CodeEntropy 2.4.3__tar.gz → 2.6.0__tar.gz

codeentropy-2.6.0/.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,
+  "reviewers": ["harryswift01", "jimboid"],
+  "minimumReleaseAge": "3 days",
+  "packageRules": [
+    {
+      "matchManagers": ["github-actions"],
+      "groupName": "GitHub Actions",
+      "addLabels": ["ci", "dependencies"]
+    },
+    {
+      "matchManagers": ["poetry", "pep621"],
+      "matchDepTypes": ["project.dependencies"],
+      "rangeStrategy": "widen",
+      "groupName": "Software Production Dependencies",
+      "addLabels": ["python", "production-deps"]
+    },
+    {
+      "matchManagers": ["poetry", "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-2.6.0}/.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:
@@ -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-2.4.3 → codeentropy-2.6.0}/.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-2.6.0/.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-2.4.3 → codeentropy-2.6.0}/.github/workflows/pr.yaml

@@ -38,9 +38,22 @@ 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-24.04
+    runs-on: ubuntu-26.04
     outputs:
       systems: ${{ steps.set-systems.outputs.systems }}
 
@@ -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: |
@@ -67,7 +80,7 @@ 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:
@@ -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
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
         with:
           name: quick-regression-failure-${{ matrix.system }}
           path: |
@@ -109,7 +122,7 @@ jobs:
   docs:
     name: Docs
     needs: unit
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     timeout-minutes: 25
 
     steps:
@@ -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
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
         with:
           name: docs-html
           path: docs/_build/html
@@ -141,7 +154,7 @@ jobs:
   pre-commit:
     name: Pre-commit
     needs: unit
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     timeout-minutes: 15
 
     steps:
@@ -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: |
@@ -170,7 +183,7 @@ jobs:
   coverage:
     name: Coverage
     needs: unit
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     timeout-minutes: 30
 
     permissions:
@@ -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-2.4.3 → codeentropy-2.6.0}/.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: 3.15.0
 
     - 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: 3.15.0
 
     - 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: "3.15"
           auto-activate: true
           activate-environment: base
           conda-remove-defaults: true

{codeentropy-2.4.3 → codeentropy-2.6.0}/.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-2.6.0}/.github/workflows/update_regression_baselines.yaml

@@ -13,19 +13,19 @@ 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 }}
 
       - 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: |
@@ -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-2.6.0}/.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@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
         with:
           name: docs-${{ matrix.os }}-py${{ matrix.python-version }}-failure
           path: |

{codeentropy-2.4.3 → codeentropy-2.6.0}/.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 }}
@@ -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: |
@@ -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:
@@ -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
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
         with:
           name: regression-${{ matrix.system }}-artifacts
           path: |

{codeentropy-2.4.3 → codeentropy-2.6.0}/CITATION.cff

@@ -76,5 +76,5 @@ keywords:
   - biomolecular simulations
   - protein flexibility
 license: MIT
-version: 2.4.3
-date-released: '2026-08-26'
+version: 2.6.0
+date-released: '2026-10-14'

{codeentropy-2.4.3 → codeentropy-2.6.0}/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__ = "2.6.0"

{codeentropy-2.4.3 → codeentropy-2.6.0}/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-2.4.3 → codeentropy-2.6.0}/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-2.4.3 → codeentropy-2.6.0}/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-2.4.3 → codeentropy-2.6.0}/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))