CodeEntropy 2.5.0__tar.gz → 2.6.1__tar.gz

{codeentropy-2.5.0 → codeentropy-2.6.1}/.github/renovate.json

@@ -7,7 +7,7 @@
   "timezone": "Europe/London",
   "schedule": ["after 9am and before 5pm every weekday"],
   "dependencyDashboard": true,
-  "assignees": ["harryswift01", "jimboid"],
+  "reviewers": ["harryswift01", "jimboid"],
   "minimumReleaseAge": "3 days",
   "packageRules": [
     {
@@ -16,14 +16,14 @@
       "addLabels": ["ci", "dependencies"]
     },
     {
-      "matchManagers": ["pep621"],
+      "matchManagers": ["poetry", "pep621"],
       "matchDepTypes": ["project.dependencies"],
       "rangeStrategy": "widen",
       "groupName": "Software Production Dependencies",
       "addLabels": ["python", "production-deps"]
     },
     {
-      "matchManagers": ["pep621"],
+      "matchManagers": ["poetry", "pep621"],
       "matchDepTypes": ["project.optional-dependencies", "build-system.requires"],
       "rangeStrategy": "replace",
       "groupName": "Python CI and Dev Tools",

{codeentropy-2.5.0 → codeentropy-2.6.1}/.github/workflows/coveralls-main.yaml

@@ -31,7 +31,7 @@ jobs:
       - name: Set up Python 3.14
         uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
         with:
-          python-version: "3.14"
+          python-version: "3.15"
 
       - name: Install testing dependencies
         run: |

codeentropy-2.6.1/.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

{codeentropy-2.5.0 → codeentropy-2.6.1}/.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
@@ -51,7 +64,7 @@ jobs:
       - name: Set up Python 3.14
         uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
         with:
-          python-version: "3.14"
+          python-version: "3.15"
 
       - name: Install testing dependencies
         run: |
@@ -82,7 +95,7 @@ jobs:
       - name: Set up Python 3.14
         uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
         with:
-          python-version: "3.14"
+          python-version: "3.15"
 
       - name: Install testing dependencies
         run: |
@@ -99,7 +112,7 @@ jobs:
 
       - name: Upload artifacts on failure
         if: failure()
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
         with:
           name: quick-regression-failure-${{ matrix.system }}
           path: |
@@ -119,7 +132,7 @@ jobs:
       - name: Set up Python 3.14
         uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
         with:
-          python-version: "3.14"
+          python-version: "3.15"
 
       - name: Install docs dependencies
         run: |
@@ -133,7 +146,7 @@ jobs:
 
       - name: Upload docs artifact
         if: always()
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
         with:
           name: docs-html
           path: docs/_build/html
@@ -151,7 +164,7 @@ jobs:
       - name: Set up Python 3.14
         uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
         with:
-          python-version: "3.14"
+          python-version: "3.15"
 
       - name: Install pre-commit dependencies
         run: |
@@ -186,7 +199,7 @@ jobs:
       - name: Set up Python 3.14
         uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
         with:
-          python-version: "3.14"
+          python-version: "3.15"
 
       - name: Install testing dependencies
         run: |

{codeentropy-2.5.0 → codeentropy-2.6.1}/.github/workflows/update_regression_baselines.yaml

@@ -25,7 +25,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
         with:
-          python-version: "3.14"
+          python-version: "3.15"
 
       - name: Install testing dependencies
         run: |

{codeentropy-2.5.0 → codeentropy-2.6.1}/.github/workflows/weekly-docs.yaml

@@ -41,7 +41,7 @@ jobs:
 
       - name: Upload docs artifacts on failure
         if: failure()
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
         with:
           name: docs-${{ matrix.os }}-py${{ matrix.python-version }}-failure
           path: |

