add tifffile pin to dev env #1541
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| name: Test and Deploy bioimageio.spec | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: ["**"] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10", "3.11","3.12", "3.13"] | |
| include: | |
| - python-version: "3.12" | |
| is-dev-version: true | |
| run_expensive_tests: true | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: "pip" | |
| - name: Install dependencies | |
| run: | | |
| pip install --upgrade pip | |
| pip install -e .[dev] | |
| - name: Get Date | |
| id: get-date | |
| run: | | |
| echo "date=$(date +'%Y-%b')" | |
| echo "date=$(date +'%Y-%b')" >> $GITHUB_OUTPUT | |
| shell: bash | |
| - uses: actions/cache/restore@v4 | |
| with: | |
| path: bioimageio_cache | |
| key: "py${{ matrix.python-version }}-${{ steps.get-date.outputs.date }}" | |
| - name: Check autogenerated imports | |
| run: python scripts/generate_version_submodule_imports.py check | |
| - run: black --check . | |
| if: matrix.is-dev-version | |
| - name: install additinal deps for a full pyright check | |
| run: pip install json_schema_for_humans | |
| if: matrix.is-dev-version | |
| - run: ruff check | |
| if: matrix.is-dev-version | |
| - run: pyright --version | |
| if: matrix.is-dev-version | |
| - run: pyright -p pyproject.toml --pythonversion ${{ matrix.python-version }} | |
| if: matrix.is-dev-version | |
| - run: pytest | |
| env: | |
| BIOIMAGEIO_CACHE_PATH: bioimageio_cache | |
| SKIP_EXPENSIVE_TESTS: ${{ matrix.run_expensive_tests && 'false' || 'true' }} | |
| - uses: actions/cache/save@v4 | |
| # explicit restore/save instead of cache action to cache even if coverage fails | |
| with: | |
| path: bioimageio_cache | |
| key: "py${{ matrix.python-version }}-${{ steps.get-date.outputs.date }}" | |
| - if: matrix.is-dev-version && github.event_name == 'pull_request' | |
| uses: orgoro/[email protected] | |
| with: | |
| coverageFile: coverage.xml | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| thresholdAll: 0.7 | |
| thresholdNew: 0.9 | |
| thresholdModified: 0.6 | |
| - if: matrix.is-dev-version | |
| run: | | |
| pip install genbadge[coverage] | |
| genbadge coverage --input-file coverage.xml --output-file ./dist/coverage/coverage-badge.svg | |
| coverage html -d dist/coverage | |
| - if: matrix.is-dev-version | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage | |
| retention-days: 1 | |
| path: dist | |
| deploy: | |
| needs: [test] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: coverage | |
| path: dist | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| cache: "pip" | |
| - name: Install dependencies | |
| run: | | |
| pip install --upgrade pip | |
| pip install -e .[dev] | |
| - name: Generate spec docs | |
| run: python scripts/generate_spec_documentation.py --dist dist/user_docs | |
| - name: Generate interactive documentation | |
| env: | |
| PYTHONPATH: "./scripts" | |
| run: python -m interactive_docs | |
| - name: Generate JSON schemas | |
| run: python scripts/generate_json_schemas.py | |
| - run: pip install json_schema_for_humans | |
| - name: Generate JSON schema documentation | |
| run: python scripts/generate_json_schema_documentation.py | |
| - name: Generate developer docs | |
| run: ./scripts/pdoc/run.sh | |
| - name: copy legacy file until BioImage.IO-packager is updated # TODO: remove if packager does not depend on it anymore | |
| run: cp weight_formats_spec.json ./dist/weight_formats_spec.json | |
| - name: Get branch name to deploy to | |
| id: get_branch | |
| shell: bash | |
| run: | | |
| if [[ -n '${{ github.event.pull_request.head.ref }}' ]]; then branch=gh-pages-${{ github.event.pull_request.head.ref }}; else branch=gh-pages; fi | |
| echo "::set-output name=branch::$branch" | |
| - name: Deploy to ${{ steps.get_branch.outputs.branch }} 🚀 | |
| uses: JamesIves/github-pages-deploy-action@v4 | |
| with: | |
| branch: ${{ steps.get_branch.outputs.branch }} | |
| folder: dist | |
| mamba-build: | |
| runs-on: ubuntu-latest | |
| needs: test | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Install Conda environment with Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| cache-downloads: true | |
| cache-environment: true | |
| environment-name: build-env | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - nodefaults | |
| create-args: >- | |
| boa | |
| - name: linux conda build | |
| run: | | |
| conda mambabuild -c conda-forge conda-recipe | |
| shell: bash -l {0} | |
| # rattler-build: | |
| # name: Build package | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # - name: Build conda package | |
| # uses: prefix-dev/[email protected] | |
| # with: | |
| # recipe-path: conda-recipe/recipe.yaml |