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Merge branch 'main' into 161-averaging-multimer
2 parents 71127da + 9087152 commit 6140253

19 files changed

Lines changed: 327 additions & 111 deletions

‎.github/renovate.json‎

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{
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"extends": [
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"config:best-practices",
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":pinAllExceptPeerDependencies",
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":dependencyDashboard",
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"group:monorepos",
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"group:recommended"
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],
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"rangeStrategy": "pin",
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"lockFileMaintenance": {
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"enabled": true
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},
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"packageRules": [
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{
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"matchUpdateTypes": ["minor", "patch"],
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"automerge": false
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}
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]
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}

‎.github/workflows/mdanalysis-compatibility-failure.md‎

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---
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title: CI Failure: MDAnalysis v{{ env.MDA_VERSION }} / Python {{ env.PYTHON_VERSION }}
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labels: CI Failure, MDAnalysis Compatibility
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title: "CI Failure: MDAnalysis v{{ env.MDA_VERSION }} / Python {{ env.PYTHON_VERSION }}"
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labels:
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- "CI Failure"
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- "MDAnalysis Compatibility"
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---
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### Automated MDAnalysis Compatibility Test Failure
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**MDAnalysis version**: `{{ env.MDA_VERSION }}`
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**Python version**: `{{ env.PYTHON_VERSION }}`
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**Workflow Run**: [Run #{{ env.RUN_NUMBER }}]({{ env.RUN_URL }})
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Automated MDAnalysis Compatibility Test Failure
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MDAnalysis version: {{ env.MDA_VERSION }}
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Python version: {{ env.PYTHON_VERSION }}
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Workflow Run: [Run #{{ env.RUN_NUMBER }}]({{ env.RUN_URL }})

‎.github/workflows/mdanalysis-compatibility.yaml‎

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name: MDAnalysis Compatibility
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on:
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schedule:
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- cron: '0 8 * * 1' # Weekly Monday checks
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workflow_dispatch:
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jobs:
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mdanalysis-compatibility:
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name: MDAnalysis Compatibility Tests
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-24.04, windows-2025, macos-15]
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python-version: ["3.11", "3.12", "3.13", "3.14"]
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mdanalysis-version: ["2.10.0"]
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steps:
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- name: Checkout repo
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uses: actions/checkout@v6
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v6.0.0
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies with MDAnalysis ${{ matrix.mdanalysis-version }}
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run: |
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pip install --upgrade pip
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pip install -e .[testing]
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pip install "MDAnalysis==${{ matrix.mdanalysis-version }}"
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- name: Run compatibility tests
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run: pytest --cov CodeEntropy --cov-report=term-missing --cov-append
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- name: Create Issue on Failure
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if: failure()
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uses: JasonEtco/create-an-issue@v2
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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PYTHON_VERSION: ${{ matrix.python-version }}
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MDA_VERSION: ${{ matrix.mdanalysis-version }}
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RUN_NUMBER: ${{ github.run_number }}
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RUN_URL: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
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with:
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filename: .github/workflows/mdanalysis-compatibility-failure.md
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update_existing: true
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search_existing: open

‎.github/workflows/project-ci.yaml‎

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@@ -6,18 +6,19 @@ on:
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pull_request:
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schedule:
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- cron: '0 8 * * 1'
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workflow_dispatch:
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jobs:
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tests:
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name: Run tests
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-24.04, windows-2025, macos-15]
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python-version: ["3.11", "3.12", "3.13"]
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python-version: ["3.11", "3.12", "3.13", "3.14"]
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steps:
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- name: Checkout repo
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uses: actions/checkout@v5.0.0
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uses: actions/checkout@v6
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v6.0.0
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run: pytest --cov CodeEntropy --cov-report term-missing --cov-append .
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- name: Coveralls GitHub Action
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uses: coverallsapp/github-action@v2.3.6
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uses: coverallsapp/github-action@v2.3.7
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with:
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github-token: ${{ secrets.GITHUB_TOKEN }}
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docs:
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runs-on: ubuntu-latest
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timeout-minutes: 15
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steps:
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- uses: actions/checkout@v5.0.0
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- name: Set up Python 3.13
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- uses: actions/checkout@v6
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- name: Set up Python 3.14
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uses: actions/setup-python@v6.0.0
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with:
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python-version: 3.13
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python-version: 3.14
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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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runs-on: ubuntu-24.04
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timeout-minutes: 15
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steps:
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- uses: actions/checkout@v5.0.0
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- name: Set up Python 3.13
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- uses: actions/checkout@v6
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- name: Set up Python 3.14
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uses: actions/setup-python@v6.0.0
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with:
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python-version: 3.13
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python-version: 3.14
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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 .[pre-commit,docs,testing]
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- name: Run pre-commit
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run: |
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pre-commit install
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pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
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mdanalysis-compatibility:
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if: github.event_name == 'schedule'
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runs-on: ubuntu-24.04
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timeout-minutes: 15
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strategy:
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matrix:
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python-version: ["3.11", "3.12", "3.13"]
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mdanalysis-version: ["2.9.0", "latest"]
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name: MDAnalysis Compatibility Tests
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steps:
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- name: Checkout repo
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uses: actions/checkout@v5.0.0
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v6.0.0
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies with MDAnalysis ${{ matrix.mdanalysis-version }}
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run: |
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pip install --upgrade pip
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pip install -e .[testing]
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if [ "${{ matrix.mdanalysis-version }}" = "latest" ]; then
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pip install MDAnalysis
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else
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pip install "MDAnalysis==${{ matrix.mdanalysis-version }}"
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fi
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- name: Run compatibility tests
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run: pytest --cov CodeEntropy --cov-report=term-missing --cov-append
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- name: Create Issue on Failure
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if: failure()
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uses: JasonEtco/create-an-issue@v2
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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PYTHON_VERSION: ${{ matrix.python-version }}
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MDA_VERSION: ${{ matrix.mdanalysis-version }}
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RUN_NUMBER: ${{ github.run_number }}
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RUN_URL: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
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with:
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filename: .github/workflows/mdanalysis-compatibility-failure.md
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update_existing: true
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search_existing: open
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pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )

