CodeEntropy 2.1.0__tar.gz → 2.2.0__tar.gz

{codeentropy-2.1.0 → codeentropy-2.2.0}/.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-2.2.0}/.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-2.2.0/.github/workflows/update_regression_baselines.yaml

@@ -0,0 +1,44 @@
+name: Update Regression Baselines
+
+on:
+  workflow_dispatch:
+
+concurrency:
+  group: update-regression-baselines-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: write
+
+jobs:
+  update-baselines:
+    name: Update regression baselines
+    runs-on: ubuntu-24.04
+    timeout-minutes: 30
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+        with:
+          ref: ${{ github.ref }}
+
+      - name: Set up Python
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+        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: Update regression baselines
+        run: pytest tests/regression --update-baselines
+
+      - name: Commit updated baselines
+        uses: stefanzweifel/git-auto-commit-action@778341af668090896ca464160c2def5d1d1a3eb0 # v6
+        with:
+          commit_message: "test(regression): update baselines"
+          commit_user_name: github-actions[bot]
+          commit_user_email: 41898282+github-actions[bot]@users.noreply.github.com

codeentropy-2.2.0/.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-2.2.0}/.gitignore

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

{codeentropy-2.1.0 → codeentropy-2.2.0}/CITATION.cff

@@ -76,5 +76,5 @@ keywords:
   - biomolecular simulations
   - protein flexibility
 license: MIT
-version: 2.1.0
-date-released: '2026-03-26'
+version: 2.2.0
+date-released: '2026-04-29'

{codeentropy-2.1.0 → codeentropy-2.2.0}/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__ = "2.2.0"

{codeentropy-2.1.0 → codeentropy-2.2.0}/CodeEntropy/config/runtime.py

@@ -335,8 +335,14 @@ class CodeEntropyRunner:
         kcal_units = args.kcal_force_units
 
         if forcefile is None:
-            logger.debug(f"Loading Universe with {tprfile} and {trrfile}")
-            return mda.Universe(tprfile, trrfile, format=fileformat)
+            if fileformat == "LAMMPSDUMP":
+                logger.debug(
+                    f"Loading Universe with {tprfile} and {trrfile} (LAMMPSDUMP)"
+                )
+                return universe_operations.convert_lammps(tprfile, trrfile, fileformat)
+            else:
+                logger.debug(f"Loading Universe with {tprfile} and {trrfile}")
+                return mda.Universe(tprfile, trrfile, format=fileformat)
 
         return universe_operations.merge_forces(
             tprfile, trrfile, forcefile, fileformat, kcal_units

{codeentropy-2.1.0 → codeentropy-2.2.0}/CodeEntropy/entropy/nodes/configurational.py

@@ -53,7 +53,7 @@ class ConfigurationalEntropyNode:
         fragments = universe.atoms.fragments
         results: dict[int, dict[str, float]] = {}
 
-        for group_id, mol_ids in groups.items():
+        for group_id, mol_ids in sorted(groups.items()):
             results[group_id] = {"ua": 0.0, "res": 0.0, "poly": 0.0}
             if not mol_ids:
                 continue

{codeentropy-2.1.0 → codeentropy-2.2.0}/CodeEntropy/entropy/nodes/orientational.py

@@ -52,7 +52,7 @@ class OrientationalEntropyNode:
 
         results: dict[int, float] = {}
 
-        for group_id, mol_ids in groups.items():
+        for group_id, mol_ids in sorted(groups.items()):
             results[group_id] = 0
             if not mol_ids:
                 continue

{codeentropy-2.1.0 → codeentropy-2.2.0}/CodeEntropy/entropy/nodes/vibrational.py

@@ -90,7 +90,7 @@ class VibrationalEntropyNode:
 
         results: dict[int, dict[str, dict[str, float]]] = {}
 
-        for group_id, mol_ids in groups.items():
+        for group_id, mol_ids in sorted(groups.items()):
             results[group_id] = {}
             if not mol_ids:
                 continue
@@ -198,7 +198,7 @@ class VibrationalEntropyNode:
         if isinstance(gid2i, dict) and gid2i:
             return gid2i
         groups = shared_data["groups"]
-        return {gid: i for i, gid in enumerate(groups.keys())}
+        return {gid: i for i, gid in enumerate(sorted(groups.keys()))}
 
     def _get_ua_frame_counts(self, shared_data: Mapping[str, Any]) -> dict[CovKey, int]:
         """Extract per-(group,residue) frame counts for united-atom covariances.

{codeentropy-2.1.0 → codeentropy-2.2.0}/CodeEntropy/entropy/workflow.py

@@ -96,7 +96,7 @@ class EntropyWorkflow:
 
         This orchestrates the complete entropy pipeline:
             1. Build trajectory slice.
-            2. Apply atom selection to create a reduced universe.
+            2. Apply atom and frame selection to create a reduced universe.
             3. Detect hierarchy levels.
             4. Group molecules.
             5. Split groups into water and non-water.
@@ -233,21 +233,31 @@ class EntropyWorkflow:
         return math.floor((end - start) / step)
 
     def _build_reduced_universe(self) -> Any:
-        """Apply atom selection and return the reduced universe.
-
-        If `selection_string` is "all", the original universe is returned.
+        """Apply atom and frame selection and return the reduced universe.
 
         Returns:
-            MDAnalysis Universe (original or reduced).
+            MDAnalysis Universe (reduced according to user selections).
         """
         selection = self._args.selection_string
+        start = self._args.start
+        end = len(self._universe.trajectory) if self._args.end == -1 else self._args.end
+        step = self._args.step
         if selection == "all":
-            return self._universe
+            reduced_atoms = self._universe
+        else:
+            reduced_atoms = self._universe_operations.select_atoms(
+                self._universe, selection
+            )
+            name = f"{len(reduced_atoms.trajectory)}_frame_dump_atom_selection"
+            self._run_manager.write_universe(reduced_atoms, name)
+
+        reduced_frames = self._universe_operations.select_frames(
+            reduced_atoms, start, end, step
+        )
+        name = f"{len(reduced_frames.trajectory)}_frame_dump_frame_selection"
+        self._run_manager.write_universe(reduced_frames, name)
 
-        reduced = self._universe_operations.select_atoms(self._universe, selection)
-        name = f"{len(reduced.trajectory)}_frame_dump_atom_selection"
-        self._run_manager.write_universe(reduced, name)
-        return reduced
+        return reduced_frames
 
     def _detect_levels(self, reduced_universe: Any) -> Any:
         """Detect hierarchy levels for each molecule in the reduced universe.
@@ -293,7 +303,7 @@ class EntropyWorkflow:
 
         water_groups = {
             gid: mol_ids
-            for gid, mol_ids in groups.items()
+            for gid, mol_ids in sorted(groups.items())
             if any(
                 res.resid in water_resids
                 for mol in [universe.atoms.fragments[i] for i in mol_ids]
@@ -301,7 +311,7 @@ class EntropyWorkflow:
             )
         }
         nonwater_groups = {
-            gid: g for gid, g in groups.items() if gid not in water_groups
+            gid: g for gid, g in sorted(groups.items()) if gid not in water_groups
         }
         return nonwater_groups, water_groups
 
@@ -354,7 +364,7 @@ class EntropyWorkflow:
             except (TypeError, ValueError):
                 logger.warning("Skipping invalid entry: %s, %s", group_id, result)
 
-        for group_id, total in entropy_by_group.items():
+        for group_id, total in sorted(entropy_by_group.items()):
             self._reporter.molecule_data.append(
                 (group_id, "Group Total", "Group Total Entropy", total)
             )