bump spec #363
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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: ${{steps.cache-key.outputs.cache-key}} | |
| - uses: actions/setup-python@v5 | |
| if: steps.look-up.outputs.cache-hit != 'true' | |
| with: | |
| python-version: '3.12' | |
| cache: 'pip' | |
| - name: Install dependencies | |
| if: steps.look-up.outputs.cache-hit != 'true' | |
| run: | | |
| pip install --upgrade pip | |
| pip install -e .[dev] | |
| - run: pytest --disable-pytest-warnings tests/test_bioimageio_collection.py::test_rdf_format_to_populate_cache | |
| if: steps.look-up.outputs.cache-hit != 'true' | |
| env: | |
| BIOIMAGEIO_POPULATE_CACHE: '1' | |
| BIOIMAGEIO_CACHE_PATH: bioimageio_cache | |
| test: | |
| needs: populate-cache | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| include: | |
| - python-version: '3.9' | |
| conda-env: dev | |
| spec: conda | |
| numpy-version: 1 | |
| - python-version: '3.9' | |
| conda-env: dev | |
| spec: main | |
| numpy-version: 2 | |
| - python-version: '3.10' | |
| conda-env: full | |
| run-expensive-tests: true | |
| report-coverage: true | |
| save-cache: true | |
| spec: conda | |
| numpy-version: 1 | |
| - python-version: '3.11' | |
| conda-env: dev | |
| spec: main | |
| numpy-version: 2 | |
| - python-version: '3.12' | |
| conda-env: dev | |
| spec: conda | |
| numpy-version: 1 | |
| # - python-version: '3.13' | |
| # conda-env: '313' | |
| # spec: main | |
| # numpy-version: 2 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - id: setup | |
| run: | | |
| echo "env-name=${{ 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 | |
| python-version: ${{ matrix.python-version }} | |
| - name: Get Date | |
| id: get-date | |
| run: | | |
| echo "today=$(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)}} | |
| -${{env.CACHE_NUMBER}} | |
| env: | |
| CACHE_NUMBER: 0 | |
| id: cache-env | |
| - name: Install env | |
| if: steps.cache-env.outputs.cache-hit != 'true' | |
| run: | | |
| conda env update --name=${{steps.setup.outputs.env-name}} --file=${{steps.setup.outputs.env-file}} | |
| - name: Ensure Python/numpy version | |
| # if: steps.cache-env.outputs.cache-hit != 'true' # TODO: skip this step on cache hits once the caches are all updated | |
| run: | | |
| conda install python=${{matrix.python-version}} numpy=${{matrix.numpy-version}} | |
| - name: Install uncached pip dependencies | |
| run: | | |
| pip install --upgrade pip | |
| pip install --no-deps -e . | |
| - name: Install uncached pip dependencies for 'full' environment | |
| if: matrix.conda-env == 'full' | |
| run: | | |
| pip install git+https://github.com/ChaoningZhang/MobileSAM.git | |
| - 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: conda list | |
| - name: Pyright | |
| if: matrix.run-expensive-tests | |
| run: | | |
| pyright --version | |
| pyright -p pyproject.toml --pythonversion ${{ matrix.python-version }} | |
| - name: Restore bioimageio cache ${{needs.populate-cache.outputs.cache-key}} | |
| uses: actions/cache/restore@v4 | |
| with: | |
| path: bioimageio_cache | |
| key: ${{needs.populate-cache.outputs.cache-key}} | |
| - name: pytest | |
| run: pytest --cov bioimageio --cov-report xml --cov-append --capture no --disable-pytest-warnings | |
| env: | |
| BIOIMAGEIO_CACHE_PATH: bioimageio_cache | |
| RUN_EXPENSIVE_TESTS: ${{ matrix.run-expensive-tests && 'true' || 'false' }} | |
| - name: Save bioimageio cache ${{needs.populate-cache.outputs.cache-key}} | |
| if: matrix.save-cache | |
| uses: actions/cache/save@v4 | |
| with: | |
| path: bioimageio_cache | |
| key: ${{needs.populate-cache.outputs.cache-key}} | |
| - 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: ${{ github.sha }}-packages | |
| - name: linux conda build test | |
| shell: bash -l {0} | |
| run: | | |
| mkdir -p ./pkgs/noarch | |
| conda-build -c conda-forge conda-recipe --no-test --output-folder ./pkgs | |
| docs: | |
| needs: test | |
| if: github.ref == 'refs/heads/main' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: coverage | |
| path: dist | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| cache: 'pip' | |
| - run: pip install -e .[dev] | |
| - name: Generate developer docs | |
| run: ./scripts/pdoc/run.sh | |
| - run: cp README.md ./dist/README.md | |
| - name: copy rendered presentations | |
| run: | | |
| mkdir ./dist/presentations | |
| cp -r ./presentations/*.html ./dist/presentations/ | |
| - name: Deploy to gh-pages 🚀 | |
| uses: JamesIves/github-pages-deploy-action@v4 | |
| with: | |
| branch: gh-pages | |
| folder: dist | |
| publish-pypi: | |
| name: Publish to PyPI | |
| needs: test | |
| if: github.ref == 'refs/heads/main' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out the repository | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 2 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip --version | |
| pip install --upgrade build | |
| pip install . | |
| pip install pytest | |
| - name: run tests | |
| run: pytest --disable-pytest-warnings | |
| - name: Check if there is a parent commit | |
| id: check-parent-commit | |
| run: | | |
| echo "sha=$(git rev-parse --verify --quiet HEAD^)" >> $GITHUB_OUTPUT | |
| - name: Detect new version | |
| id: check-version | |
| if: steps.check-parent-commit.outputs.sha | |
| uses: salsify/[email protected] | |
| with: | |
| create-tag: false | |
| version-command: | | |
| python -c "from pathlib import Path;print(Path('bioimageio/core/__init__.py').read_text().split('__version__ = \"')[1].split('\"')[0])" | |
| - name: Push tag | |
| id: tag-version | |
| if: steps.check-version.outputs.previous-version != steps.check-version.outputs.current-version | |
| uses: mathieudutour/[email protected] | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| custom_tag: ${{ steps.check-version.outputs.current-version }} | |
| - name: Build package | |
| run: | | |
| python -m build | |
| - name: Publish package on PyPI | |
| if: steps.tag-version.outputs.new_tag | |
| uses: pypa/gh-action-pypi-publish@release/v1.12 | |
| with: | |
| user: __token__ | |
| password: "${{ secrets.PYPI_TOKEN }}" | |
| packages-dir: dist/ | |
| verbose: true | |
| - name: Publish the release notes | |
| uses: release-drafter/[email protected] | |
| with: | |
| publish: "${{ steps.tag-version.outputs.new_tag != '' }}" | |
| tag: "${{ steps.tag-version.outputs.new_tag }}" | |
| env: | |
| GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}" |