‎.github/workflows/release.yaml‎

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steps:
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- name: Checkout repository
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id: repo
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uses: actions/checkout@v5.0.0
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uses: actions/checkout@v6
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- name: Set up Python
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uses: actions/setup-python@v6.0.0
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with:
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python-version: 3.13
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python-version: 3.14
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- name: Get latest release from pip
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id: latestreleased
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steps:
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- name: checkout
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uses: actions/checkout@v5.0.0
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uses: actions/checkout@v6
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- name: Change version in repo and CITATION.cff
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run: |
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runs-on: ubuntu-24.04
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steps:
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- name: Checkout repository
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uses: actions/checkout@v5.0.0
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uses: actions/checkout@v6
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with:
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ref: main
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steps:
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- name: create release
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uses: softprops/action-gh-release@v2.4.1
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uses: softprops/action-gh-release@v2.4.2
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with:
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name: v${{ github.event.inputs.version }}
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generate_release_notes: true
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steps:
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- name: checkout
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uses: actions/checkout@v5.0.0
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uses: actions/checkout@v6
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with:
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ref: main
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- name: Set up Python
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uses: actions/setup-python@v6.0.0
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with:
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python-version: 3.13
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python-version: 3.14
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- name: Install flit
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run: |

‎.github/workflows/renovate.yaml‎

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name: Renovate
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on:
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schedule:
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- cron: "0 8 * * *"
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workflow_dispatch:
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jobs:
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renovate:
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runs-on: ubuntu-24.04
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concurrency:
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group: renovate
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cancel-in-progress: true
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permissions:
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contents: write
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pull-requests: write
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issues: write
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steps:
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- uses: actions/checkout@v6
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- uses: renovatebot/github-action@v44.0.3
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with:
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token: ${{ secrets.RENOVATE_TOKEN }}
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env:
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RENOVATE_CONFIG_FILE: ".github/renovate.json"
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LOG_LEVEL: debug
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RENOVATE_REPOSITORIES: "CCPBioSim/CodeEntropy"

‎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: 1.0.3
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date-released: '2025-09-29'
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version: 1.0.5
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date-released: '2025-11-18'

‎CodeEntropy/__init__.py‎

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and statistical mechanics.
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"""
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__version__ = "1.0.3"
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__version__ = "1.0.5"

‎CodeEntropy/config/arg_config_manager.py‎

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"top_traj_file": {
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"type": str,
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"nargs": "+",
15-
"help": "Path to Structure/topology file followed by Trajectory file(s)",
15+
"help": "Path to structure/topology file followed by trajectory file",
16+
},
17+
"force_file": {
18+
"type": str,
19+
"default": None,
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"help": "Optional path to force file if forces are not in trajectory file",
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},
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"file_format": {
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"type": str,
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"default": None,
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"help": "String for file format as recognised by MDAnalysis",
26+
},
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"kcal_force_units": {
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"type": bool,
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"default": False,
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"help": "Set this to True if you have a separate force file with nonSI units.",
1631
},
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"force_file": {
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"type": str,
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268283
if args.force_partitioning != default_value:
269284
logger.warning(
270285
f"'force_partitioning' is set to {args.force_partitioning},"
271-
" which differs from the default ({default_value})."
286+
f" which differs from the default {default_value}."
272287
)

‎CodeEntropy/entropy.py‎

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)
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reduced_atom, number_molecules, levels, groups = self._initialize_molecules()
100-
100+
logger.debug(f"Universe 3: {reduced_atom}")
101101
water_atoms = self._universe.select_atoms("water")
102102
water_resids = set(res.resid for res in water_atoms.residues)
103103

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129129
end,
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step,
131131
number_frames,
132+
self._args.force_partitioning,
132133
)
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)
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543544
"""
544545
# Find the relevant force and torque matrices and tidy them up
545546
# by removing rows and columns that are all zeros
547+
546548
force_matrix = self._level_manager.filter_zero_rows_columns(force_matrix)
547549

548550
torque_matrix = self._level_manager.filter_zero_rows_columns(torque_matrix)

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