main.yml

name: Unit Tests

on:
  push:
    branches:
      - master
  pull_request:
    branches:
      - master

jobs:
  test:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest, windows-latest]
        python-version: ['3.9', '3.10', '3.11', '3.12']

    steps:
    - uses: actions/checkout@v4

    - name: Cache Python dependencies
      uses: actions/cache@v4
      with:
        path: ~/.cache/pip
        key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('**/requirements.txt') }}
        restore-keys: |
          ${{ runner.os }}-pip-${{ matrix.python-version }}-

    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install -r requirements.txt
        pip install pytest

    - name: Install cd-hit (Ubuntu)
      if: runner.os == 'Linux'
      run: |
        sudo apt-get update
        sudo apt-get install -y cd-hit

    - name: Install mmseqs2 (Ubuntu)
      if: runner.os == 'Linux'
      run: |
        sudo apt-get update
        sudo apt-get install -y mmseqs2

    - name: Install cd-hit (Windows)
      if: runner.os == 'Windows'
      shell: pwsh
      run: |
        curl -L -o cd-hit.tar.gz https://github.com/weizhongli/cdhit/releases/download/V4.8.1/cd-hit-v4.8.1-2019-0228.tar.gz
        $cdhitDir = "$Env:USERPROFILE\cdhit"
        New-Item -ItemType Directory -Force -Path $cdhitDir
        tar -xzf cd-hit.tar.gz -C $cdhitDir
        $cdhitBinPath = "$cdhitDir\cd-hit-v4.8.1-2019-0228\bin"
        Write-Host "cd-hit binary path: $cdhitBinPath"
        echo "$cdhitBinPath" | Out-File -Append -FilePath $Env:GITHUB_PATH
        [Environment]::SetEnvironmentVariable("PATH", "$Env:PATH;$cdhitBinPath", "Process")
        Write-Host "Contents of cd-hit bin directory:"
        Get-ChildItem $cdhitBinPath

    - name: Install mmseqs2 (Windows)
      if: runner.os == 'Windows'
      shell: pwsh
      run: |
        curl -L -o mmseqs2.zip https://mmseqs.com/latest/mmseqs-win64.zip
        $mmseqsDir = "$Env:USERPROFILE\mmseqs"
        New-Item -ItemType Directory -Force -Path $mmseqsDir
        Expand-Archive -Path mmseqs2.zip -DestinationPath $mmseqsDir
        $mmseqsBinPath = "$mmseqsDir\mmseqs-win64"
        Write-Host "mmseqs2 binary path: $mmseqsBinPath"
        echo "$mmseqsBinPath" | Out-File -Append -FilePath $Env:GITHUB_PATH
        [Environment]::SetEnvironmentVariable("PATH", "$Env:PATH;$mmseqsBinPath", "Process")
        Write-Host "Contents of mmseqs2 directory:"
        Get-ChildItem $mmseqsBinPath

    - name: Verify mmseqs2 installation
      if: runner.os == 'Windows'
      shell: pwsh
      run: |
        $mmseqsBinPath = "$Env:USERPROFILE\mmseqs\mmseqs-win64"
        $env:Path += ";$mmseqsBinPath"
        Write-Host "Updated PATH: $env:Path"
        Write-Host "Checking mmseqs binary in PATH:"
        if (-Not (Get-Command mmseqs -ErrorAction SilentlyContinue)) {
          Write-Error "mmseqs not found in PATH"
        } else {
          Write-Host "mmseqs found in PATH"
          mmseqs --version
        }

    - name: Verify cd-hit installation
      if: runner.os == 'Windows'
      shell: pwsh
      run: |
        $cdhitBinPath = "$Env:USERPROFILE\cdhit\cd-hit-v4.8.1-2019-0228\bin"
        $env:Path += ";$cdhitBinPath"
        Write-Host "Updated PATH: $env:Path"
        Write-Host "Checking cd-hit binary in PATH:"
        if (-Not (Get-Command cd-hit -ErrorAction SilentlyContinue)) {
          Write-Error "cd-hit not found in PATH"
        } else {
          Write-Host "cd-hit found in PATH"
          cd-hit --version
        }

    - name: Run Tests
      run: pytest tests
      env:
        HYPOTHESIS_DEADLINE: 10000000
        MPLBACKEND: Agg