nestbuildmatrix.yml

#
# detailed syntax defined in
# https://docs.github.com/en/actions/learn-github-actions/workflow-syntax-for-github-actions
#
name: "NEST CI"

on: [push, pull_request]

jobs:
  clang-format:
    runs-on: "ubuntu-22.04"
    env:
      CLANG_REQUIRE_VERSION: 17.0.4
      CLANG_FORMAT_FILE: ".clang-format"
    steps:
      - name: Harden Runner
        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
        with:
          egress-policy: audit
          disable-telemetry: true

      - name: "Checkout repository content"
        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
        with:
          fetch-depth: 0

      - name: "Install dependencies"
        run: |
          python -m pip install --force-reinstall clang-format==${{ env.CLANG_REQUIRE_VERSION }}

      - name: "Run clang-format..."
        run: |
          files=$(find . \( -iname "*.h" -o -iname "*.c" -o -iname "*.cc" -o -iname "*.cpp" \) -not -path "./thirdparty/*")
          diff -u <(cat ${files}) <(clang-format ${files})

  cppcheck:
    runs-on: "ubuntu-22.04"
    steps:
      - name: Harden Runner
        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
        with:
          egress-policy: audit
          disable-telemetry: true

      - name: "Checkout repository content"
        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
        with:
          fetch-depth: 0

      - name: "Install Linux system dependencies"
        run: |
          sudo apt-get update
          sudo apt-get install cppcheck

      - name: "Run cppcheck..."
        run: |
          cppcheck --enable=all --language=c++ --std=c++17 -i sli/ --suppressions-list=.cppcheck_suppressions ./

  rstcheck:
    runs-on: "ubuntu-22.04"
    steps:
      - name: Harden Runner
        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
        with:
          egress-policy: audit
          disable-telemetry: true

      - name: "Checkout repository content"
        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
        with:
          fetch-depth: 0

      - name: "Set up Python 3.x"
        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
        with:
          python-version: "3.10"

      - name: "Install dependencies"
        run: |
          pip install rstcheck

      - name: "Run rstcheck..."
        run: |
          rstcheck -r doc/

  vale:
    runs-on: "ubuntu-22.04"
    steps:
      - name: Harden Runner
        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
        with:
          egress-policy: audit
          disable-telemetry: true

      - name: "Checkout repository content"
        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
        with:
          fetch-depth: 0

      - name: "Set up Python 3.x"
        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
        with:
          python-version: "3.10"

      - name: "Install dependencies"
        run: |
          sudo apt update
          sudo apt install python3-docutils
          wget --progress=dot:mega 'https://github.com/errata-ai/vale/releases/download/v2.26.0/vale_2.26.0_Linux_64-bit.tar.gz'
          echo '956577b214ce3db8fb11483f99a183cf65673e3bd47423c6d4ebe37f085cadc7 vale_2.26.0_Linux_64-bit.tar.gz' | sha256sum -c
          tar -xzf 'vale_2.26.0_Linux_64-bit.tar.gz'

      - name: "Run vale..."
        run: |
          ./vale -v
          ./vale doc

  copyright_headers:
    runs-on: "ubuntu-22.04"
    steps:
      - name: Harden Runner
        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
        with:
          egress-policy: audit
          disable-telemetry: true

      - name: "Checkout repository content"
        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
        with:
          fetch-depth: 0

      - name: "Set up Python 3.x"
        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
        with:
          python-version: "3.10"

      - name: "Install dependencies"
        run: |
          pip install pydocstyle

      - name: "Check copyright headers..."
        run: |
          python build_support/check_copyright_headers.py

  unused_names:
    runs-on: "ubuntu-22.04"
    steps:
      - name: Harden Runner
        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
        with:
          egress-policy: audit
          disable-telemetry: true

      - name: "Checkout repository content"
        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
        with:
          fetch-depth: 0

      - name: "Set up Python 3.x"
        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
        with:
          python-version: "3.10"

      - name: "Check for unused nest::names..."
        run: |
          python build_support/check_unused_names.py

  forbidden_types:
    runs-on: "ubuntu-22.04"
    steps:
      - name: Harden Runner
        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
        with:
          egress-policy: audit
          disable-telemetry: true

