Adopt uv for Python package management across SmartEM ecosystem

[vredchenko]

Adopt uv for Python Package Management

Related: smartem-decisions#212 (Docker rework - separate scope)

Summary

Migrate smartem-decisions CI/CD and developer tooling from pip to uv. The repo already has uv.lock and release-smartem-decisions.yml uses uv - this work standardizes all workflows.

Note: smartem-devtools already fully adopted uv (no changes needed).

---

Design Decisions

Decision	Choice	Rationale
install_requirements action	Eliminate	uv handles everything better with astral-sh/setup-uv@v7
Tox	Eliminate	Replace with direct uv run pytest/ruff/pyright
Pre-commit ruff hooks	Official ruff-pre-commit repo	Portable, auto-updates, no uv dependency for pre-commit
Windows builds (PyInstaller)	Keep pip	PyInstaller compatibility concerns
Dockerfile	Defer to #212	Docker rework is separate scope - will use uv there

---

Implementation

Phase 1: CI Workflow Migration

1.1 Update _test.yml

File: .github/workflows/_test.yml

Replace pip+tox with uv:

- name: Install uv
  uses: astral-sh/setup-uv@v7

- name: Set up Python
  run: uv python install ${{ inputs.python-version }}

- name: Install dependencies
  run: uv sync --extra all

- name: Run tests
  run: uv run pytest --cov --cov-report=xml

1.2 Update _schema_drift.yml

File: .github/workflows/_schema_drift.yml

Replace pip install -e .[all] with uv sync --extra all.

1.3 Update _dist.yml

File: .github/workflows/_dist.yml

Replace pipx run build with uv build, pipx run twine with uvx twine.

Phase 2: Remove Obsolete Files

• Delete: .github/actions/install_requirements/ - obsolete with uv
• Delete: .github/workflows/_tox.yml - tox is being removed

Phase 3: Configuration Updates

3.1 Update pre-commit config

File: .pre-commit-config.yaml

Replace local ruff hooks (lines 28-42):

- repo: https://github.com/astral-sh/ruff-pre-commit
  rev: v0.8.6
  hooks:
    - id: ruff
      args: [--force-exclude]
    - id: ruff-format
      args: [--force-exclude]

3.2 Update pyproject.toml

File: pyproject.toml

• Remove tox-direct from dev dependencies
• Remove entire [tool.tox] section

Phase 4: Documentation Updates

4.1 REPO-GUIDELINES.md

File: claude-config/smartem-decisions/REPO-GUIDELINES.md

Update commands:

Current	New
pip install -e .[all]	uv sync --extra all
pytest	uv run pytest
ruff check	uv run ruff check
pyright	uv run pyright

4.2 for-developers.md

File: smartem-devtools/docs/getting-started/for-developers.md

Update installation instructions to use uv as primary method.

4.3 tools.md

File: smartem-devtools/docs/development/tools.md

Prefix tool commands with uv run.

---

Files Summary

Modify

File	Change
.github/workflows/_test.yml	pip+tox → uv
.github/workflows/_schema_drift.yml	pip → uv
.github/workflows/_dist.yml	pipx → uv/uvx
.pre-commit-config.yaml	local ruff → official ruff-pre-commit
pyproject.toml	Remove tox config
REPO-GUIDELINES.md	Update commands
for-developers.md	Update install docs
tools.md	Add uv run prefixes

Delete

File	Reason
.github/actions/install_requirements/	Obsolete
.github/workflows/_tox.yml	Obsolete

Keep Unchanged

File	Reason
release-smartem-decisions.yml	Already uses uv
build_win_smartem_agent.yml	Keep pip for PyInstaller
uv.lock	Already exists
Dockerfile	Defer to #212

---

Verification

1. uv sync --extra all - dependencies install correctly
2. uv run pytest - tests pass
3. uv run ruff check src tests - linting works
4. uv run pyright src tests - type checking works
5. pre-commit run --all-files - hooks pass
6. CI workflows pass on push to branch

---

Out of Scope

• Dockerfile: Separate issue #212 (rework Docker to install from PyPI)
• fandanGO-cryoem-dls: Requires coordination with upstream maintainers
• FragmentScreen repos: Read-only, conda-based
• smartem-devtools: Already fully adopted uv

---

Tasks

• Update _test.yml to use uv instead of pip+tox
• Update _schema_drift.yml to use uv
• Update _dist.yml to use uv build/uvx twine
• Delete .github/actions/install_requirements/ action
• Update .pre-commit-config.yaml to use official ruff-pre-commit
• Remove tox config from pyproject.toml
• Update REPO-GUIDELINES.md with uv commands
• Update for-developers.md with uv installation instructions
• Update tools.md with uv run prefixes

[vredchenko]

#137

[vredchenko]

DiamondLightSource/smartem-decisions#218