CodeEntropy 2.1.0__tar.gz → 2.1.1__tar.gz

{codeentropy-2.1.0 → codeentropy-2.1.1}/.github/workflows/daily.yaml

@@ -11,14 +11,16 @@ concurrency:
 
 jobs:
   unit:
-    name: Unit (${{ matrix.os }}, ${{ matrix.python-version }})
+    name: Unit (${{ matrix.os }}, py${{ matrix.python-version }})
     runs-on: ${{ matrix.os }}
     timeout-minutes: 30
+
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-24.04, macos-15, windows-2025]
         python-version: ["3.12", "3.13", "3.14"]
+
     steps:
       - name: Checkout
         uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
@@ -29,10 +31,10 @@ jobs:
           python-version: ${{ matrix.python-version }}
           cache: pip
 
-      - name: Install (testing)
+      - name: Install testing dependencies
         run: |
           python -m pip install --upgrade pip
           python -m pip install -e .[testing]
 
-      - name: Pytest (unit) • ${{ matrix.os }} • py${{ matrix.python-version }}
+      - name: Run unit tests
         run: python -m pytest tests/unit

{codeentropy-2.1.0 → codeentropy-2.1.1}/.github/workflows/pr.yaml

@@ -17,12 +17,13 @@ jobs:
       matrix:
         os: [ubuntu-24.04, macos-15, windows-2025]
         python-version: ["3.12", "3.13", "3.14"]
+
     steps:
       - name: Checkout
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
         with:
           python-version: ${{ matrix.python-version }}
           cache: pip
@@ -35,17 +36,50 @@ jobs:
       - name: Pytest (unit) • ${{ matrix.os }}, ${{ matrix.python-version }}
         run: python -m pytest tests/unit
 
+  discover-systems:
+    name: Discover regression systems
+    runs-on: ubuntu-24.04
+    outputs:
+      systems: ${{ steps.set-systems.outputs.systems }}
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+
+      - name: Set up Python 3.14
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
+        with:
+          python-version: "3.14"
+          cache: pip
+
+      - name: Install testing dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[testing]
+
+      - name: Discover systems
+        id: set-systems
+        run: |
+          SYSTEMS=$(python -m tests.regression.list_systems)
+          echo "systems=$SYSTEMS" >> $GITHUB_OUTPUT
+
   regression-quick:
-    name: Regression (quick)
-    needs: unit
+    name: Regression (fast) • ${{ matrix.system }}
+    needs: [unit, discover-systems]
     runs-on: ubuntu-24.04
     timeout-minutes: 35
+
+    strategy:
+      fail-fast: false
+      matrix:
+        system: ${{ fromJson(needs.discover-systems.outputs.systems) }}
+
     steps:
       - name: Checkout
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
 
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
         with:
           python-version: "3.14"
           cache: pip
@@ -54,28 +88,31 @@ jobs:
         uses: actions/cache@v4
         with:
           path: .testdata
-          key: codeentropy-testdata-v1-${{ runner.os }}-py3.14
+          key: codeentropy-testdata-${{ runner.os }}-py314
 
-      - name: Install (testing)
+      - name: Install testing dependencies
         run: |
           python -m pip install --upgrade pip
           python -m pip install -e .[testing]
 
-      - name: Pytest (regression quick)
-        run: python -m pytest tests/regression
+      - name: Run fast regression tests (per system)
+        run: |
+          python -m pytest tests/regression \
+            -m "not slow" \
+            -n auto \
+            --dist=loadscope \
+            -k "${{ matrix.system }}" \
+            -vv \
+            --durations=20
 
       - name: Upload artifacts (failure)
         if: failure()
         uses: actions/upload-artifact@v4
         with:
-          name: quick-regression-failure
+          name: quick-regression-failure-${{ matrix.system }}
           path: |
             .testdata/**
-            tests/regression/**/.pytest_cache/**
-            /tmp/pytest-of-*/pytest-*/**/config.yaml
-            /tmp/pytest-of-*/pytest-*/**/codeentropy_stdout.txt
-            /tmp/pytest-of-*/pytest-*/**/codeentropy_stderr.txt
-            /tmp/pytest-of-*/pytest-*/**/codeentropy_output.json
+            /tmp/pytest-of-*/pytest-*/**
 
   docs:
     name: Docs
@@ -93,7 +130,7 @@ jobs:
           python-version: "3.14"
           cache: pip
 
-      - name: Install
+      - name: Install docs dependencies
         run: |
           python -m pip install --upgrade pip
           python -m pip install -e .[docs]
@@ -114,23 +151,23 @@ jobs:
     name: Pre-commit
     runs-on: ubuntu-24.04
     timeout-minutes: 15
+
     steps:
       - name: Checkout
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
 
