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Merge pull request #281 from CCPBioSim/173-refactor-levels
Refactor workflow to DAG architecture with expanded testing, CI modernisation, and validated numerical equivalence
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‎.github/CONTRIBUTING.md‎

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## Getting Started
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Before contributing, please review the [Developer Guide](https://codeentropy.readthedocs.io/en/latest/developer_guide.html).
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Before contributing, please review the [Developer Guide](https://codeentropy.readthedocs.io/en/latest/developer_guide.html).
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It covers CodeEntropy’s architecture, setup instructions, and contribution workflow.
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If you’re new to the project, we also recommend:
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When you’re ready to submit your work:
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1. **Push your branch** to GitHub.
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2. **Open a [pull request](https://help.github.com/articles/using-pull-requests/)** against the `main` branch.
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1. **Push your branch** to GitHub.
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2. **Open a [pull request](https://help.github.com/articles/using-pull-requests/)** against the `main` branch.
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3. **Fill out the PR template**, including:
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- A concise summary of what your PR does
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- A list of all changes introduced
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- Details on how these changes affect the repository (features, tests, documentation, etc.)
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- A concise summary of what your PR does
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- A list of all changes introduced
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- Details on how these changes affect the repository (features, tests, documentation, etc.)
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4. **Verify before submission**:
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- All tests pass
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- Pre-commit checks succeed
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- Documentation is updated where applicable
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- All tests pass
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- Pre-commit checks succeed
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- Documentation is updated where applicable
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5. **Review process**:
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- Your PR will be reviewed by the core development team.
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- At least **one approval** is required before merging.
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- Your PR will be reviewed by the core development team.
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- At least **one approval** is required before merging.
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We aim to provide constructive feedback quickly and appreciate your patience during the review process.
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Found a bug or have a feature request?
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1. **Open a new issue** on GitHub.
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2. Provide a **clear and descriptive title**.
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1. **Open a new issue** on GitHub.
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2. Provide a **clear and descriptive title**.
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3. Include:
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- Steps to reproduce the issue (if applicable)
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- Expected vs. actual behavior
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- Relevant logs, screenshots, or input files
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- Steps to reproduce the issue (if applicable)
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- Expected vs. actual behavior
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- Relevant logs, screenshots, or input files
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Well-documented issues help us address problems faster and keep CodeEntropy stable and robust.
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‎.github/ISSUE_TEMPLATE/bug_report.md‎

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---
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## To Reproduce
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## To Reproduce
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<!-- Provide the YAML configuration and the exact CLI command that reproduces the issue. -->
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### YAML configuration
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<!-- Paste the YAML file or the smallest excerpt that reproduces the issue.
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<!-- Paste the YAML file or the smallest excerpt that reproduces the issue.
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Remove unrelated fields to make it minimal. -->
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```yaml
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# Paste the YAML snippet here
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- Python Version:
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- Package list:
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- If using conda, run: `conda list > packages.txt` and paste the contents here.
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``` bash
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# Paste packages.txt here
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```

‎.github/PULL_REQUEST_TEMPLATE.md‎

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<!-- List all the changes introduced in this PR. -->
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### Change 1 <!-- Rename Change 1 to reflect change title -->:
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- <!-- Bullet point the changes in update 1. -->
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## Impact
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‎.github/renovate.json‎

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"automerge": false
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}
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]
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}
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}

‎.github/workflows/daily.yaml‎

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name: CodeEntropy Daily
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on:
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schedule:
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- cron: '0 8 * * 1-5'
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workflow_dispatch:
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concurrency:
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group: daily-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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unit:
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name: Unit (${{ 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, macos-15, windows-2025]
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python-version: ["3.12", "3.13", "3.14"]
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steps:
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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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uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
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with:
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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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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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run: python -m pytest tests/unit -q

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

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‎.github/workflows/mdanalysis-compatibility.yaml‎

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‎.github/workflows/pr.yaml‎

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name: CodeEntropy CI
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on:
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pull_request:
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concurrency:
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group: pr-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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unit:
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name: Unit
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runs-on: ${{ matrix.os }}
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timeout-minutes: 25
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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, macos-15, windows-2025]
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python-version: ["3.12", "3.13", "3.14"]
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steps:
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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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uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
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with:
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python-version: ${{ matrix.python-version }}
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cache: pip
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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 }}, ${{ matrix.python-version }}
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run: python -m pytest tests/unit -q
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regression-quick:
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name: Regression (quick)
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needs: unit
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runs-on: ubuntu-24.04
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timeout-minutes: 35
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steps:
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- name: Checkout
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uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
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- name: Set up Python 3.14
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uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
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with:
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python-version: "3.14"
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cache: pip
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- name: Cache testdata
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uses: actions/cache@v4
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with:
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path: .testdata
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key: codeentropy-testdata-v1-${{ runner.os }}-py3.14
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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: Pytest (regression quick)
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run: python -m pytest tests/regression -q
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- name: Upload artifacts (failure)
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if: failure()
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uses: actions/upload-artifact@v4
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with:
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name: quick-regression-failure
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path: |
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.testdata/**
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tests/regression/**/.pytest_cache/**
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/tmp/pytest-of-*/pytest-*/**/config.yaml
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/tmp/pytest-of-*/pytest-*/**/codeentropy_stdout.txt
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/tmp/pytest-of-*/pytest-*/**/codeentropy_stderr.txt
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/tmp/pytest-of-*/pytest-*/**/codeentropy_output.json
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docs:
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name: Docs
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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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- 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 (docs)
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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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pre-commit:
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name: Pre-commit
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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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- name: Checkout
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uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
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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 (pre-commit)
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run: |
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python -m pip install --upgrade pip
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python -m pip install -e .[pre-commit]
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- name: Run pre-commit
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shell: bash
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run: |
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pre-commit install
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pre-commit run --all-files || {
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git status --short
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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

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