Move PyChaste Bindings into Chaste Trunk

[kwabenantim]

Summary
It might be a good idea to consider moving the Python bindings into the main Chaste trunk as the bindings are tightly coupled to upstream Chaste source.

Advantages:

• Easier to keep bindings in synch with develop branch and release versions.
• Bindings tests can be added to the CI on PRs to check if bindings break when other parts of Chaste are updated.
• Simpler to maintain a single documentation website.

Disadvantages:

• All developers will need to learn some python and pybind11 as well to test changes to bindings?

[kwabenantim]

We have concluded that this is a good idea.

To Do

• Release PyChaste 2024.1 #62
• Move PyChaste website #34
• Fix Automatic Wrapper Generator Bugs #40
• Add Bindings Tutorials #47
• Test Chaste/PyChaste Diff #48
• Add PyChaste Test Suite to Chaste CI #49
• Add PyChaste Support for VTK 8 #23
• Add PyChaste Support for VTK 9 #24

[kwabenantim]

Discussion @ Sheffield Hackathon

Coverage Testing

Add tests to check if there are new classes in cell_based without wrappers

Test against comprehensive list of supported use cases (100% coverage shouldn't be required initially for wrappers).

Configuring

Pybind11
Do not add Pybind11 code into trunk

Preferences in order:

1. Use scikit-build (link) to get pybind11
2. Use cmake fetchcontent
3. Do a pip install into the chaste_codegen Python env (rename env?)

Pull latest pybind11 stable version to keep up to date with latest Python and C++ version support.

cppwg
Do a pip install into the chaste_codegen Pyhton env

Conda packaging

Add Chaste developers to anaconda pychaste channel

Use GitHub actions for building conda packages

Build for Linux/MacOS amd64 and arm64 (Linux arm64 on self-hosted)

Docker

Merge into Chaste docker

Developer Documentation

• Generating wrappers automatically
• Explanation of contents of configuration file
• Code inside wrappers
• Additional code e.g. for custom PyChaste visualisation
• Fixing common problems