Merge remote-tracking branch 'origin/main' into 225-principal-axes

Author: harryswift01

.github/renovate.json

@@ -1,17 +1,17 @@
 {
   "extends": [
     "config:best-practices",
-    ":pinAllExceptPeerDependencies",
     ":dependencyDashboard",
     "group:monorepos",
     "group:recommended"
   ],
-  "rangeStrategy": "pin",
-  "schedule": ["* 8 * * 1-5"],
-  "labels": ["dependencies"],
-  "lockFileMaintenance": {
+  "enabledManagers": ["pep621"],
+  "pep621": {
     "enabled": true
   },
+  "rangeStrategy": "replace",
+  "schedule": ["* 8 * * 1-5"],
+  "labels": ["dependencies"],
   "packageRules": [
     {
       "matchUpdateTypes": ["minor", "patch"],

.github/workflows/mdanalysis-compatibility.yaml

@@ -18,7 +18,7 @@ jobs:
 
     steps:
       - name: Checkout repo
-        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6.1.0

.github/workflows/project-ci.yaml

@@ -18,7 +18,7 @@ jobs:
         python-version: ["3.11", "3.12", "3.13", "3.14"]
     steps:
       - name: Checkout repo
-        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6.1.0
@@ -40,7 +40,7 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 15
     steps:
-      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
       - name: Set up Python 3.14
         uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6.1.0
         with:
@@ -56,7 +56,7 @@ jobs:
     runs-on: ubuntu-24.04
     timeout-minutes: 15
     steps:
-      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
       - name: Set up Python 3.14
         uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6.1.0
         with:

.github/workflows/release.yaml

@@ -18,7 +18,7 @@ jobs:
     steps:
     - name: Checkout repository
       id: repo
-      uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
+      uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
 
     - name: Set up Python
       uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6.1.0
@@ -46,7 +46,7 @@ jobs:
     steps:
 
       - name: checkout
-        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
 
       - name: Change version in repo and CITATION.cff
         run: |
@@ -61,7 +61,7 @@ jobs:
 
       - name: send PR
         id: pr_id
-        uses: peter-evans/create-pull-request@84ae59a2cdc2258d6fa0732dd66352dddae2a412 # v7.0.9
+        uses: peter-evans/create-pull-request@98357b18bf14b5342f975ff684046ec3b2a07725 # v8.0.0
         with:
           commit-message: Update version to ${{ github.event.inputs.version }}
           branch: version-update
@@ -95,7 +95,7 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout repository
-        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
         with:
           ref: main
 
@@ -126,7 +126,7 @@ jobs:
     steps:
 
     - name: checkout
-      uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
+      uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
       with:
         ref: main
 

.github/workflows/update-copyright-years-in-license-file.yaml

@@ -0,0 +1,17 @@
+name: Update copyright year(s) in license file
+
+on:
+  schedule:
+    - cron: '0 3 1 1 *' # 03:00 AM on January 1
+  workflow_dispatch:
+
+jobs:
+    update-license-year:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v6
+              with:
+                  fetch-depth: 0
+            - uses: FantasticFiasco/action-update-license-year@v3
+              with:
+                  token: ${{ secrets.GITHUB_TOKEN }}

CITATION.cff

@@ -76,5 +76,5 @@ keywords:
   - biomolecular simulations
   - protein flexibility
 license: MIT
-version: 1.0.6
-date-released: '2025-11-27'
+version: 1.0.7
+date-released: '2026-01-09'

CodeEntropy/__init__.py

@@ -8,4 +8,4 @@
 and statistical mechanics.
 """
 
-__version__ = "1.0.6"
+__version__ = "1.0.7"

LICENSE

@@ -1,7 +1,7 @@
 
 MIT License
 
-Copyright (c) 2025 CCPBioSim
+Copyright (c) 2025-2026 CCPBioSim
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

pyproject.toml

@@ -38,16 +38,16 @@ classifiers = [
 keywords = ["entropy", "macromolecular systems", "MD simulation"]
 requires-python = ">=3.11"
 dependencies = [
-    "numpy==2.3.5",
-    "mdanalysis==2.10.0",
-    "pandas==2.3.3",
-    "psutil==7.1.3",
-    "PyYAML==6.0.3",
-    "python-json-logger==4.0.0",
-    "rich==14.2.0",
-    "art==6.5",
-    "waterEntropy==1.2.3",
-    "requests==2.32.5",
+    "numpy>=2.3,<3.0",
+    "mdanalysis>=2.10,<3.0",
+    "pandas>=2.3,<3.0",
+    "psutil>=7.1,<8.0",
+    "PyYAML>=6.0,<7.0",
+    "python-json-logger>=4.0,<5.0",
+    "rich>=14.2,<15.0",
+    "art>=6.5,<7.0",
+    "waterEntropy>=2,<2.1",
+    "requests>=2.32,<3.0",
 ]
 
 [project.urls]
@@ -57,24 +57,24 @@ Documentation = "https://codeentropy.readthedocs.io"
 
 [project.optional-dependencies]
 testing = [
-    "pytest==9.0.1",
-    "pytest-cov==7.0.0",
-    "pytest-sugar==1.1.1"
+    "pytest>=9.0,<10.0",
+    "pytest-cov>=7.0,<8.0",
+    "pytest-sugar>=1.1,<2.0"
 ]
 
 pre-commit = [
-    "pre-commit==4.5.0",
-    "pylint==4.0.4"
+    "pre-commit>=4.5,<5.0",
+    "pylint>=4.0,<5.0"
 ]
 docs = [
-    "sphinx",
-    "nbsphinx",
-    "sphinx_rtd_theme",
-    "sphinxcontrib-contentui",
-    "sphinxcontrib-details-directive",
-    "sphinx_copybutton",
-    "furo",
-    "markupsafe==3.0.3"
+    "sphinx>=9.1,<9.2",
+    "nbsphinx>=0.9,<1.0",
+    "sphinx_rtd_theme>=3,<3.2",
+    "sphinxcontrib-contentui>=0.2,<1.0",
+    "sphinxcontrib-details-directive>=0.1,<1.0",
+    "sphinx_copybutton>=0.5,<1.0",
+    "furo>=2025.0,<2026.0",
+    "markupsafe>=3.0,<4.0"
 ]
 
 [project.scripts]