Switched absolute to relative additional radius #2398
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| # Runs the installation tests and valgrind tests in the following cases: | |
| # 1) every day at 3 am | |
| # 2) a pull request to the master branch | |
| name: Ubuntu System CI | |
| on: | |
| schedule: | |
| # Every day at 3 am | |
| - cron: '0 3 * * *' | |
| pull_request: | |
| # Upon pull requests | |
| branches: | |
| - master | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| build: | |
| strategy: | |
| matrix: | |
| os: [ubuntu-20.04, ubuntu-22.04] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Set GHA_BRANCH_NAME | |
| run: | | |
| if [ "${{ github.event_name }}" = "pull_request" ]; then | |
| echo "GHA_BRANCH_NAME=${{ github.head_ref }}" >> $GITHUB_ENV | |
| fi | |
| if [ "${{ github.event_name }}" = "schedule" ]; then | |
| echo "GHA_BRANCH_NAME=${GITHUB_REF#refs/heads/}" >> $GITHUB_ENV | |
| fi | |
| echo "GHA_REPOSITORY=${{ github.repository }}" >> $GITHUB_ENV | |
| - name: Set OSVERS | |
| run: | | |
| ID=$(grep -oP '(?<=^ID=).+' /etc/os-release | tr -d '"') | |
| VERSION=$(grep -oP '(?<=^VERSION_ID=).+' /etc/os-release | tr -d '"') | |
| echo "OSVERS=$ID-$VERSION" >> $GITHUB_ENV | |
| - name: Start Xvfb | |
| run: | | |
| set -e | |
| sudo apt update | |
| sudo apt-get -y install xvfb | |
| XVFBARGS=":99 -ac -screen 0 2560x1440x24" | |
| /usr/bin/Xvfb $XVFBARGS >> /tmp/Xvfb.out 2>&1 & | |
| disown -ar | |
| sleep 3 | |
| - name: Install BioDynaMo | |
| shell: bash | |
| run: | | |
| sudo apt update | |
| sudo apt install -y curl | |
| curl https://raw.githubusercontent.com/${GHA_REPOSITORY}/${GHA_BRANCH_NAME}/util/install | bash | |
| # remove whole bidynamo repository to catch errors related to paths pointing into the build dir | |
| mktemp -d | |
| find /tmp -iname biodynamo -type d || true | |
| rm -rf $(find $(mktemp -d)/../* -maxdepth 1 -iname biodynamo -type d 2>/dev/null) | |
| echo "Removed" | |
| find /tmp -iname biodynamo -type d || true | |
| - name: Checkout BioDynaMo | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set INSTALL_DIR | |
| run: | | |
| if [ "${{ github.event_name }}" = "pull_request" ]; then | |
| echo "INSTALL_DIR=${GITHUB_WORKSPACE}/build" >> $GITHUB_ENV | |
| fi | |
| if [ "${{ github.event_name }}" = "schedule" ]; then | |
| echo "INSTALL_DIR=$(echo ${HOME}/biodynamo-*)" >> $GITHUB_ENV | |
| fi | |
| - name: Cache pyenv | |
| uses: actions/cache@v4 | |
| id: pyenv-cache | |
| with: | |
| path: ~/.pyenv | |
| key: ${{ env.OSVERS }}-pyenv-3.9.1 | |
| - name: Install pyenv dependency | |
| if: steps.pyenv-cache.outputs.cache-hit != 'true' | |
| run: | | |
| if [ ! -f "$HOME/.pyenv/bin/pyenv" ]; then | |
| curl https://pyenv.run | bash | |
| fi | |
| export PATH="$HOME/.pyenv/bin:$PATH" | |
| eval "$(pyenv init --path)" | |
| eval "$(pyenv init -)" | |
| if [ ! -f "$HOME/.pyenv/versions/3.9.1/lib/libpython3.so" ]; then | |
| PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.9.1 | |
| fi | |
| pyenv shell 3.9.1 | |
| - name: Cache Third Party Packages | |
| uses: actions/cache@v4 | |
| with: | |
| path: build/third_party | |
| key: ${{ env.OSVERS }}-third-party-${{ hashFiles('cmake/external/SHA256Digests.cmake') }} | |
| # Set floating point precision | |
| - name: Set floating-point-precision | |
| run: | | |
| if [ "${{ env.OSVERS }}" = "ubuntu-20.04" ]; then | |
| echo "REALT=float" >> $GITHUB_ENV | |
| fi | |
| if [ "${{ env.OSVERS }}" = "ubuntu-22.04" ]; then | |
| echo "REALT=double" >> $GITHUB_ENV | |
| fi | |
| # Don't do this in the `Build BioDynaMo step`, because notebooks might time out in GHA | |
| # runners, while waiting for other targets to be compiled. Run notebooks only | |
| # if the event is a pull request, and on ubuntu-22.04. | |
| - name: Run notebooks | |
| shell: bash | |
| run: | | |
| export PATH="$HOME/.pyenv/bin:$PATH" | |
| eval "$(pyenv init --path)" | |
| eval "$(pyenv init -)" | |
| pyenv shell 3.9.1 | |
| cmake \ | |
| -Dnotebooks=ON \ | |
| -Dsbml=OFF \ | |
| -Dnuma=OFF \ | |
| -DCMAKE_BUILD_TYPE=Release \ | |
| -Dreal_t=${{ env.REALT }} \ | |
| -B build | |
| cmake --build build --parallel --config Release --target notebooks -- -j1 | |
| if: github.event_name == 'pull_request' && matrix.os == 'ubuntu-22.04' | |
| - name: Build BioDynaMo | |
| shell: bash | |
| run: | | |
| export PATH="$HOME/.pyenv/bin:$PATH" | |
| eval "$(pyenv init --path)" | |
| eval "$(pyenv init -)" | |
| pyenv shell 3.9.1 | |
| cmake \ | |
| -Dnotebooks=OFF \ | |
| -Dparaview=ON \ | |
| -Dbenchmark=ON \ | |
| -Dlibgit2=ON \ | |
| -Dsbml=OFF \ | |
| -DCMAKE_BUILD_TYPE=Release \ | |
| -Dreal_t=${{ env.REALT }} \ | |
| -B build | |
| cmake --build build --config Release | |
| - name: Run valgrind and system tests | |
| shell: bash | |
| working-directory: build | |
| run: | | |
| . $INSTALL_DIR/bin/thisbdm.sh | |
| sudo git config --system user.name "Test User" | |
| sudo git config --system user.email user@test.com | |
| export DISPLAY=:99.0 | |
| biodynamo new test-sim | |
| . ../test/util.inc | |
| run_cmake_simulation test-sim | |
| make run-valgrind | |
| make run-demos |