include some status defaults when serializing #249
Workflow file for this run
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| name: test backoffice and build docs | |
| on: push | |
| concurrency: | |
| group: test | |
| cancel-in-progress: true | |
| jobs: | |
| initial-cleanup: | |
| environment: testing | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| cache: "pip" # caching pip dependencies | |
| - run: pip install . | |
| - run: backoffice wipe | |
| env: | |
| S3_HOST: ${{vars.S3_HOST}} | |
| S3_BUCKET: ${{vars.S3_BUCKET}} | |
| S3_FOLDER: ${{vars.S3_FOLDER}} | |
| S3_ACCESS_KEY_ID: ${{secrets.S3_ACCESS_KEY_ID}} | |
| S3_SECRET_ACCESS_KEY: ${{secrets.S3_SECRET_ACCESS_KEY}} | |
| RUN_URL: ${{github.server_url}}/${{github.repository}}/actions/runs/${{github.run_id}} | |
| BIOIMAGEIO_USER_ID: github|${{github.actor_id}} | |
| generate-initial-collection-json: | |
| needs: initial-cleanup | |
| uses: bioimage-io/collection/.github/workflows/generate_collection_json_call.yaml@main | |
| with: | |
| environment_name: testing | |
| secrets: inherit | |
| test-stage: | |
| needs: generate-initial-collection-json | |
| uses: bioimage-io/collection/.github/workflows/stage_call.yaml@main | |
| with: | |
| concept_id: 'frank-water-buffalo' | |
| package_url: 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/examples.bioimage.io/frank-water-buffalo_v1.zip' | |
| environment_name: testing | |
| secrets: inherit | |
| test-publish: | |
| needs: test-stage | |
| uses: bioimage-io/collection/.github/workflows/publish_call.yaml@main | |
| with: | |
| concept_id: 'frank-water-buffalo' | |
| reviewer: 'github|${{github.actor_id}}' | |
| environment_name: testing | |
| secrets: inherit | |
| test-generate-collection-json: | |
| needs: test-publish | |
| uses: bioimage-io/collection/.github/workflows/generate_collection_json_call.yaml@main | |
| with: | |
| environment_name: testing | |
| secrets: inherit | |
| test-generate-collection-staged-json: | |
| needs: test-publish | |
| uses: bioimage-io/collection/.github/workflows/generate_collection_json_call.yaml@main | |
| with: | |
| mode: 'staged' | |
| environment_name: testing | |
| secrets: inherit | |
| test-backup: | |
| needs: test-generate-collection-json | |
| uses: bioimage-io/collection/.github/workflows/backup_call.yaml@main | |
| with: | |
| environment_name: testing | |
| secrets: inherit | |
| build: | |
| runs-on: ubuntu-latest | |
| environment: testing | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| cache: "pip" # caching pip dependencies | |
| - run: pip install -e .[dev] | |
| - run: black . --check | |
| - run: pyright -p pyproject.toml | |
| - run: pytest | |
| env: | |
| S3_HOST: ${{vars.S3_HOST}} | |
| S3_BUCKET: ${{vars.S3_BUCKET}} | |
| S3_FOLDER: ${{vars.S3_FOLDER}} | |
| S3_ACCESS_KEY_ID: ${{secrets.S3_ACCESS_KEY_ID}} | |
| S3_SECRET_ACCESS_KEY: ${{secrets.S3_SECRET_ACCESS_KEY}} | |
| RUN_URL: ${{github.server_url}}/${{github.repository}}/actions/runs/${{github.run_id}} | |
| ZENODO_URL: ${{vars.ZENODO_URL}} | |
| ZENODO_API_ACCESS_TOKEN: ${{secrets.ZENODO_API_ACCESS_TOKEN}} | |
| BIOIMAGEIO_USER_ID: github|${{github.actor_id}} | |
| - name: export documentation | |
| run: | | |
| pdoc \ | |
| --mermaid \ | |
| --docformat google \ | |
| --logo https://bioimage.io/static/img/bioimage-io-logo.svg \ | |
| --logo-link https://bioimage.io/ \ | |
| --favicon https://bioimage.io/static/img/bioimage-io-icon-small.svg \ | |
| --footer-text 'bioimageio_collection_backoffice' \ | |
| -o ./docs bioimageio_collection_backoffice | |
| - name: Deploy to gh-pages 🚀 | |
| if: ${{ github.ref == 'refs/heads/main' }} | |
| uses: JamesIves/github-pages-deploy-action@v4 | |
| with: | |
| folder: docs |