Adopt pyproject.toml standard, fast-forward cookiecutter

[Zeitsperre]

Pull Request Checklist:

• This PR addresses an already opened issue (for bug fixes / features)
  • This PR fixes #xyz
• (If applicable) Documentation has been added / updated (for bug fixes / features).
• (If applicable) Tests have been added.
• HISTORY.rst has been updated (with summary of main changes).
  • Link to issue (:issue:number) and pull request (:pull:number) has been added.

What kind of change does this PR introduce?

• Uses the latest cookiecutter template
• Replaces setup.py, MANIFEST.in, requirements*.txt, and most configs in the setup.cfg for pyproject.toml
• Most flake8 checks are now handled via ruff
• New GitHub Workflows for automatically managing version bump and actions versions.
• Documentation adjustments
• Basic configurations for mypy-compliance

Does this PR introduce a breaking change?

Yes. We now are using pyproject.toml with flit to build the library. This will entail one or two major changes to a typical development workflow.

The main changes worth noting:

• $ pip install -e . should be substituted for $ flit install -s/--symlink when performing development installations ($ pip install . works exactly as you'd expect).
  • Alternatively, one can run $ make develop. This is documented.
• Most configurations are now found within the pyproject.toml

Other information:

https://flit.pypa.io/en/stable/index.html
https://peps.python.org/pep-0518/
https://peps.python.org/pep-0621/
https://www.mypy-lang.org/

[sarahclaude]

Is there a reason why envrionment.yml became environment-dev.yml?

[Zeitsperre]

Is there a reason why envrionment.yml became environment-dev.yml?

The reason is that the cookiecutter uses environment-dev.yml for marking dev dependencies. If it's not much trouble to adjust your routines to environment-dev.yml, the project will simply be more in sync with the template.

[sarahclaude]

Thanks for the info!

[Zeitsperre]

@sarahclaude

This is good for final review!

[sarahclaude]

Works great, flit could be added to environment-dev.yml to not have to install it after

[Zeitsperre]

@sarahclaude

Everything except the docs seems to be working. We're running into resource issues for some reason (are the notebooks too complex?). If you are happy with everything else, we can open another PR to fix that.