nestml-build.yml

name: NESTML build

on: [push, pull_request]

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

jobs:

  link_checker:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Link Checker
        uses: lycheeverse/lychee-action@v1.10.0
        with:
          args: --verbose --no-progress **/*.md **/*.html **/*.rst
          fail: true
        env:
          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}

  static_checks:
    runs-on: ubuntu-latest
    steps:
      # Checkout the repository contents
      - name: Checkout NESTML code
        uses: actions/checkout@v4

      # Setup Python version
      - name: Setup Python 3.8
        uses: actions/setup-python@v5
        with:
          python-version: 3.8

      # Install dependencies
      - name: Install apt dependencies
        run: |
          sudo apt-get update
          sudo apt-get install python3-all-dev

      # Install Python dependencies
      - name: Python dependencies
        run: |
          python -m pip install --upgrade pycodestyle
          python -m pip install -r requirements.txt

      # Static code analysis
      - name: Static code style analysis
        run: |
          python3 extras/codeanalysis/check_copyright_headers.py && python3 -m pycodestyle $GITHUB_WORKSPACE -v --ignore=E241,E501,E714,E713,E714,E252,W503 --exclude=$GITHUB_WORKSPACE/doc,$GITHUB_WORKSPACE/.git,$GITHUB_WORKSPACE/NESTML.egg-info,$GITHUB_WORKSPACE/pynestml/generated,$GITHUB_WORKSPACE/extras,$GITHUB_WORKSPACE/build,$GITHUB_WORKSPACE/.github

  build_and_test_py_standalone:
    needs: [static_checks]
    runs-on: ubuntu-latest
    steps:
      # Checkout the repository contents
      - name: Checkout NESTML code
        uses: actions/checkout@v4

      # Setup Python version
      - name: Setup Python 3.8
        uses: actions/setup-python@v5
        with:
          python-version: 3.8

      # Install dependencies
      - name: Install apt dependencies
        run: |
          sudo apt-get update
          sudo apt-get install libgsl0-dev libncurses5-dev pkg-config
          sudo apt-get install python3-all-dev python3-matplotlib python3-numpy python3-scipy ipython3

      # Install Python dependencies
      - name: Python dependencies
        run: |
          python -m pip install --upgrade pip pytest jupyterlab matplotlib pycodestyle scipy
          python -m pip install -r requirements.txt

      # Install Java
      - name: Install Java 11
        uses: actions/setup-java@v4
        with:
          distribution: 'zulu'
          java-version: '11.0.x'
          java-package: jre

      # Install Antlr4
      - name: Install Antlr4
        run: |
          wget http://www.antlr.org/download/antlr-4.13.1-complete.jar
          echo \#\!/bin/bash > antlr4
          echo java -cp \"`pwd`/antlr-4.13.1-complete.jar:$CLASSPATH\" org.antlr.v4.Tool \"\$@\" >> antlr4
          echo >> antlr4
          chmod +x antlr4
          echo PATH=$PATH:`pwd` >> $GITHUB_ENV

      # Install NESTML
      - name: Install NESTML
        run: |
          export PYTHONPATH=${{ env.PYTHONPATH }}:${{ env.NEST_INSTALL }}/lib/python3.8/site-packages
          #echo PYTHONPATH=`pwd` >> $GITHUB_ENV
          echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
          python setup.py install

      - name: Generate Lexer and Parser using Antlr4
        run: |
          cd pynestml/grammars
          ./generate_lexer_parser

      # Run integration tests
      - name: Run integration tests
        run: |
          rc=0
          for fn in $GITHUB_WORKSPACE/tests/python_standalone_tests/*.py; do
              pytest -s -o log_cli=true -o log_cli_level="DEBUG" ${fn} || rc=1
          done;
          exit $rc

  build_and_test_nest:
    needs: [static_checks]
    runs-on: ubuntu-latest
    strategy:
      matrix:
        nest_branch: ["v2.20.2", "v3.0", "v3.7", "master"]
      fail-fast: false
    steps:
      # Checkout the repository contents
      - name: Checkout NESTML code
        uses: actions/checkout@v4

