Fix CI

[kwabenantim]

Description
Currently, most failing tests are due to #11. After it is fixed, we should:

• Add GitHub actions to run tests on subsequent PRs.
• Include a ci:off tag to temporarily skip testing.
• Fix any remaining tests that are still failing.
  • TestVertexBasedCellSimulationsPythonTutorial
  • TestPetscToolsPython

[kwabenantim]

Failing Tests

• cell_based/tutorials/TestVertexBasedCellSimulationsPythonTutorial.py
• core/TestPetscToolsPython.py

[kwabenantim]

TestVertexBasedCellSimulationsPythonTutorial
Runs into a segmentation fault.

Error

[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind
[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: Run with -malloc_debug to check if memory corruption is causing the crash.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 59.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------

Trace

OffLatticeSimulation::Solve(...);
OffLatticeSimulation::ApplyBoundaries(...);
PlaneBoundaryCondition::ImposeBoundaryCondition(...);
if (dynamic_cast<AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>*>(this->mpCellPopulation) == nullptr){...}

Fix
Resolved itself after switching from C++14 to C++17 and pulling latest updates from Chaste develop branch (fast-forwarded from e1fa6a6 to 3ed690e).

[kwabenantim]

TestPetscToolsPython
Needs wrapping for PETSc Vec and Mat.

Error

======================================================================
ERROR: test_some_vecs (__main__.TestPetscTools)
----------------------------------------------------------------------
TypeError: Unregistered type : _p_Vec

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/vboxuser/PyChaste/test/python/./core/TestPetscToolsPython.py", line 44, in test_some_vecs
    vec = chaste.core.PetscTools.CreateVec(local)
TypeError: Unable to convert function return value to a Python type! The signature was
	(data: List[float]) -> _p_Vec

Maybe Useful
https://gitlab.com/petsc/petsc/-/blob/main/src/binding/petsc4py/src/petsc4py/PETSc.pxd
https://gitlab.com/petsc/petsc/-/blob/main/src/binding/petsc4py/src/petsc4py/PETSc/Mat.pyx
https://gitlab.com/petsc/petsc/-/blob/main/src/binding/petsc4py/src/petsc4py/PETSc/Vec.pyx
https://github.com/FEniCS/dolfinx/blob/main/python/dolfinx/wrappers/caster_petsc.h

[kwabenantim]

Bad X server connection
Rendering in some tests tries to open a window, which causes an error in a headless environment.

