Add min "thickness" check in CifParser to filter invalid structure which leads to infinite loop
#8190
Workflow file for this run
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| # Run 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' | |
| defaults: | |
| run: | |
| shell: bash -l {0} # Enable conda/mamba env activation by reading bash profile | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # 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 3.10) on windows (seems most likely to surface errors) and with | |
| # newest version (currently 3.12) on ubuntu (to get complete coverage on unix). | |
| config: | |
| - os: windows-latest | |
| python: "3.10" | |
| resolution: highest | |
| extras: ci,optional | |
| - os: windows-latest | |
| python: "3.10" | |
| resolution: highest | |
| extras: ci,optional,numpy-v1 # Test NP1 on Windows (quite buggy ATM) | |
| - os: ubuntu-latest | |
| python: "3.12" | |
| resolution: lowest-direct | |
| extras: ci,optional | |
| - os: macos-latest | |
| python: "3.11" | |
| resolution: lowest-direct | |
| extras: ci # test with only required dependencies installed | |
| # pytest-split automatically distributes work load so parallel jobs finish in similar time | |
| # update durations file with `pytest --store-durations --durations-path tests/files/.pytest-split-durations` | |
| split: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10] | |
| runs-on: ${{ matrix.config.os }} | |
| env: | |
| PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }} | |
| PMG_VASP_PSP_DIR: ${{ github.workspace }}/tests/files | |
| steps: | |
| - name: Check out repo | |
| uses: actions/checkout@v4 | |
| - name: Set up micromamba | |
| uses: mamba-org/setup-micromamba@main | |
| - name: Create mamba environment | |
| run: | | |
| micromamba create -n pmg python=${{ matrix.config.python }} --yes | |
| - name: Install ubuntu-only conda dependencies | |
| if: matrix.config.os == 'ubuntu-latest' | |
| run: | | |
| micromamba install -n pmg -c conda-forge bader enumlib openff-toolkit packmol pygraphviz tblite --yes | |
| - name: Install pymatgen and dependencies via uv | |
| run: | | |
| micromamba activate pmg | |
| pip install uv | |
| # TODO1 (use uv over pip) uv install torch is flaky, track #3826 | |
| # TODO2 (pin torch version): DGL library (matgl) doesn't support torch > 2.2.1, | |
| # see: https://discuss.dgl.ai/t/filenotfounderror-cannot-find-dgl-c-graphbolt-library/4302 | |
| pip install torch==2.2.1 | |
| uv pip install --editable '.[${{ matrix.config.extras }}]' --resolution=${{ matrix.config.resolution }} | |
| - name: Install optional Ubuntu dependencies | |
| if: matrix.config.os == 'ubuntu-latest' | |
| run: | | |
| # Install BoltzTraP | |
| wget -q -O BoltzTraP.tar.bz2 https://owncloud.tuwien.ac.at/index.php/s/s2d55LYlZnioa3s/download | |
| tar -jxf BoltzTraP.tar.bz2 | |
| echo "$(realpath boltztrap-1.2.5/src/)" >> $GITHUB_PATH | |
| # Install Vampire 5.0 | |
| wget -q https://vampire.york.ac.uk/resources/release-5/vampire-5.0-linux.tar.gz | |
| tar -zxf vampire-5.0-linux.tar.gz | |
| mv linux vampire-5.0 | |
| echo "$(realpath vampire-5.0/)" >> $GITHUB_PATH | |
| - name: pytest split ${{ matrix.split }} | |
| run: | | |
| micromamba activate pmg | |
| pytest --splits 10 --group ${{ matrix.split }} --durations-path tests/files/.pytest-split-durations tests | |
| trigger_atomate2_ci: | |
| needs: test | |
| runs-on: ubuntu-latest | |
| # Only run if changes are pushed to master | |
| if: github.ref == 'refs/heads/master' | |
| steps: | |
| - name: Trigger Atomate2 CI | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| curl -L \ | |
| -X POST \ | |
| -H "Accept: application/vnd.github+json" \ | |
| -H "Authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" \ | |
| -H "X-GitHub-Api-Version: 2022-11-28" \ | |
| https://api.github.com/repos/materialsproject/atomate2/dispatches \ | |
| -d '{"event_type": "pymatgen-ci-trigger", "client_payload": {"pymatgen_ref": "${{ github.sha }}"}}' |