Implement Python wrappers for cell-based simulations

[kwabenantim]

This issue continues the discussion for legacy trac ticket 3104:

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kwabenantim created the following ticket on 2022-09-02 at 11:33:49, it is owned by kwabenantim*

For those without C++ expertise, implementation of higher-level programming language bindings would offer a step change in Chaste’s usability. Extending on preliminary work in [legacy ticket 2686] on PyChaste, we will use PyBind11 to generate Python wrappers for cell-based Chaste.

[kwabenantim]

Building a conda package for PyChaste that works with develop.

So far, a manual build with these versions of dependencies from conda-forge and bioconda works:

  - python >=3.7
  - vtk ==8.2.0
  - tbb ==2019.9
  - tbb-devel ==2019.9
  - boost ==1.74.0
  - petsc ==3.10.5
  - petsc4py ==3.10.0
  - hdf5 =1.10.5=mpi_mpich_*
  - parmetis ==4.0.3
  - sundials ==5.0.0
  - xsd
  - xerces-c ==3.2.4

Note: the vtk builds from conda-forge depend on tbb, not mpi.

Trying to get conda-build to make the conda package.

[kwabenantim]

The conda package was built with conda mambabuild and is now up on a test channel. Currently testing it in a Jupyter notebook and fixing issues.

To install, run:
conda install -c kwabenantim chaste

To start a Jupyter notebook, run:
jupyter notebook

[kwabenantim]

Test	Status
ode/TestOdeSystemPython.py	passing
cell_based/tutorials/TestScratchAssayTutorial.py	passing
cell_based/tutorials/TestVertexBasedCellSimulationsPythonTutorial.py	failing
cell_based/tutorials/TestMeshBasedCellSimulationsPythonTutorial.py	passing
cell_based/tutorials/TestPottsBasedCellSimulationsPythonTutorial.py	passing
cell_based/tutorials/TestSpheroidTutorial.py	passing
cell_based/tutorials/TestCellSortingTutorial.py	passing
cell_based/tutorials/TestTensileTestTutorial.py	failing
cell_based/tutorials/TestNodeBasedCellSimulationsPythonTutorial.py	failing
cell_based/TestVertexBasedCellPopulationPython.py	failing
cell_based/TestMeshBasedCellPopulationPython.py	failing
cell_based/TestNodeBasedCellPopulationPython.py	failing
cell_based/TestCaBasedCellPopulationPython.py	failing
mesh/TestPottsMeshPython.py	passing
mesh/TestChastePointPython.py	failing
core/TestFileFinderPython.py	failing
core/TestPetscToolsPython.py	failing
core/TestRandomNumberGeneratorPython.py	passing
core/TestTimerPython.py	passing
core/TestVersionPython.py	passing
core/TestOutputFileHandlerPython.py	passing

[kwabenantim]

TestVertexBasedCellPopulationPython.py

[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 http://www.mcs.anl.gov/petsc/documentation/faq.html#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.
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=59
:
system msg for write_line failure : Bad file descriptor

This stems from the visualisation scene modifier: modifier = chaste.cell_based.VtkSceneModifier2()

[kwabenantim]

Scene rendering fixed: Chaste/PyChaste#1

[kwabenantim]

Colab notebooks enabled:
Chaste/PyChaste#2
Chaste/PyChaste#8

[kwabenantim]

Wrappers updated to Chaste/develop branch:
Chaste/PyChaste#7
Chaste/PyChaste#13

[kwabenantim]

Fixing c_vector support:
Chaste/PyChaste#11

[kwabenantim]

Remaining Tasks

• Complete c_vector support: Ublas vector wrapping support is broken PyChaste#11
• Fix PETSc Vec and Mat support and failing tests: Fix CI PyChaste#15
• Fail without crashing notebooks: Fix out-of-order crashes in notebooks PyChaste#20; Fix visualisation crashes in notebooks PyChaste#21
• Write developer documentation for adding wrappers: Update bindings documentation for developers PyChaste#19
• Move PyChaste repository to Chaste organisation: Move repository to Chaste organisation PyChaste#32

[kwabenantim]

Closing this issue as Python bindings are now implemented: https://github.com/Chaste/PyChaste. New issues will be created for further updates to the Python bindings including, but not limited to:

• Supporting new versions of dependencies
• Building conda packages for different versions of Python
• Updating the docker image
• Adding new wrappers when Chaste changes
• Adding new tutorials
• Adding new tests