Add slight delay in generate network when extra_lems_components present #330
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| 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"] | |
| 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 |