ci: add Ruff config, pre-commit hooks, and GitHub Actions lint workflow

[korbonits]

Summary

• Add Ruff config (E/F/I rules, 120-char line length, per-file ignores for __init__.py)
• Add .pre-commit-config.yaml with Ruff lint + format hooks
• Add .github/workflows/lint.yml triggering on PRs and pushes to main
• Auto-fix violations (unsorted imports, unused imports, f-string placeholders)

Note: ruff-format is excluded from pre-commit and CI — this repo uses pyink. Ruff's line-length and indent-width are set to match (80/2). F722/F821 are ignored: false positives from jaxtyping annotations (e.g. Float[Array, "b n h d"]).

Motivation

No linting or PR-level CI exists today. This PR adds lightweight enforcement using Ruff — fast, single dependency — and wires it up to run on every PR.

What's not included

• No type checking — out of scope
• No new lint rules beyond E/F/I selection

Testing

Ran ruff check . and ruff format --check . locally — all checks pass.

Co-Authored-By: Claude Sonnet 4.6 noreply@anthropic.com

[google-cla]

Thanks for your pull request! It looks like this may be your first contribution to a Google open source project. Before we can look at your pull request, you'll need to sign a Contributor License Agreement (CLA).

View this failed invocation of the CLA check for more information.

For the most up to date status, view the checks section at the bottom of the pull request.

[tomwardio]

Thanks for this PR. We already have pre-commit formatting and linter checks that use pyink and pylint respectively (https://github.com/google-deepmind/alphagenome/blob/main/pyproject.toml#L121-L122).

This aligns with our formatting and linter checks we have internally.

[korbonits]

Sorry about that! Will find something more impactful to contribute

…

On Wed, Apr 15, 2026 at 7:18 AM Tom Ward ***@***.***> wrote: *tomwardio* left a comment (google-deepmind/alphagenome#43) <#43 (comment)> Thanks for this PR. We already have pre-commit formatting and linter checks that use pyink and pylint respectively ( https://github.com/google-deepmind/alphagenome/blob/main/pyproject.toml#L121-L122 ). This aligns with our formatting and linter checks we have internally. — Reply to this email directly, view it on GitHub <#43 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABIJPHTB5M6J5IU6NJ2BOS34V6K4ZAVCNFSM6AAAAACXWUD4T6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DENJSHAZTMMZVGE> . You are receiving this because you authored the thread.Message ID: ***@***.***>