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Merge pull request #92 from CCPBioSim/90-ci-test-mdanalysis-version
Extention to CI capabilities with comparisions between CodeEntropy and MDAnalysis
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‎.github/workflows/CI.yaml‎

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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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---
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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/project-ci.yaml‎

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name: CodeEntropy CI
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on:
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push:
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branches: [main]
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pull_request:
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schedule:
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- cron: '0 8 * * 1'
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jobs:
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tests:
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runs-on: ubuntu-latest
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timeout-minutes: 30
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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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name: Run tests
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steps:
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- name: Checkout repo
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uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install CodeEntropy and its testing dependencies
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run: pip install -e .[testing]
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- name: Run test suite
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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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with:
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github-token: ${{ secrets.COVERALLS_REPO_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@v4
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- name: Set up Python 3.12
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uses: actions/setup-python@v5
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with:
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python-version: 3.12
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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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- name: Build docs
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run: cd docs && make
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pre-commit:
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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@v4
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- name: Set up Python 3.11
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uses: actions/setup-python@v5
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with:
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python-version: 3.11
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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-latest
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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: ["2.7.0", "2.8.0", "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@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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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/mdanalysis-compatibility-failure.md
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update_existing: true
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search_existing: open

‎pyproject.toml‎

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"Development Status :: 4 - Beta"
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]
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keywords = ["entropy", "macromolecular systems", "MD simulation"]
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requires-python = ">=3.8"
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requires-python = ">=3.11"
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dependencies = [
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"numpy==2.2.3",
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"mdanalysis==2.8.0",
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"mdanalysis>=2.7.0",
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"pandas==2.2.3",
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"psutil==5.9.5",
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"PyYAML==6.0.2",

‎tests/test_CodeEntropy/test_run.py‎

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run_manager._config_manager.merge_configs.return_value = mock_args
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mock_entropy_manager = MagicMock()
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with unittest.mock.patch(
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"CodeEntropy.run.EntropyManager", return_value=mock_entropy_manager
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), unittest.mock.patch("CodeEntropy.run.mda.Universe") as mock_universe:
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with (
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unittest.mock.patch(
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"CodeEntropy.run.EntropyManager", return_value=mock_entropy_manager
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),
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unittest.mock.patch("CodeEntropy.run.mda.Universe") as mock_universe,
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):
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run_manager.run_entropy_workflow()
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