fix-linting.yml

name: fix-linting
run-name: fix linting (automated)
on:
  issue_comment:
    types: [created]

permissions: {}

jobs:
  prepare-fix:
    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords.
    # The write token is used only before untrusted pull request code runs.
    if: >
      contains(github.event.comment.html_url, '/pull/') &&
      contains(github.event.comment.body, '@nf-core-bot fix linting') &&
      github.repository == 'nf-core/modules'
    permissions:
      contents: read
      issues: write
      pull-requests: read
    runs-on: ubuntu-latest
    outputs:
      head_sha: ${{ steps.pr.outputs.head_sha }}
      has_patch: ${{ steps.patch.outputs.has_patch }}
      prek_outcome: ${{ steps.prek.outcome }}
    steps:
      # indication that the linting is being fixed
      - name: React on comment
        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
        with:
          comment-id: ${{ github.event.comment.id }}
          reactions: eyes

      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
        with:
          persist-credentials: false

      # 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
        id: pr
        env:
          GH_TOKEN: ${{ github.token }}
          PR_NUMBER: ${{ github.event.issue.number }}
        run: |
          gh pr checkout "$PR_NUMBER"
          echo "head_sha=$(git rev-parse HEAD)" >> "$GITHUB_OUTPUT"

      - name: Set up Nextflow
        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
        with:
          version: "latest-stable"

      - name: Run prek
        id: prek
        uses: j178/prek-action@4e14d07f9231acabce116ccfca13b13dd9755ece # v3.0.0
        continue-on-error: true

      - name: Create lint fix patch
        id: patch
        if: steps.prek.outcome == 'failure'
        env:
          PATCH_FILE: ${{ runner.temp }}/lint-fix.patch
        run: |
          git add --all
          git diff --cached --binary --full-index --no-ext-diff > "$PATCH_FILE"
          if [ ! -s "$PATCH_FILE" ]; then
            echo "Prek failed without producing a fix."
            exit 1
          fi
          echo "has_patch=true" >> "$GITHUB_OUTPUT"

      - name: Upload lint fix patch
        if: steps.patch.outputs.has_patch == 'true'
        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
        with:
          name: lint-fix
          path: ${{ runner.temp }}/lint-fix.patch
          if-no-files-found: error
          retention-days: 1

  push-fix:
    # This job runs on a fresh runner and never executes pull request code.
    needs: prepare-fix
    if: ${{ always() && needs.prepare-fix.result != 'skipped' }}
    permissions:
      actions: read
      contents: read
      issues: write
      pull-requests: read
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
        if: needs.prepare-fix.outputs.has_patch == 'true'
        with:
          persist-credentials: false

      - name: Checkout exact pull request head
        if: needs.prepare-fix.outputs.has_patch == 'true'
        env:
          EXPECTED_HEAD_SHA: ${{ needs.prepare-fix.outputs.head_sha }}
          GH_TOKEN: ${{ github.token }}
          PR_NUMBER: ${{ github.event.issue.number }}
        run: |
          gh pr checkout "$PR_NUMBER"
          if [ "$(git rev-parse HEAD)" != "$EXPECTED_HEAD_SHA" ]; then
            echo "The pull request head changed after prek ran."
            exit 1
          fi

      - name: Download lint fix patch
        if: needs.prepare-fix.outputs.has_patch == 'true'
        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
        with:
          name: lint-fix
          path: ${{ runner.temp }}/lint-fix

      - name: Apply lint fix patch
        if: needs.prepare-fix.outputs.has_patch == 'true'
        env:
          PATCH_FILE: ${{ runner.temp }}/lint-fix/lint-fix.patch
        run: |
          if [ ! -f "$PATCH_FILE" ] || [ -L "$PATCH_FILE" ]; then
            echo "The lint fix artifact does not contain a regular patch file."
            exit 1
          fi
          git apply --check --index "$PATCH_FILE"
          git apply --index "$PATCH_FILE"

      - name: Commit and push changes
        id: commit-and-push
        if: needs.prepare-fix.outputs.has_patch == 'true'
        env:
          GH_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
        run: |
          gh auth setup-git
          git config user.email "core@nf-co.re"
          git config user.name "nf-core-bot"
          git config push.default upstream
          git status
          git -c core.hooksPath=/dev/null -c commit.gpgsign=false commit --no-verify -m "[automated] Fix code linting"
          git -c core.hooksPath=/dev/null push --no-verify

      # indication that the linting has finished
      - name: React if linting finished successfully
        if: needs.prepare-fix.outputs.prek_outcome == 'success'
        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
        with:
          comment-id: ${{ github.event.comment.id }}
          reactions: "+1"

      - name: React if linting errors were 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: ${{ always() && (failure() || needs.prepare-fix.result != 'success') }}
        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
        with:
          comment-id: ${{ github.event.comment.id }}
          reactions: confused

      - name: Comment if linting errors were not fixed
        if: ${{ always() && (failure() || needs.prepare-fix.result != 'success') }}
        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/modules/actions/runs/${{ github.run_id }}) for more details.