Merge commit '9cc63ca' into molmd_fix_3-9 #1
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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 Linux | |
| on: [ push, pull_request ] | |
| jobs: | |
| test: | |
| # prevent this action from running on forks | |
| if: github.repository == 'materialsproject/pymatgen' | |
| strategy: | |
| max-parallel: 20 | |
| matrix: | |
| # This distribution of tests is designed to ensure an approximately even time to finish for parallel jobs. | |
| include: | |
| - pkg: pymatgen/analysis/defects pymatgen/analysis/chemenv pymatgen/analysis/elasticity pymatgen/analysis/magnetism | |
| pkg_id: 1 | |
| - pkg: pymatgen/analysis --ignore=pymatgen/analysis/defects --ignore=pymatgen/analysis/chemenv --ignore=pymatgen/analysis/elasticity --ignore=pymatgen/analysis/magnetism | |
| pkg_id: 2 | |
| - pkg: pymatgen/electronic_structure pymatgen/symmetry pymatgen/command_line pymatgen/ext | |
| pkg_id: 3 | |
| - pkg: pymatgen --ignore=pymatgen/analysis --ignore=pymatgen/electronic_structure --ignore=pymatgen/symmetry --ignore=pymatgen/ext --ignore=pymatgen/command_line | |
| pkg_id: 4 | |
| runs-on: ubuntu-latest | |
| env: | |
| PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }} | |
| MPLBACKEND: "Agg" | |
| PMG_TEST_FILES_DIR: ${{ github.workspace }}/test_files | |
| GULP_LIB: ${{ github.workspace }}/cmd_line/gulp/Libraries | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: 3.9 | |
| - name: Cache pip | |
| uses: actions/cache@v2 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('requirements*.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install OpenBabel and Libs | |
| shell: bash -l {0} | |
| run: | | |
| # Required for gulp. | |
| sudo apt-get install csh gfortran | |
| conda install -c conda-forge openbabel | |
| - name: Install dependencies | |
| shell: bash -l {0} | |
| run: | | |
| # Note that this is the way to update env variables in a way that persist for the entire job. | |
| for pkg in `ls cmd_line`; do echo "`pwd`/cmd_line/$pkg/Linux_64bit" >> $GITHUB_PATH; done | |
| pip install --upgrade pip wheel | |
| pip install -r requirements.txt | |
| pip install -r requirements-optional.txt -r requirements-dev.txt | |
| pip install scikit-image==0.18.1 | |
| pip install -e . | |
| - name: pytest ${{ matrix.pkg }} | |
| shell: bash -l {0} | |
| run: | | |
| pytest ${{ matrix.pkg }} --cov=pymatgen | |
| - name: Upload coverage | |
| uses: actions/upload-artifact@v1 | |
| with: | |
| name: coverage-${{ matrix.pkg_id }} | |
| path: .coverage | |
| coverage: | |
| needs: test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: 3.9 | |
| - name: Install deps | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements-dev.txt | |
| - name: Download coverage-1 | |
| uses: actions/download-artifact@v1 | |
| with: | |
| name: coverage-1 | |
| - name: Download coverage-2 | |
| uses: actions/download-artifact@v1 | |
| with: | |
| name: coverage-2 | |
| - name: Download coverage-3 | |
| uses: actions/download-artifact@v1 | |
| with: | |
| name: coverage-3 | |
| - name: Download coverage-4 | |
| uses: actions/download-artifact@v1 | |
| with: | |
| name: coverage-4 | |
| - name: Run coverage | |
| continue-on-error: true | |
| run: | | |
| coverage combine coverage*/.coverage* | |
| coverage report | |
| coverage xml | |
| - name: Coveralls Python | |
| continue-on-error: true | |
| uses: AndreMiras/coveralls-python-action@v20201129 |