ubuntu-system-ci.yml

# 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