CodeEntropy 2.2.4__tar.gz → 2.4.1__tar.gz

{codeentropy-2.2.4 → codeentropy-2.4.1}/.github/renovate.json

@@ -5,7 +5,7 @@
     "group:monorepos",
     "group:recommended"
   ],
-  "enabledManagers": ["pep621"],
+  "enabledManagers": ["pep621", "github-actions"],
   "pep621": {
     "enabled": true
   },

codeentropy-2.4.1/.github/workflows/coveralls-main.yaml

@@ -0,0 +1,54 @@
+name: Coveralls Main
+
+on:
+  push:
+    branches: [main]
+
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: coveralls-main-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  coveralls:
+    name: Build main coverage baseline
+    runs-on: ubuntu-24.04
+    timeout-minutes: 30
+
+    permissions:
+      contents: read
+      checks: write
+      statuses: write
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+
+      - name: Set up Python 3.14
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
+        with:
+          python-version: "3.14"
+
+      - name: Install testing dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[testing]
+
+      - name: Run coverage
+        run: |
+          python -m pytest tests/unit \
+            --cov CodeEntropy \
+            --cov-report term-missing \
+            --cov-report xml \
+            -q
+
+      - name: Upload coverage to Coveralls
+        uses: coverallsapp/github-action@5cbfd81b66ca5d10c19b062c04de0199c215fb6e
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          file: coverage.xml
+          fail-on-error: false

{codeentropy-2.2.4 → codeentropy-2.4.1}/.github/workflows/daily.yaml

@@ -18,15 +18,15 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-24.04, macos-15, windows-2025]
+        os: [ubuntu-24.04, macos-26, windows-2025-vs2026]
         python-version: ["3.12", "3.13", "3.14"]
 
     steps:
       - name: Checkout
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
         with:
           python-version: ${{ matrix.python-version }}
 

{codeentropy-2.2.4 → codeentropy-2.4.1}/.github/workflows/pr.yaml

@@ -3,8 +3,11 @@ name: Pull Request CI
 on:
   pull_request:
 
+permissions:
+  contents: read
+
 concurrency:
-  group: pr-${{ github.ref }}
+  group: pr-ci-${{ github.ref }}
   cancel-in-progress: true
 
 jobs:
@@ -15,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-24.04, macos-15, windows-2025]
+        os: [ubuntu-24.04, macos-26, windows-2025-vs2026]
         python-version: ["3.12", "3.13", "3.14"]
 
     steps:
@@ -32,7 +35,7 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install -e .[testing]
 
-      - name: Pytest (unit) • ${{ matrix.os }}, ${{ matrix.python-version }}
+      - name: Pytest unit • ${{ matrix.os }}, ${{ matrix.python-version }}
         run: python -m pytest tests/unit
 
   discover-systems:
@@ -59,11 +62,11 @@ jobs:
         id: set-systems
         run: |
           SYSTEMS=$(python -m tests.regression.list_systems)
-          echo "systems=$SYSTEMS" >> $GITHUB_OUTPUT
+          echo "systems=$SYSTEMS" >> "$GITHUB_OUTPUT"
 
   regression-quick:
-    name: Regression (fast) • ${{ matrix.system }}
-    needs: [unit, discover-systems]
+    name: Regression fast • ${{ matrix.system }}
+    needs: discover-systems
     runs-on: ubuntu-24.04
     timeout-minutes: 35
 
@@ -86,19 +89,17 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install -e .[testing]
 
-      - name: Run fast regression tests (per system)
+      - name: Run fast regression tests
         run: |
           python -m pytest tests/regression \
             -m "not slow" \
-            -n auto \
-            --dist=loadscope \
-            -k "${{ matrix.system }}" \
+            --system "${{ matrix.system }}" \
             -vv \
             --durations=20
 
-      - name: Upload artifacts (failure)
+      - name: Upload artifacts on failure
         if: failure()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: quick-regression-failure-${{ matrix.system }}
           path: |
@@ -132,13 +133,14 @@ jobs:
 
       - name: Upload docs artifact
         if: always()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: docs-html
           path: docs/_build/html
 
   pre-commit:
     name: Pre-commit
+    needs: unit
     runs-on: ubuntu-24.04
     timeout-minutes: 15
 
@@ -171,6 +173,12 @@ jobs:
     runs-on: ubuntu-24.04
     timeout-minutes: 30
 
+    permissions:
+      contents: read
+      checks: write
+      statuses: write
+      pull-requests: write
+
     steps:
       - name: Checkout
         uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
@@ -187,7 +195,7 @@ jobs:
 
       - name: Run coverage
         run: |
-          pytest tests/unit \
+          python -m pytest tests/unit \
             --cov CodeEntropy \
             --cov-report term-missing \
             --cov-report xml \

{codeentropy-2.2.4 → codeentropy-2.4.1}/.github/workflows/release.yaml

@@ -18,12 +18,12 @@ jobs:
     steps:
     - name: Checkout repository
       id: repo
-      uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+      uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
     - name: Set up Python
-      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+      uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
       with:
-        python-version: 3.14.0
+        python-version: 3.14.6
 
