Switch to pyproject.toml

[ianhi]

When I tried to install in editable mode (force of habit) I ran into this deprecation warning:

DEPRECATION: Legacy editable install of sgkit==0.9.1.dev54+geef911e8.d20250401 from file:///Users/ian/Documents/dev/sgkit (setup.py develop) is deprecated.
 pip 25.1 will enforce this behaviour change. A possible replacement is to add a pyproject.toml or enable --use-pep517, and use setuptools >= 64. 
If the resulting installation is not behaving as expected, try using --config-settings editable_mode=compat. 
Please consult the setuptools documentation for more information. Discussion can be found at https://github.com/pypa/pip/issues/11457

I used ini2toml to do the initial conversion from setup.cfg to pyproject.toml then manually configured flake8 in .flake8 as flake8 does not support pyproject toml. Finally I added a line to the contributing docs about editable installs.

• [NA] Fixes #xxxx
• [NA] Tests added
• [NA] User visible changes (including notable bug fixes) are documented in changelog.rst
• [NA] New functions are listed in api.rst

[jeromekelleher]

LGTM!

[mergify]

This PR has conflicts, @ianhi please rebase and push updated version 🙏

[tomwhite]

This looks great - thanks for the contribution @ianhi!

The build was failing due to changes not related to this PR, which I have now fixed in #1297. Can you rebase this PR and change the pins to the following in pyproject.toml:

• numpy < 2.2
• xarray < 2025.03.1
• cbgen > 1.0.5

Also, it looks like Black is complaining (perhaps the settings have changed slightly?), see https://github.com/sgkit-dev/sgkit/actions/runs/14207381471/job/39820084873?pr=1300, so can you run pre-commit run --all-files please.

Thanks!

[ianhi]

Somewhat relatedly do you know the person who maintains the cbgen package? I had to install that from source when trying to follow the sgkit tutorial because it doesn't have any builds for macos 15: limix/cbgen#18

[tomwhite]

Somewhat relatedly do you know the person who maintains the cbgen package? I had to install that from source when trying to follow the sgkit tutorial because it doesn't have any builds for macos 15: limix/cbgen#18

Yes, it's @horta.