Suppress pymatgen element data warnings when imputing #958
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| # This workflow runs only on Ubuntu and aims to be more complete than the Mac and Windows workflows. | |
| # In particular, Openbabel and many of the external command line dependencies are included for testing.defaults: | |
| # The ext package is also only tested in this workflow. Coverage is also computed based on this platform. | |
| name: Testing | |
| env: | |
| PYTEST_ADDOPTS: "--color=yes" | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| workflow_dispatch: | |
| inputs: | |
| fullTest: | |
| description: "run full test" | |
| required: true | |
| default: false | |
| type: boolean | |
| jobs: | |
| test: | |
| strategy: | |
| matrix: | |
| python-version: ["3.9", "3.10", "3.11"] | |
| mongodb-version: ['4.0'] | |
| fail-fast: false | |
| runs-on: ubuntu-latest | |
| env: | |
| PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }} | |
| MPDS_KEY: ${{ secrets.MPDS_KEY }} | |
| CITRINATION_API_KEY: ${{ secrets.CITRINATION_API_KEY }} | |
| RUNNING_ON_GHACTIONS: "True" | |
| MPLBACKEND: "Agg" | |
| MATMINER_DATASET_FULL_TEST: ${{ inputs.fullTest }} | |
| services: | |
| mongo: | |
| image: mongo:4 | |
| ports: | |
| - 27017:27017 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: "pip" | |
| cache-dependency-path: '**/setup.py' | |
| - name: Install Python dependencies | |
| run: | | |
| python${{ matrix.python-version }} -m pip install --upgrade pip pip-tools setuptools setuptools_scm | |
| python${{ matrix.python-version }} -m piptools sync --user requirements/ubuntu-latest_py${{ matrix.python-version }}.txt | |
| # Using non-editable install for testing building of MANIFEST files | |
| python${{ matrix.python-version }} -m pip install --no-deps . | |
| python${{ matrix.python-version }} -m pip install pre-commit | |
| - name: linting | |
| run: | | |
| pre-commit run --all-files | |
| - name: Run tests | |
| run: | | |
| python${{ matrix.python-version }} -m pytest --cov=matminer matminer --durations=0 --timeout=360 | |
| - name: Build package | |
| if: matrix.python-version == 3.9 | |
| run: | | |
| python${{ matrix.python-version }} -m pip install --upgrade pip build setuptools setuptools_scm wheel | |
| python${{ matrix.python-version }} -m build | |
| - name: Publish distribution 📦s to Test PyPI | |
| if: matrix.python-version == 3.9 && github.repository == 'hackingmaterials/matminer' | |
| uses: pypa/gh-action-pypi-publish@release/v1.5 | |
| with: | |
| skip_existing: true | |
| repository_url: https://test.pypi.org/legacy/ | |
| user: __token__ | |
| password: ${{ secrets.TEST_PYPI_TOKEN }} | |
| auto-gen-release: | |
| needs: | |
| - test | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.PAT }} | |
| steps: | |
| - uses: rymndhng/[email protected] | |
| with: | |
| bump_version_scheme: norelease |