Add dependency floor checks and generate conda recipe dependencies from pyproject.toml

.github/workflows/dependency-floors.yaml

@@ -0,0 +1,50 @@
+name: Dependency Floors
+
+on:
+  schedule:
+    - cron: '0 8 * * 1'
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: dependency-floors-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lowest:
+    name: Lowest dependencies (${{ matrix.os }}, py${{ matrix.python-version }})
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 30
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-26.04, macos-26, windows-2025-vs2026]
+        python-version: ["3.12", "3.13", "3.14"]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install uv
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install uv
+
+      - name: Resolve lowest dependencies as wheels
+        run: |
+          uv pip compile pyproject.toml --resolution lowest-direct --only-binary :all: --output-file lowest.txt
+          cat lowest.txt
+
+      - name: Install lowest dependencies
+        run: uv pip install --system --resolution lowest-direct -e ".[testing]"
+
+      - name: Run unit tests
+        run: python -m pytest tests/unit

.github/workflows/pr.yaml

@@ -38,6 +38,19 @@ jobs:
       - name: Pytest unit • ${{ matrix.os }}, ${{ matrix.python-version }}
         run: python -m pytest tests/unit
 
+      - name: Install uv
+        run: python -m pip install uv
+
+      - name: Resolve lowest dependencies as wheels
+        run: |
+          uv pip compile pyproject.toml --resolution lowest-direct --only-binary :all: --output-file lowest.txt
+
+      - name: Install lowest dependencies
+        run: uv pip install --system --reinstall --resolution lowest-direct -e ".[testing]"
+
+      - name: Pytest unit at lowest dependencies • ${{ matrix.os }}, ${{ matrix.python-version }}
+        run: python -m pytest tests/unit
+
   discover-systems:
     name: Discover regression systems
     runs-on: ubuntu-26.04

README.md

@@ -3,7 +3,7 @@ CodeEntropy
 
 | Category       | Badges |
 |----------------|--------|
-| **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) |
+| **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) |
 | **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) |
 | **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) |
 | **Citation**      | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17570721.svg)](https://doi.org/10.5281/zenodo.17570721) |

conda-recipe/meta.yaml

@@ -1,5 +1,12 @@
 {% set name = "codeentropy" %}
 {% set version = "0.0.0" %}
+{% set pyproject = load_file_data("../pyproject.toml", from_recipe_dir=True) %}
+{% set pip_only = namespace(water_entropy="") %}
+{% for dependency in pyproject["project"]["dependencies"] %}
+{% if dependency.startswith("waterEntropy") %}
+{% set pip_only.water_entropy = dependency %}
+{% endif %}
+{% endfor %}
 
 package:
   name: {{ name }}
@@ -12,7 +19,7 @@ build:
   noarch: python
   script: |
     python -m pip install . -vv --no-deps
-    PIP_NO_INDEX=0 python -m pip install -vv --index-url https://pypi.org/simple "waterEntropy>=2,<3.0"
+    PIP_NO_INDEX=0 python -m pip install -vv --index-url https://pypi.org/simple "{{ pip_only.water_entropy }}"
   entry_points:
     - CodeEntropy=CodeEntropy.cli:main
 
@@ -22,21 +29,14 @@ requirements:
     - pip
     - flit-core >=4,<5
   run:
-    - python >=3.12
-    - numpy >=2.3.2,<2.5.0
-    - mdanalysis >=2.10,<3.0
-    - pandas >=2.3.3,<4.0
-    - psutil >=5.9.4,<8.0
-    - pyyaml >=6.0.3,<7.0
-    - rich >=13.0.0,<16.0
-    - python-art >=5.0,<7.0
-    - networkx >=2.8,<4.0
-    - requests >=2.32.2,<3.0
-    - rdkit >=2025.3.4,<2026
-    - dask >=2025.4.0,<2027.1.0
-    - distributed >=2025.4.0,<2027.1.0
-    - dask-jobqueue >=0.9.0,<1.0
-    - numba >=0.63.0,<0.70
+    - python {{ pyproject["project"]["requires-python"] }}
+    {% for dependency in pyproject["project"]["dependencies"] %}
+    {% if dependency.startswith("art>") %}
+    - python-{{ dependency }}
+    {% elif not dependency.startswith("waterEntropy") %}
+    - {{ dependency | lower }}
+    {% endif %}
+    {% endfor %}
 
 test:
   imports:

docs/developer_guide.rst

@@ -167,9 +167,30 @@ Weekly workflows:
 
 - Full regression suite including slow tests
 - Documentation build across all Python versions
+- Dependency floor checks (see :ref:`dependency-policy`)
 
 CI also caches regression datasets to improve performance.
 
+.. _dependency-policy:
+
+Dependency Policy
+-----------------
+
+Runtime dependencies in ``pyproject.toml`` are declared as ranges. The lower
+bound (floor) is the oldest release CodeEntropy is known to work with, so that it
+stays installable alongside other scientific packages. Floors are only raised
+when the code needs a newer release. Upper bounds are widened by Renovate.
+
+The unit job in the pull request workflow and the weekly ``dependency-floors.yaml``
+workflow check this. They check that the lowest allowed versions resolve to
+installable wheels on each platform and Python version, and that the unit tests
+pass with them installed.
+
+Run the same checks locally with `uv <https://docs.astral.sh/uv/>`_::
+
+    uv pip install --resolution lowest-direct -e ".[testing]"
+    python -m pytest tests/unit
+
 Building Documentation
 ----------------------
 

pyproject.toml

@@ -37,10 +37,10 @@ classifiers = [
 keywords = ["entropy", "macromolecular systems", "MD simulation"]
 requires-python = ">=3.12"
 dependencies = [
-    "numpy>=2.3.2,<2.6.0",
+    "numpy>=2.3.5,<2.6.0",
     "mdanalysis>=2.10,<3.0",
     "pandas>=2.3.3,<4.0",
-    "psutil>=5.9.4,<8.0",
+    "psutil>=7.1.3,<8.0",
     "PyYAML>=6.0.3,<7.0",
     "rich>=13.0.0,<16.0",
     "art>=5.0,<7.0",
@@ -49,9 +49,9 @@ dependencies = [
     "requests>=2.32.2,<3.0",
     "rdkit>=2025.3.4,<2027",
     "numba>=0.63.0,<0.70",
-    "dask>=2025.4.0,<2027.1.0",
+    "dask>=2025.7.0,<2027.1.0",
     "dask-jobqueue>=0.9.0,<1.0",
-    "distributed>=2025.4.0,<2027.1.0",
+    "distributed>=2025.7.0,<2027.1.0",
 ]
 
 [project.urls]