Migrate dev tooling from pip-tools/tox to uv

[hf-krechan]

Summary

• Moves dev-tool extras (tests, coverage, formatting, linting, spell_check, type_check, init_bo4e) from [project.optional-dependencies] to PEP 735 [dependency-groups], plus a bundled dev group; drops the test_packaging extra (build/twine) entirely.
• Replaces tox.ini and requirements.txt with uv.lock.
• Rewrites all GitHub Actions workflows to use astral-sh/setup-uv + uv sync --group X / uv run instead of pip install tox && tox -e X, inlining the docker-compose/BO4E-model-generation steps that tox used to chain via nested tox -e calls.
• packaging_test.yml now uses native uv build + uv publish --dry-run instead of build/twine.
• Updates .github/dependabot.yml ecosystem from pip to uv.
• Updates .pre-commit-config.yaml (bumps black rev to match new pins, adds the uv-lock hook).
• Updates README.md dev setup instructions from tox -e ... to uv run/uv sync.

Dependency pins (final state, after CI debugging)

• datamodel-code-generator stays pinned at ==0.25.9 (not bumped). An earlier attempt to bump it to resolve an isort conflict broke bo4e-python-generator==0.0.10, which relies on datamodel-code-generator internals that changed across releases. Fixed the original isort conflict instead by pinning the formatting group's isort to 5.13.2 (last release compatible with datamodel-code-generator==0.25.9's isort<6.0 constraint).
• sqlmodel pinned to ==0.0.24 and python-dotenv pinned to ==1.0.1 in [project.dependencies]. Both were previously open-ended constraints that only got frozen for CI via the now-removed requirements.txt; without that freeze, uv lock picked newer versions that break mypy (sqlmodel) and .env loading under coverage run -m pytest (python-dotenv). See PR comments below for the full debugging trail.

No workflow matrix structures were changed, so existing required status checks on main should still match by name.

Test plan

• uv lock resolves cleanly
• uv sync --group dev succeeds
• Spot-checked each group syncs independently (tests, linting, type_check, spell_check, coverage, formatting, init_bo4e)
• Ran black --check, isort --check, codespell, pylint, mypy, pytest import, bost --help, bo4e-generator --help through uv run
• uv build and uv publish --dry-run succeed locally
• CI passes on this PR (all checks green, including docker-based integration/coverage jobs)

🤖 Generated with Claude Code

[hf-krechan]

CI status: all checks green ✅

Summary of the full fix chain that came out of debugging CI after the initial migration:

1. Reverted the datamodel-code-generator bump. My first fix for an isort conflict bumped datamodel-code-generator from 0.25.9 to >=0.27.1, which resolved to the latest release (0.70.0) and broke bo4e-python-generator==0.0.10 (DataModelSet.__new__() missing 2 required positional arguments). Even the minimal bump to 0.27.1 breaks it differently (type_map_factory() got an unexpected keyword target_datetime_class) — bo4e-python-generator reaches into datamodel-code-generator internals that shift across releases, so it's tightly locked to exactly 0.25.9. Resolved the original isort conflict instead by downgrading the formatting group's isort pin to 5.13.2 (last release satisfying datamodel-code-generator==0.25.9's isort<6.0 constraint).

2. Pinned sqlmodel==0.0.24 in [project.dependencies]. The dependency was always the open-ended sqlmodel>=0.0.14 — requirements.txt is what silently froze it at 0.0.24 for CI. Without that freeze, uv lock resolved to 0.0.39, which breaks mypy against the bo4e-generated models (SQLModelConfig/ConfigDict incompatibilities, 459 errors).

3. Pinned python-dotenv==1.0.1, for the same reason — resolved to 1.2.2 without the requirements.txt freeze, which broke load_dotenv()'s implicit path discovery specifically when pytest runs wrapped by coverage run -m pytest from the tests/ directory (OSError: Could not load .env file.).

All three were cases where requirements.txt had silently pinned a version that pyproject.toml's own (looser) constraint didn't capture, and this repo's generated model code (via bo4e-python-generator/datamodel-code-generator) turns out to be fragile against drift in any of them — confirmed by this repo's own Dependabot history, which already has failed, unmerged bump attempts for python-dotenv, datamodel-code-generator, and pydantic.

🤖 Generated with Claude Code

[Copilot]

Pull request overview

This PR migrates the repository’s Python dev tooling from pip-tools/tox to uv, centralizing dependency resolution in uv.lock and updating CI + documentation accordingly.

Changes:

• Replace tox env orchestration and requirements.txt with uv dependency groups and uv.lock.
• Rewrite GitHub Actions workflows to use astral-sh/setup-uv, uv sync --group …, and uv run ….
• Update developer-facing tooling and docs (pyproject.toml dependency groups, pre-commit hooks, README).

Reviewed changes

Copilot reviewed 12 out of 14 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
tox.ini	Removes legacy tox environments in favor of uv-based workflow steps.
requirements.txt	Removes pip-tools generated requirements in favor of uv.lock.
README.md	Updates dev setup and common commands to use uv sync / uv run.
pyproject.toml	Moves dev extras to [dependency-groups] and adjusts some pins.
.pre-commit-config.yaml	Updates formatter hook versions and adds uv-lock hook.
.github/workflows/unittests.yml	Migrates unit-test job to uv (but currently does not run tests).
.github/workflows/pythonlint.yml	Migrates lint/type/spell jobs to uv and inlines BO4E model generation.
.github/workflows/python-publish.yml	Migrates release workflow steps to uv and inlines checks.
.github/workflows/packaging_test.yml	Switches packaging test to uv build + uv publish --dry-run.
.github/workflows/integrationtests.yml	Migrates integration tests to uv and inlines DB/model setup.
.github/workflows/formatting.yml	Migrates formatting checks to uv groups and uv run.
.github/workflows/coverage.yml	Migrates coverage job to uv and inlines DB/model setup.
.github/dependabot.yml	Switches Dependabot ecosystem entry from pip to uv.

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[hf-krechan]

Confirmed accurate, but this is pre-existing behavior, not something this migration changed — the old tox.ini's [testenv:unittests] also only ran tox -e setup_testpostgresql + tox -e remove_testpostgresql, never pytest (there's no separate unit-test suite in this repo, only tests/integrationtests, which is what integrationtests.yml actually exercises). I translated the tox behavior 1:1 rather than silently changing what this check does, since pytest (3.11, ubuntu-latest) is a required status check on main and I didn't want to risk changing its semantics without a separate discussion. Worth a follow-up issue if the maintainers want this job renamed or made to actually assert something.