Regenerated all NML cells & updated networks #242
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| 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: [ 3.8, 3.9, "3.10" ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install OMV | |
| run: | | |
| pip install git+https://github.com/OpenSourceBrain/osb-model-validation | |
| - name: Download some data | |
| run: | | |
| pip install allensdk==2.15.2 | |
| cd CellTypesDatabase/data | |
| python download.py -test | |
| ls -alt | |
| - name: Analyse data | |
| run: | | |
| cd CellTypesDatabase/data | |
| pip install pyelectro | |
| python extract_data.py -test | |
| - name: Generate plots of data | |
| run: | | |
| cd CellTypesDatabase/data | |
| pip install pyneuroml airspeed | |
| python data_summary.py -test | |
| - name: Download selected NEURON models | |
| run: | | |
| pip install neuron | |
| cd CellTypesDatabase/models | |
| pip install markupsafe==2.0.1 | |
| python download.py | |
| ls -alt 4* | |
| echo "Downloading GLIF models" | |
| cd GLIF | |
| python download_glif.py -test | |
| - name: Simulate selected NEURON models | |
| run: | | |
| echo "Simulating a GLIF cell" | |
| cd CellTypesDatabase/models/GLIF | |
| python run_glif.py -test | |
| - name: Extract NeuroML2 models from NEURON files | |
| run: | | |
| cd CellTypesDatabase/models | |
| nrnivmodl NEURON | |
| echo "----- Parsing perisomatic and all active.." | |
| python ParseAll.py -all_active | |
| ls -alt NeuroML2 | |
| echo "----- Parsing GLIF.." | |
| cd GLIF | |
| pip install git+https://github.com/OpenSourceBrain/OpenCortex | |
| export NEURON_HOME=$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 |