PyNN/.github/workflows/full-test.yml at 23c3411dcc26ea7d966d472969fbb960078171b9 · NeuralEnsemble/PyNN · GitHub

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# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: Run all tests

on:
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]

jobs:
  test:
    name: Test on ${{ matrix.os }} with Python ${{ matrix.python-version }}
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: true
      matrix:
        python-version: ["3.10", "3.12", "3.14"]
        os: ["ubuntu-latest", "windows-latest"]
    steps:
    - uses: actions/checkout@v6
    - uses: mpi4py/setup-mpi@v1
      if: startsWith(matrix.os, 'ubuntu')
      with:
        mpi: openmpi
    - uses: mpi4py/setup-mpi@v1
      if: startsWith(matrix.os, 'windows')
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v6
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install Linux system dependencies
      if: startsWith(matrix.os, 'ubuntu')
      run: |
        sudo apt-get install libltdl-dev libgsl0-dev python3-all-dev openmpi-bin libopenmpi-dev libboost-dev
    - name: Install basic Python dependencies
      run: |
        python -m pip install --upgrade pip
        python -m pip install pytest pytest-cov coveralls flake8
    - name: Install Brian 2
      run: |
        python -m pip install brian2
    - name: Install NEURON
      if: startsWith(matrix.os, 'ubuntu')
      run: |
        python -m pip install "neuron>=9.0.0" morphio
        python -m pip install "nrnutils>0.2.0"
    - name: Install NEST
      if: startsWith(matrix.os, 'ubuntu')
      run: |
        python -m pip install "cython<3.1.0"
        wget https://github.com/nest/nest-simulator/archive/refs/tags/v3.10.tar.gz -O nest-simulator-3.10.tar.gz
        tar xzf nest-simulator-3.10.tar.gz
        cmake -DCMAKE_INSTALL_PREFIX=$HOME/.local -Dwith-mpi=ON ./nest-simulator-3.10
        make
        make install
    - name: Install Arbor
      if: startsWith(matrix.os, 'ubuntu')
      run: |
        python -m pip install arbor==0.10.0 libNeuroML morphio
    - name: Install NESTML
      if: startsWith(matrix.os, 'ubuntu')
      run: |
        python -m pip install https://github.com/nest/nestml/archive/refs/tags/v8.3.0.tar.gz
    - name: Install PyNN itself
      run: |
        python -m pip install -e ".[test,nestml]"
    - name: Test installation has worked (Ubuntu)
      # this is needed because the PyNN tests are just skipped if the simulator
      # fails to install, so we need to catch import failures separately
      if: startsWith(matrix.os, 'ubuntu')
      run: |
        python -c "import pyNN.nest"
        python -c "import pyNN.neuron"
        python -c "import pyNN.brian2"
        python -c "import pyNN.arbor"
    - name: Test installation has worked (Windows)
      if: startsWith(matrix.os, 'windows')
      run: |
        python -c "import pyNN.brian2"
    - name: Lint with flake8
      run: |
        # stop the build if there are Python syntax errors or undefined names
        flake8 pyNN --count --select=E9,F63,F7,F82 --ignore=F821,F824 --show-source --statistics
        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
        flake8 pyNN --count --exit-zero --max-complexity=20 --max-line-length=127 --statistics
    - name: Run unit and system tests
      run: |
        pytest -v -n auto --cov=pyNN --cov-report=term test
    - name: Upload coverage data
      run: |
        coveralls --service=github
      env:
        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        COVERALLS_FLAG_NAME: ${{ matrix.test-name }}
        COVERALLS_PARALLEL: true
  arbor-versions:
    # Check that the Arbor backend works across the supported version range
    name: Arbor ${{ matrix.arbor-version }} (Ubuntu, Python 3.12)
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        arbor-version: ["0.10.0", "0.12.2"]
    steps:
    - uses: actions/checkout@v6
    - name: Set up Python 3.12
      uses: actions/setup-python@v6
      with:
        python-version: "3.12"
    - name: Install Arbor ${{ matrix.arbor-version }} and dependencies
      run: |
        python -m pip install --upgrade pip
        python -m pip install pytest scipy
        python -m pip install "arbor==${{ matrix.arbor-version }}" libNeuroML morphio
    - name: Install PyNN itself
      run: |
        python -m pip install -e ".[test]"
    - name: Test that the Arbor backend imports (builds the catalogue)
      run: |
        python -c "import arbor; print('arbor', arbor.__version__)"
        python -c "import pyNN.arbor"
    - name: Run Arbor unit and scenario tests
      run: |
        pytest -v test/unittests/test_arbor.py test/system/scenarios -k arbor
  coveralls:
    name: Indicate completion to coveralls.io
    needs: test
    runs-on: ubuntu-latest
    container: python:3-slim
    steps:
    - name: Finished
      run: |
        pip3 install --upgrade coveralls
        coveralls --service=github --finish
      env:
        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}