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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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|
@@ -4,7 +4,7 @@ on: | |
| types: [created] | ||
|
|
||
| jobs: | ||
| deploy: | ||
| fix-linting: | ||
| # Only run if comment is on a PR with the main repo, and if it contains the magic keywords | ||
| if: > | ||
| contains(github.event.comment.html_url, '/pull/') && | ||
|
|
@@ -13,36 +13,77 @@ jobs: | |
| runs-on: ubuntu-latest | ||
| steps: | ||
| # Use the @nf-core-bot token to check out so we can push later | ||
| - uses: actions/checkout@v4 | ||
| - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | ||
| with: | ||
| token: ${{ secrets.nf_core_bot_auth_token }} | ||
|
|
||
| # indication that the linting is being fixed | ||
| - name: React on comment | ||
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | ||
| with: | ||
| comment-id: ${{ github.event.comment.id }} | ||
| reactions: eyes | ||
|
|
||
| # Action runs on the issue comment, so we don't get the PR by default | ||
| # Use the gh cli to check out the PR | ||
| - name: Checkout Pull Request | ||
| run: gh pr checkout ${{ github.event.issue.number }} | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} | ||
|
|
||
| - name: Set up Python 3.11 | ||
| uses: actions/setup-python@v5 | ||
| # Install and run pre-commit | ||
| - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 | ||
| with: | ||
| python-version: 3.11 | ||
| cache: "pip" | ||
| python-version: "3.12" | ||
|
|
||
| - name: Install pre-commit | ||
| run: pip install pre-commit | ||
|
|
||
| - name: Run pre-commit | ||
| run: pre-commit run --all-files || echo "status=fail" >> $GITHUB_ENV | ||
| id: pre-commit | ||
| run: pre-commit run --all-files | ||
| continue-on-error: true | ||
|
|
||
| # indication that the linting has finished | ||
| - name: react if linting finished succesfully | ||
| if: steps.pre-commit.outcome == 'success' | ||
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | ||
| with: | ||
| comment-id: ${{ github.event.comment.id }} | ||
| reactions: "+1" | ||
|
|
||
| - name: Commit & push changes | ||
| if: env.status == 'fail' | ||
| id: commit-and-push | ||
| if: steps.pre-commit.outcome == 'failure' | ||
| run: | | ||
| git config user.email "[email protected]" | ||
| git config user.name "nf-core-bot" | ||
| git config push.default upstream | ||
| git add . | ||
| git status | ||
| git commit -m "[automated] Fix linting with pre-commit" | ||
| git commit -m "[automated] Fix code linting" | ||
| git push | ||
| - name: react if linting errors were fixed | ||
| id: react-if-fixed | ||
| if: steps.commit-and-push.outcome == 'success' | ||
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | ||
| with: | ||
| comment-id: ${{ github.event.comment.id }} | ||
| reactions: hooray | ||
|
|
||
| - name: react if linting errors were not fixed | ||
| if: steps.commit-and-push.outcome == 'failure' | ||
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | ||
| with: | ||
| comment-id: ${{ github.event.comment.id }} | ||
| reactions: confused | ||
|
|
||
| - name: react if linting errors were not fixed | ||
| if: steps.commit-and-push.outcome == 'failure' | ||
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | ||
| with: | ||
| issue-number: ${{ github.event.issue.number }} | ||
| body: | | ||
| @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually. | ||
| See [CI log](https://github.com/plant-food-research-open/assemblyqc/actions/runs/${{ github.run_id }}) for more details. | ||
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