Configured a continuous integration (CI) workflow #1
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| name: CI | |
| on: | |
| pull_request: | |
| push: | |
| workflow_dispatch: | |
| permissions: | |
| contents: read | |
| env: | |
| ENV_NAME: aenet-torch | |
| PYTHON_VERSION: "3.11" | |
| jobs: | |
| unit-tests: | |
| name: Unit Tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Set up micromamba environment | |
| uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| environment-name: ${{ env.ENV_NAME }} | |
| create-args: >- | |
| python=${{ env.PYTHON_VERSION }} | |
| pip | |
| cache-environment: true | |
| cache-downloads: true | |
| init-shell: bash | |
| - name: Install project and dependencies | |
| run: | | |
| micromamba run -n "${ENV_NAME}" python -m pip install --upgrade pip | |
| micromamba run -n "${ENV_NAME}" python -m pip install -e ".[dev,torch]" | |
| - name: Run general pytest suite | |
| run: | | |
| micromamba run -n "${ENV_NAME}" pytest -q -m "not docs_examples" | |
| docs: | |
| name: Docs | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Set up micromamba environment | |
| uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| environment-name: ${{ env.ENV_NAME }} | |
| create-args: >- | |
| python=${{ env.PYTHON_VERSION }} | |
| pip | |
| cache-environment: true | |
| cache-downloads: true | |
| init-shell: bash | |
| - name: Install project and dependencies | |
| run: | | |
| micromamba run -n "${ENV_NAME}" python -m pip install --upgrade pip | |
| micromamba run -n "${ENV_NAME}" python -m pip install -e ".[dev,torch]" | |
| - name: Run pytest docs examples | |
| run: | | |
| micromamba run -n "${ENV_NAME}" pytest -q -m docs_examples | |
| - name: Run Sphinx doctest | |
| run: | | |
| micromamba run -n "${ENV_NAME}" \ | |
| python -m sphinx -b doctest docs/source docs/build/doctest | |
| - name: Run warning-clean Sphinx HTML build | |
| run: | | |
| micromamba run -n "${ENV_NAME}" \ | |
| python -m sphinx -W --keep-going -b html docs/source docs/build/html | |
| notebooks: | |
| name: Notebook (${{ matrix.notebook_name }}) | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - notebook: notebooks/example-01-featurization.ipynb | |
| notebook_name: example-01-featurization | |
| - notebook: notebooks/example-04-torch-featurization.ipynb | |
| notebook_name: example-04-torch-featurization | |
| - notebook: notebooks/example-05-torch-training.ipynb | |
| notebook_name: example-05-torch-training | |
| - notebook: notebooks/example-06-torch-inference.ipynb | |
| notebook_name: example-06-torch-inference | |
| - notebook: notebooks/example-07-neighbor-list.ipynb | |
| notebook_name: example-07-neighbor-list | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Set up micromamba environment | |
| uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| environment-name: ${{ env.ENV_NAME }} | |
| create-args: >- | |
| python=${{ env.PYTHON_VERSION }} | |
| pip | |
| cache-environment: true | |
| cache-downloads: true | |
| init-shell: bash | |
| - name: Install project and dependencies | |
| run: | | |
| micromamba run -n "${ENV_NAME}" python -m pip install --upgrade pip | |
| micromamba run -n "${ENV_NAME}" python -m pip install -e ".[dev,torch]" | |
| - name: Prepare disposable notebook worktree | |
| run: | | |
| mkdir -p "${RUNNER_TEMP}/notebook-worktree" | |
| rsync -a --delete --exclude ".git" ./ "${RUNNER_TEMP}/notebook-worktree/" | |
| - name: Execute notebook | |
| run: | | |
| mkdir -p "${RUNNER_TEMP}/executed-notebooks" | |
| micromamba run -n "${ENV_NAME}" \ | |
| python -m jupyter nbconvert --to notebook --execute \ | |
| "${RUNNER_TEMP}/notebook-worktree/${{ matrix.notebook }}" \ | |
| --output-dir "${RUNNER_TEMP}/executed-notebooks" \ | |
| --ExecutePreprocessor.timeout=600 |