Merge branch 'development' into experimental #331
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |