centos-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: CentOS 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:
    runs-on: ubuntu-latest
    container:
      image: centos:7

    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

      # Do this prior to Checkout BioDynaMo, because the CentOS docker container
      # does not come with git preinstalled. This would mess up later calls to
      # `git describe --tags`
    - name: Install latest version of git
      shell: bash
      run: |
        yum install -y http://opensource.wandisco.com/centos/7/git/x86_64/wandisco-git-release-7-2.noarch.rpm
        yum install -y git

    - name: Start Xvfb
      run: |
        set -e
        yum -y install xorg-x11-server-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: |
        yum update -y
        yum install -y sudo curl
        curl https://raw.githubusercontent.com/${GHA_REPOSITORY}/${GHA_BRANCH_NAME}/util/install | bash
        # remove whole BioDynaMo 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@v3
      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@v2
      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@v2
      with:
        path: build/third_party
        key: ${{ env.OSVERS }}-third-party-${{ hashFiles('cmake/external/SHA256Digests.cmake') }}

    - name: Build BioDynaMo
      shell: bash
      run: |
        export PATH="$HOME/.pyenv/bin:$PATH"
        eval "$(pyenv init --path)"
        eval "$(pyenv init -)"
        pyenv shell 3.9.1
        . scl_source enable devtoolset-10 || true
        . /etc/profile.d/modules.sh || true
        module load mpi
        cmake \
          -Dparaview=ON \
          -Dbenchmark=ON \
          -Dsbml=OFF \
          -Dnuma=OFF \
          -Dlibgit2=OFF \
          -DCMAKE_BUILD_TYPE=Release \
          -B build
        cmake --build build --config Release

    # # 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
    # - name: Run notebooks
    #   shell: bash
    #   run: |
    #     export PATH="$HOME/.pyenv/bin:$PATH"
    #     eval "$(pyenv init --path)"
    #     eval "$(pyenv init -)"
    #     pyenv shell 3.9.1
    #     . scl_source enable devtoolset-10 || true
    #     . /etc/profile.d/modules.sh || true
    #     module load mpi
    #     cmake \
    #       -Dnotebooks=ON \
    #       -B build
    #     cmake --build build --config Release --target notebooks -- -j1

    - name: Run system tests
      shell: bash
      working-directory: build
      run: |
        yum install -y xorg-x11-server-Xvfb fontconfig mesa-dri-drivers
        . $INSTALL_DIR/bin/thisbdm.sh
        git config --system user.name "Test User"
        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-demos