      - name: "Checkout repository content"
        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
        with:
          fetch-depth: 0

      - name: "Check for forbidden types..."
        run: |
          ./build_support/check_forbidden_types.sh

  lychee_IGNORED:
    runs-on: "ubuntu-22.04"
    steps:
      - name: Harden Runner
        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
        with:
          egress-policy: audit
          disable-telemetry: true

      - name: "Checkout repository content"
        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
        with:
          fetch-depth: 0

      - name: "Install dependencies"
        run: |
          wget --progress=dot:mega 'https://github.com/lycheeverse/lychee/releases/download/v0.8.2/lychee-v0.8.2-x86_64-unknown-linux-gnu.tar.gz'
          echo '12c27c9b6d551aea9178080d27de75ed26125b130722153399259432f723e606  lychee-v0.8.2-x86_64-unknown-linux-gnu.tar.gz' | sha256sum -c
          tar -xzf 'lychee-v0.8.2-x86_64-unknown-linux-gnu.tar.gz'

      - name: "Run lychee..."
        continue-on-error: true
        run: "pwd; ls -l; ./lychee build_support/ doc/{*.txt,*.md,htmldoc} examples/ lib* models/ nest* pynest/ testsuite/ *.md"
        # TODO: doc/auto_examples and doc/models need to be added here, but exists only after a `make html`
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

  pydocstyle:
    runs-on: "ubuntu-22.04"
    steps:
      - name: Harden Runner
        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
        with:
          egress-policy: audit
          disable-telemetry: true

      - name: "Checkout repository content"
        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
        with:
          fetch-depth: 0

      - name: "Set up Python 3.x"
        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
        with:
          python-version: "3.10"

      - name: "Install dependencies"
        run: |
          pip install pydocstyle

      - name: "Run pydocstyle..."
        run: |
          pydocstyle pynest/

  mypy:
    runs-on: "ubuntu-22.04"
    steps:
      - name: Harden Runner
        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
        with:
          egress-policy: audit
          disable-telemetry: true

      - name: "Checkout repository content"
        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
        with:
          fetch-depth: 0

      - name: "Set up Python 3.x"
        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
        with:
          python-version: "3.10"

      - name: "Install dependencies"
        run: |
          pip install mypy matplotlib numpy scipy data-science-types

      - name: "Run mypy..."
        run: |
          mypy pynest/

  # pytest-linux:
  #   runs-on: "ubuntu-22.04"
  #   needs: [build_linux]
  #   env:
  #     NEST_VPATH: "build"
  #     NEST_RESULT: "result"

  #   strategy:
  #     fail-fast: true
  #     matrix:
  #       os: ["ubuntu-22.04"]
  #       cpp_compiler: ["gcc"]

  #       # available use flags (all default to "OFF"):
  #       use:
  #         - "boost, optimize, warning"  # formerly "minimal"
  #       #  - "openmp, python, gsl, ltdl, boost, optimize, warning"  # formerly "openmp_only"
  #       #  - "mpi, python, gsl, ltdl, boost, optimize, warning"  # formerly "mpi_only"
  #       #  - "openmp, mpi, python, gsl, ltdl, boost, sionlib, libneurosim, optimize, warning"  # formerly "full"

  #   steps:
  #     - name: "Download binary artifacts"
  #       uses: actions/download-artifact@v3
  #       with:
  #         name: "build-${{ matrix.os }}-${{ matrix.cpp_compiler }}-${{ matrix.use }}"

  #     - name: "Set up Python 3.x"
  #       uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
  #       with:
  #         python-version: "3.10"

  #     - name: "Install dependencies"
  #       run: |
  #         pip install pytest pytest-cov pytest-doctestplus

  #     - name: "Run pytest..."
  #       run: |
  #         pwd
  #         ls -lisa
  #         cd "$NEST_VPATH"
  #         pwd
  #         ls -lisa
  #         pytest testsuite/pytests/

  # pytest-mac:
  #   runs-on: "macos-latest"
  #   needs: [build_macos]
  #   steps:
  #     - name: "Checkout repository content"
  #       uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
  #       with:
  #         fetch-depth: 0

