adding echos to env variables #153
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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: ${{ matrix.python-version }} # install the python version needed | |
| cache: "pip" | |
| - name: Install dependencies | |
| shell: bash -el {0} | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install openmpi mpi4py neuron | |
| # - name: Set environment variables | |
| # run: | | |
| # echo "export MPI_HOME=$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 | |
| echo $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 |