksMembraneBbar.py RUNTIME 1)
355-
NotebookTest(NOTEBOOKFILE Mechanics/Linear/SimpleMechanics.ipynb RUNTIME 5)
355+
NotebookTest(NOTEBOOKFILE Mechanics/Linear/SimpleMechanics.py RUNTIME 5)
356356
NotebookTest(NOTEBOOKFILE Mechanics/EvaluatingBbarWithSimpleExamples/evaluating_bbbar_with_simple_examples.py RUNTIME 5)
357-
NotebookTest(NOTEBOOKFILE Mechanics/Linear/DiscWithHole/Linear_Disc_with_hole.md RUNTIME 15)
357+
NotebookTest(NOTEBOOKFILE Mechanics/Linear/DiscWithHole/Linear_Disc_with_hole.py RUNTIME 15)
358358
if(NOT WIN32)
359-
NotebookTest(NOTEBOOKFILE Mechanics/Linear/DiscWithHole/Linear_Disc_with_hole_convergence_analysis.ipynb RUNTIME 40)
359+
NotebookTest(NOTEBOOKFILE Mechanics/Linear/DiscWithHole/Linear_Disc_with_hole_convergence_analysis.py RUNTIME 40)
360360
endif()
361361
if (OGS_USE_MFRONT)
362-
NotebookTest(NOTEBOOKFILE Mechanics/PLLC/PLLC.ipynb RUNTIME 7)
362+
NotebookTest(NOTEBOOKFILE Mechanics/PLLC/PLLC.py RUNTIME 7)
363363
if(TFEL_WITH_PYTHON)
364-
NotebookTest(NOTEBOOKFILE Mechanics/HoekBrown/HoekBrownYieldCriterion.md RUNTIME 20)
364+
NotebookTest(NOTEBOOKFILE Mechanics/HoekBrown/HoekBrownYieldCriterion.py RUNTIME 20)
365365
endif()
366366
endif()
367367
endif()

‎ProcessLib/SteadyStateDiffusion/Tests.cmake

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Original file line numberDiff line numberDiff line change
@@ -1048,7 +1048,7 @@ AddTest(
10481048
)
10491049

10501050
if(OGS_USE_MPI)
1051-
NotebookTest(NOTEBOOKFILE Notebooks/SimplePETSc.ipynb RUNTIME 10)
1051+
NotebookTest(NOTEBOOKFILE Notebooks/SimplePETSc.py RUNTIME 10)
10521052
else()
10531053
NotebookTest(
10541054
NOTEBOOKFILE Elliptic/cube_1x1x1_SteadyStateDiffusion/ssd-cube.ipynb

‎ProcessLib/TH2M/Tests.cmake

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@ if (NOT OGS_USE_MPI)
1313
OgsTest(PROJECTFILE TH2M/THM/Confined_Compression/THM_confined_compression_liquid.prj RUNTIME 55)
1414
OgsTest(PROJECTFILE TH2M/TH/idealGasLaw/compression_gas.prj RUNTIME 1)
1515
OgsTest(PROJECTFILE TH2M/H2M/Liakopoulos/liakopoulos_TH2M.prj RUNTIME 15)
16-
NotebookTest(NOTEBOOKFILE TH2M/H2M/Liakopoulos/ogs-jupyter-lab-h2m-2d-liakopoulos.ipynb RUNTIME 15)
16+
NotebookTest(NOTEBOOKFILE TH2M/H2M/Liakopoulos/ogs-jupyter-lab-h2m-2d-liakopoulos.py RUNTIME 15)
1717
if(NOT ENABLE_ASAN)
1818
OgsTest(PROJECTFILE TH2M/H2M/Liakopoulos/liakopoulos_newton.xml RUNTIME 5)
1919
endif()
@@ -25,13 +25,13 @@ if (NOT OGS_USE_MPI)
2525
OgsTest(PROJECTFILE TH2M/TH2/heatpipe/heat_pipe_strict.prj RUNTIME 80)
2626
OgsTest(PROJECTFILE TH2M/H2/dissolution_diffusion/continuous_injection.prj RUNTIME 60)
2727
OgsTest(PROJECTFILE TH2M/H2/dissolution_diffusion/bourgeat.prj RUNTIME 60)
28-
NotebookTest(NOTEBOOKFILE TH2M/H2/dissolution_diffusion/phase_appearance.ipynb RUNTIME 60)
29-
NotebookTest(NOTEBOOKFILE TH2M/H2/mcWhorter/mcWhorter.ipynb RUNTIME 55)
28+
NotebookTest(NOTEBOOKFILE TH2M/H2/dissolution_diffusion/phase_appearance.py RUNTIME 60)
29+
NotebookTest(NOTEBOOKFILE TH2M/H2/mcWhorter/mcWhorter.py RUNTIME 55)
3030
OgsTest(PROJECTFILE TH2M/H/diffusion/diffusion.prj RUNTIME 10)
31-
NotebookTest(NOTEBOOKFILE TH2M/H/diffusion/diffusion.ipynb RUNTIME 30)
31+
NotebookTest(NOTEBOOKFILE TH2M/H/diffusion/diffusion.py RUNTIME 30)
3232
OgsTest(PROJECTFILE TH2M/TH/Ogata-Banks/ogata-banks.prj RUNTIME 60)
33-
NotebookTest(NOTEBOOKFILE TH2M/TH/Ogata-Banks/Ogata-Banks.ipynb RUNTIME 120)
34-
NotebookTest(NOTEBOOKFILE TH2M/TH/idealGasLaw/confined_gas_compression.ipynb RUNTIME 10)
33+
NotebookTest(NOTEBOOKFILE TH2M/TH/Ogata-Banks/Ogata-Banks.py RUNTIME 120)
34+
NotebookTest(NOTEBOOKFILE TH2M/TH/idealGasLaw/confined_gas_compression.py RUNTIME 10)
3535
# submesh residuum output
3636
OgsTest(PROJECTFILE TH2M/submesh_residuum_assembly/T.xml RUNTIME 1)
3737
OgsTest(PROJECTFILE TH2M/submesh_residuum_assembly/p_G.xml RUNTIME 1)
@@ -454,5 +454,5 @@ AddTest(
454454
)
455455

456456
if(NOT OGS_USE_PETSC)
457-
NotebookTest(NOTEBOOKFILE TH2M/TH2/heatpipe/heatpipe.ipynb RUNTIME 140)
457+
NotebookTest(NOTEBOOKFILE TH2M/TH2/heatpipe/heatpipe.py RUNTIME 140)
458458
endif()

‎ProcessLib/Tests.cmake

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Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ if(TARGET ThermoHydroMechanics
66
)
77
NotebookTest(
88
NOTEBOOKFILE
9-
ThermoHydroMechanics/Linear/Point_injection/SaturatedPointheatsource.ipynb
9+
ThermoHydroMechanics/Linear/Point_injection/SaturatedPointheatsource.py
1010
RUNTIME 1800
1111
PROPERTIES PROCESSORS 4
1212
)

‎ProcessLib/TwoPhaseFlowWithPrho/Tests.cmake

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Original file line numberDiff line numberDiff line change
@@ -45,5 +45,5 @@ AddTest(
4545
)
4646

4747
if(NOT WIN32 AND NOT OGS_USE_MPI)
48-
NotebookTest(NOTEBOOKFILE Parabolic/TwoPhaseFlowPrho/MoMaS/MoMaS.ipynb RUNTIME 10)
48+
NotebookTest(NOTEBOOKFILE Parabolic/TwoPhaseFlowPrho/MoMaS/MoMaS.py RUNTIME 10)
4949
endif()

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