  #     - name: "Set up Python 3.x"
  #       uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
  #       with:
  #         python-version: "3.10"

  #     - name: "Install dependencies"
  #       run: |
  #         pip install pytest pytest-cov pytest-doctestplus

  #     - name: "Run pytest..."
  #       run: |
  #         pytest pynest/

  pylint:
    runs-on: "ubuntu-22.04"
    steps:
      - name: Harden Runner
        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
        with:
          egress-policy: audit
          disable-telemetry: true

      - name: "Checkout repository content"
        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
        with:
          fetch-depth: 0

      - name: "Set up Python 3.x"
        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
        with:
          python-version: "3.10"

      - name: "Install dependencies"
        run: |
          pip install pylint

      - name: "Run pylint..."
        run: |
          pylint --jobs=$(nproc) pynest/ testsuite/pytests/*.py testsuite/regressiontests/*.py

  isort:
    runs-on: "ubuntu-20.04"
    steps:
      - name: "Checkout repository content"
        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
        with:
          fetch-depth: 0

      - name: "Run isort..."
        uses: isort/isort-action@f14e57e1d457956c45a19c05a89cccdf087846e5  # 1.1.0
        with:
          configuration: --profile=black --thirdparty="nest" --check-only --diff

  black:
    runs-on: "ubuntu-22.04"
    steps:
      - name: Harden Runner
        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
        with:
          egress-policy: audit
          disable-telemetry: true

      - name: "Checkout repository content"
        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
        with:
          fetch-depth: 0

      - name: "Run black..."
        uses: psf/black@d9ad09a32b0e0481bb4fef548d35b7a49cc03c5d  # 23.12.0
        with:
          jupyter: true

  flake8:
    runs-on: "ubuntu-22.04"
    steps:
      - name: Harden Runner
        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
        with:
          egress-policy: audit
          disable-telemetry: true

      - name: "Checkout repository content"
        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
        with:
          fetch-depth: 0

      - name: "Set up Python 3.x"
        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
        with:
          python-version: "3.10"

      - name: "Install dependencies"
        run: |
          pip install flake8

      - name: "Run flake8..."
        run: |
          flake8 .

  sphinx-rtd:
    # as close as possible to the Readthedocs setup (system install cmake, pip install -r doc/requirements.txt)
    runs-on: "ubuntu-22.04"
    needs: [pydocstyle, rstcheck, vale]
    steps:
      - name: Harden Runner
        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
        with:
          egress-policy: audit
          disable-telemetry: true

      - name: "Checkout repository content"
        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
        with:
          fetch-depth: 0

      - name: "Set up Python 3.x"
        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
        with:
          # Using 3.8 because Read the docs does not work with higher versions.
          # See also: https://github.com/nest/nest-simulator/pull/2744
          python-version: "3.10"

      - name: "Install dependencies"
        run: |
          sudo apt update
          pip install -r doc/requirements.txt
          # The pandoc executable, which is required, cannot be installed via pip see: https://stackoverflow.com/a/71585691
          sudo apt install pandoc

      - name: "Test-build documentation"
        run: |
          mkdir -pv build
          cd build
          cmake -Dwith-userdoc=ON -DCMAKE_INSTALL_PREFIX=../install ..
          make docs |& tee sphinx-output.log

      - name: Upload artifacts
        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
        with:
          name: "sphinx-rtd output"
          path: |
            build/sphinx-output.log
            build/doc/_build/html/

  sphinx-conda:
    # as close as possible to the suggested user docs build in the documentation
    runs-on: "ubuntu-22.04"
    if: false
    needs: [pydocstyle, rstcheck, vale]
    steps:
      - name: Harden Runner
        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
        with:
          egress-policy: audit
          disable-telemetry: true

      - name: "Checkout repository content"
        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
        with:
          fetch-depth: 0

      - name: Install Conda
        uses: conda-incubator/setup-miniconda@030178870c779d9e5e1b4e563269f3aa69b04081   # v3.0.3
        with:
          auto-update-conda: true
          python-version: "3.10"

      - name: Install conda dependencies
        shell: bash -l {0}
        run: |
          conda info
          conda env create -p conda