{codeentropy-2.5.0 → codeentropy-2.6.1}/.github/workflows/weekly-regression.yaml

@@ -24,7 +24,7 @@ jobs:
       - name: Set up Python 3.14
         uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
         with:
-          python-version: "3.14"
+          python-version: "3.15"
 
       - name: Install testing dependencies
         run: |
@@ -55,7 +55,7 @@ jobs:
       - name: Set up Python 3.14
         uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
         with:
-          python-version: "3.14"
+          python-version: "3.15"
 
       - name: Install testing dependencies
         run: |
@@ -72,7 +72,7 @@ jobs:
 
       - name: Upload regression artifacts (failure)
         if: failure()
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
         with:
           name: regression-${{ matrix.system }}-artifacts
           path: |

{codeentropy-2.5.0 → codeentropy-2.6.1}/CITATION.cff

@@ -76,5 +76,5 @@ keywords:
   - biomolecular simulations
   - protein flexibility
 license: MIT
-version: 2.5.0
-date-released: '2026-10-09'
+version: 2.6.1
+date-released: '2026-10-15'

{codeentropy-2.5.0 → codeentropy-2.6.1}/CodeEntropy/__init__.py

@@ -8,4 +8,4 @@ entropy estimates, supporting a wide range of applications in molecular simulati
 and statistical mechanics.
 """
 
-__version__ = "2.5.0"
+__version__ = "2.6.1"

{codeentropy-2.5.0 → codeentropy-2.6.1}/CodeEntropy/cli.py

@@ -4,16 +4,18 @@ This module provides the CLI entry point used to run the multiscale cell
 correlation entropy workflow.
 
 The entry point is intentionally small and only responsible for:
-  1) Creating a job folder.
-  2) Constructing a CodeEntropyRunner.
-  3) Executing the entropy workflow.
-  4) Handling fatal errors with a non-zero exit code.
+  1) Handling informational flags such as ``--version``.
+  2) Creating a job folder.
+  3) Constructing a CodeEntropyRunner.
+  4) Executing the entropy workflow.
+  5) Handling fatal errors with a non-zero exit code.
 """
 
 from __future__ import annotations
 
 import logging
 
+from CodeEntropy.config.argparse import ConfigResolver
 from CodeEntropy.config.runtime import CodeEntropyRunner
 
 logger = logging.getLogger(__name__)
@@ -22,9 +24,15 @@ logger = logging.getLogger(__name__)
 def main() -> None:
     """Run the entropy workflow.
 
+    Arguments are parsed before any side effects so that informational flags such
+    as ``--version`` and ``--help`` exit without creating a job folder or
+    rendering the splash screen.
+
     Raises:
         SystemExit: Exits with status code 1 on any unhandled exception.
     """
+    ConfigResolver().build_parser().parse_known_args()
+
     folder = CodeEntropyRunner.create_job_folder()
 
     try:

{codeentropy-2.5.0 → codeentropy-2.6.1}/CodeEntropy/config/argparse.py

@@ -31,6 +31,7 @@ from typing import Any
 
 import yaml
 
+from CodeEntropy import __version__
 from CodeEntropy.core.dask_clusters import HPCDaskManager
 
 logger = logging.getLogger(__name__)
@@ -318,6 +319,11 @@ class ConfigResolver:
         parser = argparse.ArgumentParser(
             description="CodeEntropy: entropy calculation with the MCC method."
         )
+        parser.add_argument(
+            "--version",
+            action="version",
+            version=f"CodeEntropy {__version__}",
+        )
 
         for name, spec in self._arg_specs.items():
             arg_name = f"--{name}"

{codeentropy-2.5.0 → codeentropy-2.6.1}/CodeEntropy/config/runtime.py

@@ -32,6 +32,7 @@ from rich.rule import Rule
 from rich.table import Table
 from rich.text import Text
 
