tests-conda.yml

name: Tests

on:
  workflow_dispatch:
  pull_request:
    branches:
      - dev
      - master
  push:
    branches:
      - dev
      - master

jobs:
  build-linux:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 5
      matrix:
        python-version: [3.8, 3.9]
    timeout-minutes: 60 # add a timeout

    steps:
    - uses: actions/checkout@v2
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}
    - name: Display Python version
      run: python -c "import sys; print(sys.version)"
    - name: Install dependencies
      shell: bash -l {0}
      run: |
        sudo apt-get update
        sudo apt-get install openslide-tools
        sudo apt-get install pandoc
    - name: Setup Miniconda
      uses: conda-incubator/setup-miniconda@v2
      with:
        auto-activate-base: false
        activate-environment: pathml
        environment-file: environment.yml
        mamba-version: "*"
        python-version: ${{ matrix.python-version }}
    - name: Debugging
      run: |
        echo "Printing the environment.yml file..."
        cat environment.yml
        echo "Checking the status of mamba..."
        mamba --version
        echo "Checking the available disk space..."
        df -h
    - name: Install dependencies with mamba
      shell: bash -l {0}
      run: mamba env update --file environment.yml --name pathml
    - name: Conda info
      shell: bash -l {0}
      run: |
        conda info
        conda list
    
    - name: Set default Temurin JDK 17
      run: |
        sudo update-java-alternatives --set temurin-17-jdk-amd64 || true
        java -version
        
    - name: Install PathML
      shell: bash -l {0}      
      run: pip install -e .
      
    - name: Install python-spams
      shell: bash -l {0}      
      run: pip install spams
      
    - name: disk usage
      shell: bash -l {0}
      run: |
        sudo df -h
        sudo du -h

    # - name: Check Coverage Command
    #   run: |
    #     which coverage
    #     coverage --version
        
    # - name: Test with pytest for tile_stitcher
    #   run: |
    #     java -version
    #     python -m pytest tests/preprocessing_tests/test_tilestitcher.py
        
    # - name: Test with pytest and generate coverage report
    #   shell: bash -l {0}
    #   run: |
    #     coverage run -m pytest -m "not slow and not exclude"
    #     coverage xml
    # - name: Upload coverage to Codecov
    #   uses: codecov/codecov-action@v2
    #   with:
    #     token: ${{ secrets.CODECOV_TOKEN }}
    #     env_vars: OS,PYTHON
    #     fail_ci_if_error: true
    #     files: ./coverage.xml
    #     name: codecov-umbrella
    #     verbose: true

    - name: Test other modules with pytest and generate coverage
      shell: bash -l {0}
      run: |
        COVERAGE_FILE=.coverage_others coverage run -m pytest -m "not slow and not exclude"

    - name: Test tile_stitcher with pytest and generate coverage
      shell: bash -l {0}
      run: |
        COVERAGE_FILE=.coverage_tilestitcher coverage run -m pytest tests/preprocessing_tests/test_tilestitcher.py
    
    - name: List Files in Directory
      shell: bash -l {0}
      run: |
        ls -la

    - name: Combine Coverage Data
      shell: bash -l {0}
      run: |
        coverage combine .coverage_tilestitcher .coverage_others

    - name: Generate Combined Coverage Report
      shell: bash -l {0}
      run: |
        coverage xml -o combined_coverage.xml
    
    # - name: Combine coverage data
    #   shell: bash -l {0}
    #   run: |
    #     coverage combine coverage_tilestitcher.xml coverage_others.xml
    #     coverage xml -o coverage_combined.xml

    - name: Upload combined coverage to Codecov
      uses: codecov/codecov-action@v2
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        env_vars: OS,PYTHON
        fail_ci_if_error: true
        files: ./combined_coverage.xml
        name: codecov-umbrella
        verbose: true

    - name: Compile docs
      shell: bash -l {0}
      run: |
        cd docs
        pip install -r readthedocs-requirements.txt
        make html