Refactor and small updates to OpenMM and OpenFF task documents #3726
Workflow file for this run
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| name: testing | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| test: | |
| name: ${{ matrix.package }} (${{ matrix.os }}/py${{ matrix.python-version }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: ["ubuntu-latest"] # TODO openbabel for windows and mac | |
| package: ["emmet-core", "emmet-builders", "emmet-api"] | |
| python-version: ["3.10", "3.11"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| channels: anaconda, conda-forge | |
| - name: Install all conda requirements | |
| shell: bash -l {0} | |
| run: | | |
| conda install openbabel openff-toolkit>=0.14.0 openff-interchange>=0.3.22 sqlite -y | |
| # - uses: actions/setup-python@v5 | |
| # with: | |
| # python-version: ${{ matrix.python-version }} | |
| # cache: 'pip' | |
| # - name: Install OpenBabel on Ubuntu | |
| # if: matrix.os == 'ubuntu-latest' | |
| # env: | |
| # cc_compiler: "gcc" | |
| # cxx_compiler: "g++" | |
| # cmake_flags: "-DPYTHON_BINDINGS=ON -DRUN_SWIG=ON" | |
| # shell: bash -l {0} | |
| # run: | | |
| # sudo apt-get update && sudo apt-get -qq install ninja-build swig libeigen3-dev libboost-all-dev libopenbabel-dev | |
| # git clone https://github.com/openbabel/openbabel.git ${{ runner.workspace }}/openbabel | |
| # mkdir "${{ runner.workspace }}/openbabel/build" | |
| # cd "${{ runner.workspace }}/openbabel/build" | |
| # cmake -DCMAKE_C_COMPILER=$cc_compiler -DCMAKE_CXX_COMPILER=$cxx_compiler $cmake_flags .. | |
| # sudo make | |
| # sudo make install | |
| # echo "PYTHONPATH=/usr/local/lib:/usr/local/include/openbabel3:$PYTHONPATH" >> $GITHUB_PATH | |
| # sudo ln -s /usr/include/openbabel3 /usr/local/include/openbabel3 | |
| # echo "LD_LIBRARY_PATH=/usr/local/lib:/usr/include/openbabel3:$LD_LIBRARY_PATH" >> $GITHUB_PATH | |
| # - name: Install OpenBabel on MacOS | |
| # if: matrix.os == 'macos-latest' | |
| # env: | |
| # cc_compiler: "clang" | |
| # cxx_compiler: "clang++" | |
| # shell: bash -l {0} | |
| # run: | | |
| # brew install ninja swig eigen boost | |
| # echo "/Users/runner/Library/Python/${{ matrix.python-version }}/bin" >> $GITHUB_PATH | |
| # git clone https://github.com/openbabel/openbabel.git ${{ runner.workspace }}/openbabel | |
| # mkdir "${{ runner.workspace }}/openbabel/build" | |
| # cd "${{ runner.workspace }}/openbabel/build" | |
| # cmake -DCMAKE_C_COMPILER=$cc_compiler -DCMAKE_CXX_COMPILER=$cxx_compiler $cmake_flags .. | |
| # sudo make | |
| # sudo make install | |
| # echo "PYTHONPATH=/usr/local/lib:/usr/local/include/openbabel3:$PYTHONPATH" >> $GITHUB_PATH | |
| # sudo ln -s /usr/include/openbabel3 /usr/local/include/openbabel3 | |
| # echo "LD_LIBRARY_PATH=/usr/local/lib:/usr/include/openbabel3:$LD_LIBRARY_PATH" >> $GITHUB_PATH | |
| - name: Install Python dependencies | |
| shell: bash -l {0} | |
| run: | | |
| python${{ matrix.python-version }} -m pip install --upgrade pip pip-tools | |
| python${{ matrix.python-version }} -m pip install --user `grep numpy ${{ matrix.package }}/requirements/${{ matrix.os }}_py${{ matrix.python-version }}_extras.txt` | |
| python${{ matrix.python-version }} -m pip install --user -r ${{ matrix.package }}/requirements/${{ matrix.os }}_py${{ matrix.python-version }}_extras.txt | |
| - name: Install editable emmet-core if needed | |
| shell: bash -l {0} | |
| if: matrix.package != 'emmet-core' | |
| run: python${{ matrix.python-version }} -m pip install --user --no-deps ./emmet-core | |
| - name: Install ${{ matrix.package }} | |
| shell: bash -l {0} | |
| run: python${{ matrix.python-version }} -m pip install --user --no-deps -e ./${{ matrix.package }} | |
| - name: Lint with mypy | |
| shell: bash -l {0} | |
| run: python${{ matrix.python-version }} -m mypy --namespace-package ${{ matrix.package }}/emmet | |
| - name: Test with pytest | |
| if: always() # run tests even if linting failed | |
| shell: bash -l {0} | |
| run: python${{ matrix.python-version }} -m pytest --cov=emmet --cov-report=xml ${{ matrix.package }}/tests | |
| - uses: codecov/[email protected] | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| # docs: | |
| # needs: test | |
| # runs-on: ubuntu-latest | |
| # strategy: | |
| # matrix: | |
| # python-version: ["3.8"] | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - uses: actions/setup-python@v5 | |
| # with: | |
| # python-version: ${{ matrix.python-version }} | |
| # cache: 'pip' | |
| # - name: Install OpenBabel | |
| # run: | | |
| # sudo apt-get update && sudo apt-get install openbabel libopenbabel-dev | |
| # sudo ln -s /usr/include/openbabel3 /usr/local/include/openbabel3 | |
| # - name: Install dependencies | |
| # run: | | |
| # python${{ matrix.python-version }} -m pip install --upgrade pip pip-tools | |
| # python${{ matrix.python-version }} -m piptools sync --user emmet-*/requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt | |
| # python${{ matrix.python-version }} -m pip install --user --no-deps -e ./emmet-core ./emmet-api ./emmet-builders | |
| # - name: Build | |
| # run: mkdocs build |