Update cd-hit and mmseq installation20 #563
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| 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: matrix.os == 'windows-latest' | |
| 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: $cdhitBinPath" | |
| [Environment]::SetEnvironmentVariable("PATH", "$Env:PATH;$cdhitBinPath", [System.EnvironmentVariableTarget]::Machine) | |
| Write-Host "Contents of cd-hit bin directory:" | |
| Get-ChildItem $cdhitBinPath | |
| - name: Install mmseqs2 (Windows) | |
| if: matrix.os == 'windows-latest' | |
| 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: $mmseqsBinPath" | |
| [Environment]::SetEnvironmentVariable("PATH", "$Env:PATH;$mmseqsBinPath", [System.EnvironmentVariableTarget]::Machine) | |
| Write-Host "Contents of mmseqs2 directory:" | |
| Get-ChildItem $mmseqsBinPath | |
| - name: Verify mmseqs2 installation | |
| if: matrix.os == 'windows-latest' | |
| 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: matrix.os == 'windows-latest' | |
| 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 |