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Merge pull request #458 from CCPBioSim/457-feature-monitor-dependency-lower-bounds-in-ci
Add dependency floor checks and generate conda recipe dependencies from `pyproject.toml`
2 parents 7745ef8 + 4fd7965 commit f5ba2aa

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‎.github/workflows/dependency-floors.yaml‎

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name: Dependency Floors
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on:
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schedule:
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- cron: '0 8 * * 1'
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workflow_dispatch:
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permissions:
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contents: read
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concurrency:
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group: dependency-floors-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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lowest:
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name: Lowest dependencies (${{ matrix.os }}, py${{ 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-26.04, macos-26, windows-2025-vs2026]
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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@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install uv
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run: |
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python -m pip install --upgrade pip
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python -m pip install uv
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- name: Resolve lowest dependencies as wheels
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run: |
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uv pip compile pyproject.toml --resolution lowest-direct --only-binary :all: --output-file lowest.txt
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cat lowest.txt
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- name: Install lowest dependencies
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run: uv pip install --system --resolution lowest-direct -e ".[testing]"
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- name: Run unit tests
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run: python -m pytest tests/unit

‎.github/workflows/pr.yaml‎

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- name: Pytest unit • ${{ matrix.os }}, ${{ matrix.python-version }}
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run: python -m pytest tests/unit
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- name: Install uv
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run: python -m pip install uv
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- name: Resolve lowest dependencies as wheels
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run: |
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uv pip compile pyproject.toml --resolution lowest-direct --only-binary :all: --output-file lowest.txt
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- name: Install lowest dependencies
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run: uv pip install --system --reinstall --resolution lowest-direct -e ".[testing]"
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- name: Pytest unit at lowest dependencies • ${{ matrix.os }}, ${{ matrix.python-version }}
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run: python -m pytest tests/unit
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discover-systems:
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name: Discover regression systems
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runs-on: ubuntu-26.04

‎README.md‎

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| Category | Badges |
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|----------------|--------|
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| **Build** | [![PR Checks](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/pr.yaml/badge.svg)](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/pr.yaml) [![Daily Tests](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/daily.yaml/badge.svg)](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/daily.yaml) |
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| **Build** | [![PR Checks](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/pr.yaml/badge.svg)](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/pr.yaml) [![Daily Tests](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/daily.yaml/badge.svg)](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/daily.yaml) [![Dependency Floors](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/dependency-floors.yaml/badge.svg)](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/dependency-floors.yaml) |
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| **Regression** | [![Weekly Regression](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/weekly-regression.yaml/badge.svg)](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/weekly-regression.yaml) |
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| **Documentation** | [![Weekly Docs](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/weekly-docs.yaml/badge.svg)](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/weekly-docs.yaml) [![Docs - Status](https://app.readthedocs.org/projects/codeentropy/badge/?version=latest)](https://codeentropy.readthedocs.io/en/latest/?badge=latest) |
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| **Citation** | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17570721.svg)](https://doi.org/10.5281/zenodo.17570721) |

‎conda-recipe/meta.yaml‎

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{% set name = "codeentropy" %}
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{% set version = "0.0.0" %}
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{% set pyproject = load_file_data("../pyproject.toml", from_recipe_dir=True) %}
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{% set pip_only = namespace(water_entropy="") %}
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{% for dependency in pyproject["project"]["dependencies"] %}
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{% if dependency.startswith("waterEntropy") %}
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{% set pip_only.water_entropy = dependency %}
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{% endif %}
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{% endfor %}
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package:
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name: {{ name }}
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noarch: python
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script: |
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python -m pip install . -vv --no-deps
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PIP_NO_INDEX=0 python -m pip install -vv --index-url https://pypi.org/simple "waterEntropy>=2,<3.0"
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PIP_NO_INDEX=0 python -m pip install -vv --index-url https://pypi.org/simple "{{ pip_only.water_entropy }}"
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entry_points:
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- CodeEntropy=CodeEntropy.cli:main
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- pip
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- flit-core >=4,<5
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run:
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- python >=3.12
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- numpy >=2.3.2,<2.5.0
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- mdanalysis >=2.10,<3.0
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- pandas >=2.3.3,<4.0
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- psutil >=5.9.4,<8.0
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- pyyaml >=6.0.3,<7.0
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- rich >=13.0.0,<16.0
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- python-art >=5.0,<7.0
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- networkx >=2.8,<4.0
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- requests >=2.32.2,<3.0
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- rdkit >=2025.3.4,<2026
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- dask >=2025.4.0,<2027.1.0
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- distributed >=2025.4.0,<2027.1.0
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- dask-jobqueue >=0.9.0,<1.0
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- numba >=0.63.0,<0.70
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- python {{ pyproject["project"]["requires-python"] }}
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{% for dependency in pyproject["project"]["dependencies"] %}
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{% if dependency.startswith("art>") %}
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- python-{{ dependency }}
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{% elif not dependency.startswith("waterEntropy") %}
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- {{ dependency | lower }}
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{% endif %}
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{% endfor %}
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test:
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imports:

‎docs/developer_guide.rst‎

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- Full regression suite including slow tests
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- Documentation build across all Python versions
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- Dependency floor checks (see :ref:`dependency-policy`)
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CI also caches regression datasets to improve performance.
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.. _dependency-policy:
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Dependency Policy
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-----------------
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Runtime dependencies in ``pyproject.toml`` are declared as ranges. The lower
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bound (floor) is the oldest release CodeEntropy is known to work with, so that it
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stays installable alongside other scientific packages. Floors are only raised
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when the code needs a newer release. Upper bounds are widened by Renovate.
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The unit job in the pull request workflow and the weekly ``dependency-floors.yaml``
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workflow check this. They check that the lowest allowed versions resolve to
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installable wheels on each platform and Python version, and that the unit tests
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pass with them installed.
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Run the same checks locally with `uv <https://docs.astral.sh/uv/>`_::
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uv pip install --resolution lowest-direct -e ".[testing]"
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python -m pytest tests/unit
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Building Documentation
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----------------------
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‎pyproject.toml‎

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keywords = ["entropy", "macromolecular systems", "MD simulation"]
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requires-python = ">=3.12"
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dependencies = [
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"numpy>=2.3.2,<2.6.0",
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"numpy>=2.3.5,<2.6.0",
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"mdanalysis>=2.10,<3.0",
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"pandas>=2.3.3,<4.0",
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"psutil>=5.9.4,<8.0",
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"psutil>=7.1.3,<8.0",
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"PyYAML>=6.0.3,<7.0",
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"rich>=13.0.0,<16.0",
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"art>=5.0,<7.0",
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"requests>=2.32.2,<3.0",
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"rdkit>=2025.3.4,<2027",
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"numba>=0.63.0,<0.70",
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"dask>=2025.4.0,<2027.1.0",
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"dask>=2025.7.0,<2027.1.0",
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"dask-jobqueue>=0.9.0,<1.0",
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"distributed>=2025.4.0,<2027.1.0",
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"distributed>=2025.7.0,<2027.1.0",
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]
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[project.urls]

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