CodeEntropy 2.0.0__tar.gz → 2.1.1__tar.gz

{codeentropy-2.0.0 → 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 }}
-        run: python -m pytest tests/unit -q
+      - name: Run unit tests
+        run: python -m pytest tests/unit

{codeentropy-2.0.0 → 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
@@ -33,19 +34,52 @@ jobs:
           python -m pip install -e .[testing]
 
       - name: Pytest (unit) • ${{ matrix.os }}, ${{ matrix.python-version }}
-        run: python -m pytest tests/unit -q
+        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 -q
+      - 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-2.0.0 → codeentropy-2.1.1}/.github/workflows/release.yaml

@@ -163,30 +163,36 @@ jobs:
           sed -i "s/^{% set version = \".*\" %}$/{% set version = \"${{ github.event.inputs.version }}\" %}/" conda-recipe/meta.yaml
           grep '{% set version' conda-recipe/meta.yaml
 
-      - name: Setup Conda
+      - name: Setup Conda (conda-forge only)
         uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-variant: Miniforge3
           python-version: "3.12"
-          auto-activate-base: false
+          auto-activate: false
+          conda-remove-defaults: true
+          channels: conda-forge
+          channel-priority: strict
 
       - name: Install build tools
         shell: bash -l {0}
         run: |
           conda install -y conda-build anaconda-client
-          conda config --add channels conda-forge
-          conda config --set channel_priority strict
           conda config --set anaconda_upload no
 
       - name: Build package
         shell: bash -l {0}
+        env:
+          PIP_NO_INDEX: "0"
         run: |
+          PKG_PATH=$(conda build conda-recipe --output)
+          echo "PKG_PATH=$PKG_PATH" >> "$GITHUB_ENV"
           conda build conda-recipe
+          test -f "$PKG_PATH"
+          echo "Built: $PKG_PATH"
 
       - name: Upload to Anaconda
         shell: bash -l {0}
         env:
           ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
         run: |
-          PKG_PATH=$(conda build conda-recipe --output)
           anaconda -t "$ANACONDA_API_TOKEN" upload "$PKG_PATH" --user CCPBioSim --force

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-2.0.0 → codeentropy-2.1.1}/.gitignore

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

{codeentropy-2.0.0 → codeentropy-2.1.1}/CITATION.cff

@@ -76,5 +76,5 @@ keywords:
   - biomolecular simulations
   - protein flexibility
 license: MIT
-version: 2.0.0
-date-released: '2026-02-27'
+version: 2.1.1
+date-released: '2026-04-01'

{codeentropy-2.0.0 → 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__ = "2.0.0"
+__version__ = "2.1.1"

{codeentropy-2.0.0 → codeentropy-2.1.1}/CodeEntropy/config/argparse.py

@@ -25,7 +25,7 @@ import glob
 import logging
 import os
 from dataclasses import dataclass
-from typing import Any, Dict, Optional, Set
+from typing import Any
 
 import yaml
 
@@ -48,11 +48,11 @@ class ArgSpec:
     help: str
     default: Any = None
     type: Any = None
-    action: Optional[str] = None
-    nargs: Optional[str] = None
+    action: str | None = None
+    nargs: str | None = None
 
 
-ARG_SPECS: Dict[str, ArgSpec] = {
+ARG_SPECS: dict[str, ArgSpec] = {
     "top_traj_file": ArgSpec(
         type=str,
         nargs="+",
@@ -145,6 +145,12 @@ ARG_SPECS: Dict[str, ArgSpec] = {
         default=True,
         help="Use bonded axes to rotate forces for UA level vibrational entropies",
     ),
+    "search_type": ArgSpec(
+        type=str,
+        default="RAD",
+        help="Type of neighbor search to use."
+        "Default RAD; grid search is also available",
+    ),
 }
 
 
@@ -159,7 +165,7 @@ class ConfigResolver:
       - validating trajectory-related numeric parameters
     """
 
-    def __init__(self, arg_specs: Optional[Dict[str, ArgSpec]] = None) -> None:
+    def __init__(self, arg_specs: dict[str, ArgSpec] | None = None) -> None:
         """Initialize the manager.
 
         Args:
@@ -168,7 +174,7 @@ class ConfigResolver:
         """
         self._arg_specs = dict(arg_specs or ARG_SPECS)
 
-    def load_config(self, directory_path: str) -> Dict[str, Any]:
+    def load_config(self, directory_path: str) -> dict[str, Any]:
         """Load the first YAML config file found in a directory.
 
