build.yaml

name: Test and Deploy bioimageio.core

on:
  push:
    branches: [ main ]
  pull_request:
    branches: [ "**" ]

defaults:
  run:
    shell: micromamba-shell {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-spec-conda:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
    steps:
    - uses: actions/checkout@v4
    - name: Install Conda environment with Micromamba
      if: matrix.python-version != '3.8'
      uses: mamba-org/setup-micromamba@v1
      with:
        cache-downloads: true
        cache-environment: true
        environment-file: dev/env-wo-python.yaml
        create-args: >-
          python=${{ matrix.python-version }}
        post-cleanup: 'all'
    - name: Install py3.8 environment
      if: matrix.python-version == '3.8'
      uses: mamba-org/setup-micromamba@v1
      with:
        cache-downloads: true
        cache-environment: true
        environment-file: dev/env-py38.yaml
        post-cleanup: 'all'
    - name: additional setup
      run: pip install --no-deps -e .
    - name: Get Date
      id: get-date
      run: |
        echo "date=$(date +'%Y-%b')"
        echo "date=$(date +'%Y-%b')" >> $GITHUB_OUTPUT
      shell: bash
    - uses: actions/cache@v4
      with:
        path: bioimageio_cache
        key: "test-spec-conda-${{ steps.get-date.outputs.date }}"
    - name: pytest-spec-conda
      run: pytest --disable-pytest-warnings
      env:
        BIOIMAGEIO_CACHE_PATH: bioimageio_cache

  test-spec-main:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.8', '3.12']
        include:
          - python-version: '3.12'
            is-dev-version: true
    steps:
    - uses: actions/checkout@v4
    - name: Install Conda environment with Micromamba
      if: matrix.python-version != '3.8'
      uses: mamba-org/setup-micromamba@v1
      with:
        cache-downloads: true
        cache-environment: true
        environment-file: dev/env-wo-python.yaml
        create-args: >-
          python=${{ matrix.python-version }}
        post-cleanup: 'all'
    - name: Install py3.8 environment
      if: matrix.python-version == '3.8'
      uses: mamba-org/setup-micromamba@v1
      with:
        cache-downloads: true
        cache-environment: true
        environment-file: dev/env-py38.yaml
        post-cleanup: 'all'
    - name: additional setup spec
      run: |
        conda remove --yes --force bioimageio.spec || true  # allow failure for cached env
        pip install --no-deps git+https://github.com/bioimage-io/spec-bioimage-io
    - name: additional setup core
      run: pip install --no-deps -e .
    - name: Get Date
      id: get-date
      run: |
        echo "date=$(date +'%Y-%b')"
        echo "date=$(date +'%Y-%b')" >> $GITHUB_OUTPUT
      shell: bash
    - uses: actions/cache@v4
      with:
        path: bioimageio_cache
        key: "test-spec-main-${{ steps.get-date.outputs.date }}"
    - name: pytest-spec-main
      run: pytest --disable-pytest-warnings
      env:
        BIOIMAGEIO_CACHE_PATH: bioimageio_cache
    - if: matrix.is-dev-version && github.event_name == 'pull_request'
      uses: orgoro/coverage@v3.2
      with:
        coverageFile: coverage.xml
        token: ${{ secrets.GITHUB_TOKEN }}
    - if: matrix.is-dev-version && 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.is-dev-version && github.ref == 'refs/heads/main'
      uses: actions/upload-artifact@v4
      with:
        name: coverage
        retention-days: 1
        path: dist


  test-spec-main-tf:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.9', '3.12']
    steps:
    - uses: actions/checkout@v4
    - uses: mamba-org/setup-micromamba@v1
      with:
        cache-downloads: true
        cache-environment: true
        environment-file: dev/env-tf.yaml
        condarc: |
          channel-priority: flexible
        create-args: >-
          python=${{ matrix.python-version }}
        post-cleanup: 'all'
    - name: additional setup spec
      run: |
        conda remove --yes --force bioimageio.spec || true  # allow failure for cached env
        pip install --no-deps git+https://github.com/bioimage-io/spec-bioimage-io
    - name: additional setup core
      run: pip install --no-deps -e .
    - name: Get Date
      id: get-date
      run: |
        echo "date=$(date +'%Y-%b')"
        echo "date=$(date +'%Y-%b')" >> $GITHUB_OUTPUT
      shell: bash
    - uses: actions/cache@v4
      with:
        path: bioimageio_cache
        key: "test-spec-main-tf-${{ steps.get-date.outputs.date }}"
    - run: pytest --disable-pytest-warnings
      env:
        BIOIMAGEIO_CACHE_PATH: bioimageio_cache

  test-spec-conda-tf:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.9', '3.12']
    steps:
    - uses: actions/checkout@v4
    - uses: mamba-org/setup-micromamba@v1
      with:
        cache-downloads: true
        cache-environment: true
        environment-file: dev/env-tf.yaml
        condarc: |
          channel-priority: flexible
        create-args: >-
          python=${{ matrix.python-version }}
        post-cleanup: 'all'
    - name: additional setup
      run: pip install --no-deps -e .
    - name: Get Date
      id: get-date
      run: |
        echo "date=$(date +'%Y-%b')"
        echo "date=$(date +'%Y-%b')" >> $GITHUB_OUTPUT
      shell: bash
    - uses: actions/cache@v4
      with:
        path: bioimageio_cache
        key: "test-spec-conda-tf-${{ steps.get-date.outputs.date }}"
    - name: pytest-spec-tf
      run: pytest --disable-pytest-warnings
      env:
        BIOIMAGEIO_CACHE_PATH: bioimageio_cache

  conda-build:
    runs-on: ubuntu-latest
    needs: test-spec-conda
    steps:
    - name: checkout
      uses: actions/checkout@v4
      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
        create-args: |
          boa
    - name: linux conda build
      run: |
        conda mambabuild -c conda-forge conda-recipe

  docs:
    needs: [test-spec-main]
    if: github.ref == 'refs/heads/main'
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}
    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