mypy: analyze types in all possible libraries

[rominf]

Preparation for #646

• Remove ignore_missing_imports = true from mypy configuration.
• Run mypy in the same environment instead of separate to check types
  in dependencies like fastapi.
• Move mypy dependencies from pre-commit configuration to setup.cfg.
• Update mypy dependencies there.
• Move rq from environment.yml to setup.cfg: conda-forge version:
  1.9.0, pypi version : 1.15.1 (two years difference; types were added).
• Add libraries with missing types to ignore list in mypy
  configuration.
• Add pydantic mypy plugin.
• Allow running mypy without explicit paths.
• Update GitHub Actions.
• Temporarily add ignore annotation-unchecked to make mypy pass.
• Fix new mypy issues:
  • Use https://github.com/hauntsaninja/no_implicit_optional to make
    Optional explicit.
  • If there is no default, the first pydantic.Field argument should
    be omitted (None means that the default argument is None).
  • Refactor _run_migrations. There were two different paths: one for
    normal execution and another one for testing. Simplify arguments and
    the function code, and introduce a new mock run_migrations.
  • To preserve compatibility, introduce ChannelWithOptionalName for
    the /channels patch method. Note that the solution is a bit dirty
    (I had to use type: ignore[assignment]) to minimize the number of
    models and the diff.
  • Trivial errors.

[codecov-commenter]

Codecov Report

Patch coverage: 95.65% and project coverage change: -0.03% ⚠️

Comparison is base (7501519) 83.64% compared to head (deda79d) 83.61%.

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Additional details and impacted files

@@            Coverage Diff             @@
##             main     #658      +/-   ##
==========================================
- Coverage   83.64%   83.61%   -0.03%     
==========================================
  Files          79       79              
  Lines        6230     6239       +9     
==========================================
+ Hits         5211     5217       +6     
- Misses       1019     1022       +3     

Files Changed	Coverage Δ
quetz/dao.py	88.74% <ø> (ø)
quetz/main.py	89.89% <ø> (ø)
quetz/cli.py	74.68% <75.00%> (-0.08%)	⬇️
quetz/config.py	90.20% <100.00%> (ø)
quetz/hooks.py	82.60% <100.00%> (ø)
quetz/jobs/rest_models.py	87.17% <100.00%> (ø)
quetz/metrics/view.py	68.75% <100.00%> (ø)
quetz/pkgstores.py	68.01% <100.00%> (ø)
quetz/rest_models.py	98.20% <100.00%> (+0.02%)	⬆️
quetz/tasks/mirror.py	88.09% <100.00%> (-1.03%)	⬇️
... and 1 more

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[rominf]

If there is no default, first pydantic.Field argument should be omitted (None means that the default argument is None).

but

To preserve compatibility, introduce the ChannelWithOptionalName for /channels patch method.

I'm relying on the test suite and/or your knowledge of what's Optional and what's not since the codebase is new to me, and I might miss something.

cc @beenje

[rominf]

It looks like the test test_download_remote_file_in_parallel is flaky: there is a problem in the test or the code. I haven't touched this place, and the previous run with the same code succeeded (I just fixed the commit message in the last force push).

The link to the job: https://github.com/mamba-org/quetz/actions/runs/6065939126/job/16455972862?pr=658

[wolfv]

Hey @rominf indeed, that test is unfortunately flaky (has been this way since a rather long time).

[rominf]

Rebased, now tests pass.

[rominf]

A reminder about the PR.

Feel free to close the PR if its continuation is not beneficial. I am open to rebasing and improving it though.