Migrate linting CI from pre-commit to prek#151
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Use the prek-action (a faster, drop-in reimplementation of pre-commit) in both the lint check and the @nf-core-bot autofix workflow. prek reads the existing .pre-commit-config.yaml and runs the same hooks, so the config is kept unchanged and contributors can still run pre-commit locally. - pre-commit.yml: replace setup-python + pip install pre-commit with j178/prek-action (runs prek run --all-files). - fix-linting.yml: install prek via the action (install-only) and run it, preserving the continue-on-error outcome that drives the commit/react logic. - Keep the 'pre-commit' job name so required-status-check protection is unaffected. Addresses #150 (CI swap, keeping .pre-commit-config.yaml).
mashehu
approved these changes
Jun 17, 2026
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| - name: Run prek | ||
| id: prek | ||
| run: prek run --all-files | ||
| continue-on-error: true |
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not needed if we run the setup step without the added install-only
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Good call — done in 9f456e2. Dropped install-only and the separate run step; the action now runs prek run --all-files directly with id: prek + continue-on-error, so the existing steps.prek.outcome autofix/commit logic is unchanged.
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Address review feedback: drop the install-only + separate run step and let j178/prek-action run prek run --all-files itself, with id + continue-on-error driving the existing autofix/commit logic.
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Summary
Migrate the linting CI from
pre-committoprek— a faster, single-binary, drop-in reimplementation of pre-commit written in Rust.prekreads the existing.pre-commit-config.yamland runs the same hooks, so the config is kept unchanged and contributors can still usepre-commitlocally if they prefer. Noprek.toml, no forced tooling change.Changes
.github/workflows/pre-commit.yml— replaceactions/setup-python+pip install pre-commit+pre-commit run --all-fileswithj178/prek-action(which runsprek run --all-files)..github/workflows/fix-linting.yml(the@nf-core-bot fix lintingautofix) — install prek via the action (install-only: true) and runprek run --all-files, preserving thecontinue-on-erroroutcome that drives the commit/react logic.pre-commitjob name so any required-status-check branch protection keeps matching.prek-actionis pinned to a commit SHA (v2.0.4) to match the repo's other pinned actions.Why
.pre-commit-config.yaml, same hooks (prettier, editorconfig-checker, actionlint).Notes
https://claude.ai/code/session_01DGsyWUGbsvfkJDgdcaYLxv
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