CodeEntropy 2.4.3__tar.gz → 2.5.0__tar.gz

codeentropy-2.5.0/.github/renovate.json

@@ -0,0 +1,33 @@
+{
+  "$schema": "https://docs.renovatebot.com/renovate-schema.json",
+  "extends": [
+    "config:best-practices",
+    "helpers:pinGitHubActionDigestsToSemver"
+  ],
+  "timezone": "Europe/London",
+  "schedule": ["after 9am and before 5pm every weekday"],
+  "dependencyDashboard": true,
+  "assignees": ["harryswift01", "jimboid"],
+  "minimumReleaseAge": "3 days",
+  "packageRules": [
+    {
+      "matchManagers": ["github-actions"],
+      "groupName": "GitHub Actions",
+      "addLabels": ["ci", "dependencies"]
+    },
+    {
+      "matchManagers": ["pep621"],
+      "matchDepTypes": ["project.dependencies"],
+      "rangeStrategy": "widen",
+      "groupName": "Software Production Dependencies",
+      "addLabels": ["python", "production-deps"]
+    },
+    {
+      "matchManagers": ["pep621"],
+      "matchDepTypes": ["project.optional-dependencies", "build-system.requires"],
+      "rangeStrategy": "replace",
+      "groupName": "Python CI and Dev Tools",
+      "addLabels": ["python", "dev-dependencies"]
+    }
+  ]
+}

{codeentropy-2.4.3 → codeentropy-2.5.0}/.github/workflows/coveralls-main.yaml

@@ -16,7 +16,7 @@ concurrency:
 jobs:
   coveralls:
     name: Build main coverage baseline
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     timeout-minutes: 30
 
     permissions:

{codeentropy-2.4.3 → codeentropy-2.5.0}/.github/workflows/daily.yaml

@@ -23,7 +23,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0

{codeentropy-2.4.3 → codeentropy-2.5.0}/.github/workflows/pr.yaml

@@ -40,7 +40,7 @@ jobs:
 
   discover-systems:
     name: Discover regression systems
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     outputs:
       systems: ${{ steps.set-systems.outputs.systems }}
 
@@ -67,7 +67,7 @@ jobs:
   regression-quick:
     name: Regression fast • ${{ matrix.system }}
     needs: discover-systems
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     timeout-minutes: 35
 
     strategy:
@@ -99,7 +99,7 @@ jobs:
 
       - name: Upload artifacts on failure
         if: failure()
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
         with:
           name: quick-regression-failure-${{ matrix.system }}
           path: |
@@ -109,7 +109,7 @@ jobs:
   docs:
     name: Docs
     needs: unit
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     timeout-minutes: 25
 
     steps:
@@ -133,7 +133,7 @@ jobs:
 
       - name: Upload docs artifact
         if: always()
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
         with:
           name: docs-html
           path: docs/_build/html
@@ -141,7 +141,7 @@ jobs:
   pre-commit:
     name: Pre-commit
     needs: unit
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     timeout-minutes: 15
 
     steps:
@@ -170,7 +170,7 @@ jobs:
   coverage:
     name: Coverage
     needs: unit
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     timeout-minutes: 30
 
     permissions:

{codeentropy-2.4.3 → codeentropy-2.5.0}/.github/workflows/release.yaml

@@ -14,16 +14,16 @@ permissions:
 jobs:
   checks:
     name: Version check
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     steps:
     - name: Checkout repository
       id: repo
-      uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+      uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
 
     - name: Set up Python
       uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
       with:
-        python-version: 3.14.6
+        python-version: 3.14.8
 
     - name: Get latest release from pip
       id: latestreleased
@@ -42,11 +42,11 @@ jobs:
   version:
     name: prepare ${{ github.event.inputs.version }}
     needs: checks
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     steps:
 
       - name: checkout
-        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
 
       - name: Change version in repo and CITATION.cff
         run: |
@@ -92,10 +92,10 @@ jobs:
   tag:
     name: tag release
     needs: version
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     steps:
       - name: Checkout repository
-        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           ref: main
 
@@ -109,11 +109,11 @@ jobs:
   release:
     name: make github release
     needs: tag
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     steps:
       - name: create release
         id: create_release
-        uses: softprops/action-gh-release@3d0d9888cb7fd7b750713d6e236d1fcb99157228 # v3.0.2
+        uses: softprops/action-gh-release@efb35369e0ad2afab669f228072c1b0d510eae64 # v3.0.3
         with:
           name: v${{ github.event.inputs.version }}
           generate_release_notes: true
@@ -128,7 +128,7 @@ jobs:
         run: |
           # generate_release_notes builds the changelog server-side, so pull
           # it back down here rather than trying to reconstruct it locally.
-          gh release view "${{ github.event.inputs.version }}" --json body -q .body > changelog.txt
+          gh release view "${{ github.event.inputs.version }}" --repo "${{ github.repository }}" --json body -q .body > changelog.txt
 
       - name: notify Zulip of release
         if: steps.create_release.outcome == 'success'
@@ -158,18 +158,18 @@ jobs:
   pypi:
     name: make pypi release
     needs: [tag, release]
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     steps:
 
     - name: checkout
-      uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+      uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
       with:
         ref: main
 
     - name: Set up Python
       uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
       with:
-        python-version: 3.14.6
+        python-version: 3.14.8
 
     - name: Install flit
       run: |
@@ -186,11 +186,11 @@ jobs:
   conda:
     name: publish conda to anaconda.org
     needs: [tag, release]
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
 
     steps:
       - name: Checkout
-        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           ref: main
 
