CodeEntropy 2.3.0__tar.gz → 2.4.2__tar.gz

{codeentropy-2.3.0 → codeentropy-2.4.2}/.github/renovate.json

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

{codeentropy-2.3.0 → codeentropy-2.4.2}/.github/workflows/daily.yaml

@@ -23,10 +23,10 @@ jobs:
 
     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-2.3.0 → codeentropy-2.4.2}/.github/workflows/pr.yaml

@@ -93,15 +93,13 @@ jobs:
         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 on failure
         if: failure()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: quick-regression-failure-${{ matrix.system }}
           path: |
@@ -135,7 +133,7 @@ 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

{codeentropy-2.3.0 → codeentropy-2.4.2}/.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
 
@@ -111,14 +111,50 @@ jobs:
     needs: tag
     runs-on: ubuntu-24.04
     steps:
-
       - name: create release
+        id: create_release
         uses: softprops/action-gh-release@a06a81a03ee405af7f2048a818ed3f03bbf83c7b # v2.5.0
         with:
           name: v${{ github.event.inputs.version }}
           generate_release_notes: true
           tag_name: ${{ github.event.inputs.version }}
 
+      - name: fetch generated changelog
+        id: changelog
+        if: steps.create_release.outcome == 'success'
+        continue-on-error: true
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          # generate_release_notes builds the changelog server-side, so pull
+          # it back down here rather than trying to reconstruct it locally.
+          gh release view "${{ github.event.inputs.version }}" --json body -q .body > changelog.txt
+
+      - name: notify Zulip of release
+        if: steps.create_release.outcome == 'success'
+        continue-on-error: true
+        env:
+          ZULIP_BOT_EMAIL: ${{ secrets.ZULIP_BOT_EMAIL }}
+          ZULIP_BOT_API_KEY: ${{ secrets.ZULIP_BOT_API_KEY }}
+          ZULIP_SITE: ${{ secrets.ZULIP_SITE }}
+          REPO: ${{ github.event.repository.name }}
+          TAG: v${{ github.event.inputs.version }}
+          RELEASE_URL: ${{ steps.create_release.outputs.url }}
+        run: |
+          CONTENT=$(cat <<EOF
+          **${REPO}** [${TAG}](${RELEASE_URL}) has been released 🎉
+
+          $(cat changelog.txt)
+          EOF
+          )
+
+          curl -sSf "${ZULIP_SITE}/api/v1/messages" \
+            -u "${ZULIP_BOT_EMAIL}:${ZULIP_BOT_API_KEY}" \
+            --data-urlencode type=stream \
+            --data-urlencode "to=announcement" \
+            --data-urlencode "topic=software releases" \
+            --data-urlencode "content=${CONTENT}"
+
   pypi:
     name: make pypi release
     needs: [tag, release]
@@ -126,23 +162,23 @@ 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 +190,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           ref: main
 
@@ -164,7 +200,7 @@ 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-2.3.0 → codeentropy-2.4.2}/.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-2.3.0 → codeentropy-2.4.2}/.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"
 
@@ -36,7 +36,7 @@ jobs:
         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-2.3.0 → codeentropy-2.4.2}/.github/workflows/weekly-docs.yaml

@@ -22,10 +22,10 @@ jobs:
 
     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-2.3.0 → codeentropy-2.4.2}/.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-2.3.0 → codeentropy-2.4.2}/CITATION.cff

@@ -76,5 +76,5 @@ keywords:
   - biomolecular simulations
   - protein flexibility
 license: MIT
-version: 2.3.0
-date-released: '2026-06-26'
+version: 2.4.2
+date-released: '2026-08-26'

{codeentropy-2.3.0 → codeentropy-2.4.2}/CodeEntropy/__init__.py

@@ -8,4 +8,4 @@ entropy estimates, supporting a wide range of applications in molecular simulati
 and statistical mechanics.
 """
 
-__version__ = "2.3.0"
+__version__ = "2.4.2"