      - name: "Test-build documentation"
        shell: bash -l {0}
        run: |
          conda activate conda/
          mkdir -pv build
          cd build
          cmake -DCMAKE_INSTALL_PREFIX=../install ..
          make html |& tee sphinx-output.log

      - name: Upload artifacts
        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
        with:
          path: |
            build/sphinx-output.log
            build/doc/_build/html/

  build_linux:
    if: ${{ !contains(github.event.head_commit.message, 'ci skip') }}
    runs-on: ${{ matrix.os }}
    needs: [clang-format, mypy, copyright_headers, unused_names, forbidden_types, pylint, isort, black, flake8]
    env:
      CXX_FLAGS: "-pedantic -Wextra -Woverloaded-virtual -Wno-unknown-pragmas"
      NEST_VPATH: "build"
      NEST_RESULT: "result"

    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-22.04"]
        cpp_compiler: ["gcc"]

        # available use flags (all default to "OFF"):
        # openmp, mpi, python, gsl, ltdl, boost, sionlib, libneurosim, optimize, warning, userdoc, music, readline
        use:
          - "optimize, warning"
          - "boost, optimize, warning"
          - "openmp, python, gsl, ltdl, boost, optimize, warning"
          - "mpi, python, gsl, ltdl, boost, optimize, warning"
          - "openmp, mpi, python, gsl, ltdl, boost, hdf5, sionlib, libneurosim, optimize, warning, music"

    steps:
      - name: Harden Runner
        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
        with:
          egress-policy: audit
          disable-telemetry: true

      - name: "Checkout repository content"
        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
        with:
          fetch-depth: 0

      - name: "Set up Python 3.x"
        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
        with:
          python-version: "3.10"

      - name: "Restore apt cache"
        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
        env:
          cache-name: "apt-cache"
        with:
          path: |
            !/var/cache/apt/archives/lock
            !/var/cache/apt/archives/partial
            /var/cache/apt
          key: ${{ runner.os }}-system-${{ env.cache-name }}-${{ hashFiles('**/environment.yml') }}
          restore-keys: |
            ${{ runner.os }}-system-${{ env.cache-name }}-
            ${{ runner.os }}-system-

      - name: "Install Linux system dependencies"
        run: |
          # https://github.com/actions/virtual-environments/blob/main/images/linux/Ubuntu2004-README.md
          sudo apt-get update
          sudo apt-get install \
                           ccache \
                           python3-all-dev \
                           jq \
                           libpcre3 libpcre3-dev \
                           pkg-config
          # not sure why these would be required:
          #   sudo apt-get install tcl8.6 tcl8.6-dev tk8.6-dev
          sudo ldconfig

      - name: "Install Readline dependencies"
        if: "${{ contains(matrix.use, 'readline') }}"
        run: "sudo apt-get install libreadline6-dev libncurses5-dev"

      - name: "Install LTDL dependencies"
        if: "${{ contains(matrix.use, 'ltdl') }}"
        run: "sudo apt-get install libltdl-dev"

      - name: "Uninstall Boost development libraries"
        if: "${{ ! contains(matrix.use, 'boost') }}"
        run: |
          apt list --installed 'libboost*'
          sudo apt-get remove --autoremove 'libboost*-dev'

      - name: "Install Boost dependencies"
        if: "${{ contains(matrix.use, 'boost') }}"
        run: "sudo apt-get install libboost-filesystem-dev libboost-regex-dev libboost-wave-dev libboost-python-dev libboost-program-options-dev libboost-test-dev"

      - name: "Install OpenMPI development dependencies"
        if: "${{ contains(matrix.use, 'mpi') }}"
        run: "sudo apt-get install openmpi-bin libopenmpi-dev"

      - name: "Install GSL system dependencies"
        if: "${{ contains(matrix.use, 'gsl') }}"
        run: "sudo apt-get install libgsl0-dev"

      - name: "Install HDF5 system dependencies"
        if: "${{ contains(matrix.use, 'hdf5') }}"
        run: "sudo apt-get install libhdf5-dev"