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
         with:
           python-version: "3.14"
           cache: pip
 
-      - name: Install (pre-commit)
+      - name: Install pre-commit dependencies
         run: |
           python -m pip install --upgrade pip
           python -m pip install -e .[pre-commit]
 
       - name: Run pre-commit
-        shell: bash
         run: |
           pre-commit install
           pre-commit run --all-files || {
@@ -144,8 +181,9 @@ jobs:
     needs: unit
     runs-on: ubuntu-24.04
     timeout-minutes: 30
+
     steps:
-      - name: Checkout repo
+      - name: Checkout
         uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
 
       - name: Set up Python 3.14
@@ -154,12 +192,12 @@ jobs:
           python-version: "3.14"
           cache: pip
 
-      - name: Install (testing)
+      - name: Install testing dependencies
         run: |
           python -m pip install --upgrade pip
           python -m pip install -e .[testing]
 
-      - name: Run unit test suite with coverage
+      - name: Run coverage
         run: |
           pytest tests/unit \
             --cov CodeEntropy \
@@ -167,7 +205,7 @@ jobs:
             --cov-report xml \
             -q
 
-      - name: Upload to Coveralls
+      - name: Upload coverage to Coveralls
         uses: coverallsapp/github-action@5cbfd81b66ca5d10c19b062c04de0199c215fb6e
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}

codeentropy-2.1.1/.github/workflows/weekly-regression.yaml

@@ -0,0 +1,90 @@
+name: Weekly Regression Tests
+
+on:
+  schedule:
+    - cron: '0 8 * * 1'
+  workflow_dispatch:
+
+concurrency:
+  group: weekly-regression-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  discover:
+    name: Discover regression systems
+    runs-on: ubuntu-24.04
+
+    outputs:
+      systems: ${{ steps.set.outputs.systems }}
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+
+      - name: Set up Python 3.14
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
+        with:
+          python-version: "3.14"
+          cache: pip
+
+      - name: Install testing dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[testing]
+
+      - name: Generate system matrix
+        id: set
+        run: |
+          systems=$(python -m tests.regression.list_systems)
+          echo "systems=$systems" >> $GITHUB_OUTPUT
+
+  regression:
+    name: Regression (${{ matrix.system }})
+    needs: discover
+    runs-on: ubuntu-24.04
+    timeout-minutes: 360
+
+    strategy:
+      fail-fast: false
+      matrix:
+        system: ${{ fromJson(needs.discover.outputs.systems) }}
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+
+      - name: Set up Python 3.14
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
+        with:
+          python-version: "3.14"
+          cache: pip
+
+      - name: Cache regression test data
+        uses: actions/cache@v4
+        with:
+          path: .testdata
+          key: codeentropy-testdata-${{ runner.os }}-py314
+
+      - name: Install testing dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[testing]
+
+      - name: Run regression tests (slow, per system)
+        run: |
+          pytest tests/regression \
+            -k "${{ matrix.system }}" \
+            --run-slow \
+            -n auto \
+            --dist=loadscope \
+            -vv \
+            --durations=20
+
+      - name: Upload regression artifacts (failure)
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: regression-${{ matrix.system }}-artifacts
+          path: |
+            .testdata/**
+            /tmp/pytest-of-*/pytest-*/**

{codeentropy-2.1.0 → codeentropy-2.1.1}/.gitignore

@@ -129,4 +129,4 @@ job*
 .testdata/
 
 !tests/regression/baselines/
-!tests/regression/baselines/*.json
+!tests/regression/baselines/*/*.json

{codeentropy-2.1.0 → codeentropy-2.1.1}/CITATION.cff

@@ -76,5 +76,5 @@ keywords:
   - biomolecular simulations
   - protein flexibility
 license: MIT
-version: 2.1.0
-date-released: '2026-03-26'
+version: 2.1.1
+date-released: '2026-04-01'

{codeentropy-2.1.0 → codeentropy-2.1.1}/CodeEntropy/__init__.py

@@ -8,4 +8,4 @@ entropy estimates, supporting a wide range of applications in molecular simulati
 and statistical mechanics.
 """
 
-__version__ = "2.1.0"
+__version__ = "2.1.1"

