coreneuron-ci.yml

name: CoreNEURON CI

concurrency:
  group: ${{ github.workflow }}#${{ github.ref }}
  cancel-in-progress: true

on:
  push:
    branches:
      - master
      - release/**
  pull_request:
    branches:
      - master
      - release/**

env:
  BUILD_TYPE: Release
  DEVELOPER_DIR: /Applications/Xcode_11.3.1.app/Contents/Developer
  DEFAULT_PY_VERSION: 3.8

jobs:
  ci:
    runs-on: ${{ matrix.os }}

    name: ${{ matrix.os }} - ${{ toJson(matrix.config) }})

    env:
      INSTALL_DIR: install
      SDK_ROOT: $(xcrun --sdk macosx --show-sdk-path)

    strategy:
      matrix:
        os: [ ubuntu-18.04, macOS-10.15 ]
        config:
          # Defaults: CORENRN_ENABLE_MPI=ON
          - {cmake_option: "-DCORENRN_ENABLE_DEBUG_CODE=ON -DTEST_EXEC_PREFIX='mpiexec;-n;2'", documentation: ON}
          - {cmake_option: "-DCORENRN_ENABLE_MPI_DYNAMIC=ON -DTEST_EXEC_PREFIX='mpiexec;-n;2'"}
          - {cmake_option: "-DCORENRN_ENABLE_MPI_DYNAMIC=ON -DCORENRN_ENABLE_SHARED=OFF -DTEST_EXEC_PREFIX='mpiexec;-n;2'"}
          - {cmake_option: "-DCORENRN_ENABLE_MPI=OFF"}
          - {use_nmodl: ON, py_version: 3.6.7}
          - {use_nmodl: ON}
          - {use_ispc: ON, py_version: 3.6.7}
          - {gcc_version: 9}
      fail-fast: false

    steps:

      - name: Install homebrew packages
        if: startsWith(matrix.os, 'macOS')
        run: |
          brew update
          brew install coreutils bison flex boost openmpi
        shell: bash

      - name: Install apt packages
        if: startsWith(matrix.os, 'ubuntu')
        run: |
          sudo apt-get install doxygen bison flex libboost-all-dev libopenmpi-dev openmpi-bin python3-dev python3-pip libfl-dev
        shell: bash

      - name: Install specific apt packages
        if: startsWith(matrix.os, 'ubuntu') && matrix.config.gcc_version
        run: |
          sudo apt-get install g++-${GCC_VERSION}
        shell: bash
        env:
          GCC_VERSION: ${{ matrix.config.gcc_version }}

      - name: Set up Python3
        uses: actions/setup-python@v2
        with:
          python-version: ${{ env.PYTHON_VERSION }}
        env:
          PYTHON_VERSION:  ${{ matrix.config.py_version || env.DEFAULT_PY_VERSION }}

      - name: Install ISPC
        if: ${{ matrix.config.use_ispc == 'ON' }}
        working-directory: ${{runner.workspace}}
        run: |
          ispc_version="v1.12.0";
          if [ "${{ startsWith(matrix.os, 'ubuntu') }}" == "true" ]; then
            url_os="linux";
            ispc_version_suffix="b";
          else
            url_os="macOS";
            ispc_version_suffix="";
          fi;
          url="https://github.com/ispc/ispc/releases/download/${ispc_version}/ispc-${ispc_version}${ispc_version_suffix}-${url_os}.tar.gz";
          wget -O ispc.tar.gz $url;
          mkdir ispc && tar -xvzf ispc.tar.gz -C ispc --strip 1;
      - name: Install NMODL dependencies
        if: ${{ matrix.config.use_nmodl == 'ON' ||  matrix.config.use_ispc == 'ON' }}
        run: |
          python3 -m pip install --upgrade pip jinja2 pyyaml pytest "sympy<1.6";

      - uses: actions/checkout@v2

      - name: Install Python3 documentation dependencies
        if: ${{ startsWith(matrix.os, 'ubuntu') && matrix.config.documentation == 'ON' }}
        working-directory: ${{runner.workspace}}/CoreNeuron
        run: |
          python3 -m pip install --upgrade pip
          python3 -m pip install --upgrade -r docs/docs_requirements.txt

      - name: Build and Test
        id: build-test
        shell: bash
        working-directory: ${{runner.workspace}}/CoreNeuron
        run:  |
          if [ -n "$GCC_VERSION" ]; then
              export CXX="g++-${GCC_VERSION}" CC="gcc-${GCC_VERSION}";
          fi
          
          if [[ "${{ startsWith(matrix.os, 'macOS') }}" = "true" ]]; then
              export PATH=/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:$PATH;
              export CXX=g++;
              export CC=gcc;
          fi
          
          echo "------- Build, Test and Install -------"
          mkdir build && cd build
          if [[ "$USE_ISPC" == "ON" ]]; then
              cmake -DCORENRN_ENABLE_ISPC=ON -DCMAKE_ISPC_COMPILER=${{runner.workspace}}/ispc/bin/ispc -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DPYTHON_EXECUTABLE=$(which python3) ..;
          elif [[ "$USE_NMODL" == "ON" ]]; then
              cmake -DCORENRN_ENABLE_NMODL=ON -DCORENRN_NMODL_FLAGS="sympy --analytic" -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DPYTHON_EXECUTABLE=$(which python3) ..;
          else
              cmake ${cmake_option} -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DPYTHON_EXECUTABLE=$(which python3) ..;
          fi
          make
          ctest --output-on-failure
          make install
        env:
          cmake_option: ${{ matrix.config.cmake_option }}
          USE_ISPC: ${{ matrix.config.use_ispc }}
          USE_NMODL: ${{ matrix.config.use_nmodl }}
          INSTALL_DIR: ${{ runner.workspace }}/install
          GCC_VERSION: ${{ matrix.config.gcc_version }}
          PYTHON_VERSION:  ${{ matrix.config.py_version || env.DEFAULT_PY_VERSION }}

      # This step will set up an SSH connection on tmate.io for live debugging.
      # To enable it, you have to:
      #   * add 'live-debug-ci' to your PR title
      #   * push something to your PR branch (note that just re-running the pipeline disregards the title update)
      - name: live debug session on failure (manual steps required, check `.github/workflows/coreneuron-ci.yml`)
        if: failure() && contains(github.event.pull_request.title, 'live-debug-ci')
        uses: mxschmitt/action-tmate@v3

      - name: Documentation
        if: ${{ startsWith(matrix.os, 'ubuntu') && matrix.config.documentation == 'ON' }}
        id: documentation
        working-directory: ${{runner.workspace}}/CoreNeuron
        run: |
          echo "------- Build Doxygen Documentation -------";
          pushd build;
          make docs;
          echo "-------- Disable jekyll --------";
          pushd docs;
          touch .nojekyll;
          echo ::set-output name=status::done
          
      - name: Deploy 🚀
        uses: JamesIves/github-pages-deploy-action@4.1.5
        if: steps.documentation.outputs.status == 'done' && github.ref == 'refs/heads/master'
        with:
          branch: gh-pages # The branch the action should deploy to.
          folder: ${{runner.workspace}}/CoreNeuron/build/docs  # The folder the action should deploy.
          single-commit: true #have a single commit on the deployment branch instead of maintaining the full history