      - name: "Restore ccache"
        # Using CCache to re-use compiled objects from prior runs that have the same
        # source (hashed), compiler (mtime+size) and compile flags.
        env:
          cache-name: "ccache"
        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
        with:
          path: |
            $HOME/.ccache
            .ccache
            /home/runner/.ccache
          key: ${{ runner.os }}-${{ env.cache-name }}-${{ matrix.cpp_compiler }}-${{ matrix.NEST_BUILD_TYPE }}
          restore-keys: |
            ${{ runner.os }}-${{ env.cache-name }}-${{ matrix.cpp_compiler }}-${{ matrix.NEST_BUILD_TYPE }}
            ${{ runner.os }}-${{ env.cache-name }}-${{ matrix.cpp_compiler }}
            ${{ runner.os }}-${{ env.cache-name }}
            ${{ runner.os }}

      - name: "Restore pip cache"
        env:
          cache-name: "pip-cache"
        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
        with:
          path: |
            /opt/hostedtoolcache/Python/**/site-packages/*
            $HOME/.cache/pip
          key: ${{ runner.os }}-python-${{ env.cache-name }}-${{ hashFiles('**/requirements.txt') }}
          restore-keys: |
            ${{ runner.os }}-python-${{ env.cache-name }}-
            ${{ runner.os }}-python-

      - name: "Install Python dependencies"
        run: |
          python -m pip install --upgrade pip setuptools
          python -m pip install --force-reinstall --upgrade cython  # this finds a broken preinstall if not explicitly forced
          python -c "import setuptools; print('package location:', setuptools.__file__)"
          pip list

      - name: "Install Python test dependencies" 
        # These could go to a separate venv…
        run: |
          python -m pip install 'junitparser>=2' pytest pytest-timeout pytest-xdist terminaltables 
          python -m pip install numpy scipy pandas matplotlib
          test \! -e "=2"   # assert junitparser is correctly quoted and '>' is not interpreted as shell redirect
          python -c "import pytest; print('package location:', pytest.__file__)"

      - name: "Install Python doc dependencies"
        run: "python -m pip install pandoc"
        
      - name: "Install Python mpi dependencies" 
        if: "${{ contains(matrix.use, 'mpi') }}"
        run: "python -m pip install --force-reinstall --upgrade mpi4py"

      - name: "Install h5py"
        if: "${{ contains(matrix.use, 'hdf5') }}"
        run: |
          python -m pip install --force-reinstall --upgrade --no-binary=h5py h5py

      - name: "Install MUSIC"
        if: "${{ contains(matrix.use, 'music') }}"
        run: |
          chmod +x build_support/install_music.sh
          ./build_support/install_music.sh

      - name: "Install SIONlib"
        if: "${{ contains(matrix.use, 'sionlib') }}"
        run: |
          chmod +x build_support/install_sionlib.sh
          ./build_support/install_sionlib.sh

      - name: "Install LibNeurosim – WARNING WARNING NO PROPER PYTHON INSTALL!"
        if: "${{ contains(matrix.use, 'libneurosim') }}"
        run: |
          chmod +x build_support/install_csa-libneurosim.sh
          PYLIB_DIR="$(python3 -c "import sysconfig; print(sysconfig.get_path('include'))" | sed 's/include/lib/')"
          ./build_support/install_csa-libneurosim.sh $PYLIB_DIR

      - name: "List available packages"
        run: |
          gcc --version
          python --version
          apt list
          pip list

      - name: "Configure NEST build"
        env:
          CMAKE_C_COMPILER_LAUNCHER: ccache
          CMAKE_CXX_COMPILER_LAUNCHER: ccache
        run: |
          mkdir -p "$NEST_VPATH/reports" "$NEST_RESULT"

          if [ "$xNEST_BUILD_COMPILER" = "CLANG" ]; then
              export CC=clang-11
              export CXX=clang++-11
          fi
          export CXX_FLAGS="-pedantic -Wextra -Wno-unknown-pragmas -D_GLIBCXX_ASSERTIONS"

