* Fixed bug where kallisto quantification would sometimes fail to sum… #602
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| name: Build CI | |
| on: | |
| push: | |
| pull_request: | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-latest, windows-latest, macos-latest ] | |
| python-version: ['3.10', '3.11', '3.12' ] | |
| exclude: | |
| - os: macos-latest | |
| python-version: '3.10' | |
| env: | |
| DISPLAY: ':99.0' | |
| steps: | |
| - name: Configure pagefile | |
| if: runner.os == 'Windows' | |
| uses: al-cheb/[email protected] | |
| - name: Set up pagefile | |
| if: runner.os == 'Windows' | |
| run: | | |
| (Get-CimInstance Win32_PageFileUsage).AllocatedBaseSize | |
| - name: Get repository | |
| uses: actions/checkout@v4 | |
| - name: apt-get update (Linux) | |
| if: runner.os == 'Linux' | |
| run: sudo apt-get update | |
| - name: Setup Qt requirements for Linux | |
| uses: tlambert03/setup-qt-libs@v1 | |
| - name: Setup Graphviz | |
| uses: ts-graphviz/setup-graphviz@v2 | |
| with: | |
| # Skip to run brew update command on macOS. | |
| macos-skip-brew-update: 'true' # defalt false | |
| - name: Cache LLVM and Clang | |
| if: runner.os != 'macOS' | |
| id: cache-llvm | |
| uses: actions/cache@v2 | |
| with: | |
| path: ${{ runner.temp }}/llvm | |
| key: llvm | |
| - name: Install LLVM and Clang | |
| if: runner.os != 'macOS' | |
| uses: KyleMayes/install-llvm-action@v2 | |
| with: | |
| version: "14.0" | |
| directory: ${{ runner.temp }}/llvm | |
| cached: ${{ steps.cache-llvm.outputs.cache-hit }} | |
| - name: Install R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: '4.4' # The R version to download (if necessary) and use. | |
| - name: Install homebrew on Linux | |
| if: runner.os == 'Linux' | |
| uses: Homebrew/actions/setup-homebrew@master | |
| - name: Install cURL on Linux | |
| if: runner.os == 'Linux' | |
| run: sudo apt-get install libcurl4-openssl-dev | |
| - name: Install cURL on Windows | |
| if: runner.os == 'Windows' | |
| run: choco install openssl | |
| - name: Install libxml on MacOS | |
| if: runner.os == 'macOS' | |
| run: brew install libxml2 | |
| - name: command line tools on MacOS | |
| if: runner.os == 'macOS' | |
| run: | | |
| gcc -v -xc++ /dev/null -fsyntax-only | |
| - name: Test R installation | |
| run: Rscript -e "print('R script ran successfully')" | |
| - name: Install kallisto | |
| run: | | |
| if [ "$RUNNER_OS" == "Linux" ]; then | |
| wget https://github.com/pachterlab/kallisto/releases/download/v0.50.1/kallisto_linux-v0.50.1.tar.gz | |
| tar -xvzf kallisto*.gz | |
| echo "${GITHUB_WORKSPACE}/kallisto" >> $GITHUB_PATH | |
| elif [ "$RUNNER_OS" == "macOS" ]; then | |
| brew install hdf5 | |
| wget https://github.com/pachterlab/kallisto/releases/download/v0.50.1/kallisto_mac_m1-v0.50.1.tar.gz | |
| tar -xvzf kallisto*.gz | |
| echo "${GITHUB_WORKSPACE}/kallisto" >> $GITHUB_PATH | |
| elif [ "$RUNNER_OS" == "Windows" ]; then | |
| choco install wget -y | |
| wget https://github.com/pachterlab/kallisto/releases/download/v0.50.1/kallisto_windows-v0.50.1.zip | |
| 7z x kallisto*.zip | |
| echo "${GITHUB_WORKSPACE}/kallisto" >> $GITHUB_PATH | |
| else | |
| echo "$RUNNER_OS not supported" | |
| exit 1 | |
| fi | |
| shell: bash | |
| continue-on-error: true | |
| - name: Test kallisto installation | |
| run: kallisto version | |
| - name: Install bowtie2 | |
| run: | | |
| if [ "$RUNNER_OS" == "Linux" ]; then | |
| brew install bowtie2 | |
| elif [ "$RUNNER_OS" == "macOS" ]; then | |
| brew install bowtie2 | |
| elif [ "$RUNNER_OS" == "Windows" ]; then | |
| choco install wget -y | |
| wget https://github.com/BenLangmead/bowtie2/releases/download/v2.5.1/bowtie2-2.5.1-mingw-x86_64.zip | |
| 7z x bowtie2-2.5.1-mingw-x86_64.zip | |
| echo "${GITHUB_WORKSPACE}/bowtie2-2.5.1-mingw-x86_64" >> $GITHUB_PATH | |
| else | |
| echo "$RUNNER_OS not supported" | |
| exit 1 | |
| fi | |
| shell: bash | |
| - name: Test bowtie2 installation | |
| run: | | |
| bowtie2 --version | |
| bowtie2-build-s --version | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install --upgrade -r requirements_dev.txt | |
| python -m pip install .[all] | |
| - name: Test with pytest | |
| run: | | |
| coverage run --source=rnalysis/ -m pytest tests/ | |
| continue-on-error: false | |
| - name: Generate lcov file | |
| run: coverage lcov | |
| - name: Coveralls Parallel | |
| uses: coverallsapp/github-action@v2 | |
| if: runner.os != 'macOS' | |
| continue-on-error: true | |
| with: | |
| flag-name: run-${{ join(matrix.*, '-') }} | |
| parallel: true | |
| path-to-lcov: ./coverage.lcov | |
| finish: | |
| name: Finish submitting coverage | |
| if: ${{ always() }} | |
| needs: build | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Coveralls Finished | |
| uses: coverallsapp/github-action@v2 | |
| continue-on-error: true | |
| with: | |
| parallel-finished: true |