Update adapters and converters #299
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| name: Test and Deploy bioimageio.core | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ "**" ] | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| jobs: | |
| black: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: psf/black@stable | |
| with: | |
| options: "--check" | |
| src: "." | |
| jupyter: true | |
| version: "24.3" | |
| populate-cache: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| cache-key: ${{steps.cache-key.outputs.cache-key}} | |
| steps: | |
| - name: Get Date | |
| id: get-date | |
| run: | | |
| echo "date=$(date +'%Y-%b')" | |
| echo "date=$(date +'%Y-%b')" >> $GITHUB_OUTPUT | |
| - id: cache-key | |
| run: echo "cache-key=test-${{steps.get-date.outputs.date}}" >> $GITHUB_OUTPUT | |
| - uses: actions/cache/restore@v4 | |
| id: look-up | |
| with: | |
| path: bioimageio_cache | |
| key: ${{steps.cache-key.outputs.cache-key}} | |
| lookup-only: true | |
| - uses: actions/checkout@v4 | |
| if: steps.look-up.outputs.cache-hit != 'true' | |
| - uses: actions/cache@v4 | |
| if: steps.look-up.outputs.cache-hit != 'true' | |
| with: | |
| path: bioimageio_cache | |
| key: ${{steps.cache-key.outputs.cache-key}} | |
| - uses: actions/setup-python@v5 | |
| if: steps.look-up.outputs.cache-hit != 'true' | |
| with: | |
| python-version: '3.12' | |
| cache: 'pip' | |
| - name: Install dependencies | |
| if: steps.look-up.outputs.cache-hit != 'true' | |
| run: | | |
| pip install --upgrade pip | |
| pip install -e .[dev] | |
| - run: pytest --disable-pytest-warnings tests/test_bioimageio_collection.py::test_rdf_format_to_populate_cache | |
| if: steps.look-up.outputs.cache-hit != 'true' | |
| env: | |
| BIOIMAGEIO_POPULATE_CACHE: '1' | |
| BIOIMAGEIO_CACHE_PATH: bioimageio_cache | |
| test: | |
| needs: populate-cache | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| include: | |
| - python-version: '3.8' | |
| conda-env: py38 | |
| spec: conda | |
| - python-version: '3.8' | |
| conda-env: py38 | |
| spec: main | |
| - python-version: '3.9' | |
| conda-env: dev | |
| spec: conda | |
| - python-version: '3.10' | |
| conda-env: dev | |
| spec: conda | |
| - python-version: '3.11' | |
| conda-env: full | |
| spec: main | |
| run-expensive-tests: true | |
| report-coverage: true | |
| - python-version: '3.12' | |
| conda-env: dev | |
| spec: conda | |
| - python-version: '3.13' | |
| conda-env: dev | |
| spec: main | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - id: setup | |
| run: | | |
| echo "env-name=${{ matrix.spec }}-${{ matrix.conda-env }}-${{ matrix.python-version }}" | |
| echo "env-name=${{ matrix.spec }}-${{ matrix.conda-env }}-${{ matrix.python-version }}" >> $GITHUB_OUTPUT | |
| echo "env-file=dev/env-${{ matrix.conda-env }}.yaml" | |
| echo "env-file=dev/env-${{ matrix.conda-env }}.yaml" >> $GITHUB_OUTPUT | |
| - name: check on env-file | |
| shell: python | |
| run: | | |
| from pathlib import Path | |
| from pprint import pprint | |
| if not (env_path:=Path("${{steps.setup.outputs.env-file}}")).exists(): | |
| if env_path.parent.exists(): | |
| pprint(env_path.parent.glob("*")) | |
| else: | |
| pprint(Path().glob("*")) | |
| raise FileNotFoundError(f"{env_path} does not exist") | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| auto-activate-base: true | |
| activate-environment: ${{steps.setup.outputs.env-name}} | |
| channel-priority: strict | |
| miniforge-version: latest | |
| - name: Get Date | |
| id: get-date | |
| run: | | |
| echo "today=$(date -u '+%Y%m%d')" | |
| echo "today=$(date -u '+%Y%m%d')" >> $GITHUB_OUTPUT | |
| - name: Restore cached env | |