          cd "$NEST_VPATH"
          cmake \
              -DCMAKE_INSTALL_PREFIX="$NEST_RESULT" \
              -DCMAKE_CXX_FLAGS="$CXX_FLAGS" \
              -Dwith-optimize=${{ contains(matrix.use, 'optimize') && 'ON' || 'OFF' }} \
              -Dwith-warning=${{ contains(matrix.use, 'warning') && 'ON' || 'OFF' }} \
              -Dwith-boost=${{ contains(matrix.use, 'boost') && 'ON' || 'OFF' }} \
              -Dwith-openmp=${{ contains(matrix.use, 'openmp') && 'ON' || 'OFF' }} \
              -Dwith-mpi=${{ contains(matrix.use, 'mpi') && 'ON' || 'OFF' }} \
              -Dwith-python=${{ contains(matrix.use, 'python') && 'ON' || 'OFF' }} \
              -Dwith-gsl=${{ contains(matrix.use, 'gsl') && 'ON' || 'OFF' }} \
              -Dwith-ltdl=${{ contains(matrix.use, 'ltdl') && 'ON' || 'OFF' }} \
              -Dwith-readline=${{ contains(matrix.use, 'readline') && 'ON' || 'OFF' }} \
              -Dwith-hdf5=${{ contains(matrix.use, 'hdf5') && 'ON' || 'OFF' }} \
              -Dwith-sionlib=${{ contains(matrix.use, 'sionlib') && '$HOME/.cache/sionlib.install' || 'OFF' }} \
              -Dwith-libneurosim=${{ contains(matrix.use, 'libneurosim') && '$HOME/.cache/libneurosim.install' || 'OFF' }} \
              -Dwith-music=${{ contains(matrix.use, 'music') && '$HOME/.cache/music.install' || 'OFF' }} \
              ..

      - name: "Add GCC problem matcher"
        run: |
          echo "::add-matcher::gcc_problem_matcher.json"

      - name: "Build NEST"
        run: |
          cd "$NEST_VPATH"
          env
          make VERBOSE=1

      - name: "Remove GCC problem matcher"
        run: |
          echo "::remove-matcher owner=gcc-problem-matcher::"

      - name: "Install NEST"
        run: |
          cd "$NEST_VPATH"
          make install

      - name: "Initialize Matplotlibrc"
        run: |
          # initialize matplotlib backend
          mkdir -p $HOME/.matplotlib
          echo "backend : svg" > $HOME/.matplotlib/matplotlibrc

      - name: "Run NEST testsuite"
        env:
          DO_TESTS_SKIP_TEST_REQUIRING_MANY_CORES: ${{ contains(matrix.use, 'mpi') && contains(matrix.use, 'openmp') }}
        run: |
          pwd
          cd "$NEST_VPATH"
          chmod -v u+x ${NEST_RESULT}/share/nest/testsuite/do_tests.sh
          make VERBOSE=1 installcheck

      - name: "Upload install and test results"
        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
        if: always()
        with:
          name: "build-logs-${{ matrix.os }}-${{ matrix.cpp_compiler }}-${{ matrix.use }}"
          path: |
            build/install_manifest.txt
            build/test_report_*/

  build_macos:
    if: ${{ !contains(github.event.head_commit.message, 'ci skip') }}
    runs-on: ${{ matrix.os }}
    needs: [clang-format, mypy, copyright_headers, unused_names, forbidden_types, pylint, isort, black, flake8]
    env:
      CXX_FLAGS: "-pedantic -Wextra -Woverloaded-virtual -Wno-unknown-pragmas"
      NEST_VPATH: "build"
      NEST_RESULT: "result"

    strategy:
      fail-fast: false
      matrix:
        os: [macos-latest]
        cpp_compiler: ["clang"]

        # available use flags (all default to "OFF"):
        # openmp, mpi, python, gsl, ltdl, boost, hdf5, sionlib, libneurosim, optimize, warning, userdoc, music
        use:
          - "openmp, mpi, python, gsl, ltdl, boost, hdf5, optimize, warning"

    steps:
      - name: Harden Runner
        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
        with:
          egress-policy: audit
          disable-telemetry: true

      - name: "Checkout repository content"
        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
        with:
          fetch-depth: 0

      - name: "Set up Python 3.x"
        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
        with:
          python-version: 3.12

      - name: "Install MacOS system dependencies"
        run: |
          brew install coreutils gsl open-mpi libomp automake autoconf libtool boost hdf5