{codeentropy-2.1.0 → codeentropy-2.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: CodeEntropy
-Version: 2.1.0
+Version: 2.1.1
 Summary: CodeEntropy is a Python package for computing the configurational entropy of macromolecular systems using forces sampled from molecular dynamics (MD) simulations. It implements the multiscale cell correlation method to provide accurate and efficient entropy estimates, supporting a wide range of applications in molecular simulation and statistical mechanics.
 Keywords: entropy,macromolecular systems,MD simulation
 Author-email: Arghya 'Argo' Chakravorty <arghyac@umich.edu>, Donald Chung-HK <donald.chung@stfc.ac.uk>, Sarah Fegan <sarah.fegan@stfc.ac.uk>, James Gebbie-Rayet <james.gebbie@stfc.ac.uk>, Sarah Harris <sarah.harris@sheffield.ac.uk>, Richard Henchman <rhen7213@uni.sydney.edu.au>, Jonathan Higham <j.higham4@lancaster.ac.uk>, Jas Kalayan <jas.kalayan@stfc.ac.uk>, Ioana Papa <iapapa1@sheffield.ac.uk>
@@ -44,6 +44,7 @@ Requires-Dist: rstcheck>=6.2,<7.0 ; extra == "pre-commit"
 Requires-Dist: pytest>=9.0,<10.0 ; extra == "testing"
 Requires-Dist: pytest-cov>=7.0,<8.0 ; extra == "testing"
 Requires-Dist: pytest-sugar>=1.1,<2.0 ; extra == "testing"
+Requires-Dist: pytest-xdist ; extra == "testing"
 Project-URL: Documentation, https://codeentropy.readthedocs.io
 Project-URL: Homepage, https://ccpbiosim.github.io/CodeEntropy/
 Project-URL: Repository, https://github.com/CCPBioSim/CodeEntropy

{codeentropy-2.1.0 → codeentropy-2.1.1}/conda-recipe/meta.yaml

@@ -38,6 +38,7 @@ requirements:
     - dask >=2026.1.2,<2026.2.0
     - distributed >=2026.1.2,<2026.2.0
     - dask-jobqueue >=0.9,<0.10
+    - pytest-xdist >=3.8, <3.9
 
 test:
   imports:

{codeentropy-2.1.0 → codeentropy-2.1.1}/docs/developer_guide.rst

@@ -54,7 +54,7 @@ Run regression tests excluding slow systems::
 
 Run slow regression tests::
 
-    pytest tests/regression -m slow
+    pytest tests/regression --run-slow
 
 Run tests with coverage::
 

{codeentropy-2.1.0 → codeentropy-2.1.1}/pyproject.toml

@@ -61,7 +61,8 @@ Documentation = "https://codeentropy.readthedocs.io"
 testing = [
     "pytest>=9.0,<10.0",
     "pytest-cov>=7.0,<8.0",
-    "pytest-sugar>=1.1,<2.0"
+    "pytest-sugar>=1.1,<2.0",
+    "pytest-xdist"
 ]
 pre-commit = [
     "pre-commit>=4.5,<5.0",
@@ -83,6 +84,16 @@ docs = [
 [project.scripts]
 CodeEntropy = "CodeEntropy.cli:main"
 
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+
+addopts = "-n auto -vv -ra"
+
+markers = [
+  "regression: end-to-end regression tests against baselines",
+  "slow: long-running regression tests (20-30+ minutes)",
+]
+
 [tool.ruff]
 line-length = 88
 target-version = "py311"

codeentropy-2.1.1/tests/__init__.py

@@ -0,0 +1 @@
+""" """

codeentropy-2.1.1/tests/regression/baselines/benzaldehyde/axes_off.json

@@ -0,0 +1,45 @@
+{
+  "args": {
+    "top_traj_file": [
+      "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/molecules.top",
+      "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/trajectory.crd"
+    ],
+    "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/forces.frc",
+    "file_format": "MDCRD",
+    "kcal_force_units": true,
+    "selection_string": "resid 1:10",
+    "start": 0,
+    "end": 1,
+    "step": 1,
+    "bin_width": 30,
+    "temperature": 298.0,
+    "verbose": false,
+    "output_file": "/tmp/pytest-of-harry-swift/pytest-53/test_regression_matches_baseli0/job001/output_file.json",
+    "force_partitioning": 0.5,
+    "water_entropy": true,
+    "grouping": "molecules",
+    "combined_forcetorque": true,
+    "customised_axes": false,
+    "search_type": "grid"
+  },
+  "provenance": {
+    "python": "3.14.3",
+    "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39",
+    "codeentropy_version": "2.1.0",
+    "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590"
+  },
+  "groups": {
+    "0": {
+      "components": {
+        "united_atom:Transvibrational": 0.08982962903796131,
+        "united_atom:Rovibrational": 32.16018134884085,
+        "residue:FTmat-Transvibrational": 88.7671666695003,
+        "residue:FTmat-Rovibrational": 61.61036267672132,
+        "united_atom:Conformational": 0.0,
+        "residue:Conformational": 0.0,
+        "residue:Orientational": 7.791711490122748
+      },
+      "total": 190.41925181422317
+    }
+  }
+}

codeentropy-2.1.1/tests/regression/baselines/benzaldehyde/combined_forcetorque_false.json

