Build conda packages for Python 3.8 - 3.11

[kwabenantim]

Summary

• Supports Build conda packages for Python 3.8 - 3.12 #42
• Supports Update PyChaste docker image #28

[kwabenantim]

Failure to resolve conda build dependencies
The minimum version of petsc4py on conda-forge that supports Python 3.11 is petsc4py 3.17.4 which depends on:

libgcc-ng >=12, libgfortran-ng, libgfortran5 >=10.4.0, mpich >=4.0.2,<5.0a0, numpy >=1.21.6,<2.0a0, 
petsc >=3.17.4,<3.18.0a0 real_*, python >=3.10,<3.11.0a0, python >=3.10,<3.11.0a0 *_cpython, python_abi 3.10.* *_cp310

In turn, petsc 3.17.4 from conda-forge depends on:

fftw * mpi_openmpi_*, hdf5 * mpi_openmpi_*, hdf5 >=1.12.2,<1.12.3.0a0 mpi_openmpi_*, 
hypre >=2.25.0,<2.25.1.0a0, libblas >=3.9.0,<4.0a0, libcblas >=3.9.0,<4.0a0, libgcc-ng >=12, 
libgfortran-ng, libgfortran5 >=10.4.0, liblapack >=3.9.0,<4.0a0, libstdcxx-ng >=12, 
metis >=5.1.0,<5.2.0a0, mumps-mpi >=5.2.1,<5.2.2.0a0, openmpi >=4.1.4,<5.0a0, 
parmetis >=4.0.3,<4.1.0a0, ptscotch >=6.0.9,<6.0.10.0a0, scalapack >=2.2.0,<2.3.0a0, 
scotch >=6.0.9,<6.0.10.0a0, suitesparse >=5.10.1,<5.11.0a0, superlu, superlu_dist >=7.1.1,<8.0a0, 
yaml >=0.2.5,<0.3.0a0

However, Chaste does not yet support hdf5 1.12.

[bdevans]

Ok, good investigating! Maybe time to open an issue in the main repo to add support for hdf5>=1.12 then?

[kwabenantim]

The investigation for supporting HDF 1.12 had already started on an old trac ticket (now a github issue):

• HDF5 1.12 support Chaste#163

[kwabenantim]

We now have vtk 7.1.1 built for Python 3.11 (https://anaconda.org/PyChaste/vtk/files).
Next step is to build PyChaste for Python 3.11.

[kwabenantim]

The VTK conda build has some fixed paths in its generated CMake configuration that need fixing.

make[3]: *** No rule to make target 
'/home/conda/feedstock_root/build_artifacts/vtk_1696254766018/_build_env/x86_64-conda-linux-gnu/sysroot/usr/lib/libSM.so', 
needed by 'projects/PyChaste/libchaste_project_PyChaste.so'.  Stop.

[kwabenantim]

Fixes

VTKConfig.cmake

-if (VTK_USE_CXX11_FEATURES)
-  if (CMAKE_VERSION VERSION_LESS "3.1")
-    message(FATAL_ERROR "VTK was built with C++11 features using CMake's CXX_STANDARD_REQUIRED feature.  Configuring projects this way requires a newer version of CMake.  Please update to CMake 3.1 or newer")
-  endif()
-  set(CMAKE_CXX_STANDARD 11)
-  set(CMAKE_CXX_STANDARD_REQUIRED 11)
-endif()

VTKTargets.cmake
Remove /home/conda/feedstock_root/build_artifacts/vtk_1696254766018/_build_env/x86_64-conda-linux-gnu/sysroot/usr/lib/ from all paths passed to the linker.

[kwabenantim]

Need to update build scripts to narrow down dependencies due to installation issues:

• Broken pychaste conda install #55

[kwabenantim]

Conda Builds for PyChaste and VTK

• Python 3.8
• Python 3.9
• Python 3.10
• Python 3.11
• Python 3.12 (skipped)

[kwabenantim]

Colab Notebook for Immersed Boundary tutorial working okay.

[kwabenantim]

Skipping Python 3.12 as vtk 7 python wrapping contains deprecated functionality. Support for newer vtk versions should fix this in #23 and #24