Update the manifest with DL4MicEverywhere information #369
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Update the manifest with DL4MicEverywhere information | |
| on: | |
| # At 05:30 AM of every day | |
| schedule: | |
| - cron: "30 5 * * *" | |
| workflow_dispatch: | |
| jobs: | |
| update_manifest: | |
| name: Update the manifest.bioimage.io.yaml with DL4MicEverywhere information | |
| outputs: | |
| matrix: ${{ steps.create_json.outputs.matrix }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Clone ZeroCostDL4Mic repository | |
| uses: actions/checkout@v4 | |
| with: | |
| path: ZeroCostDL4Mic | |
| - name: Clone DL4MicEverywhere repository | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: HenriquesLab/DL4MicEverywhere | |
| path: DL4MicEverywhere | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.9' | |
| - name: Install requirements | |
| working-directory: ./ZeroCostDL4Mic | |
| run: pip install -r Tools/CI_requirements.txt | |
| - name: Update the versioning on the manifest | |
| working-directory: ./ZeroCostDL4Mic | |
| run: python3 Tools/update_manifest_versioning.py | |
| - name: Update the DL4MicEverywhere information on the manifest | |
| working-directory: ./ZeroCostDL4Mic | |
| id: updated_notebooks | |
| run: | | |
| output=$(python3 Tools/update_manifest_dl4miceverywhere.py) | |
| echo "$output" | |
| echo "value=$output" >> $GITHUB_OUTPUT | |
| - if: ${{ steps.updated_notebooks.outputs.value != '' }} | |
| name: List and extract all notebook with new version | |
| id: create_json | |
| run: | | |
| echo "Start" | |
| files_json="{\"include\":[{\"notebook\":\"" | |
| echo "$files_json" | |
| first=true | |
| for file in ${{ steps.updated_notebooks.outputs.value }}; do | |
| echo "$file was changed" | |
| if [ "$first" = true ]; then | |
| files_json+=$file | |
| first=false | |
| else | |
| files_json+="\"},{\"notebook\":\""$file | |
| fi | |
| echo "$files_json" | |
| done | |
| files_json+="\"}]}" | |
| echo "$files_json" | |
| echo "matrix=$files_json" >> $GITHUB_OUTPUT | |
| echo "END" | |
| - name: Commit the changes | |
| uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| repository: ./ZeroCostDL4Mic | |
| commit_message: GitHub Action - Update manifest with DL4MicEverywhere information | |
| config_matrix: | |
| if: ${{ needs.update_manifest.outputs.matrix != '' }} | |
| name: Call the building and pushing, and possible update configuration | |
| needs: update_manifest | |
| strategy: | |
| # put fail-fast as false if you want to see all results even if one fails, | |
| # fail-fast is true by default | |
| fail-fast: false | |
| matrix: ${{ fromJson(needs.update_manifest.outputs.matrix) }} | |
| uses: ./.github/workflows/export_notebook.yml # calls the one above ^ | |
| with: | |
| notebook_name: ${{ matrix.notebook }} | |
| secrets: inherit |