fix-the-autoannotate-metadata-workflow #86
Workflow file for this run
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| name: AutocompleteMetadata | |
| on: | |
| pull_request_target: | |
| paths: | |
| - 'Molecules/membrane/**/metadata.yaml' | |
| - 'Molecules/solution/**/metadata.yaml' | |
| permissions: | |
| contents: read | |
| pull-requests: write | |
| jobs: | |
| add-metadata: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout BilayerData | |
| uses: actions/checkout@v6 | |
| with: | |
| repository: ${{ github.event.pull_request.head.repo.full_name }} | |
| ref: ${{ github.event.pull_request.head.ref }} | |
| persist-credentials: false | |
| - name: Clone Databank and install | |
| run: | | |
| git clone --depth 1 https://github.com/NMRlipids/FAIRMD_lipids.git "$RUNNER_TEMP/Databank" | |
| pip install "$RUNNER_TEMP/Databank" | |
| - name: Install the gh cli | |
| uses: ksivamuthu/actions-setup-gh-cli@v3 | |
| with: | |
| version: 2.83.0 | |
| - name: Find changed metadata.yaml files | |
| id: files | |
| env: | |
| GH_TOKEN: ${{ github.token }} | |
| run: | | |
| changed_files=$(gh api --paginate \ | |
| "repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/files" \ | |
| --jq '.[] | select(.status != "removed") | .filename' \ | |
| | grep -E '^Molecules/(membrane|solution)/[^/]+/metadata\.yaml$' || true) | |
| { | |
| echo "changed_files<<EOF" | |
| echo "$changed_files" | |
| echo "EOF" | |
| } >> "$GITHUB_OUTPUT" | |
| echo "Changed files:" | |
| echo "$changed_files" | |
| - name: Run AddMetadata.py and create suggestions | |
| if: steps.files.outputs.changed_files != '' | |
| env: | |
| CHANGED_FILES: ${{ steps.files.outputs.changed_files }} | |
| run: | | |
| printf '%s\n' "$CHANGED_FILES" | while IFS= read -r f; do | |
| [ -n "$f" ] && python "$RUNNER_TEMP/Databank/developer/autocomplete_metadata.py" "$f" | |
| done | |
| - name: Suggest changes on PR | |
| if: steps.files.outputs.changed_files != '' | |
| uses: reviewdog/action-suggester@v1 | |
| with: | |
| tool_name: addmetadata | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| fail_level: any # surface errors instead of exiting 0 | |
| reviewdog_flags: -tee # echo reviewdog's stdout/stderr to the log |