Add NEST examples #161
Workflow file for this run
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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: ["3.8", "3.10", "3.12"] | |
| os: ["ubuntu-latest", "windows-latest"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Linux system dependencies | |
| if: startsWith(matrix.os, 'ubuntu') | |
| run: | | |
| sudo apt-get install libltdl-dev libgsl0-dev python3-all-dev openmpi-bin libopenmpi-dev | |
| - name: Install basic Python dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install pytest pytest-cov coveralls flake8 | |
| - name: Install Brian 2 | |
| run: | | |
| python -m pip install brian2 | |
| - name: Install NEURON | |
| if: startsWith(matrix.os, 'ubuntu') | |
| run: | | |
| python -m pip install neuron==8.2.4 | |
| python -m pip install "nrnutils>0.2.0" | |
| - name: Install NEST | |
| if: startsWith(matrix.os, 'ubuntu') | |
| run: | | |
| python -m pip install cython | |
| wget https://github.com/nest/nest-simulator/archive/refs/tags/v3.7.tar.gz -O nest-simulator-3.7.tar.gz | |
| tar xzf nest-simulator-3.7.tar.gz | |
| cmake -DCMAKE_INSTALL_PREFIX=$HOME/.local -Dwith-mpi=ON ./nest-simulator-3.7 | |
| make | |
| make install | |
| - name: Install PyNN itself | |
| run: | | |
| pip install -e ".[test]" | |
| - name: Test installation has worked | |
| # this is needed because the PyNN tests are just skipped if the simulator | |
| # fails to install, so we need to catch import failures separately | |
| run: | | |
| python -c "import pyNN.nest" | |
| python -c "import pyNN.neuron" | |
| 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 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 pyNN --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Run unit and system tests | |
| run: | | |
| pytest -v --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 | |
| 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 }} |