Build larch on linux and run tests #3
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Build larch on linux and run tests | |
| on: | |
| workflow_dispatch: | |
| jobs: | |
| build-larch: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| environment: [build-larch-debug, build-larch-release] | |
| environment: ${{ matrix.environment }} | |
| steps: | |
| - name: Check out code | |
| uses: actions/checkout@v2 | |
| with: | |
| submodules: true | |
| - name: Prepare build environment | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install build-essential zlib1g-dev python3-pip python3-pytest git git-lfs | |
| - name: Install conda | |
| run: | | |
| curl -L https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh > Miniconda3-latest-Linux-x86_64.sh | |
| bash Miniconda3-latest-Linux-x86_64.sh -b -p ~/miniconda | |
| ~/miniconda/bin/conda update -n base -c defaults conda | |
| mkdir build | |
| - name: Create conda env | |
| run: | | |
| source ~/miniconda/etc/profile.d/conda.sh | |
| conda config --prepend channels conda-forge | |
| conda config --prepend channels bioconda | |
| conda config --show channels | |
| conda env create -f environment-dev.yml | |
| - name: Build (cmake step) | |
| env: | |
| CMAKE_BUILD_TYPE: ${{ vars.CMAKE_BUILD_TYPE }} | |
| CMAKE_NUM_THREADS: ${{ vars.CMAKE_NUM_THREADS }} | |
| USE_USHER: ${{ vars.USE_USHER }} | |
| run: | | |
| source ~/miniconda/etc/profile.d/conda.sh | |
| conda activate larch-dev | |
| cd build | |
| export CMAKE_NUM_THREADS=${CMAKE_NUM_THREADS} | |
| cmake -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DUSE_USHER=${USE_USHER} .. | |
| - name: Build (make step) | |
| env: | |
| MAKE_NUM_THREADS: ${{ vars.MAKE_NUM_THREADS }} | |
| run: | | |
| source ~/miniconda/etc/profile.d/conda.sh | |
| conda activate larch-dev | |
| cd build | |
| make VERBOSE=1 -j${MAKE_NUM_THREADS} | |
| - name: Run tests | |
| env: | |
| LARCH_TEST_FLAGS: ${{ vars.LARCH_TEST_FLAGS }} | |
| run: | | |
| source ~/miniconda/etc/profile.d/conda.sh | |
| conda activate larch-dev | |
| cd build | |
| ln -s ../data | |
| ./larch-test ${LARCH_TEST_FLAGS} |