non-omv.yml

name: Testing non OMV based scripts

on:
  push:
    branches: [ master, development, experimental, pg*, add* ]
  pull_request:
    branches: [ master, development, experimental, pg*, add* ]

jobs:
  build:

    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: [ 3.7, 3.8, 3.9 ]

    steps:
    - uses: actions/checkout@v3

    - name: Set up Python  ${{ matrix.python-version }}
      uses: actions/setup-python@v3
      with:
        python-version:  ${{ matrix.python-version }}

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

    - name: Download some data
      run: |
         pip install allensdk==2.15.1

         cd CellTypesDatabase/data
         python download.py -test
         ls -alt

    - name: Analyse data
      run: |
         cd CellTypesDatabase/data
         pip install pyelectro

         python extract_data.py -test

    - name: Generate plots of data
      run: |

         cd CellTypesDatabase/data

         pip install pyneuroml airspeed
         python data_summary.py -test

    - name: Download selected NEURON models
      run: |
         pip install neuron
         cd CellTypesDatabase/models
         pip install markupsafe==2.0.1
         python download.py
         ls -alt 4*

         echo "Downloading GLIF models"
         cd GLIF
         python download_glif.py -test

    - name: Simulate selected NEURON models
      run: |
          echo "Simulating a GLIF cell"
          cd CellTypesDatabase/models/GLIF
          python run_glif.py -test


    - name: Extract NeuroML2 models from NEURON files
      run: |
         cd CellTypesDatabase/models
         nrnivmodl  NEURON

         echo "-----   Parsing perisomatic and all active.."
         python ParseAll.py -all_active
         ls -alt NeuroML2

         echo "-----   Parsing GLIF.."
         cd GLIF
         pip install git+https://github.com/OpenSourceBrain/OpenCortex
         export NEURON_HOME=$pythonLocation
         python parse_glif.py -test

    - name: Tune data
      run: |
         cd CellTypesDatabase/tune
         git clone https://github.com/NeuralEnsemble/neurotune.git
         cd neurotune/
         pip install .
         cd ..
         rm -rf neurotune
         export NEURON_HOME=$pythonLocation
         python tuneAllen.py -izhone

    - name: Final version info
      run: |
        pip list
        env