tests-windows.yml

name: Tests windows

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

jobs:
  build:
    runs-on: windows-latest
    strategy:
      max-parallel: 5
      matrix:
        python-version: ["3.8", "3.9", "3.10"]
    timeout-minutes: 120

    steps:

      - uses: actions/checkout@v2

      - name: Set up JDK 17
        uses: actions/setup-java@v2
        with:
          java-version: '17'
          distribution: 'temurin'

      - name: Print JAVA_HOME and PATH
        run: |
          echo "JAVA_HOME: $env:JAVA_HOME"
          echo "PATH: $env:PATH"
        shell: pwsh

      - name: Set JDK_HOME environment variable
        run: echo "JDK_HOME=${JAVA_HOME}" >> $GITHUB_ENV
        shell: bash

      
      - name: Setup Micromamba
        uses: mamba-org/setup-micromamba@v1
        with:
          micromamba-version: '1.5.6-0'
          environment-name: pathml
          environment-file: environment.yml
          init-shell: >-
            bash
          create-args: >-
            python=${{ matrix.python-version }}


      - name: Run Python script to find JVM path
        shell: bash -l {0}
        run: |
          python -c "import javabridge; print('javabridge.locate.find_javahome():', javabridge.locate.find_javahome()); print('javabridge.jutil._find_jvm_windows():', javabridge.jutil._find_jvm_windows())"
    
      - name: Print JAVA_HOME and PATH Second
        run: |
          echo "JAVA_HOME: $env:JAVA_HOME"
          echo "PATH: $env:PATH"
        shell: pwsh


      - name: Download and Setup OpenSlide
        run: |
          # $zipFile = "openslide-win64-20231011.zip"
          $zipFile = "openslide-win64-20230414.zip"
          $extractPath = Join-Path $env:GITHUB_WORKSPACE "openslide-binaries"
          # Invoke-WebRequest -Uri "https://github.com/openslide/openslide-bin/releases/download/v20231011/$zipFile" -OutFile $zipFile
          Invoke-WebRequest -Uri "https://github.com/openslide/openslide-bin/releases/download/v20230414/$zipFile" -OutFile $zipFile
          Expand-Archive -Path $zipFile -DestinationPath $extractPath
          # $binPath = Join-Path $extractPath "openslide-win64-20231011/bin"
          $binPath = Join-Path $extractPath "openslide-win64-20230414/bin"
          Write-Host "Adding to PATH: $binPath"
          echo "OPENSLIDE_PATH=$binPath" | Out-File -Append -FilePath $env:GITHUB_ENV
          # echo "$binPath" | Out-File -Append -FilePath $env:GITHUB_PATH
        shell: pwsh

      # Optional: List files in OpenSlide bin directory to verify
      - name: List files in OpenSlide bin directory
        run: |
          Get-ChildItem -Path $env:OPENSLIDE_PATH
        shell: pwsh
        env:
          OPENSLIDE_PATH: ${{ env.OPENSLIDE_PATH }}

      - name: Mamba info
        shell: bash -l {0}
        run: |
          micromamba info
          micromamba config
          micromamba list

      - name: Install PathML
        shell: bash -l {0}      
        run: pip install -e .

      - name: Install torchvision
        shell: bash -l {0}
        run: pip install torchvision==0.14.1
        
      - name: Set OPENSLIDE_PATH
        run: echo "OPENSLIDE_PATH=D:\a\pathml\pathml\openslide-binaries\openslide-win64-20231011\bin" >> $GITHUB_ENV
        shell: pwsh

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

      - name: Test tile_stitcher with pytest and generate coverage
        shell: bash -l {0}
        run: |
          coverage run --data-file=.coverage_tilestitcher -m pytest tests/preprocessing_tests/test_tilestitcher.py