+from CodeEntropy import __version__
 from CodeEntropy.config.argparse import ConfigResolver
 from CodeEntropy.core.dask_clusters import HPCDaskManager
 from CodeEntropy.core.logging import LoggingConfig
@@ -135,20 +136,21 @@ class CodeEntropyRunner:
             return None
 
     def show_splash(self) -> None:
-        """Render a Rich splash screen with optional citation metadata."""
+        """Render a Rich splash screen.
+
+        The version shown is that of the locally installed package. Remaining
+        metadata (authors, description, URL) comes from the online citation file
+        when it is reachable.
+        """
         citation = self.load_citation_data()
+        version_text = Align.center(Text(f"Version {__version__}", style="green"))
 
         if citation:
             ascii_title = text2art(citation.get("title", "CodeEntropy"))
             ascii_render = Align.center(Text(ascii_title, style="bold white"))
 
-            version = citation.get("version", "?")
-            release_date = citation.get("date-released", "?")
             url = citation.get("url", citation.get("repository-code", ""))
 
-            version_text = Align.center(
-                Text(f"Version {version} | Released {release_date}", style="green")
-            )
             url_text = Align.center(Text(url, style="blue underline"))
 
             abstract = citation.get("abstract", "No description available.")
@@ -193,7 +195,7 @@ class CodeEntropyRunner:
         else:
             ascii_title = text2art("CodeEntropy")
             ascii_render = Align.center(Text(ascii_title, style="bold white"))
-            splash_content = Group(ascii_render)
+            splash_content = Group(ascii_render, Rule(style="cyan"), version_text)
 
         splash_panel = Panel(
             splash_content,

{codeentropy-2.5.0 → codeentropy-2.6.1}/CodeEntropy/levels/dihedrals/conformational_state_builder.py

@@ -46,7 +46,12 @@ class ConformationStateBuilder(ConformationPeakDetector, ConformationStateAssign
         frame_selection: FrameSelection,
         progress: _RichProgressSink | None = None,
         chunk_size: int | None = None,
-    ) -> tuple[dict[UAKey, list[str]], list[list[str]], dict[UAKey, int], list[int]]:
+    ) -> tuple[
+        dict[UAKey, list[str]],
+        dict[int, list[str]],
+        dict[UAKey, int],
+        dict[int, int],
+    ]:
         """Build conformational state labels from selected trajectory frames.
 
         Args:
@@ -87,7 +92,12 @@ class ConformationStateBuilder(ConformationPeakDetector, ConformationStateAssign
         frame_selection: FrameSelection,
         chunk_size: int,
         progress: _RichProgressSink | None = None,
-    ) -> tuple[dict[UAKey, list[str]], list[list[str]], dict[UAKey, int], list[int]]:
+    ) -> tuple[
+        dict[UAKey, list[str]],
+        dict[int, list[str]],
+        dict[UAKey, int],
+        dict[int, int],
+    ]:
         """Build conformational states with serial frame-chunk map-reduce.
 
         Args:
@@ -108,11 +118,10 @@ class ConformationStateBuilder(ConformationPeakDetector, ConformationStateAssign
         if chunk_size < 1:
             raise ValueError("chunk_size must be >= 1")
 
-        number_groups = len(groups)
         states_ua: dict[UAKey, list[str]] = {}
-        states_res: list[list[str]] = [[] for _ in range(number_groups)]
+        states_res: dict[int, list[str]] = {}
         flexible_ua: dict[UAKey, int] = {}
-        flexible_res: list[int] = []
+        flexible_res: dict[int, int] = {}
 
         task: TaskID | None = None
         if progress is not None:
@@ -186,6 +195,7 @@ class ConformationStateBuilder(ConformationPeakDetector, ConformationStateAssign
             state_data = self._reduce_state_partials(state_partials)
 
             self._merge_group_state_data(
+                group_id=group_id,
                 state_data=state_data,
                 states_ua=states_ua,
                 states_res=states_res,

{codeentropy-2.5.0 → codeentropy-2.6.1}/CodeEntropy/levels/dihedrals/state_assignment.py

@@ -170,20 +170,23 @@ class ConformationStateAssigner:
 
     @staticmethod
     def _merge_group_state_data(
+        group_id: int,
         state_data: ConformationStateData,
         states_ua: dict[UAKey, list[str]],
-        states_res: list[list[str]],
+        states_res: dict[int, list[str]],
         flexible_ua: dict[UAKey, int],
-        flexible_res: list[int],
+        flexible_res: dict[int, int],
     ) -> None:
         """Merge one group's state data into final output accumulators.
 
