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Update PyRadiomics and SlicerRadiomics build and CI

Key Investigators

• Joost van Griethuysen (The Netherlands Cancer Institute, The Netherlands)
• Jean-Christophe Fillion-Robin (Kitware Inc., USA)

Project Description

PyRadiomics was first introduced in 2017 and remains a very popular python package to compute radiomics features. It is integrated into 3D slicer via the SlicerRadiomics module. However, both projects are not heavily maintained anymore, causing the CI chain and build tools to be out of date.

Objective

Update build tools and CI pipelines for both PyRadiomics and SlicerRadiomics to be up to date with the latest python versions and build tools

Approach and Plan

• Scikit-ci is deprecated and should be replaced
• Invesitate option of using cibuildwheel
• Update metadata to adhere to new standards.

Progress and Next Steps

• Update pyproject.toml and remove deprecated files (e.g. setup.py, setup.cfg, requirements*.txt, MANIFEST)
• Run cookiecutter from Scientific Python Library Development Guide separately and use it to update pyradiomics structure.
  • Change build system to scikit-build-core
  • Build C-extensions using CMake
  • Moves CI/CD from CircleCI/AppVeyor to GitHub Actions.
• Create PR #203 in pykwalify to deal with deprecation warning. Ignore this warning in the build process of pyradiomics for the time being.
• Disable pre-commit part of CI pending the correct setup of CI/CD.
• Local build & test now passing.
• CI passing on pull request branch

ToDo:

• Update CI configuration to match supported python versions enabled in CircleCI/AppVeyor builds.PyRadiomics PR #898
• Currently, CI is failing on METADATA mismatch in wheel generation. This is due to a mismatch in generated version string (a version parsed from a metadata dir doesn’t contain the date suffix, whereas the on in the generated wheel does). Fix the version string error to allow CI to pass.
• Add exceptions for style errors in pre-commit to allow it to pass initially. PyRadiomics issue #899
• Later, apply style changes to make pyradiomics adhere to the configured style.
• Review readthedocs documentation generation.
• Review CD configuration to publish releases on tags pushed onto the master branch in the main repo.

Illustrations

Background and References

Documentation

• https://pyradiomics.readthedocs.io
• https://cibuildwheel.pypa.io

Source code

• https://github.com/AIM-harvard/pyradiomics
• https://github.com/AIM-harvard/slicerradiomics

Misc

• Scientific Python Library Development Guide