Implement bond interactions #646
Workflow file for this run
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| name: test | |
| on: | |
| pull_request: | |
| push: | |
| branches: | |
| - main | |
| schedule: | |
| - cron: "18 10 1,15 * *" | |
| workflow_call: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: unit test [python-${{ matrix.python-version }}, ${{ matrix.mpi }}] | |
| runs-on: ubuntu-latest | |
| env: | |
| MPIEXEC_TIMEOUT: 300 | |
| RDMAV_FORK_SAFE: 1 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] | |
| mpi: ["nompi", "mpich", "openmpi"] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Setup MPI | |
| if: ${{ matrix.mpi != 'nompi' }} | |
| uses: mpi4py/setup-mpi@v1 | |
| with: | |
| mpi: ${{ matrix.mpi }} | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install test dependencies | |
| run: | | |
| pip install -r tests/requirements.txt | |
| - name: Install | |
| run: | | |
| pip install . | |
| - name: Test | |
| run: | | |
| python -m unittest discover -v -s ./tests -p "test_*.py" | |
| - name: Install mpi4py | |
| if: ${{ matrix.mpi != 'nompi' }} | |
| run: | | |
| pip install --no-cache-dir mpi4py | |
| - name: Test MPI | |
| if: ${{ matrix.mpi != 'nompi' }} | |
| run: | | |
| mpiexec -n 2 python -m unittest discover -v -s ./tests -p "test_*.py" | |
| test-hoomd: | |
| name: unit test [python-${{ matrix.python-version }}, hoomd-${{ matrix.hoomd-version }}] | |
| needs: test | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10", "3.11"] | |
| hoomd-version: ["2.9.7", "3.11.0", "4.7.0"] | |
| include: | |
| - python-version: "3.12" | |
| hoomd-version: "4.7.0" | |
| exclude: | |
| - python-version: "3.11" | |
| hoomd-version: "2.9.7" | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| channels: conda-forge | |
| channel-priority: true | |
| mamba-version: "*" | |
| python-version: ${{ matrix.python-version }} | |
| - name: Force HOOMD 2 NumPy version | |
| if: ${{ matrix.hoomd-version == '2.9.7' || matrix.hoomd-version == '3.11.0' }} | |
| run: | | |
| mamba install "numpy<2" "gsd<3.4" | |
| - name: Install test dependencies | |
| run: | | |
| mamba install hoomd=${{ matrix.hoomd-version }} --no-update-deps | |
| pip install -r tests/requirements.txt --upgrade-strategy only-if-needed | |
| - name: Install | |
| run: | | |
| pip install . | |
| - name: Test | |
| run: | | |
| python -m unittest -v tests/simulate/test_hoomd.py | |
| test-lammps: | |
| name: unit test [python-${{ matrix.python-version }}, lammps-${{ matrix.lammps-version }}, ${{ matrix.mpi }}] | |
| needs: test | |
| runs-on: ubuntu-latest | |
| env: | |
| MPIEXEC_TIMEOUT: 300 | |
| RDMAV_FORK_SAFE: 1 | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10", "3.11"] | |
| lammps-version: ["2022.06.23", "2023.08.02"] | |
| mpi: ["mpich", "openmpi"] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| channels: conda-forge | |
| channel-priority: true | |
| mamba-version: "*" | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install LAMMPS | |
| run: | | |
| mamba install "lammps=${{ matrix.lammps-version }}=*${{ matrix.mpi }}*" mpi4py | |
| - name: Force libpnetcdf version | |
| if: ${{ matrix.lammps-version == '2023.08.02' }} | |
| run: | | |
| mamba install "libpnetcdf<1.13.0" | |
| - name: Install test dependencies | |
| run: | | |
| pip install -r tests/requirements.txt | |
| - name: Install | |
| run: | | |
| pip install . | |
| - name: Test | |
| run: | | |
| python -m unittest -v tests/simulate/test_lammps.py | |
| - name: Test executable | |
| run: | | |
| python tests/simulate/test_lammps.py -v --lammps ${{ matrix.lammps-version == '2022.06.23' && 'lmp_serial' || 'lmp' }} | |
| - name: Test MPI | |
| run: | | |
| mpiexec -n 2 python -m unittest -v tests/simulate/test_lammps.py | |
| - name: Test MPI executable | |
| run: | | |
| python tests/simulate/test_lammps.py -v --lammps "mpiexec -n 2 lmp_mpi" | |
| test-examples: | |
| name: test examples | |
| needs: [test, test-hoomd] | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Setup Python 3.8 | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| channels: conda-forge | |
| channel-priority: true | |
| mamba-version: "*" | |
| python-version: 3.8 | |
| - name: Install test dependencies | |
| run: | | |
| mamba install hoomd=3 | |
| pip install -r doc/requirements.txt | |
| - name: Install | |
| run: | | |
| pip install . | |
| - name: Run notebooks | |
| run: | | |
| for nb in doc/source/guide/examples/*/*.ipynb | |
| do | |
| jupyter nbconvert \ | |
| --ExecutePreprocessor.timeout=120 \ | |
| --to notebook \ | |
| --execute $nb | |
| done | |
| # final exit point for unit tests on PRs, which can be a required check | |
| test-exit: | |
| name: unit test | |
| needs: [test, test-hoomd, test-lammps, test-examples] | |
| if: ${{ always() && github.event_name == 'pull_request' }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check core tests | |
| if: needs.test.result != 'success' | |
| run: echo "::error ::core tests failed." && exit 1 | |
| - name: Check hoomd tests | |
| if: needs.test-hoomd.result != 'success' | |
| run: echo "::error ::hoomd tests failed." && exit 1 | |
| - name: Check lammps tests | |
| if: needs.test-lammps.result != 'success' | |
| run: echo "::error ::lammps tests failed." && exit 1 |