build: adopt PEP 735 dependency groups for dev/test/doc

[Marius1311]

Aligns cell-annotator with cookiecutter-scverse v0.7.0 by moving development-only dependencies from [project.optional-dependencies] to [dependency-groups] (PEP 735). Provider layers stay as optional-dependencies since end users install them via pip install cell-annotator[openai] etc.

New layout

[dependency-groups] (dev-only — not shipped in the wheel metadata):

• dev = pre-commit, twine
• test = pytest, coverage, flaky, pytest-cov
• doc = Sphinx stack

[project.optional-dependencies] (install-time extras, unchanged for end users):

• provider layers: openai, anthropic, gemini, all-providers, colors, gpu, tutorials
• test — thinned to a pointer at cell-annotator[all-providers] + cell-annotator[colors]. The Python test packages no longer live here, so there's a single source of truth per audience.

[tool.hatch.envs.*] — switched features = [...] to dependency-groups = [...] for the default, docs, and hatch-test envs. hatch-test also keeps features = [ "test" ] so the provider extras flow in via the thin pointer above.

Docs

• docs/contributing.md — pip recipe updated to pip install --group dev --group test --group doc -e ".[test]" (requires pip 25.1+).
• docs/contributing.md — uv recipe updated to uv sync --all-extras --all-groups.

Validation

• uv sync --all-extras --all-groups resolves cleanly.
• uv run --group test --extra test pytest → 188 passed.
• hatch env show -i renders the hatch-test matrix with the expected dependencies.
• sphinx-build -M html docs docs/_build succeeds with no warnings.

Notes

• End users are unaffected: pip install cell-annotator[openai] still works exactly as before.
• External CI that installs cell-annotator[test] will continue to get the provider extras, but will now need to also pull --group test (or switch to uv / hatch) to get the Python test packages. We have no external consumer of [test] that I'm aware of.

Part of #73. Stacks on #74.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 79.95%. Comparing base (daf4b1c) to head (ecb4382).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #75   +/-   ##
=======================================
  Coverage   79.95%   79.95%           
=======================================
  Files          15       15           
  Lines        1237     1237           
=======================================
  Hits          989      989           
  Misses        248      248           

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