@@ -200,10 +200,10 @@ jobs:
           grep '{% set version' conda-recipe/meta.yaml
 
       - name: Setup Conda (conda-forge only)
-        uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4
+        uses: conda-incubator/setup-miniconda@be893c923ea9cf1cf7cd510fbdde27c7e18cbdcb # v4.1.0
         with:
           miniforge-variant: Miniforge3
-          python-version: "3.12"
+          python-version: "3.14"
           auto-activate: true
           activate-environment: base
           conda-remove-defaults: true

{codeentropy-2.4.3 → codeentropy-2.5.0}/.github/workflows/update-copyright-years-in-license-file.yaml

@@ -9,9 +9,9 @@ jobs:
     update-license-year:
         runs-on: ubuntu-latest
         steps:
-            - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+            - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
               with:
                   fetch-depth: 0
-            - uses: FantasticFiasco/action-update-license-year@f180e962fa988db222d8f03ef4636750312d1b3d # v3
+            - uses: FantasticFiasco/action-update-license-year@f180e962fa988db222d8f03ef4636750312d1b3d # v3.0.4
               with:
                   token: ${{ secrets.GITHUB_TOKEN }}

{codeentropy-2.4.3 → codeentropy-2.5.0}/.github/workflows/update_regression_baselines.yaml

@@ -13,12 +13,12 @@ permissions:
 jobs:
   update-baselines:
     name: Update regression baselines
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     timeout-minutes: 30
 
     steps:
       - name: Checkout
-        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           ref: ${{ github.ref }}
 
@@ -36,7 +36,7 @@ jobs:
         run: pytest tests/regression --update-baselines --run-slow
 
       - name: Commit updated baselines
-        uses: stefanzweifel/git-auto-commit-action@4a55954c782fc1ea30b9056cd3e7a2b40ca8887d # v7
+        uses: stefanzweifel/git-auto-commit-action@4a55954c782fc1ea30b9056cd3e7a2b40ca8887d # v7.2.0
         with:
           commit_message: "test(regression): update baselines"
           commit_user_name: github-actions[bot]

{codeentropy-2.4.3 → codeentropy-2.5.0}/.github/workflows/weekly-docs.yaml

@@ -22,7 +22,7 @@ jobs:
 
     steps:
       - name: Checkout repo
-        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
@@ -41,7 +41,7 @@ jobs:
 
       - name: Upload docs artifacts on failure
         if: failure()
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
         with:
           name: docs-${{ matrix.os }}-py${{ matrix.python-version }}-failure
           path: |

{codeentropy-2.4.3 → codeentropy-2.5.0}/.github/workflows/weekly-regression.yaml

@@ -12,7 +12,7 @@ concurrency:
 jobs:
   discover:
     name: Discover regression systems
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
 
     outputs:
       systems: ${{ steps.set.outputs.systems }}
@@ -40,7 +40,7 @@ jobs:
   regression:
     name: Regression (${{ matrix.system }})
     needs: discover
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     timeout-minutes: 360
 
     strategy:
@@ -72,7 +72,7 @@ jobs:
 
       - name: Upload regression artifacts (failure)
         if: failure()
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
         with:
           name: regression-${{ matrix.system }}-artifacts
           path: |

{codeentropy-2.4.3 → codeentropy-2.5.0}/CITATION.cff

@@ -76,5 +76,5 @@ keywords:
   - biomolecular simulations
   - protein flexibility
 license: MIT
-version: 2.4.3
-date-released: '2026-08-26'
+version: 2.5.0
+date-released: '2026-10-09'

{codeentropy-2.4.3 → codeentropy-2.5.0}/CodeEntropy/__init__.py

@@ -8,4 +8,4 @@ entropy estimates, supporting a wide range of applications in molecular simulati
 and statistical mechanics.
 """
 
-__version__ = "2.4.3"
+__version__ = "2.5.0"

{codeentropy-2.4.3 → codeentropy-2.5.0}/CodeEntropy/entropy/vibrational.py

@@ -148,7 +148,7 @@ class VibrationalEntropy:
             Eigenvalues as a NumPy array.
         """
         matrix = np.asarray(matrix, dtype=float)
-        return la.eigvals(matrix)
+        return la.eigvalsh(matrix)
 
     def _convert_lambda_units(self, lambdas: np.ndarray) -> np.ndarray:
         """Convert eigenvalues into SI units using run_manager.
@@ -185,7 +185,10 @@ class VibrationalEntropy:
         """Convert eigenvalues to frequencies with robust filtering.
 
         Filters out eigenvalues that are complex, non-positive, or near-zero to
-        avoid invalid frequencies and unstable entropies.
+        avoid invalid frequencies and unstable entropies. The near-zero
+        tolerance scales with the spectrum's own magnitude (as in
+        ``numpy.linalg.matrix_rank``) rather than using a fixed cutoff, since
+        the eigensolver noise floor around a true null mode is not constant.
 
         Args:
             lambdas: Eigenvalues (post unit conversion).
@@ -197,8 +200,11 @@ class VibrationalEntropy:
         lambdas = np.asarray(lambdas)
         lambdas = np.real_if_close(lambdas, tol=1000)
 
+        scale = float(np.max(np.abs(lambdas))) if lambdas.size else 0.0
+        atol = lambdas.size * np.finfo(float).eps * scale
+
         valid_mask = (
-            np.isreal(lambdas) & (lambdas > 0) & (~np.isclose(lambdas, 0, atol=1e-7))
+            np.isreal(lambdas) & (lambdas > 0) & (~np.isclose(lambdas, 0, atol=atol))
         )
 
         removed = int(len(lambdas) - np.count_nonzero(valid_mask))