fix simularium file generation #371
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| name: Build and test | |
| on: [push, pull_request] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [ '3.7.15', '3.8.12', '3.9.7', '3.10.4', '3.11.0' ] | |
| # python-version: [ '3.7', '3.8', '3.9', '3.10' ] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: "Setup Python ${{ matrix.python-version }}" | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Start Xvfb | |
| run: | | |
| export DISPLAY=:99.0 | |
| Xvfb -ac :99 -screen 0 1280x1024x16 > /dev/null 2>&1 & | |
| - name: Install dependencies | |
| run: | | |
| sudo apt -y update | |
| sudo apt -y install cmake libjpeg-dev libtiff-dev freeglut3-dev libxi-dev libxmu-dev | |
| sudo apt -y install libvtk7-dev vtk7 | |
| sudo apt -y install xvfb | |
| - name: Configure smoldyn | |
| run: | | |
| cmake --version | |
| PYTHON=$(which python) | |
| $PYTHON -c "import sys; print(sys.version)" | |
| $PYTHON -m pip install pytest matplotlib numpy wheel flaky | |
| mkdir build && cd build | |
| cmake -DOPTION_PYTHON=ON \ | |
| -DOPTION_EXAMPLES=ON \ | |
| -DPython3_EXECUTABLE=$PYTHON .. | |
| - name: Build smoldyn | |
| run: | | |
| cd build && make -j2 && make wheel && sudo make install | |
| - name: Test smoldyn | |
| run: | | |
| cd build && xvfb-run --auto-servernum ctest --output-on-failure -j2 | |
| python -m pip install smoldyn*.whl | |
| python -c "import smoldyn; print(smoldyn.__file__); print(smoldyn.__version__)" | |
| # BioSimulators | |
| - name: Build BioSimulators Docker image | |
| if: matrix.python-version >= '3.9' | |
| run: | | |
| cp build/smoldyn*.whl scripts/ | |
| cd scripts | |
| docker build \ | |
| --file Dockerfile-BioSimulators \ | |
| --tag ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:latest \ | |
| . | |
| - name: Lint BioSimulators | |
| if: matrix.python-version >= '3.9' | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 | |
| flake8 source/python/smoldyn/biosimulators/ --ignore E501,W503 | |
| - name: Install BioSimulators | |
| if: matrix.python-version >= '3.9' | |
| run: | | |
| cd build | |
| WHEEL_PATH=$(ls smoldyn*.whl) | |
| python -m pip install --force-reinstall "${WHEEL_PATH}[biosimulators,biosimulators-tests]" | |
| - name: Test BioSimulators | |
| if: matrix.python-version >= '3.9' | |
| run: | | |
| python -m pip install pytest flaky | |
| xvfb-run --auto-servernum python -m pytest tests/test_biosimulators.py --verbose |