more printouts #155
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name: Unit tests | |
on: | |
push: | |
branches: ['**'] | |
pull_request: | |
branches: ['**'] | |
jobs: | |
build: | |
runs-on: ${{ matrix.os }} | |
strategy: | |
matrix: | |
os: [ubuntu-latest, macos-latest] | |
python-version: [3.8] | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Install ubuntu dependencies | |
shell: bash -el {0} | |
run: | | |
if [ "${{ matrix.os }}" == "ubuntu-latest" ]; then | |
sudo add-apt-repository ppa:ubuntu-toolchain-r/test | |
sudo apt-get update | |
sudo apt-get install build-essential wget | |
sudo apt-get install libopenmpi-dev openmpi-bin | |
fi; | |
- name: Install macos dependencies | |
shell: bash -el {0} | |
run: | | |
if [ "${{ matrix.os }}" == "macos-latest" ]; then | |
brew install open-mpi | |
echo "export DYLD_LIBRARY_PATH=/usr/local/lib:$DYLD_LIBRARY_PATH" >> $GITHUB_ENV | |
echo "export MPI_LIB_NRN_PATH=/usr/local/lib" >> $GITHUB_ENV | |
echo "List /opt/homebrew/lib" | |
ls /opt/homebrew/lib | |
echo "List /opt/homebrew/Cellar/open-mpi/5.0.3_1/lib" | |
ls /opt/homebrew/Cellar/open-mpi/5.0.3_1/lib | |
export MPI_LIB_NRN_PATH=/opt/homebrew/Cellar/open-mpi/5.0.3_1/lib | |
export DYLD_LIBRARY_PATH=/opt/homebrew/Cellar/open-mpi/5.0.3_1/lib:$DYLD_LIBRARY_PATH | |
echo "DYLD_LIBRARY_PATH $DYLD_LIBRARY_PATH" | |
fi; | |
- name: Print which mpirun mpiexec | |
shell: bash -el {0} | |
run: | | |
mpiexec --version | |
which mpirun mpiexec | |
if [ "${{ matrix.os }}" == "macos-latest" ]; then | |
echo $DYLD_LIBRARY_PATH | |
echo $MPI_LIB_NRN_PATH | |
fi; | |
# - name: Install dependencies | |
# shell: bash -el {0} | |
# run: | | |
# python -m pip install --upgrade pip | |
# pip install --yes -c conda-forge mpi4py openmpi | |
# - uses: conda-incubator/setup-miniconda@v2 | |
# with: | |
# activate-environment: test | |
# python-version: ${{ matrix.python-version }} | |
# fetch-depth: 2 | |
- name: setup python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} # install the python version needed | |
cache: "pip" | |
- name: Install dependencies | |
shell: bash -el {0} | |
run: | | |
python -m pip install --upgrade pip | |
python -m pip install openmpi mpi4py neuron | |
export MPI_LIB_NRN_PATH=/opt/homebrew/Cellar/open-mpi/5.0.3_1/lib | |
echo $MPI_LIB_NRN_PATH | |
- name: Install dependencies | |
shell: bash -el {0} | |
run: | | |
python -m pip install --upgrade pip | |
python -m pip install openmpi mpi4py neuron | |
# - name: Set environment variables | |
# run: | | |
# echo "export MPI_HOME=$CONDA_PREFIX" >> $GITHUB_ENV | |
# echo "export PATH=$MPI_HOME/bin:$PATH" >> $GITHUB_ENV | |
# echo "export LD_LIBRARY_PATH=$MPI_HOME/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV | |
- name: Check MPI version | |
shell: bash -el {0} | |
run: | | |
mpiexec --version | |
- name: Print mpi4py config | |
shell: bash -el {0} | |
run: | | |
python ./hnn_core/mpi4py_test.py | |
- name: Install HNN-core | |
shell: bash -el {0} | |
run: | | |
pip install --verbose '.[opt, parallel, test, gui]' | |
- name: Run MPI application | |
shell: bash -el {0} | |
run: | | |
mpiexec -np 2 python ./hnn_core/mpi_test.py | |
- name: Verify NEURON installation | |
shell: bash -el {0} | |
run: | | |
echo "MPI_LIB_NRN_PATH $MPI_LIB_NRN_PATH" | |
echo "DYLD_LIBRARY_PATH $DYLD_LIBRARY_PATH" | |
nrniv -python -nobanner -mpi -c "from neuron import h; print(h)" | |
- name: Run MPI application with NEURON | |
shell: bash -el {0} | |
run: | | |
mpiexec -np 2 -verbose nrniv -python -mpi -nobanner python ./hnn_core/mpi_test.py | |
#- name: Lint with flake8 | |
# shell: bash -el {0} | |
# run: | | |
# flake8 --count hnn_core | |
- name: Test with pytest | |
shell: bash -el {0} | |
run: | | |
python -m pytest ./hnn_core/tests/test_dipole.py --cov=hnn_core --cov-report=xml -s | |
# # - name: Upload coverage to Codecov | |
# shell: bash -el {0} | |
# run: | | |
# bash <(curl -s https://codecov.io/bash) -f ./coverage.xml |