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Migrate linting CI from pre-commit to prek #151

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Merged
edmundmiller merged 2 commits into from
Jun 17, 2026
+9 −21
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Migrate linting CI from pre-commit to prek #151

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513bf5c
Migrate linting CI from pre-commit to prek
claude Jun 16, 2026
9f456e2
fix-linting: run prek via the action directly
claude Jun 17, 2026
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19 changes: 6 additions & 13 deletions .github/workflows/fix-linting.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -31,30 +31,23 @@ jobs:
env:
GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}

# Install and run pre-commit
- uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6
with:
python-version: 3.11

- name: Install pre-commit
run: pip install pre-commit

- name: Run pre-commit
id: pre-commit
run: pre-commit run --all-files
# Run prek (drop-in, faster pre-commit; reads the same
# .pre-commit-config.yaml). The action runs `prek run --all-files`.
- uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2.0.4
id: prek
continue-on-error: true

# indication that the linting has finished
- name: react if linting finished succesfully
if: steps.pre-commit.outcome == 'success'
if: steps.prek.outcome == 'success'
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
with:
comment-id: ${{ github.event.comment.id }}
reactions: "+1"

- name: Commit & push changes
id: commit-and-push
if: steps.pre-commit.outcome == 'failure'
if: steps.prek.outcome == 'failure'
run: |
git config user.email "core@nf-co.re"
git config user.name "nf-core-bot"
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11 changes: 3 additions & 8 deletions .github/workflows/pre-commit.yml
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Expand Up @@ -10,11 +10,6 @@ jobs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6
with:
python-version: 3.11
- name: Install pre-commit
run: pip install pre-commit

- name: Run pre-commit
run: pre-commit run --all-files
# prek is a drop-in, faster reimplementation of pre-commit; it reads the
# existing .pre-commit-config.yaml and runs the same hooks.
- uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2.0.4
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