Move dependency management to uv

[molpopgen]

• Move contents from setup.[py|cfg] into pyproject.toml
• Update github workflows
• Delete old requirements files

See #589

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.06%. Comparing base (4bc3f95) to head (e5be9c0).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #590      +/-   ##
==========================================
- Coverage   99.81%   99.06%   -0.75%     
==========================================
  Files           5        5              
  Lines        1600     1600              
==========================================
- Hits         1597     1585      -12     
- Misses          3       15      +12     

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[molpopgen]

Issues:

• Our use of jupyter-book requires pinning ipython to a version that requires python >= 3.10. While it may be true that the package itself works as far back as 3.7, we do not test that that is true and it appears that current tooling includes the entire development environment as having the same minimum version.
• It is not clear that dev.yaml is needed in the work flows any longer?
• The window tests are failing sporadically.

[molpopgen]

@grahamgower @apragsdale -- this is ready for a look.

I have shoe-horned most tasks into a place where they now work. The problem is the windows tests. They fail because the modules in demes-spec are not finding ruamel. I cannot reproduce this issue locally, which makes sense because I'm on Linux and the Linux tests are also passing in CI.

[grahamgower]

The failing tests are in test_cli.py and test_spec.py. What these tests have in common is that they use subprocess.* to run python. These subprocesses are unable to import basic dependencies such as attr and ruamel, so my guess is that the uv virtual environment is not active for the subprocess. I don't think the previous tests used a virtual environment, and so didn't encounter this issue? This is likely a common problem experienced by other projects using uv and running cli tests, so it might be worth finding out what others have done here.

[grahamgower]

There seems to be a lot of duplication between the _setup.cfg and pyproject.toml - is this intentional? And what's the role of _setup.cfg here, versus setup.cfg? Which files are generated by uv? Is it just uv.lock?

[grahamgower]

I reckon we're out of beta now.

[grahamgower]

This doesn't match the _setup.cfg file.

[grahamgower]

No longer in beta.