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Merge branch 'main' into 27-orientational-entropy
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‎.github/workflows/daily.yaml‎

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name: CodeEntropy Daily Checks
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name: Daily Unit Tests
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on:
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schedule:
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jobs:
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unit:
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name: Daily unit tests
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name: Unit (${{ matrix.os }}, ${{ matrix.python-version }})
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runs-on: ${{ matrix.os }}
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timeout-minutes: 30
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-24.04, windows-2025, macos-15]
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os: [ubuntu-24.04, macos-15, windows-2025]
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python-version: ["3.12", "3.13", "3.14"]
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timeout-minutes: 30
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steps:
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- name: Checkout repo
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- name: Checkout
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uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
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- name: Set up Python ${{ matrix.python-version }}
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python-version: ${{ matrix.python-version }}
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cache: pip
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- name: Install CodeEntropy and its testing dependencies
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- name: Install (testing)
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run: |
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pip install --upgrade pip
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pip install -e .[testing]
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- name: Run unit test suite
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run: pytest tests/unit -q
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coverage:
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name: Coverage (ubuntu, latest python)
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runs-on: ubuntu-24.04
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timeout-minutes: 30
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steps:
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- name: Checkout repo
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uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
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python -m pip install --upgrade pip
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python -m pip install -e .[testing]
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- name: Set up Python 3.14
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uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
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with:
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python-version: "3.14"
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cache: pip
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- name: Install CodeEntropy and its testing dependencies
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run: |
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pip install --upgrade pip
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pip install -e .[testing]
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- name: Run unit test suite with coverage
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run: pytest tests/unit --cov CodeEntropy --cov-report term-missing --cov-report xml -q
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- name: Coveralls GitHub Action
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uses: coverallsapp/github-action@5cbfd81b66ca5d10c19b062c04de0199c215fb6e # v2.3.7
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with:
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github-token: ${{ secrets.GITHUB_TOKEN }}
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file: coverage.xml
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- name: Pytest (unit) • ${{ matrix.os }} • py${{ matrix.python-version }}
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run: python -m pytest tests/unit -q

‎.github/workflows/pr.yaml‎

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name: CodeEntropy CI
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name: Pull Request CI
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on:
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pull_request:
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python-version: ${{ matrix.python-version }}
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cache: pip
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- name: Install (testing)
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- name: Install testing dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install -e .[testing]
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- name: Pytest (unit) • ${{ matrix.os }} • py${{ matrix.python-version }}
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- name: Pytest (unit) • ${{ matrix.os }}, ${{ matrix.python-version }}
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run: python -m pytest tests/unit -q
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regression-quick:
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docs:
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name: Docs
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needs: unit
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runs-on: ubuntu-24.04
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timeout-minutes: 25
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steps:
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- name: Checkout
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uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
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uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
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- name: Set up Python 3.14
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uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
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uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
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with:
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python-version: "3.14"
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cache: pip
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- name: Install (docs)
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- name: Install
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run: |
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python -m pip install --upgrade pip
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python -m pip install -e .[docs]
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- name: Build docs
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run: |
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cd docs
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make
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make -C docs clean
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make -C docs html SPHINXOPTS="-W --keep-going"
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- name: Upload docs artifact
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if: always()
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uses: actions/upload-artifact@v4
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with:
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name: docs-html
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path: docs/_build/html
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pre-commit:
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name: Pre-commit
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git diff
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exit 1
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}
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coverage:
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name: Coverage
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needs: unit
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runs-on: ubuntu-24.04
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timeout-minutes: 30
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steps:
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- name: Checkout repo
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uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
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- name: Set up Python 3.14
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uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
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with:
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python-version: "3.14"
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cache: pip
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- name: Install (testing)
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run: |
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python -m pip install --upgrade pip
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python -m pip install -e .[testing]
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- name: Run unit test suite with coverage
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run: |
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pytest tests/unit \
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--cov CodeEntropy \
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--cov-report term-missing \
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--cov-report xml \
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-q
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- name: Upload to Coveralls
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uses: coverallsapp/github-action@5cbfd81b66ca5d10c19b062c04de0199c215fb6e
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with:
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github-token: ${{ secrets.GITHUB_TOKEN }}
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file: coverage.xml
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fail-on-error: false

