fix_linting.yml

name: Fix linting
on:
  issue_comment:
    types: [created]

jobs:
  fix_linting:
    runs-on: ubuntu-latest
    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
    if: >
      github.repository_owner == 'MultiQC' &&
      github.event.issue.pull_request &&
      startsWith(github.event.comment.body, '@multiqc-bot fix linting')

    steps:
      - uses: actions/checkout@v4
        with:
          token: ${{ secrets.MQC_BOT_GITHUB_TOKEN }}

      # Action runs on the issue comment, so we don't get the PR by default.
      # Use the GitHub CLI to check out the PR:
      - name: Checkout Pull Request
        env:
          GITHUB_TOKEN: ${{ secrets.MQC_BOT_GITHUB_TOKEN }}
        run: gh pr checkout ${{ github.event.issue.number }}

      - uses: actions/setup-python@v5
        with:
          python-version: "3.12"
          cache: "pip"

      - name: Install pre-commit
        run: |
          python -m pip install --upgrade pip
          pip install pre-commit
          pre-commit install

      - name: Run pre-commit
        run: |
          pre-commit run --all-files || true

      - name: Check if any files changed
        run: |
          git diff --exit-code || echo "changed=YES" >> $GITHUB_ENV
          echo "Files changed: ${{ env.changed }}"

      - name: Commit and push changes
        if: env.changed == 'YES'
        run: |
          git config user.name 'MultiQC Bot'
          git config user.email 'multiqc-bot@seqera.io'
          git config push.default upstream
          git add .
          git status
          git commit -m "[automated] Fix code linting"
          git push