Model with CAR-T cells #135
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number }} | |
| cancel-in-progress: true | |
| jobs: | |
| build: | |
| name: ${{ matrix.name }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - name: ubu22-gcc | |
| os: ubuntu-22.04 | |
| compiler: gcc | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.9 | |
| - name: Install dependencies | |
| run: | | |
| #sudo apt-get update | |
| if [ "${{ matrix.compiler }}" = "gcc" ]; then | |
| sudo apt-get install -y gcc g++ cmake make | |
| echo "CC=gcc" >> $GITHUB_ENV | |
| echo "CXX=g++" >> $GITHUB_ENV | |
| else | |
| sudo apt-get install -y clang cmake make | |
| echo "CC=clang" >> $GITHUB_ENV | |
| echo "CXX=clang++" >> $GITHUB_ENV | |
| fi | |
| sudo apt-get install curl freeglut3-dev g++ gcc git libblas-dev \ | |
| libbz2-dev liblapack-dev libnuma-dev libomp5 \ | |
| libomp-dev libopenmpi-dev libpthread-stubs0-dev \ | |
| make wget zlib1g-dev python3-dev libbz2-dev \ | |
| libffi-dev liblzma-dev libreadline-dev \ | |
| libsqlite3-dev libssl-dev python3-openssl tk-dev \ | |
| xz-utils zlib1g-dev | |
| curl https://pyenv.run | bash | |
| - name: Cache Third Party Packages | |
| uses: actions/cache@v4 | |
| with: | |
| path: build/third_party | |
| key: ${{ matrix.os }}-third-party-${{ hashFiles('cmake/external/SHA256Digests.cmake') }} | |
| - name: Restore BDM Cache | |
| uses: actions/cache/restore@v4 | |
| id: cache | |
| with: | |
| path: | | |
| biodynamo | |
| key: ${{ matrix.os }}-bdm | |
| - name: Build BDM if Cache is not found | |
| if: ${{ steps.cache.outputs.cache-hit != 'true' }} | |
| run: | | |
| git clone --depth=1 https://github.com/vgvassilev/biodynamo.git | |
| cd biodynamo | |
| cmake \ | |
| -Dnotebooks=OFF \ | |
| -Dparaview=OFF \ | |
| -Dbenchmark=ON \ | |
| -Dlibgit2=ON \ | |
| -Dsbml=OFF \ | |
| -DCMAKE_BUILD_TYPE=Release \ | |
| -B build | |
| cmake --build build --config Release | |
| cd .. | |
| - name: Save Cache BDM | |
| uses: actions/cache/save@v4 | |
| if: ${{ steps.cache.outputs.cache-hit != 'true' }} | |
| with: | |
| path: | | |
| biodynamo | |
| key: ${{ steps.cache.outputs.cache-primary-key }} | |
| - name: Configure project | |
| run: | | |
| #FIXME: Drop this requirement by passing to cmake -DNOPYENV=Yes | |
| export PATH="$HOME/.pyenv/bin:$PATH" | |
| eval "$(pyenv init --path)" | |
| eval "$(pyenv init -)" | |
| pyenv install 3.9 | |
| pyenv shell 3.9 | |
| source $GITHUB_WORKSPACE/biodynamo/build/bin/thisbdm.sh | |
| cmake . -B build \ | |
| -DBioDynaMo_DIR="$GITHUB_WORKSPACE/biodynamo/build/share/cmake/" \ | |
| -DCMAKE_BUILD_TYPE="Release" | |
| - name: Build project | |
| run: | | |
| cmake --build build -- -j$(nproc) | |
| - name: Run tests | |
| run: | | |
| # FIXME: Enable. | |
| # ctest --test-dir build --output-on-failure | |
| - name: Setup tmate session | |
| if: ${{ !cancelled() && runner.debug }} | |
| uses: mxschmitt/action-tmate@v3 | |
| # When debugging increase to a suitable value! | |
| timeout-minutes: 30 |