Move PyChaste Bindings into Chaste Trunk about pychaste HOT 6 OPEN

Rather than listing python3-notebook as a dependency (which I believe is deprecated), shouldn't we use jupyter lab? It might in general be better to install python packages with pip (in a virtual environment) rather than through (slowly updated) ubuntu packages.

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Thanks @bdevans. I'll update the package list.

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We have concluded that this is a good idea.

To Do

• #62
• #34
• #40
• #47
• #48
• #49
• #23
• #24

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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 Python 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

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Directory structure:

Chaste/pychaste
│
├── dynamic
│   ├── config.yaml
│   ├── templates
│   └── wrappers
│       ├── cell_based
│       ├── core
│       ├── mesh
│       ├── ode
│       ├── pde
│       └── visualization
├── src
│   ├── cpp
│   │   ├── cell_based
│   │   ├── ode
│   │   └── visualization
│   └── py
│       ├── chaste
│       │   ├── cell_based
│       │   ├── core
│       │   ├── external
│       │   ├── mesh
│       │   ├── ode
│       │   ├── pde
│       │   └── visualization
│       ├── docs
│       │   ├── api
│       │   └── tutorial
│       ├── LICENSE
│       ├── MANIFEST.in
│       ├── pyproject.toml
│       ├── setup.cfg
│       └── setup.py
└── test
    ├── cell_based
    ├── core
    ├── data
    ├── mesh
    ├── ode
    ├── tutorial
    └── visualization

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Notes from Nottingham Hackathon

• Add xvfb to recommended packages in chaste-dependencies
• More informative error message about files and methods that needs changing
• Error message should say how to fix the problem
• Put PyChaste dev documentation on developer wiki
• Update PyChaste web pages

• Create a pychaste-dependencies ubuntu package in addition to chaste-dependencies

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