tests-conda.yml

name: Tests Cross-Platform

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: [3.9]
    timeout-minutes: 60

    steps:
      - uses: actions/checkout@v2

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

      - name: Debug JAVA_HOME
        run: |
          echo $env:JAVA_HOME
          echo $env:PATH
        shell: pwsh

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

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

      - name: Download and Setup OpenSlide
        run: |
          $zipFile = "openslide-win64-20231011.zip"
          $extractPath = Join-Path $env:GITHUB_WORKSPACE "openslide-binaries"
          Invoke-WebRequest -Uri "https://github.com/openslide/openslide-bin/releases/download/v20231011/$zipFile" -OutFile $zipFile
          Expand-Archive -Path $zipFile -DestinationPath $extractPath
          $binPath = Join-Path $extractPath "openslide-win64-20231011/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: Download and Setup OpenSlide
      #   run: |
      #     Invoke-WebRequest -Uri "https://github.com/openslide/openslide-bin/releases/download/v20231011/openslide-win64-20231011.zip" -OutFile "openslide-win64-20231011.zip"
      #     # Expand-Archive -Path "openslide-win64-20231011.zip" -DestinationPath "${{ github.workspace }}/openslide-binaries"
      #     # echo "${{ github.workspace }}/openslide-binaries/openslide-win64-20231011" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8
      #   shell: pwsh

      # - name: Extract OpenSlide Binaries
      #   run: |
      #     Expand-Archive -Path "openslide-win64-20231011.zip" -DestinationPath "${{ github.workspace }}/openslide-binaries"
      #     $binPath = Join-Path ${{ github.workspace }} "openslide-binaries/openslide-win64-20231011/bin"
      #     Write-Host "Adding to PATH: $binPath"
      #     echo "$binPath" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8
      #   shell: pwsh

      # - name: List files in OpenSlide bin directory
      #   run: |
      #     $binPath = Join-Path ${{ github.workspace }} "openslide-binaries/openslide-win64-20231011/bin"
      #     Get-ChildItem -Path $binPath
      #   shell: pwsh
        
      - name: Check PATH
        run: |
          # echo $env:JAVA_HOME
          echo $env:PATH
        shell: pwsh
        
      - name: Setup Miniconda
        uses: conda-incubator/setup-miniconda@v2
        with:
          auto-activate-base: false
          activate-environment: pathml
          environment-file: '.github/ci-environments/env-py39.yml'
          mamba-version: "*"
          python-version: ${{ matrix.python-version }}

      - name: Debugging
        shell: bash -l {0}
        run: |
          echo "Checking the status of mamba..."
          mamba --version
          echo "Checking the available disk space..."
          df -h

      - name: Conda info
        shell: bash -l {0}
        run: |
          conda info
          conda 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: Download and Setup OpenSlide
      #   run: |
      #     Invoke-WebRequest -Uri "https://github.com/openslide/openslide-bin/releases/download/v20231011/openslide-win64-20231011.zip" -OutFile "openslide-win64-20231011.zip"
      #     Expand-Archive -Path "openslide-win64-20231011.zip" -DestinationPath "${{ github.workspace }}/openslide-binaries"
      #     echo "${{ github.workspace }}/openslide-binaries/openslide-win64-20231011" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8
      #   shell: pwsh

      - name: Set OPENSLIDE_PATH
        run: echo "OPENSLIDE_PATH=D:\a\pathml\pathml\openslide-binaries\openslide-win64-20231011\bin" >> $GITHUB_ENV
        shell: pwsh

      - name: Check PATH
        run: |
          # echo $env:JAVA_HOME
          echo $env:PATH
        shell: pwsh
      
      - 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
        continue-on-error: true

      - 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"
        continue-on-error: true


# name: Tests Cross-Platform

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

# jobs:
#   build:
#     runs-on: windows-latest  # Use Ubuntu if you're building on Linux, or keep windows-latest if you're targeting Windows.
#     strategy:
#       max-parallel: 5
#       matrix:
#         python-version: [3.9]
#     timeout-minutes: 60

#     steps:
#     - uses: actions/checkout@v2
    
#     - name: Set up JDK 17
#       uses: actions/setup-java@v2
#       with:
#         java-version: '17'
#         distribution: 'temurin' # Use 'temurin' for Eclipse Temurin distribution
#       id: setup-java

#     - name: Debug JAVA_HOME
#       run: |
#         echo $env:JAVA_HOME
#         echo $env:PATH
#       shell: pwsh

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

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

#     - name: vcpkg build
#       uses: johnwason/vcpkg-action@v6
#       id: vcpkg
#       with:
#         pkgs: openslide
#         triplet: x64-windows
#         token: ${{ github.token }}
#         github-binarycache: true
        
#     - name: Setup Miniconda
#       uses: conda-incubator/setup-miniconda@v2
#       with:
#         auto-activate-base: false
#         activate-environment: pathml
#         environment-file: '.github/ci-environments/env-py39.yml'  # Directly specify the env-py39.yml file
#         mamba-version: "*"
#         python-version: ${{ matrix.python-version }}

#     - name: Debugging
#       shell: bash -l {0}
#       run: |
#         echo "Checking the status of mamba..."
#         mamba --version
#         echo "Checking the available disk space..."
#         df -h

#     - name: Conda info
#       shell: bash -l {0}
#       run: |
#         conda info
#         conda list

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

#     # - name: Install python-spams
#     #   shell: bash -l {0}      
#     #   run: pip install spams
    
#     - name: Install torchvision
#       shell: bash -l {0}
#       run: pip install torchvision==0.14.1

#     - name: Set up vcpkg
#       uses: lukka/run-vcpkg@v10
#       with:
#         # Setup vcpkg directory
#         vcpkgDirectory: '${{ github.workspace }}/vcpkg'
#         # Clone vcpkg repo
#         setupOnly: true
        
#     - name: Install OpenSlide with vcpkg
#       run: |
#         ./vcpkg/vcpkg install openslide
#       working-directory: ${{ github.workspace }}
      
#     - 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
#         coverage run --data-file=.coverage_tilestitcher -m pytest tests/preprocessing_tests/test_tilestitcher.py

#     - 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"
#           # COVERAGE_FILE=.coverage_others coverage run -m pytest -m "not slow and not exclude"