         The current behavior matches your existing workflow:
@@ -188,7 +194,7 @@ class ConfigResolver:
 
         config_path = yaml_files[0]
         try:
-            with open(config_path, "r", encoding="utf-8") as file:
+            with open(config_path, encoding="utf-8") as file:
                 config = yaml.safe_load(file) or {"run1": {}}
             logger.info("Loaded configuration from: %s", config_path)
             return config
@@ -253,7 +259,7 @@ class ConfigResolver:
                 )
                 continue
 
-            kwargs: Dict[str, Any] = {}
+            kwargs: dict[str, Any] = {}
             if spec.type is not None:
                 kwargs["type"] = spec.type
             if spec.default is not None:
@@ -266,7 +272,7 @@ class ConfigResolver:
         return parser
 
     def resolve(
-        self, args: argparse.Namespace, run_config: Optional[Dict[str, Any]]
+        self, args: argparse.Namespace, run_config: dict[str, Any] | None
     ) -> argparse.Namespace:
         """Merge CLI arguments with YAML configuration and adjust logging level.
 
@@ -306,8 +312,8 @@ class ConfigResolver:
 
     @staticmethod
     def _detect_cli_overrides(
-        args_dict: Dict[str, Any], default_dict: Dict[str, Any]
-    ) -> Set[str]:
+        args_dict: dict[str, Any], default_dict: dict[str, Any]
+    ) -> set[str]:
         """Detect which args were explicitly overridden in the CLI.
 
         Args:
@@ -322,8 +328,8 @@ class ConfigResolver:
     def _apply_yaml_defaults(
         self,
         args: argparse.Namespace,
-        run_config: Dict[str, Any],
-        cli_provided: Set[str],
+        run_config: dict[str, Any],
+        cli_provided: set[str],
     ) -> None:
         """Apply YAML values onto args for keys not provided by CLI.
 
@@ -336,7 +342,7 @@ class ConfigResolver:
             if yaml_value is None or key in cli_provided:
                 continue
             if key in self._arg_specs:
-                logger.debug("Using YAML value for %s: %s", key, yaml_value)
+                logger.debug(f"Using YAML value for {key}: {yaml_value}")
                 setattr(args, key, yaml_value)
 
     def _ensure_defaults(self, args: argparse.Namespace) -> None:

{codeentropy-2.0.0 → codeentropy-2.1.1}/CodeEntropy/config/runtime.py

@@ -18,7 +18,7 @@ from __future__ import annotations
 import logging
 import os
 import pickle
-from typing import Any, Dict, Optional
+from typing import Any
 
 import MDAnalysis as mda
 import requests
@@ -112,7 +112,7 @@ class CodeEntropyRunner:
 
         return new_folder_path
 
-    def load_citation_data(self) -> Optional[Dict[str, Any]]:
+    def load_citation_data(self) -> dict[str, Any] | None:
         """Load CITATION.cff from GitHub.
 
         If the request fails (offline, blocked, etc.), returns None.
@@ -335,7 +335,7 @@ class CodeEntropyRunner:
         kcal_units = args.kcal_force_units
 
         if forcefile is None:
-            logger.debug("Loading Universe with %s and %s", tprfile, trrfile)
+            logger.debug(f"Loading Universe with {tprfile} and {trrfile}")
             return mda.Universe(tprfile, trrfile, format=fileformat)
 
         return universe_operations.merge_forces(

{codeentropy-2.0.0 → codeentropy-2.1.1}/CodeEntropy/core/logging.py

@@ -16,7 +16,6 @@ from __future__ import annotations
 
 import logging
 import os
-from typing import Dict, Optional
 
 from rich.console import Console
 from rich.logging import RichHandler
@@ -55,7 +54,7 @@ class LoggingConfig:
         handlers: Mapping of handler name to handler instance.
     """
 
-    _console: Optional[Console] = None
+    _console: Console | None = None
 
     @classmethod
     def get_console(cls) -> Console:
@@ -80,7 +79,7 @@ class LoggingConfig:
 
         self.level = level
         self.console = self.get_console()
-        self.handlers: Dict[str, logging.Handler] = {}
+        self.handlers: dict[str, logging.Handler] = {}
 
         self._setup_handlers()
 