| uses: actions/cache/restore@v4 | |
| with: | |
| path: ${{env.CONDA}}/envs/${{steps.setup.outputs.env-name}} | |
| key: >- | |
| conda-${{runner.os}}-${{runner.arch}} | |
| -${{steps.get-date.outputs.today}} | |
| -${{hashFiles(steps.setup.outputs.env-file)}} | |
| -${{env.CACHE_NUMBER}} | |
| env: | |
| CACHE_NUMBER: 0 | |
| id: cache-env | |
| - name: Install env | |
| run: conda env update --name=${{steps.setup.outputs.env-name}} --file=${{steps.setup.outputs.env-file}} python=${{matrix.python-version}} | |
| if: steps.cache-env.outputs.cache-hit != 'true' | |
| - name: Cache env | |
| if: steps.cache-env.outputs.cache-hit != 'true' | |
| uses: actions/cache/save@v4 | |
| with: | |
| path: ${{env.CONDA}}/envs/${{steps.setup.outputs.env-name}} | |
| key: >- | |
| conda-${{runner.os}}-${{runner.arch}} | |
| -${{steps.get-date.outputs.today}} | |
| -${{hashFiles(steps.setup.outputs.env-file)}} | |
| -${{env.CACHE_NUMBER}} | |
| env: | |
| CACHE_NUMBER: 0 | |
| - run: | | |
| pyright --version | |
| pyright -p pyproject.toml --pythonversion ${{ matrix.python-version }} | |
| if: matrix.run-expensive-tests | |
| - name: Restore bioimageio cache | |
| uses: actions/cache/restore@v4 | |
| id: bioimageio-cache | |
| with: | |
| path: bioimageio_cache | |
| key: ${{needs.populate-cache.outputs.cache-key}} | |
| fail-on-cache-miss: true | |
| - name: pytest | |
| run: pytest --disable-pytest-warnings --cov=bioimageio --cov-report=xml --cov-append --capture=no --failed-first --doctest-modules --ignore=bioimageio/core/backends --ignore=bioimageio/core/weight_converters | |
| env: | |
| BIOIMAGEIO_CACHE_PATH: bioimageio_cache | |
| RUN_EXPENSIVE_TESTS: ${{ matrix.run-expensive-tests && 'true' || 'false' }} | |
| - if: matrix.report-coverage && github.event_name == 'pull_request' | |
| uses: orgoro/[email protected] | |
| with: | |
| coverageFile: coverage.xml | |
| token: ${{secrets.GITHUB_TOKEN}} | |
| - if: matrix.report-coverage && github.ref == 'refs/heads/main' | |
| run: | | |
| pip install genbadge[coverage] | |
| genbadge coverage --input-file coverage.xml --output-file ./dist/coverage/coverage-badge.svg | |
| coverage html -d dist/coverage | |
| - if: matrix.report-coverage && github.ref == 'refs/heads/main' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage | |
| retention-days: 1 | |
| path: dist | |
| conda-build: | |
| needs: test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| auto-activate-base: true | |
| activate-environment: "" | |
| channel-priority: strict | |
| miniforge-version: latest | |
| conda-solver: libmamba | |
| - name: install common conda dependencies | |
| run: conda install -n base -c conda-forge conda-build -y | |
| - uses: actions/cache@v4 | |
| with: | |
| path: | | |
| pkgs/noarch | |
| pkgs/channeldata.json | |
| key: ${{ github.sha }}-packages | |
| - name: linux conda build test | |
| shell: bash -l {0} | |
| run: | | |
| mkdir -p ./pkgs/noarch | |
| conda-build -c conda-forge conda-recipe --no-test --output-folder ./pkgs | |
| docs: | |
| needs: test | |
| if: github.ref == 'refs/heads/main' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: coverage | |
| path: dist | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| cache: 'pip' | |
| - run: pip install -e .[dev] | |
| - name: Generate developer docs | |
| run: ./scripts/pdoc/run.sh | |
| - run: cp README.md ./dist/README.md | |
| - name: copy rendered presentations | |
| run: | | |
| mkdir ./dist/presentations | |
| cp -r ./presentations/*.html ./dist/presentations/ | |
| - name: Deploy to gh-pages 🚀 | |
| uses: JamesIves/github-pages-deploy-action@v4 | |
| with: | |
| branch: gh-pages | |
| folder: dist |