      # Setup Python version
      - name: Setup Python 3.8
        uses: actions/setup-python@v5
        with:
          python-version: 3.8

      # Install dependencies
      - name: Install apt dependencies
        run: |
          sudo apt-get update
          sudo apt-get install libltdl7-dev libgsl0-dev libncurses5-dev libreadline6-dev pkg-config
          sudo apt-get install python3-all-dev python3-matplotlib python3-numpy python3-scipy ipython3

      # Install Python dependencies
      - name: Python dependencies
        run: |
          python -m pip install --upgrade pip pytest jupyterlab matplotlib pycodestyle scipy pandas
          python -m pip install -r requirements.txt

      # Install Java
      - name: Install Java 11
        uses: actions/setup-java@v4
        with:
          distribution: 'zulu'
          java-version: '11.0.x'
          java-package: jre

      # Install Antlr4
      - name: Install Antlr4
        run: |
          wget http://www.antlr.org/download/antlr-4.13.1-complete.jar
          echo \#\!/bin/bash > antlr4
          echo java -cp \"`pwd`/antlr-4.13.1-complete.jar:$CLASSPATH\" org.antlr.v4.Tool \"\$@\" >> antlr4
          echo >> antlr4
          chmod +x antlr4
          echo PATH=$PATH:`pwd` >> $GITHUB_ENV

      # Install NEST simulator
      - name: NEST simulator
        run: |
          python -m pip install cython
          echo "GITHUB_WORKSPACE = $GITHUB_WORKSPACE"
          NEST_SIMULATOR=$(pwd)/nest-simulator
          NEST_INSTALL=$(pwd)/nest_install
          echo "NEST_SIMULATOR = $NEST_SIMULATOR"
          echo "NEST_INSTALL = $NEST_INSTALL"

          git clone --depth=1 https://github.com/nest/nest-simulator --branch ${{ matrix.nest_branch }}
          mkdir nest_install
          echo "NEST_INSTALL=$NEST_INSTALL" >> $GITHUB_ENV
          cd nest_install
          cmake -DCMAKE_INSTALL_PREFIX=$NEST_INSTALL $NEST_SIMULATOR
          make && make install
          cd ..

      # Install NESTML (repeated)
      - name: Install NESTML
        run: |
          export PYTHONPATH=${{ env.PYTHONPATH }}:${{ env.NEST_INSTALL }}/lib/python3.8/site-packages
          #echo PYTHONPATH=`pwd` >> $GITHUB_ENV
          echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
          python setup.py install

      - name: Generate Lexer and Parser using Antlr4
        run: |
          cd pynestml/grammars
          ./generate_lexer_parser

      # Unit tests
      - name: Run unit tests
        run: |
          pytest -s -o norecursedirs='*' -o log_cli=true -o log_cli_level="DEBUG" tests

      # Integration tests: prepare (make module containing all NESTML models)
      - name: Setup integration tests
        run: |
          # exclude third factor plasticity models; these will only compile successfully if code generation is as a neuron+synapse pair
          export ALL_MODEL_FILENAMES=`find models/neurons -name "*.nestml" | paste -sd " "`
          echo $ALL_MODEL_FILENAMES
          echo "NEST_INSTALL = ${{ env.NEST_INSTALL }}"
          echo "NEST_VERSION = ${{ matrix.nest_branch }}"
          sed -i 's|%NEST_PATH%|${{ env.NEST_INSTALL }}|' tests/nest_tests/resources/nest_codegen_opts.json
          sed -i 's|%NEST_VERSION%|${{ matrix.nest_branch }}|' tests/nest_tests/resources/nest_codegen_opts.json
          nestml --input_path $ALL_MODEL_FILENAMES --target_path target --suffix _nestml --logging_level INFO --module_name nestml_allmodels_module --codegen_opts tests/nest_tests/resources/nest_codegen_opts.json

