Update adapters and converters #280
Workflow file for this run
This file contains hidden or 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: 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" | |
| test: | |
| 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" >> $GITHUB_OUTPUT | |
| - shell: python | |
| run: | | |
| from pathlib import Path | |
| from pprint import pprint | |
| if not (env_path:=Path("${{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: ${{steps.setup.outputs.env-name}} | |
| channel-priority: strict | |
| miniforge-version: latest | |
| - name: Get Date | |
| id: get-date | |
| run: | | |
| echo "date=$(date +'%Y-%b')" | |
| echo "date=$(date +'%Y-%b')" >> $GITHUB_OUTPUT | |
| echo "today=$(date -u '+%Y%m%d')" | |
| echo "today=$(date -u '+%Y%m%d')" >> $GITHUB_OUTPUT | |
| - name: Cache env | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.CONDA }}/envs/${{steps.setup.outputs.env-name}} | |
| key: >- | |
| conda-${{ runner.os }}-${{ runner.arch }}- | |
| -${{steps.get-date.outputs.today }}- | |
| -${{ hashFiles(matrix.conda-env) }}- | |
| -${{env.CACHE_NUMBER }} | |
| env: | |
| CACHE_NUMBER: 0 | |
| id: cache | |
| - name: Update env | |
| run: conda env update --name=${{steps.setup.outputs.env-name}} --file=${{steps.setup.outputs.env-file}} python=${{matrix.python-version}} | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| - run: | | |
| pyright --version | |
| pyright | |
| if: matrix.run-expensive-tests | |
| - uses: actions/cache@v4 | |
| with: | |
| path: bioimageio_cache | |
| key: "test-${{matrix.spec}}-${{ steps.get-date.outputs.date }}" | |
| - name: pytest | |
| run: pytest --disable-pytest-warnings | |
| 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 |