build.yml

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/coverage@v3.2
        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/rattler-build-action@v0.2.2
#      with:
#        recipe-path: conda-recipe/recipe.yaml