codeentropy-2.1.1/CodeEntropy/entropy/configurational.py

@@ -0,0 +1,86 @@
+"""Conformational entropy utilities.
+
+This module provides:
+
+- Assignment of discrete conformational states for a single dihedral time series.
+- Computation of conformational entropy from a sequence of state labels.
+
+"""
+
+from __future__ import annotations
+
+import logging
+from typing import Any
+
+import numpy as np
+
+logger = logging.getLogger(__name__)
+
+
+class ConformationalEntropy:
+    """Compute conformational entropy from states information."""
+
+    _GAS_CONST: float = 8.3144598484848
+
+    def __init__(self) -> None:
+        """Math-only engine.
+
+        This class assigns conformational states and computes conformational entropy.
+        It does not depend on the workflow runner, universe, grouping, or reporting.
+        """
+        pass
+
+    def conformational_entropy_calculation(self, states: Any) -> float:
+        """Compute conformational entropy for a sequence of state labels.
+
+        Entropy is computed as:
+
+            S = -R * sum_i p_i * ln(p_i)
+
+        where p_i is the observed probability of state i in ``states``.
+
+        Args:
+            states: Sequence/array of discrete state labels. Empty/None yields 0.0.
+            number_frames: Frame count metadata.
+
+        Returns:
+            float: Conformational entropy in J/mol/K.
+        """
+        arr = self._to_1d_array(states)
+        if arr is None or arr.size == 0:
+            return 0.0
+
+        values, counts = np.unique(arr, return_counts=True)
+        total_count = int(np.sum(counts))
+        if total_count <= 0 or values.size <= 1:
+            return 0.0
+
+        probs = counts.astype(float) / float(total_count)
+        probs = probs[probs > 0.0]
+
+        s_conf = -self._GAS_CONST * float(np.sum(probs * np.log(probs)))
+        logger.debug(f"Total conformational entropy: {s_conf}")
+        return s_conf
+
+    @staticmethod
+    def _to_1d_array(states: Any) -> np.ndarray | None:
+        """Convert a state sequence into a 1D numpy array.
+
+        Args:
+            states: Input sequence/array.
+
+        Returns:
+            1D numpy array, or None if input is not usable.
+        """
+        if states is None:
+            return None
+
+        if isinstance(states, np.ndarray):
+            arr = states.reshape(-1)
+        else:
+            try:
+                arr = np.asarray(list(states)).reshape(-1)
+            except TypeError:
+                return None
+
+        return arr

{codeentropy-2.0.0 → codeentropy-2.1.1}/CodeEntropy/entropy/graph.py

@@ -15,18 +15,19 @@ from __future__ import annotations
 
 import logging
 from dataclasses import dataclass
-from typing import Any, Dict
+from typing import Any
 
 import networkx as nx
 
 from CodeEntropy.entropy.nodes.aggregate import AggregateEntropyNode
 from CodeEntropy.entropy.nodes.configurational import ConfigurationalEntropyNode
+from CodeEntropy.entropy.nodes.orientational import OrientationalEntropyNode
 from CodeEntropy.entropy.nodes.vibrational import VibrationalEntropyNode
 
 logger = logging.getLogger(__name__)
 
 
-SharedData = Dict[str, Any]
+SharedData = dict[str, Any]
 
 
 @dataclass(frozen=True)
@@ -57,9 +58,9 @@ class EntropyGraph:
     def __init__(self) -> None:
         """Initialize an empty entropy graph."""
         self._graph: nx.DiGraph = nx.DiGraph()
-        self._nodes: Dict[str, Any] = {}
+        self._nodes: dict[str, Any] = {}
 
-    def build(self) -> "EntropyGraph":
+    def build(self) -> EntropyGraph:
         """Populate the graph with the standard entropy workflow.
 
         Returns:
@@ -68,10 +69,15 @@ class EntropyGraph:
         specs = (
             NodeSpec("vibrational_entropy", VibrationalEntropyNode()),
             NodeSpec("configurational_entropy", ConfigurationalEntropyNode()),
+            NodeSpec("orientational_entropy", OrientationalEntropyNode()),
             NodeSpec(
                 "aggregate_entropy",
                 AggregateEntropyNode(),
-                deps=("vibrational_entropy", "configurational_entropy"),
+                deps=(
+                    "vibrational_entropy",
+                    "configurational_entropy",
+                    "orientational_entropy",
+                ),
             ),
         )
 
@@ -82,7 +88,7 @@ class EntropyGraph:
 
     def execute(
         self, shared_data: SharedData, *, progress: object | None = None
-    ) -> Dict[str, Any]:
+    ) -> dict[str, Any]:
         """Execute the entropy graph in topological order.
 
         Nodes are executed in dependency order (topological sort). Each node reads
@@ -105,7 +111,7 @@ class EntropyGraph:
         Raises:
             KeyError: If a node name is missing from the internal node registry.
         """
-        results: Dict[str, Any] = {}
+        results: dict[str, Any] = {}
 
         for node_name in nx.topological_sort(self._graph):
             node = self._nodes[node_name]