Refactor CI to use micromamba instead of docker containers. #16
Workflow file for this run
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| name: Test | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| on: | |
| pull_request: | |
| push: | |
| branches: | |
| - "trunk-minor" | |
| - "trunk-major" | |
| workflow_dispatch: | |
| schedule: | |
| - cron: '0 18 * * 1' | |
| jobs: | |
| execute_notebooks: | |
| name: Execute notebooks | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - name: Checkout hoomd | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6 | |
| with: | |
| path: code | |
| ref: ${{ github.event_name == 'pull_request' && github.base_ref || github.ref_name }} | |
| repository: glotzerlab/hoomd-blue | |
| submodules: true | |
| - name: Determine hoomd hash | |
| id: hoomd | |
| run: echo "sha=$(git rev-parse HEAD)" >> $GITHUB_OUTPUT | |
| working-directory: code | |
| - name: Restore cached HOOMD-blue build | |
| id: cache | |
| uses: actions/cache/restore@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2 | |
| with: | |
| path: install | |
| key: hoomd-blue-${{ steps.hoomd.outputs.sha }} | |
| - name: Checkout notebooks | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6 | |
| with: | |
| path: notebooks | |
| - name: Create Python Environment | |
| uses: mamba-org/setup-micromamba@f8b8a1e23a26f60a44c853292711bacfd3eac822 # v1.9.0 | |
| with: | |
| environment-name: test | |
| environment-file: notebooks/.github/workflows/environments/py312-conda-lock.yml | |
| micromamba-root-path: ${{ github.workspace }}/micromamba | |
| - name: Configure conda environment variables | |
| run: | | |
| echo "PYTHONPATH=$GITHUB_WORKSPACE/install" >> $GITHUB_ENV | |
| echo "CONDA_PREFIX=$MAMBA_ROOT_PREFIX/envs/test" >> $GITHUB_ENV | |
| echo "CMAKE_PREFIX_PATH=$MAMBA_ROOT_PREFIX/envs/test" >> $GITHUB_ENV | |
| echo "$MAMBA_ROOT_PREFIX/envs/test/bin" >> $GITHUB_PATH | |
| - name: Configure | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: >- | |
| cmake -B hoomd/build -S code -GNinja | |
| -DCMAKE_BUILD_TYPE=Release | |
| -DENABLE_GPU=off | |
| -DENABLE_MPI=on | |
| -DENABLE_TBB=off | |
| -DBUILD_TESTING=off | |
| -DENABLE_LLVM=off | |
| -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/install | |
| - name: Compile | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2)) | |
| working-directory: hoomd/build | |
| - name: Cache HOOMD-blue build | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| uses: actions/cache/save@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2 | |
| with: | |
| path: install | |
| key: hoomd-blue-${{ steps.hoomd.outputs.sha }} | |
| - name: Display hoomd version | |
| run: python3 -c "import hoomd; print(hoomd.version.version, hoomd.version.git_sha1)" | |
| - name: List notebooks | |
| run: ls **/*.ipynb | |
| working-directory: notebooks | |
| - name: Execute notebooks | |
| run: | | |
| for i in */ | |
| do | |
| # Skip CPPPotential examples until they are rewritten. | |
| if [[ $i == "07-Modelling-Patchy-Particles"* ]]; then | |
| echo "Skipping notebooks in $i" | |
| else | |
| echo "Running notebooks in: $i" && jupyter nbconvert --execute --inplace $i/*.ipynb || exit 1 | |
| fi | |
| done | |
| working-directory: notebooks | |
| # This check is very basic, but we don't want to use `python -W error` as it will also catch any | |
| # warnings generated inside nbconvert and its dependencies. | |
| - name: Check for warnings | |
| run: | | |
| has_warnings=0 | |
| for file in **/*.ipynb | |
| do | |
| grep Warning $file && echo "::warning file=${file}::Has deprecation warnings" && has_warnings=1 | |
| done | |
| # Allow deprecation warnings for now. | |
| # exit ${has_warnings} | |
| working-directory: notebooks |