Support publishing to PyPI

[ebrahimebrahim]

This adds support for publishing to PyPI by transitioning from the legacy setup.py to pyproject.toml.

The changes are adapted from the output of cookiecutter scientific-python/cookie based off scientific-python/cookie@8c0a1627. See https://learn.scientific-python.org/development/

Changes include:

• GitHub workflows for continuous integration (ci.yml) and continuous development (cd.yml). Each time a GitHub Release is created, it triggers the build, test, and publishing of wheels.
  • (The pytest CI is placeholder infrastructure in case there is a desire to add unit tests in the future)
• Infrastructure for building sphinx-based documentation.
• Extraction of package version from source control by leveraging setuptools-scm. Note that generated source distribution will include the relevant version metadata.
• Pre-commit hooks for checking style.
  • To start with, linting exceptions have been added to pyproject.toml to ignore the style constraints that are not initially satisfied and that could not be safely auto-fixed. Subsequent commits can remove the exceptions and make style changes if there is a desire to do that in the future.
• Dependabot configuration

The major benefit of this proposed update is that HD_BET can be more easily maintained and automatically published to PyPI upon release. This helps bring HD_BET further into the larger python neuroimaging ecosystem by allowing other packages to mark it as a dependency.

The only required step on your side will be to create a pending publisher on PyPI so that the GitHub workflow can automatically publish the package upon release creation. Would be happy to provide more details on any of this.

[ebrahimebrahim]

@FabianIsensee What do you think of this approach to publishing the project and automating some of the routine maintenance? Happy to provide some help in keeping this wonderful project alive!

[FabianIsensee]

Hey, thanks for the PR. This project is no longer actively developed and I welcome ways of reducing the amount of work we have to invest into keeping it running for everyone.
Can you please enlighten me how I can integrate the automatic pypi publishing once it is merged?

[ebrahimebrahim]

Once it is merged the steps to publish would be:

• (Once) Create a pending publisher on PyPI (essentially linking this repo to a project on your PyPI account)
• (Every time you want to publish a new version) Release a version of the software using github

(The "automatic" aspect of it is that the publish step is triggered automatically whenever you create a release on github. This is achieved by the configuration in the cd.yml file that is added in this PR)

[FabianIsensee]

Thanks, will do.
Might need some more days because I need to fix some things on our end

[ebrahimebrahim]

@FabianIsensee Let me know if there are any more questions I can answer or anything I can help with to move this along