CodeEntropy 2.1.1__tar.gz → 2.2.0__tar.gz

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-2.1.1 → codeentropy-2.2.0}/CITATION.cff

@@ -76,5 +76,5 @@ keywords:
   - biomolecular simulations
   - protein flexibility
 license: MIT
-version: 2.1.1
-date-released: '2026-04-01'
+version: 2.2.0
+date-released: '2026-04-29'

{codeentropy-2.1.1 → 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__ = "2.1.1"
+__version__ = "2.2.0"

{codeentropy-2.1.1 → 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-2.1.1 → 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-2.1.1 → 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-2.1.1 → 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-2.1.1 → 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)
             )