     - name: Get latest release from pip
       id: latestreleased
@@ -46,7 +46,7 @@ jobs:
     steps:
 
       - name: checkout
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - 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@c0f553fe549906ede9cf27b5156039d195d2ece0 # v8.1.0
+        uses: peter-evans/create-pull-request@5f6978faf089d4d20b00c7766989d076bb2fc7f1 # v8.1.1
         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@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           ref: main
 
@@ -113,7 +113,7 @@ jobs:
     steps:
 
       - name: create release
-        uses: softprops/action-gh-release@a06a81a03ee405af7f2048a818ed3f03bbf83c7b # v2.5.0
+        uses: softprops/action-gh-release@3d0d9888cb7fd7b750713d6e236d1fcb99157228 # v3.0.2
         with:
           name: v${{ github.event.inputs.version }}
           generate_release_notes: true
@@ -126,23 +126,23 @@ jobs:
     steps:
 
     - name: checkout
-      uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+      uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
       with:
         ref: main
 
     - name: Set up Python
-      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+      uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
       with:
-        python-version: 3.14.0
+        python-version: 3.14.6
 
     - name: Install flit
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flit~=3.9
+        python -m pip install "flit>=4,<5" "flit_core>=4,<5"
 
     - name: Build and publish
       run: |
-        flit publish
+        flit publish --use-vcs
       env:
         FLIT_USERNAME: __token__
         FLIT_PASSWORD:  ${{ secrets.PYPI_API_TOKEN }}
@@ -154,7 +154,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           ref: main
 
@@ -164,7 +164,7 @@ jobs:
           grep '{% set version' conda-recipe/meta.yaml
 
       - name: Setup Conda (conda-forge only)
-        uses: conda-incubator/setup-miniconda@v3
+        uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4
         with:
           miniforge-variant: Miniforge3
           python-version: "3.12"

{codeentropy-2.2.4 → codeentropy-2.4.1}/.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@v6
+            - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
               with:
                   fetch-depth: 0
-            - uses: FantasticFiasco/action-update-license-year@v3
+            - uses: FantasticFiasco/action-update-license-year@f180e962fa988db222d8f03ef4636750312d1b3d # v3
               with:
                   token: ${{ secrets.GITHUB_TOKEN }}

{codeentropy-2.2.4 → codeentropy-2.4.1}/.github/workflows/update_regression_baselines.yaml

@@ -18,12 +18,12 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           ref: ${{ github.ref }}
 
       - name: Set up Python
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
         with:
           python-version: "3.14"
 
@@ -33,10 +33,10 @@ jobs:
           python -m pip install -e .[testing]
 
       - name: Update regression baselines
-        run: pytest tests/regression --update-baselines
+        run: pytest tests/regression --update-baselines --run-slow
 
       - name: Commit updated baselines
-        uses: stefanzweifel/git-auto-commit-action@778341af668090896ca464160c2def5d1d1a3eb0 # v6
+        uses: stefanzweifel/git-auto-commit-action@4a55954c782fc1ea30b9056cd3e7a2b40ca8887d # v7
         with:
           commit_message: "test(regression): update baselines"
           commit_user_name: github-actions[bot]

{codeentropy-2.2.4 → codeentropy-2.4.1}/.github/workflows/weekly-docs.yaml

@@ -16,16 +16,16 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-24.04, windows-2025, macos-15]
+        os: [ubuntu-24.04, windows-2025-vs2026, macos-26]
         python-version: ["3.12", "3.13", "3.14"]
     timeout-minutes: 30
 
     steps:
       - name: Checkout repo
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -41,7 +41,7 @@ jobs:
 
       - name: Upload docs artifacts on failure
         if: failure()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: docs-${{ matrix.os }}-py${{ matrix.python-version }}-failure
           path: |

{codeentropy-2.2.4 → codeentropy-2.4.1}/.github/workflows/weekly-regression.yaml

@@ -64,17 +64,15 @@ jobs:
 
       - name: Run regression tests (slow, per system)
         run: |
-          pytest tests/regression \
-            -k "${{ matrix.system }}" \
+          python -m pytest tests/regression \
+            --system "${{ matrix.system }}" \
             --run-slow \
-            -n auto \
-            --dist=loadscope \
             -vv \
             --durations=20
 
       - name: Upload regression artifacts (failure)
         if: failure()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: regression-${{ matrix.system }}-artifacts
           path: |

{codeentropy-2.2.4 → codeentropy-2.4.1}/CITATION.cff

@@ -76,5 +76,5 @@ keywords:
   - biomolecular simulations
   - protein flexibility
 license: MIT
-version: 2.2.4
-date-released: '2026-05-15'
+version: 2.4.1
+date-released: '2026-08-18'

{codeentropy-2.2.4 → codeentropy-2.4.1}/CodeEntropy/__init__.py

@@ -8,4 +8,4 @@ entropy estimates, supporting a wide range of applications in molecular simulati
 and statistical mechanics.
 """
 
-__version__ = "2.2.4"
+__version__ = "2.4.1"