      - name: "Restore pip cache"
        env:
          cache-name: "pip-cache"
        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
        with:
          path: |
            /opt/hostedtoolcache/Python/**/site-packages/*
            $HOME/.cache/pip
          key: ${{ runner.os }}-python-${{ env.cache-name }}-${{ hashFiles('**/requirements.txt') }}
          restore-keys: |
            ${{ runner.os }}-python-${{ env.cache-name }}-
            ${{ runner.os }}-python-

      - name: "Install Python dependencies"
        run: |
          python -m pip install --upgrade pip setuptools
          python -c "import setuptools; print('package location:', setuptools.__file__)"
          python -m pip install --force-reinstall --upgrade scipy 'junitparser>=2' numpy pytest pytest-timeout pytest-xdist mpi4py h5py cython matplotlib terminaltables pandoc pandas
          test \! -e "=2"   # assert junitparser is correctly quoted and '>' is not interpreted as shell redirect
          python -c "import pytest; print('package location:', pytest.__file__)"
          pip list

      - name: "Configure NEST build"
        run: |
          mkdir -p "$NEST_VPATH/reports" "$NEST_RESULT"

          cd "$NEST_VPATH"
          cmake \
              -DCMAKE_INSTALL_PREFIX="$NEST_RESULT" \
              -DCMAKE_CXX_FLAGS="$CXX_FLAGS" \
              -Dwith-optimize=${{ contains(matrix.use, 'optimize') && 'ON' || 'OFF' }} \
              -Dwith-warning=${{ contains(matrix.use, 'warning') && 'ON' || 'OFF' }} \
              -Dwith-boost=${{ contains(matrix.use, 'boost') && 'ON' || 'OFF' }} \
              -Dwith-openmp=${{ contains(matrix.use, 'openmp') && 'ON' || 'OFF' }} \
              ${{ contains(matrix.use, 'openmp') && '-DOpenMP_ROOT=$(brew --prefix libomp)' }} \
              -Dwith-mpi=${{ contains(matrix.use, 'mpi') && 'ON' || 'OFF' }} \
              -Dwith-python=${{ contains(matrix.use, 'python') && 'ON' || 'OFF' }} \
              -Dwith-gsl=${{ contains(matrix.use, 'gsl') && 'ON' || 'OFF' }} \
              -Dwith-ltdl=${{ contains(matrix.use, 'ltdl') && 'ON' || 'OFF' }} \
              -Dwith-readline=${{ contains(matrix.use, 'readline') && 'ON' || 'OFF' }} \
              -Dwith-hdf5=${{ contains(matrix.use, 'hdf5') && 'ON' || 'OFF' }} \
              -Dwith-sionlib=${{ contains(matrix.use, 'sionlib') && '$HOME/.cache/sionlib.install' || 'OFF' }} \
              -Dwith-libneurosim=${{ contains(matrix.use, 'libneurosim') && '$HOME/.cache/libneurosim.install' || 'OFF' }} \
              -Dwith-music=${{ contains(matrix.use, 'music') && '$HOME/.cache/music.install' || 'OFF' }} \
              ..

      - name: "Add GCC problem matcher"
        run: |
          echo "::add-matcher::gcc_problem_matcher.json"

      - name: "Build NEST"
        run: |
          cd "$NEST_VPATH"
          env
          make VERBOSE=1

      - name: "Remove GCC problem matcher"
        run: |
          echo "::remove-matcher owner=gcc-problem-matcher::"

      - name: "Install NEST"
        run: |
          cd "$NEST_VPATH"
          make install

      - name: "Initialize Matplotlibrc"
        run: |
          # initialize matplotlib backend
          mkdir -p $HOME/.matplotlib
          echo "backend : svg" > $HOME/.matplotlib/matplotlibrc

      - name: "Run NEST testsuite"
        run: |
          pwd
          cd "$NEST_VPATH"
          chmod -v u+x ${NEST_RESULT}/share/nest/testsuite/do_tests.sh
          make VERBOSE=1 installcheck

      - name: "Upload install and test results"
        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
        if: ${{ always() }}
        with:
          name: "${{ matrix.NEST_BUILD_TYPE }}-build-logs-${{ matrix.os }}-${{ matrix.cpp_compiler }}"
          path: |
            build/install_manifest.txt
            build/test_report_*/