@@ -0,0 +1,45 @@
+{
+  "args": {
+    "top_traj_file": [
+      "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/molecules.top",
+      "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/trajectory.crd"
+    ],
+    "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/forces.frc",
+    "file_format": "MDCRD",
+    "kcal_force_units": true,
+    "selection_string": "resid 1:10",
+    "start": 0,
+    "end": 1,
+    "step": 1,
+    "bin_width": 30,
+    "temperature": 298.0,
+    "verbose": false,
+    "output_file": "/tmp/pytest-of-harry-swift/pytest-53/test_regression_matches_baseli1/job001/output_file.json",
+    "force_partitioning": 0.5,
+    "water_entropy": true,
+    "grouping": "molecules",
+    "combined_forcetorque": false,
+    "customised_axes": true,
+    "search_type": "grid"
+  },
+  "provenance": {
+    "python": "3.14.3",
+    "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39",
+    "codeentropy_version": "2.1.0",
+    "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590"
+  },
+  "groups": {
+    "0": {
+      "components": {
+        "united_atom:Transvibrational": 0.07119323721997475,
+        "united_atom:Rovibrational": 49.68669738152346,
+        "residue:Transvibrational": 69.48692941204929,
+        "residue:Rovibrational": 68.46147102540942,
+        "united_atom:Conformational": 0.0,
+        "residue:Conformational": 0.0,
+        "residue:Orientational": 7.791711490122748
+      },
+      "total": 195.49800254632487
+    }
+  }
+}

codeentropy-2.1.0/tests/regression/baselines/benzaldehyde.json → codeentropy-2.1.1/tests/regression/baselines/benzaldehyde/default.json

@@ -1,10 +1,10 @@
 {
   "args": {
     "top_traj_file": [
-      "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/molecules.top",
-      "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/trajectory.crd"
+      "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/molecules.top",
+      "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/trajectory.crd"
     ],
-    "force_file": "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/forces.frc",
+    "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/forces.frc",
     "file_format": "MDCRD",
     "kcal_force_units": true,
     "selection_string": "all",
@@ -14,7 +14,7 @@
     "bin_width": 30,
     "temperature": 298.0,
     "verbose": false,
-    "output_file": "/tmp/pytest-of-ogo12949/pytest-5/test_regression_matches_baseli1/job001/output_file.json",
+    "output_file": "/tmp/pytest-of-harry-swift/pytest-53/test_regression_matches_baseli2/job001/output_file.json",
     "force_partitioning": 0.5,
     "water_entropy": true,
     "grouping": "molecules",
@@ -23,10 +23,10 @@
     "search_type": "grid"
   },
   "provenance": {
-    "python": "3.13.5",
-    "platform": "Linux-6.17.0-1012-oem-x86_64-with-glibc2.39",
-    "codeentropy_version": "2.0.0",
-    "git_sha": "697cc5da0af766f2f69b0fa31254f2ce7b2b1141"
+    "python": "3.14.3",
+    "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39",
+    "codeentropy_version": "2.1.0",
+    "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590"
   },
   "groups": {
     "0": {

codeentropy-2.1.1/tests/regression/baselines/benzaldehyde/frame_window.json

@@ -0,0 +1,45 @@
+{
+  "args": {
+    "top_traj_file": [
+      "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/molecules.top",
+      "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/trajectory.crd"
+    ],
+    "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzaldehyde/forces.frc",
+    "file_format": "MDCRD",
+    "kcal_force_units": true,
+    "selection_string": "resid 1:10",
+    "start": 0,
+    "end": 5,
+    "step": 2,
+    "bin_width": 30,
+    "temperature": 298.0,
+    "verbose": false,
+    "output_file": "/tmp/pytest-of-harry-swift/pytest-53/test_regression_matches_baseli3/job001/output_file.json",
+    "force_partitioning": 0.5,
+    "water_entropy": true,
+    "grouping": "molecules",
+    "combined_forcetorque": true,
+    "customised_axes": true,
+    "search_type": "grid"
+  },
+  "provenance": {
+    "python": "3.14.3",
+    "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39",
+    "codeentropy_version": "2.1.0",
+    "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590"
+  },
+  "groups": {
+    "0": {
+      "components": {
+        "united_atom:Transvibrational": 40.30267601961045,
+        "united_atom:Rovibrational": 38.21906858443615,
+        "residue:FTmat-Transvibrational": 73.41098578352612,
+        "residue:FTmat-Rovibrational": 57.881504393660364,
+        "united_atom:Conformational": 0.0,
+        "residue:Conformational": 0.0,
+        "residue:Orientational": 7.791711490122748
+      },
+      "total": 217.60594627135583
+    }
+  }
+}