Error

test_construct (cell_based.TestCaBasedCellPopulationPython.TestPottsMesh) ... ERROR: In ./Rendering/OpenGL2/vtkXOpenGLRenderWindow.cxx, line 300
vtkXOpenGLRenderWindow (0x5555b3b08a80): bad X server connection. DISPLAY=[fv-az438-312:17440] *** Process received signal ***
[fv-az438-312:17440] Signal: Aborted (6)
[fv-az438-312:17440] Signal code:  (-6)
[fv-az438-312:17440] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7f29080c4520]
[fv-az438-312:17440] [ 1] /lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x12c)[0x7f2908118a7c]
[fv-az438-312:17440] [ 2] /lib/x86_64-linux-gnu/libc.so.6(raise+0x16)[0x7f29080c4476]
[fv-az438-312:17440] [ 3] /lib/x86_64-linux-gnu/libc.so.6(abort+0xd3)[0x7f29080aa7f3]
[fv-az438-312:17440] [ 4] /lib/x86_64-linux-gnu/libvtkRenderingOpenGL2-7.1.so.7.1p(+0x900a5)[0x7f28fae310a5]
[fv-az438-312:17440] [ 5] /lib/x86_64-linux-gnu/libvtkRenderingOpenGL2-7.1.so.7.1p(_ZN22vtkXOpenGLRenderWindow15GetDesiredDepthEv+0x12)[0x7f28fafbaa12]
[fv-az438-312:17440] [ 6] /lib/x86_64-linux-gnu/libvtkRenderingOpenGL2-7.1.so.7.1p(_ZN26vtkXRenderWindowInteractor10InitializeEv+0x22d)[0x7f28fafb211d]
[fv-az438-312:17440] [ 7] /lib/x86_64-linux-gnu/libvtkRenderingCore-7.1.so.7.1p(_ZN15vtkRenderWindow6RenderEv+0x430)[0x7f28faaf4d90]
[fv-az438-312:17440] [ 8] /lib/x86_64-linux-gnu/libvtkRenderingOpenGL2-7.1.so.7.1p(_ZN22vtkXOpenGLRenderWindow6RenderEv+0x31)[0x7f28fafc0e51]
[fv-az438-312:17440] [ 9] /home/runner/work/PyChaste/PyChaste/Chaste/build/projects/PyChaste/libchaste_project_PyChaste.so(_ZN8VtkSceneILj3EE13ResetRendererEj+0x12b)[0x7f28fc37a21b]
[fv-az438-312:17440] [10] /home/runner/work/PyChaste/PyChaste/Chaste/build/projects/PyChaste/libchaste_project_PyChaste.so(_ZN8VtkSceneILj3EE5StartEv+0xf4)[0x7f28fc379c74]
[fv-az438-312:17440] [11] /home/runner/.local/lib/python3.10/site-packages/chaste/visualization/_chaste_project_PyChaste_visualization.so(+0x3f8a4)[0x7f28f6b908a4]
[fv-az438-312:17440] [12] /home/runner/.local/lib/python3.10/site-packages/chaste/visualization/_chaste_project_PyChaste_visualization.so(+0x20eac)[0x7f28f6b71eac]
[fv-az438-312:17440] [13] python3(+0x15cc9e)[0x5555afe8ec9e]
[fv-az438-312:17440] [14] python3(_PyObject_MakeTpCall+0x25b)[0x5555afe8572b]
[fv-az438-312:17440] [15] python3(+0x16b1eb)[0x5555afe9d1eb]
[fv-az438-312:17440] [16] python3(_PyEval_EvalFrameDefault+0x640a)[0x5555afe7d75a]
[fv-az438-312:17440] [17] python3(+0x16af11)[0x5555afe9cf11]
[fv-az438-312:17440] [18] python3(_PyEval_EvalFrameDefault+0x6cd)[0x5555afe77a1d]
[fv-az438-312:17440] [19] python3(_PyFunction_Vectorcall+0x7c)[0x5555afe8f4ec]
[fv-az438-312:17440] [20] python3(_PyEval_EvalFrameDefault+0x8c4)[0x5555afe77c14]
[fv-az438-312:17440] [21] python3(+0x16b05e)[0x5555afe9d05e]
[fv-az438-312:17440] [22] python3(_PyEval_EvalFrameDefault+0x2a37)[0x5555afe79d87]
[fv-az438-312:17440] [23] python3(_PyObject_FastCallDictTstate+0xc4)[0x5555afe848b4]
[fv-az438-312:17440] [24] python3(_PyObject_Call_Prepend+0x5c)[0x5555afe99f9c]
[fv-az438-312:17440] [25] python3(+0x285050)[0x5555affb7050]
[fv-az438-312:17440] [26] python3(_PyObject_MakeTpCall+0x25b)[0x5555afe8572b]
[fv-az438-312:17440] [27] python3(_PyEval_EvalFrameDefault+0x67dc)[0x5555afe7db2c]
[fv-az438-312:17440] [28] python3(+0x16b05e)[0x5555afe9d05e]
[fv-az438-312:17440] [29] python3(_PyEval_EvalFrameDefault+0x2a37)[0x5555afe79d87]
[fv-az438-312:17440] *** End of error message ***
/home/runner/work/_temp/88502592-3561-46f5-a073-165fa7e5765a.sh: line 6: 17440 Aborted                 (core dumped) python3 -m unittest -v cell_based/Test*.py cell_based/tutorials/Test*.py core/Test*.py mesh/Test*.py ode/Test*.py

Maybe Useful
https://discourse.vtk.org/t/offscreen-rendering-opening-window/1660

Fix
Use xvfb-run to run tests

[kwabenantim]

TestPetscToolsPython Needs wrapping for PETSc Vec and Mat.

It's not clear why this test is needed since we rely on petsc4py. Perhaps better to re-implement PetscTools.{hpp|cpp} in Python using petsc4py?

[kwabenantim]

It's not clear why this test is needed since we rely on petsc4py. Perhaps better to re-implement PetscTools.{hpp|cpp} in Python using petsc4py?

Vet and Mat are wrapped opaquely, so no conversions needed.