         Args:
+            group_id: Id of the group the state data belongs to.
             state_data: Serial conformational state data for one group.
             states_ua: UA state accumulator to mutate.
-            states_res: Residue state accumulator to mutate.
+            states_res: Residue state accumulator, keyed by group id, to mutate.
             flexible_ua: UA flexible-dihedral accumulator to mutate.
-            flexible_res: Residue flexible-dihedral accumulator to mutate.
+            flexible_res: Residue flexible-dihedral accumulator, keyed by group id,
+                to mutate.
 
         Returns:
             None. Mutates the provided accumulators.
@@ -199,8 +202,8 @@ class ConformationStateAssigner:
                     state_data.flexible_ua_updates[key],
                 )
 
-        states_res.append(state_data.state_res)
-        flexible_res.append(state_data.flex_res)
+        states_res[group_id] = state_data.state_res
+        flexible_res[group_id] = state_data.flex_res
 
     def _process_conformations_from_angles(
         self,

{codeentropy-2.5.0 → codeentropy-2.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: CodeEntropy
-Version: 2.5.0
+Version: 2.6.1
 Summary: CodeEntropy is a Python package for computing the configurational entropy of macromolecular systems using forces sampled from molecular dynamics (MD) simulations. It implements the multiscale cell correlation method to provide accurate and efficient entropy estimates, supporting a wide range of applications in molecular simulation and statistical mechanics.
 Keywords: entropy,macromolecular systems,MD simulation
 Author-email: Arghya 'Argo' Chakravorty <arghyac@umich.edu>, Donald Chung-HK <donald.chung@stfc.ac.uk>, Sarah Fegan <sarah.fegan@stfc.ac.uk>, James Gebbie-Rayet <james.gebbie@stfc.ac.uk>, Sarah Harris <sarah.harris@sheffield.ac.uk>, Richard Henchman <rhen7213@uni.sydney.edu.au>, Jonathan Higham <j.higham4@lancaster.ac.uk>, Jas Kalayan <jas.kalayan@stfc.ac.uk>, Ioana Papa <iapapa1@sheffield.ac.uk>
@@ -16,21 +16,21 @@ Classifier: License :: OSI Approved :: MIT License
 Classifier: Natural Language :: English
 Classifier: Development Status :: 5 - Production/Stable
 License-File: LICENSE
-Requires-Dist: numpy>=2.3.2,<2.5.0
+Requires-Dist: numpy>=2.3.5,<2.6.0
 Requires-Dist: mdanalysis>=2.10,<3.0
 Requires-Dist: pandas>=2.3.3,<4.0
-Requires-Dist: psutil>=5.9.4,<8.0
+Requires-Dist: psutil>=7.1.3,<8.0
 Requires-Dist: PyYAML>=6.0.3,<7.0
 Requires-Dist: rich>=13.0.0,<16.0
 Requires-Dist: art>=5.0,<7.0
 Requires-Dist: networkx>=2.8,<4.0
 Requires-Dist: waterEntropy>=2,<3.0
 Requires-Dist: requests>=2.32.2,<3.0
-Requires-Dist: rdkit>=2025.3.4,<2026
+Requires-Dist: rdkit>=2025.3.4,<2027
 Requires-Dist: numba>=0.63.0,<0.70
-Requires-Dist: dask>=2025.4.0,<2027.1.0
+Requires-Dist: dask>=2025.7.0,<2027.1.0
 Requires-Dist: dask-jobqueue>=0.9.0,<1.0
-Requires-Dist: distributed>=2025.4.0,<2027.1.0
+Requires-Dist: distributed>=2025.7.0,<2027.1.0
 Requires-Dist: sphinx>=8.0.0,<10.0 ; extra == "docs"
 Requires-Dist: nbsphinx>=0.9.3,<1.0 ; extra == "docs"
 Requires-Dist: sphinx_copybutton>=0.5,<1.0 ; extra == "docs"
@@ -56,7 +56,7 @@ 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) |

