unit_tests.yml

name: Unit tests

on:
  push:
    branches: ['**']
  pull_request:
    branches: ['**']

jobs:
  build:

    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest, macos-latest]
        python-version: [3.8]

    steps:
      - uses: actions/checkout@v4
      - name: Install ubuntu dependencies
        shell: bash -el {0}
        run: |
          if [ "${{ matrix.os }}" == "ubuntu-latest" ]; then
          sudo add-apt-repository ppa:ubuntu-toolchain-r/test
          sudo apt-get update
          sudo apt-get install build-essential wget
          sudo apt-get install libopenmpi-dev openmpi-bin
          fi;
      # - name: Install dependencies
      #   shell: bash -el {0}
      #   run: |
      #     python -m pip install --upgrade pip
      #     pip install --yes -c conda-forge mpi4py openmpi    
      # - uses: conda-incubator/setup-miniconda@v2
      #   with:
      #     activate-environment: test
      #     python-version: ${{ matrix.python-version }}
      #     fetch-depth: 2
      - name: setup python
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }} # install the python version needed
          cache: "pip"
      - name: Install dependencies
        shell: bash -el {0}
        run: |
          python -m pip install --upgrade pip
          python -m pip install openmpi mpi4py neuron
      # - name: Set environment variables
      #   run: |
      #     echo "export MPI_HOME=$CONDA_PREFIX" >> $GITHUB_ENV
      #     echo "export PATH=$MPI_HOME/bin:$PATH" >> $GITHUB_ENV
      #     echo "export LD_LIBRARY_PATH=$MPI_HOME/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
      - name: Check MPI version
        shell: bash -el {0}
        run: |
          mpiexec --version
      - name: Print mpi4py config
        shell: bash -el {0}
        run: |
          python ./hnn_core/mpi4py_test.py
      - name: Print which mpirun mpiexec
        shell: bash -el {0}
        run: |
          mpiexec --version
          which mpirun mpiexec
      - name: Install HNN-core
        shell: bash -el {0}
        run: |
          pip install --verbose '.[opt, parallel, test, gui]'
      - name: Run MPI application
        shell: bash -el {0}
        run: |
          mpiexec -np 2 python ./hnn_core/mpi_test.py
      - name: Verify NEURON installation
        shell: bash -el {0}
        run: |
          nrniv -python -nobanner -mpi -c "from neuron import h; print(h)"
      - name: Run MPI application with NEURON
        shell: bash -el {0}
        run: |
          mpiexec -np 2 -verbose nrniv -python -mpi -nobanner python ./hnn_core/mpi_test.py
      #- name: Lint with flake8
      #  shell: bash -el {0}
      #  run: |
      #    flake8 --count hnn_core
      - name: Test with pytest
        shell: bash -el {0}
        run: |
          python -m pytest ./hnn_core/tests/test_dipole.py  --cov=hnn_core --cov-report=xml -s
      # # - name:  Upload coverage to Codecov
      #   shell: bash -el {0}
      #   run: |
      #     bash <(curl -s https://codecov.io/bash) -f ./coverage.xml