Clean up core.surface comments and docstrings
#5339
Workflow file for this run
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| # Runs the complete test suite incl. many external command line dependencies (like Openbabel) | |
| # as well as the pymatgen.ext package. Coverage used to be computed based on this workflow. | |
| name: Tests | |
| on: | |
| push: | |
| branches: [master] | |
| paths-ignore: ["**/*.md", docs/**] | |
| pull_request: | |
| branches: [master] | |
| paths-ignore: ["**/*.md", docs/**] | |
| workflow_dispatch: | |
| workflow_call: # make this workflow reusable by release.yml | |
| permissions: | |
| contents: read | |
| jobs: | |
| test: | |
| # prevent this action from running on forks | |
| if: github.repository == 'materialsproject/pymatgen' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # pytest-split automatically distributes work load so parallel jobs finish in similar time | |
| os: [ubuntu-latest, windows-latest] | |
| python-version: ["3.9", "3.11"] | |
| split: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10] | |
| # include/exclude is meant to maximize CI coverage of different platforms and python | |
| # versions while minimizing the total number of jobs. We run all pytest splits with the | |
| # oldest supported python version (currently 3.9) on windows (seems most likely to surface | |
| # errors) and with newest version (currently 3.11) on ubuntu (to get complete and speedy | |
| # coverage on unix). We ignore mac-os, which is assumed to be similar to ubuntu. | |
| exclude: | |
| - os: windows-latest | |
| python-version: "3.11" | |
| - os: ubuntu-latest | |
| python-version: "3.9" | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }} | |
| GULP_LIB: ${{ github.workspace }}/cmd_line/gulp/Libraries | |
| PMG_VASP_PSP_DIR: ${{ github.workspace }}/tests/files | |
| steps: | |
| - name: Check out repo | |
| uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: pip | |
| cache-dependency-path: setup.py | |
| - name: Install uv | |
| run: pip install uv | |
| - name: Copy GULP to bin | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| sudo cp cmd_line/gulp/Linux_64bit/* /usr/local/bin/ | |
| - name: Install Bader | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| wget https://theory.cm.utexas.edu/henkelman/code/bader/download/bader_lnx_64.tar.gz | |
| tar xvzf bader_lnx_64.tar.gz | |
| sudo mv bader /usr/local/bin/ | |
| continue-on-error: true # This is not critical to succeed. | |
| - name: Install Enumlib | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| git clone --recursive https://github.com/msg-byu/enumlib | |
| cd enumlib/symlib/src | |
| export F90=gfortran | |
| make | |
| cd ../../src | |
| make enum.x | |
| sudo mv enum.x /usr/local/bin/ | |
| cd .. | |
| sudo cp aux_src/makeStr.py /usr/local/bin/ | |
| continue-on-error: true # This is not critical to succeed. | |
| - name: Install Packmol | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| wget -O packmol.tar.gz https://github.com/m3g/packmol/archive/refs/tags/v20.14.2.tar.gz | |
| tar xvzf packmol.tar.gz | |
| export F90=gfortran | |
| cd packmol-20.14.2 | |
| ./configure | |
| make | |
| sudo mv packmol /usr/local/bin/ | |
| cd .. | |
| continue-on-error: true # This is not critical to succeed. | |
| - name: Install dependencies | |
| run: | | |
| # TODO remove temporary fix. added since uv install torch is flaky. | |
| # track https://github.com/astral-sh/uv/issues/1921 for resolution | |
| pip install torch | |
| uv pip install numpy cython --system | |
| uv pip install -e '.[dev,optional]' --system | |
| # TODO remove next line installing ase from main branch when FrechetCellFilter is released | |
| uv pip install --upgrade 'git+https://gitlab.com/ase/ase' --system | |
| - name: pytest split ${{ matrix.split }} | |
| run: | | |
| pytest --splits 10 --group ${{ matrix.split }} --durations-path tests/files/.pytest-split-durations tests |