{codeentropy-2.5.0 → codeentropy-2.6.1}/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) |

{codeentropy-2.5.0 → codeentropy-2.6.1}/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:

{codeentropy-2.5.0 → codeentropy-2.6.1}/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
 ----------------------
 

{codeentropy-2.5.0 → codeentropy-2.6.1}/pyproject.toml

@@ -37,21 +37,21 @@ classifiers = [
 keywords = ["entropy", "macromolecular systems", "MD simulation"]
 requires-python = ">=3.12"
 dependencies = [
-    "numpy>=2.3.2,<2.5.0",
+    "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",
     "networkx>=2.8,<4.0",
     "waterEntropy>=2,<3.0",
     "requests>=2.32.2,<3.0",
-    "rdkit>=2025.3.4,<2026",
+    "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]

{codeentropy-2.5.0 → codeentropy-2.6.1}/tests/regression/baselines/benzaldehyde/axes_off.json

@@ -3,14 +3,14 @@
     "0": {
       "components": {
         "united_atom:Transvibrational": 0.06950663196232491,
-        "united_atom:Rovibrational": 35.19655714759131,
-        "residue:FTmat-Transvibrational": 86.6413638447789,
-        "residue:FTmat-Rovibrational": 62.24303760058523,
+        "united_atom:Rovibrational": 35.19655714759134,
+        "residue:FTmat-Transvibrational": 86.64136384477892,
+        "residue:FTmat-Rovibrational": 62.24303760058521,
         "united_atom:Conformational": 0.0,
         "residue:Conformational": 0.0,
         "residue:Orientational": 20.481571492615355
       },
-      "total": 204.6320367175331
+      "total": 204.63203671753317
     }
   }
 }

{codeentropy-2.5.0 → codeentropy-2.6.1}/tests/regression/baselines/benzaldehyde/combined_forcetorque_false.json

@@ -3,14 +3,14 @@
     "0": {
       "components": {
         "united_atom:Transvibrational": 0.06817494136874551,
-        "united_atom:Rovibrational": 49.686697381523466,
+        "united_atom:Rovibrational": 49.686697381523516,
         "residue:Transvibrational": 69.25273989458984,
-        "residue:Rovibrational": 68.64810133422232,
+        "residue:Rovibrational": 68.6481013342223,
         "united_atom:Conformational": 0.0,
         "residue:Conformational": 0.0,
         "residue:Orientational": 20.481571492615355
       },
-      "total": 208.13728504431973
+      "total": 208.13728504431975
     }
   }
 }

{codeentropy-2.5.0 → codeentropy-2.6.1}/tests/regression/baselines/benzaldehyde/default.json

@@ -2,9 +2,9 @@
   "groups": {
     "0": {
       "components": {
-        "united_atom:Transvibrational": 24.921822103314035,
-        "united_atom:Rovibrational": 27.950376507672594,
-        "residue:FTmat-Transvibrational": 70.97090266225699,
+        "united_atom:Transvibrational": 24.92182210331405,
+        "united_atom:Rovibrational": 27.950376507672583,
+        "residue:FTmat-Transvibrational": 70.97090266225698,
         "residue:FTmat-Rovibrational": 59.588669973122094,
         "united_atom:Conformational": 7.522643899702263,
         "residue:Conformational": 0.0,