Add CI, a tests stub, and a project README template

[gmermoud]

This repo is the base template for the lab's Python projects, but it had no tests, no CI, and its README described the template itself rather than the project built from it. It also picks up the pre-commit and container work that was sitting uncommitted in the tree.

What's here

CI — .github/workflows/ci.yml runs two jobs on every push to main and every PR: pre-commit (every hook over all files) and pytest (uv sync --frozen then the suite). The Python version is pinned via PYTHON_VERSION at the top of the workflow and should be kept in step with containers/apptainer.def.

Tests — tests/test_hello.py is a stub covering the example hello(). pytest is a dev dependency rather than a uvx tool: unlike the linters, it has to import the project, so it needs the environment.

Package rename — src/python-base/ → src/package_name/. The old name contained a hyphen, so it was not a valid module name and import python_base failed on a fresh clone. The placeholder is now importable and project-agnostic (python-base is the repo name, not the package name). This also made ruff start checking the package, surfacing a D104 that had been silently skipped — hence the new __init__.py docstring.

Docs — README.md becomes a fill-in-the-blanks template for downstream projects, with the template's own documentation moved to GUIDELINES.md. GUIDELINES.md gains sections on populating tests/ and on how CI works; setup step 2 now explains the underscore rule for package names. AGENTS.md now points at src/package_name/ instead of the leftover src/jaxifer-harness/.

Verification

uvx pre-commit run --all-files passes all 8 hooks, uv sync --frozen && uv run pytest passes, and actionlint reports no findings on the workflow. The action versions (checkout@v7, setup-uv@v8, cache@v6) were checked against the API rather than guessed.

Notes for review

• The mdformat hook reflowed AGENTS.md and GUIDELINES.md to 100 columns, which accounts for much of the diff noise in those files.
• .gitignore no longer ignores docs/, containers/, and models/, so containers/ is now tracked.
• The commit was made with --no-verify because the installed .git/hooks/pre-commit is stale (it points at an absolute path from another machine). The hooks were run manually over all files instead, with the results above. Running uvx pre-commit install will regenerate the hook locally.

🤖 Generated with Claude Code