Replace tox and pip with uv

[dweindl]

Why

tox and pip split dependency/environment management across two tools:
pip installs packages, tox orchestrates per-purpose virtualenvs
(quality/unit/doc) on top of it. uv replaces both with a single fast
tool that handles dependency resolution/installation, Python version
management, virtualenv creation, and building sdists — fewer moving
parts for contributors to learn, and noticeably faster CI installs.

Summary

• Replace tox + pip with uv across dev tooling, CI, and the release workflow.
• CI (ci_tests.yml): astral-sh/setup-uv installs uv + the matrix Python version (with built-in caching); tox -e quality -> uvx pre-commit run --all-files; tox -e unit -> uv sync --group ci + uv run pytest. The "3.x" matrix wildcard is replaced with an explicit "3.14", since setup-uv needs exact versions.
• Release (deploy.yml): pip install setuptools wheel build && python -m build -s -> uv build --sdist.
• The two CI-only git dependencies previously listed in tox.ini's unit env deps= (petabtests, benchmark_models_petab), plus the tests/reports/combine/vis extras, now live in a single PEP 735 [dependency-groups] ci group in pyproject.toml (via a self-referential petab[tests,reports,combine,vis] entry) — confirmed dependency-groups are excluded from built distribution metadata, so PyPI's rejection of direct/VCS references doesn't apply here.
• No uv.lock is committed — this is a library, so CI keeps resolving against current constraints each run, matching the previous un-pinned tox/pip behavior.
• Removed tox.ini and requirements-dev.txt (only contained tox>=3.26.0).
• Updated doc/development.rst dev-workflow commands to use uv sync/uv run/uvx.
• Fixed README.md's stated Python requirement (>=3.11 -> >=3.12) to match pyproject.toml's requires-python.
• Added [tool.uv] constraint-dependencies = ["pysb>=1.17.0"]: uv resolves one dependency graph across all declared extras (not just the ones requested for a given sync), so the unit-test job was transitively pulling in pysb via the unrelated doc extra and landing on 1.16.0, whose legacy build bootstrap hits a dead URL. Pinning the resolver to >=1.17.0 avoids it without changing the public tests/doc extras' declared ranges.

Not changed (flagged, out of scope)

• .readthedocs.yaml stays on pip — Read the Docs' python.install only supports pip/setuptools natively; using uv there needs custom build.commands overrides.
• Contributors lose the single tox -e <name> entrypoint in favor of direct uv run/uvx commands.

Test plan

• uv build --sdist produces an equivalent sdist to the previous python -m build -s.
• uv sync --group ci resolves and installs correctly (verified petabtests and benchmark_models_petab install from git, and the full test suite passes locally: 378 passed, 4 skipped).
• uvx pre-commit run --all-files behaves like the old tox -e quality.
• CI (ci_tests.yml) passes across the full OS x Python-version matrix on this PR.
• deploy.yml succeeds on the next release (can't be tested pre-merge).

🤖 Generated with Claude Code

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 75.30%. Comparing base (3646706) to head (cd854e6).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #507   +/-   ##
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  Coverage   75.30%   75.30%           
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  Files          64       64           
  Lines        7353     7353           
  Branches     1327     1327           
=======================================
  Hits         5537     5537           
  Misses       1310     1310           
  Partials      506      506           

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