Update code quality configuration

[khaeru]

• Bump mypy, ruff versions and update config.
  • We now follow the configuration recommended in Using mypy via pre-commit python/mypy#13916, such that all files are checked with mypy, even if only a few are edited in a particular commit. This, for instance, avoids the situation that a change to type hints in one file causes typing errors in other files that are not checked.
  • IPython/Jupyter notebooks are now included in ruff formatting.
• Update copyright year.
• Work around Tags no longer fetch with Git v2.48.0 actions/checkout#2041.

How to review

TBD

PR checklist

• Continuous integration checks all ✅
• Add or expand tests; coverage checks both ✅
• Add, expand, or update documentation. N/A, formatting only
• Update release notes.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.9%. Comparing base (3fa1191) to head (96407b5).
Report is 7 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##            main    #555     +/-   ##
=======================================
- Coverage   98.9%   98.9%   -0.1%     
=======================================
  Files         44      44             
  Lines       4790    4790             
=======================================
- Hits        4740    4738      -2     
- Misses        50      52      +2     

Files with missing lines	Coverage Δ
ixmp/backend/jdbc.py	97.2% <100.0%> (ø)
ixmp/cli.py	100.0% <ø> (ø)
ixmp/tests/backend/test_jdbc.py	100.0% <ø> (ø)
ixmp/tests/core/test_scenario.py	100.0% <100.0%> (ø)

... and 1 file with indirect coverage changes

[khaeru]

@glatterf42 I could, optionally, expand this PR with 2 kinds of improvements to the GitHub Actions workflows that I have prototyped in genno and elsewhere:

1. pytest.yaml: use uv to set up Python and invoke pytest and pre-commit. As advertised, this seems to be very fast.

   It doesn't require any changes to code or packaging, so it seems to be a no-regret change.

2. publish.yaml: use uv build and uv publish instead of other tools; drop chaining to our iiasa/actions reusable workflow; use PyPI×GitHub "trusted publishing".

   However, because of upstream issues (metadata version missmatch in uv 0.5.5 astral-sh/uv#9513 → [BUG] tool.setuptools.license-files results in invalid metadata pypa/setuptools#4759) this requires a change in the build-backend, for which I went with hatchling as suggested in comments on those issues. This isn't a major change, especially as I only used the build backend and did not attempt to use any of the other features that hatch advertises. But I think it begins to collide with our discussion of whether to adopt hatch, pdm, poetry, or something else, where we still don't have a clear "yes" on any option. Also, uv publish is marked experimental for the time being.

   So I would maybe avoid to do this one in ixmp and the rest of the stack, for the moment.

Please let me know briefly what you think, and I'll proceed and also make parallel changes to message_ix.

[glatterf42]

Thanks for this PR :)

I agree with what you say, 1. sounds good, 2. can likely wait a little. Though I have already thought about migrating our package management to uv completely myself, i.e. migrate the pyproject.toml, generate a lock file, etc. But this can also wait until we can do 2. at least, I think.

[khaeru]

Okay, now in place. Compared to this run:

• macOS:
  • actions/setup-python: 2:49–5:33
  • astral-sh/setup-uv: 4:11–5:07
• Linux:
  • actions/setup-python: 2:29–4:30
  • astral-sh/setup-uv: 2:38–4:08
• Windows:
  • actions/setup-python: 13:08–15:58
  • astral-sh/setup-uv: 11:39–12:19

So only clear daylight on Windows, but by a few minutes. However there's a lot of variability in the unrelated steps. For the ubuntu-latest-py3.13 jobs, the times for the setup step + "Install the package and dependencies":

• actions/setup-python: 11 seconds + 53 seconds.
• astral-sh/setup-uv: 2 seconds + 6 seconds.

So that's a clear improvement.

[glatterf42]

Thanks, looks great to me :)
Hopeful that this will stabilize our CI :)