ci.yml

name: TileDB-BioImaging CI

on: [push]

jobs:
  build:
    name: ${{ matrix.sys.os }}
    runs-on: ${{ matrix.sys.os }}
    timeout-minutes: 25
    strategy:
      matrix:
        sys:
          - { os: windows-latest, shell: 'cmd /C call {0}' }
          - { os: ubuntu-latest,  shell: "bash -l {0}" }
      fail-fast: false
    defaults:
      run:
        shell: ${{ matrix.sys.shell }}

    env:
      run_coverage: ${{ github.ref == 'refs/heads/main' }}

    outputs:
      coverage: ${{ steps.stats.outputs.coverage }}

    steps:
    - uses: actions/checkout@v2

    - name: Install Conda environment with Micromamba
      uses: mamba-org/setup-micromamba@v1.9.0
      with:
        micromamba-version:  1.5.10-0
        environment-name: test
        cache-downloads: true
        create-args: >-
          python=3.9
          pre-commit
          pytest-cov
          pytest-mock
    
    - name: Install openslide for non-Win
      run: |
        sudo apt install openslide-tools
        micromamba install openslide
        echo ${{ matrix.sys.os }}
      if: ${{ matrix.sys.os != 'windows-latest' }}

    - name: Install openslide for Win 
      run: |
        choco install wget --no-progress
        wget https://github.com/openslide/openslide-winbuild/releases/download/v20221217/openslide-win64-20221217.zip
        7z x openslide-win64-20221217.zip -oD:\openslide\
        mklink /D C:\openslide-win64\ D:\openslide\openslide-win64-20221217\
        cd C:\openslide-win64\
        dir
        set openslide_path=%cd%
        echo %openslide_path%
      if: ${{ matrix.sys.os == 'windows-latest' }}

    - name: Run pre-commit hooks
      run: | 
        micromamba run -n test pre-commit run -a

    - name: Install package
      shell: "bash -l {0}"
      run: |
        pip install --no-cache-dir --upgrade tifffile "imagecodecs>=2023.7.10"
        pip install .[full]

    - name: Run tests with coverage
      id: stats
      env:
        AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
        AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
      run: |
        : # This GITHUB_WORKSPACE is bydefault set to D: driver whereas pytest's tmp_dir 
        : # default is C: ,thus we create a temp_test folder for pytest's tmp_dir to run on D: as well 
        pytest -v --cov=tiledb --cov-report=term-missing --durations=0 tests/ > coverage.txt
        exit_code=$?
        TEST_COVERAGE="$(grep '^TOTAL' coverage.txt | awk -v N=4 '{print $N}')"
        echo "coverage=$TEST_COVERAGE" >> $GITHUB_OUTPUT
        exit $exit_code
      if: ${{ matrix.sys.os != 'windows-latest' }}

    - name: Run tests with coverage WINDOWS
      id: stats-win
      env:
        AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
        AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
      run: |
        mkdir test_temp
        micromamba run -n test pytest --basetemp=test_temp -v --cov=tiledb --cov-report=term-missing --durations=0 tests/ --ignore=tests/integration/converters/test_ome_tiff_experimental.py
      if: ${{ matrix.sys.os == 'windows-latest' }}

    - name: Run notebook examples
      run: |
        micromamba run -n test pip install opencv-python-headless matplotlib nbmake
        micromamba run -n test pytest --nbmake examples

    - name: Create Test Coverage Badge
      if: ${{ fromJSON(env.run_coverage) && matrix.sys.os == 'ubuntu-latest'}}
      uses: schneegans/dynamic-badges-action@v1.1.0
      with:
        auth: ${{ secrets.COVERAGE_SECRET }}
        gistID: 32d48185733a4e7375e80e3e35fab452
        filename: gist_bioimg.json
        label: Test Coverage
        message: ${{ steps.stats.outputs.coverage }}
        color: green
        namedLogo: pytest