Build larch on linux and run tests #5
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| 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} |