‎.github/workflows/release.yaml‎

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name: release
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name: Release CodeEntropy
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workflow_dispatch:
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env:
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FLIT_USERNAME: __token__
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FLIT_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
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conda:
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name: publish conda to anaconda.org
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needs: [tag, release]
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runs-on: ubuntu-24.04
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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with:
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ref: main
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- name: Set version in conda recipe
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run: |
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sed -i "s/^{% set version = \".*\" %}$/{% set version = \"${{ github.event.inputs.version }}\" %}/" conda-recipe/meta.yaml
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grep '{% set version' conda-recipe/meta.yaml
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- name: Setup Conda
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uses: conda-incubator/setup-miniconda@v3
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with:
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miniforge-variant: Miniforge3
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python-version: "3.12"
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auto-activate-base: false
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- name: Install build tools
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shell: bash -l {0}
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run: |
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conda install -y conda-build anaconda-client
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conda config --add channels conda-forge
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conda config --set channel_priority strict
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conda config --set anaconda_upload no
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- name: Build package
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shell: bash -l {0}
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run: |
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conda build conda-recipe
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- name: Upload to Anaconda
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shell: bash -l {0}
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env:
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ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
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run: |
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PKG_PATH=$(conda build conda-recipe --output)
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anaconda -t "$ANACONDA_API_TOKEN" upload "$PKG_PATH" --user CCPBioSim --force

‎.github/workflows/weekly-docs.yaml‎

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name: CodeEntropy Weekly Docs
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name: Weekly Docs Build
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schedule:
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os: [ubuntu-24.04, windows-2025, macos-15]
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python-version: ["3.12", "3.13", "3.14"]
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timeout-minutes: 30
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steps:
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- name: Checkout repo
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uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
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- name: Install python dependencies
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run: |
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pip install --upgrade pip
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pip install -e .[docs]
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python -m pip install --upgrade pip
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python -m pip install -e .[docs]
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- name: Build docs
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run: cd docs && make
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- name: Build docs (warnings as errors)
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run: |
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make -C docs clean
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make -C docs html SPHINXOPTS="-W --keep-going"
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- name: Upload docs artifacts on failure
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if: failure()

‎.github/workflows/weekly-regression.yaml‎

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name: CodeEntropy Weekly Regression
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name: Weekly Regression Tests
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on:
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schedule:

‎.pre-commit-config.yaml‎

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- id: check-added-large-files
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- id: check-merge-conflict
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- id: check-yaml
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exclude: ^conda-recipe/meta\.yaml$
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- id: check-toml
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- id: check-case-conflict
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- id: check-ast
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- id: end-of-file-fixer
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- id: trailing-whitespace
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- repo: https://github.com/rstcheck/rstcheck
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rev: v6.2.0
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hooks:
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- id: rstcheck
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name: rstcheck (docstrings only)
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files: \.py$
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args: ["--report-level", "warning"]
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- repo: local
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hooks:
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- id: sphinx-docs
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name: sphinx-build (pre-push, warnings as errors)
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entry: bash -lc 'make -C docs clean && make -C docs html SPHINXOPTS="-W --keep-going"'
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language: system
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pass_filenames: false
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stages: [pre-push]

‎CITATION.cff‎

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- biomolecular simulations
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- protein flexibility
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license: MIT
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version: 1.0.7
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date-released: '2026-01-09'
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version: 2.0.0
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date-released: '2026-02-27'

‎CodeEntropy/__init__.py‎

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and statistical mechanics.
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"""
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__version__ = "1.0.7"
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__version__ = "2.0.0"

‎CodeEntropy/config/argparse.py‎

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1) A declarative argument specification (`ARG_SPECS`) used to build an
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``argparse.ArgumentParser``.
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2) A `ConfigResolver` that:
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- loads YAML configuration (if present),
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- merges YAML values with CLI values (CLI wins),
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- adjusts logging verbosity,
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- validates a subset of runtime inputs against the trajectory.
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Notes:
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common string forms like "true"/"false".
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"""

‎CodeEntropy/entropy/configurational.py‎

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"""Conformational entropy utilities.
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This module provides:
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* Assigning discrete conformational states for a single dihedral time series.
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* Computing conformational entropy from a sequence of state labels.
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The public surface area is intentionally small to keep responsibilities clear.
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- Assignment of discrete conformational states for a single dihedral time series.
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- Computation of conformational entropy from a sequence of state labels.
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"""
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"""Compute conformational entropy for a sequence of state labels.
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Entropy is computed as:
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S = -R * sum_i p_i * ln(p_i)
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where p_i is the observed probability of state i in `states`.
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where p_i is the observed probability of state i in ``states``.
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Args:
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states: Sequence/array of discrete state labels. Empty/None yields 0.0.
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number_frames: Frame count metadata.
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Returns:
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Conformational entropy in J/mol/K.
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float: Conformational entropy in J/mol/K.
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"""
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_ = number_frames
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