      # Integration tests
      - name: Run integration tests
        if: ${{ matrix.nest_branch == 'master' || matrix.nest_branch == 'v2.20.2' }}
        env:
          LD_LIBRARY_PATH: ${{ env.NEST_INSTALL }}/lib/nest
        run: |
          rc=0
          for fn in $GITHUB_WORKSPACE/tests/nest_tests/*.py; do
              pytest -s -o log_cli=true -o log_cli_level="DEBUG" ${fn} || rc=1
          done;
          exit $rc

      # Run only the nest integration tests for NEST versions other than master and 2.20.2
      - name: Run integration tests
        if: ${{ !(matrix.nest_branch == 'master' || matrix.nest_branch == 'v2.20.2') }}
        env:
          LD_LIBRARY_PATH: ${{ env.NEST_INSTALL }}/lib/nest
        run: |
          pytest -s -o log_cli=true -o log_cli_level="DEBUG" tests/nest_tests/nest_integration_test.py

      # Run IPython/Jupyter notebooks
      - name: Run Jupyter notebooks
        if: ${{ matrix.nest_branch == 'master' }}
        run: |
          ipynb_fns=$(find $GITHUB_WORKSPACE/doc/tutorials -name '*.ipynb')
          rc=0
          for fn in $ipynb_fns; do
              echo "Now running Jupyter notebook: ${fn}"
              cd `dirname ${fn}`
              ipython3 ${fn}
              if [ $? -ne 0 ]; then
                  echo "Error running Jupyter notebook: ${fn}"
                  rc=1
              fi
          done;
          cd $GITHUB_WORKSPACE
          exit $rc


  build_and_test_nest_compartmental:
    needs: [static_checks]
    runs-on: ubuntu-latest
    strategy:
      matrix:
        nest_branch: ["master"]
      fail-fast: false
    steps:
      # Checkout the repository contents
      - name: Checkout NESTML code
        uses: actions/checkout@v4

      # Setup Python version
      - name: Setup Python 3.8
        uses: actions/setup-python@v5
        with:
          python-version: 3.8

      # Install dependencies
      - name: Install apt dependencies
        run: |
          sudo apt-get update
          sudo apt-get install libltdl7-dev libgsl0-dev libncurses5-dev libreadline6-dev pkg-config
          sudo apt-get install python3-all-dev python3-matplotlib python3-numpy python3-scipy ipython3

      # Install Python dependencies
      - name: Python dependencies
        run: |
          python -m pip install --upgrade pip pytest jupyterlab matplotlib pycodestyle scipy pandas
          python -m pip install -r requirements.txt

      # Install NEST simulator
      - name: NEST simulator
        run: |
          python -m pip install cython
          echo "GITHUB_WORKSPACE = $GITHUB_WORKSPACE"
          NEST_SIMULATOR=$(pwd)/nest-simulator
          NEST_INSTALL=$(pwd)/nest_install
          echo "NEST_SIMULATOR = $NEST_SIMULATOR"
          echo "NEST_INSTALL = $NEST_INSTALL"

          git clone --depth=1 https://github.com/nest/nest-simulator --branch ${{ matrix.nest_branch }}
          mkdir nest_install
          echo "NEST_INSTALL=$NEST_INSTALL" >> $GITHUB_ENV
          cd nest_install
          cmake -DCMAKE_INSTALL_PREFIX=$NEST_INSTALL $NEST_SIMULATOR
          make && make install
          cd ..

      # Install NESTML (repeated)
      - name: Install NESTML
        run: |
          export PYTHONPATH=${{ env.PYTHONPATH }}:${{ env.NEST_INSTALL }}/lib/python3.8/site-packages
          #echo PYTHONPATH=`pwd` >> $GITHUB_ENV
          echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
          python setup.py install

      # Integration tests
      - name: Run integration tests
        env:
          LD_LIBRARY_PATH: ${{ env.NEST_INSTALL }}/lib/nest
        run: |
          rc=0
          for fn in $GITHUB_WORKSPACE/tests/nest_compartmental_tests/*.py; do
              pytest -s -o log_cli=true -o log_cli_level="DEBUG" ${fn} || rc=1
          done;
          exit $rc