updated regression baselines for ethyl acetate

Author: ioanaapapa

.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",

.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: |

.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
@@ -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: |

.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: |

.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: |

.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: |

CITATION.cff

@@ -76,5 +76,5 @@ keywords:
   - biomolecular simulations
   - protein flexibility
 license: MIT
-version: 2.4.3
-date-released: '2026-08-26'
+version: 2.6.1
+date-released: '2026-10-15'

CodeEntropy/__init__.py

@@ -8,4 +8,4 @@
 and statistical mechanics.
 """
 
-__version__ = "2.4.3"
+__version__ = "2.6.1"

CodeEntropy/cli.py

@@ -4,16 +4,18 @@
 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 @@
 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: