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Configured a continuous integration (CI) workflow
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‎.github/workflows/ci.yml‎

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

‎.gitignore‎

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outputs/
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.virtual_documents
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# Notebook-generated outputs
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notebooks/features.h5
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notebooks/features_torch.h5
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notebooks/generate.out
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notebooks/predict.out
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notebooks/run/
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notebooks/example-01-outputs/
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notebooks/example-05-outputs/
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notebooks/example-08-outputs/
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debug/
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profiling/
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fortran/

‎docs/source/api/trainset.rst‎

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See Also
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--------
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* :doc:`torch_featurization` - PyTorch-based featurization APIs
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* :doc:`/usage/torch_featurization` - PyTorch-based featurization APIs

‎docs/source/dev/docs_examples.rst‎

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/Users/aurban/.local/bin/micromamba run -n aenet-torch \
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pytest -q src/aenet/geometry/tests/test_docs_transformations_basic.py
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Run the maintained notebook-first examples without mutating tracked notebooks:
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.. code-block:: bash
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mkdir -p /tmp/aenet-doc-notebooks
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/Users/aurban/.local/bin/micromamba run -n aenet-torch \
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python -m jupyter nbconvert --to notebook --execute \
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notebooks/example-01-featurization.ipynb \
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--output-dir /tmp/aenet-doc-notebooks
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Repeat the same pattern for:
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- ``notebooks/example-04-torch-featurization.ipynb``
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- ``notebooks/example-05-torch-training.ipynb``
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- ``notebooks/example-06-torch-inference.ipynb``
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- ``notebooks/example-07-neighbor-list.ipynb``
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This avoids overwriting the source ``.ipynb`` files. Some notebooks still
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write side-effect artifacts such as HDF5 files or checkpoints relative to the
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notebook directory, so use a disposable worktree or temporary copy when you
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need a perfectly clean checkout.
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CI Coverage
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-----------
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The repository CI is split into three layers so failures are easy to localize:
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- general unit tests: ``pytest -q -m "not docs_examples"``
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- docs checks: ``pytest -q -m docs_examples`` plus Sphinx doctest and
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warning-clean HTML builds
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- notebook checks: execution of the maintained notebook-first examples listed
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above via ``nbconvert --execute`` from a disposable worktree with a
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temporary output directory
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Repo-wide ``ruff check .`` is intentionally not a required CI gate yet because
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the repository still has a substantial backlog of pre-existing lint violations.
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Treat lint as a follow-up ratchet by directory or subsystem rather than
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blocking the initial test/docs CI path on legacy cleanup.
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Authoring Policy
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----------------
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‎notebooks/example-01-outputs/features.h5‎

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