Add --help-json flag for machine-readable CLI help
#5370
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| name: Fix linting from a comment | |
| on: | |
| issue_comment: | |
| types: [created] # Add "@nf-core-bot fix linting" as a PR comment to trigger this workflow. | |
| jobs: | |
| fix-linting: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| pull-requests: write | |
| steps: | |
| - name: branch-deploy | |
| id: branch-deploy | |
| uses: github/branch-deploy@fded0351b6b79f854b335c11b3d93063461dd288 # v11.1.2 | |
| with: | |
| trigger: "@nf-core-bot fix linting" | |
| reaction: "eyes" | |
| stable_branch: "dev" | |
| # Use the @nf-core-bot token to check out so we can push later | |
| - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 | |
| with: | |
| token: ${{ secrets.nf_core_bot_auth_token }} | |
| # 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 }} | |
| # Install and run prek | |
| - name: Run prek | |
| id: prek | |
| uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2 | |
| with: | |
| extra-args: --config .pre-commit-config.yaml --all-files | |
| continue-on-error: true | |
| # indication that the linting has finished | |
| - name: react if linting finished succesfully | |
| if: steps.prek.outcome == 'success' | |
| uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 | |
| with: | |
| comment-id: ${{ github.event.comment.id }} | |
| reactions: "+1" | |
| - name: Commit & push changes | |
| id: commit-and-push | |
| if: steps.prek.outcome == 'failure' | |
| run: | | |
| git config user.email "core@nf-co.re" | |
| git config user.name "nf-core-bot" | |
| git config push.default upstream | |
| git add . | |
| git status | |
| 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@e8674b075228eee787fea43ef493e45ece1004c9 # v5 | |
| 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@e8674b075228eee787fea43ef493e45ece1004c9 # v5 | |
| 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@e8674b075228eee787fea43ef493e45ece1004c9 # v5 | |
| 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/nf-core/tools/actions/runs/${{ github.run_id }}) for more details. |