ci.yml

name: Continuous builds

on:
  push:
    branches: [ master, development, experimental, modelspec ]
  pull_request:
    branches: [ master, development, experimental, modelspec ]

jobs:
  build:

    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
    env:
      JNML_HOME: "/home/runner/work/NeuroMLlite/NeuroMLlite/jNeuroML"
      HDF5_DISABLE_VERSION_CHECK: 1

    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 some dependencies
      run: |
        python -m pip install --upgrade pip
        pip install flake8

    - name: Install NeuroMLlite and extra requirements
      run: |
          pip install .
          pip install -r requirements-extra.txt
                  
          pip install 'numpy<=1.23.0' # temp fix, see https://github.com/OpenSourceBrain/osb-model-validation/issues/91


    - name: Lint with flake8
      run: |
        flake8 . --count --exit-zero --show-source --max-line-length=127 --statistics

    - name: Install correct branch of pyneuroml etc.
      run: |
        env

        # Check to see if on development/experimental branches
        export jnml_branches="development"
        export pynml_branch="development"
        echo "JNML_HOME: $JNML_HOME"
        echo "Will use jNeuroML from branches $jnml_branches"
        echo "Will use pyNeuroML from branch $pynml_branch"

        # Install pyNeuroML
        git clone https://github.com/NeuroML/pyNeuroML.git
        cd pyNeuroML
        git checkout $pynml_branch
        pip install pandas==1.3.5
        pip install NEURON==8.2.2 # Specify version of neuron - 8.2.1 fails
        #pip install -r requirements-dev.txt
        pip install .
        cd -

        # Install latest jnml...
        git clone https://github.com/NeuroML/jNeuroML.git
        cd jNeuroML
        git checkout $jnml_branches
        python getNeuroML.py $jnml_branches  # will call mvn install on this & other repos
        echo "Installed!"
        ls -alth

        export PATH=$PATH:$JNML_HOME
        ./jnml -v
        which jnml
        env
        cd ..

    - name: List packages so far
      run: |
        pip list

    - name: Install OMV
      run: |
        # Install OMV
        pip install git+https://github.com/OpenSourceBrain/osb-model-validation

        export PATH=$PATH:$JNML_HOME

        omv list -V  # list all currently known...
        env

    - name: Install some simulators for testing
      run: |
        #pip install cython
        omv install NEURON
        pip install NetPyNE  # strange issues on py3.7 with omv install...
        omv install PyNN
        omv install jNeuroML
        omv install Brian2
        omv install arbor
        omv install eden
        
        #### HDF5_DISABLE_VERSION_CHECK set globally...
        #pip uninstall h5py -y
        #sudo apt install -y python3-h5py # issue when building nest
        #export HDF5_DISABLE_VERSION_CHECK=1
        if [[ ${{ matrix.python-version }} != 2.7 ]]; then omv install PyNEST; fi
        #pip install h5py
        omv list -V # list installed engines

    - name: Run pytest
      run: |
        pip install pytest tables # tables for Sonata test file
        cd neuromllite/test/
        pytest -v

    - name: Regenerate and test
      run: |

        export PATH=$PATH:$JNML_HOME
        export NEURON_HOME=$pythonLocation
        env
        echo "===================="
        # All tests
        ./regenerateAndTest.sh

    - name: Run OMV tests
      run: |
        omv all -V --engine=jNeuroML # limited for now, issues with nest...
        omv all -V --engine=jNeuroML_NEURON # limited for now, issues with nest...

    - name: OMV final version info
      run: |
        omv list -V # list installed engines