Merge pull request #294 from CCPBioSim/27-orientational-entropy

Introduce Basic Orientational Entropy Calculations

Author: skfegan

.github/workflows/daily.yaml

@@ -35,4 +35,4 @@ jobs:
           python -m pip install -e .[testing]
 
       - name: Pytest (unit) • ${{ matrix.os }} • py${{ matrix.python-version }}
-        run: python -m pytest tests/unit -q
+        run: python -m pytest tests/unit

.github/workflows/pr.yaml

@@ -33,7 +33,7 @@ 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
 
   regression-quick:
     name: Regression (quick)
@@ -62,7 +62,7 @@ jobs:
           python -m pip install -e .[testing]
 
       - name: Pytest (regression quick)
-        run: python -m pytest tests/regression -q
+        run: python -m pytest tests/regression
 
       - name: Upload artifacts (failure)
         if: failure()

.github/workflows/weekly-regression.yaml

@@ -13,7 +13,6 @@ jobs:
   regression:
     name: Regression tests (including slow)
     runs-on: ubuntu-24.04
-    timeout-minutes: 180
     steps:
       - name: Checkout repo
         uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
@@ -36,7 +35,7 @@ jobs:
           pip install -e .[testing]
 
       - name: Run regression test suite
-        run: pytest tests/regression -q --run-slow
+        run: pytest tests/regression --run-slow
 
       - name: Upload regression artifacts on failure
         if: failure()

CodeEntropy/config/argparse.py

@@ -25,7 +25,7 @@
 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 @@ class 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 @@ def __init__(self, arg_specs: Optional[Dict[str, ArgSpec]] = None) -> None:
         """
         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 @@ def load_config(self, directory_path: str) -> Dict[str, Any]:
 
         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 @@ def build_parser(self) -> argparse.ArgumentParser:
                 )
                 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 @@ def build_parser(self) -> argparse.ArgumentParser:
         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 @@ def resolve(
 
     @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 @@ def _detect_cli_overrides(
     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 @@ def _apply_yaml_defaults(
             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/config/runtime.py

@@ -18,7 +18,7 @@
 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 @@ def create_job_folder() -> str:
 
         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 @@ def _build_universe(
         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/core/logging.py

@@ -16,7 +16,6 @@
 
 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 @@ def __init__(self, folder: str, level: int = logging.INFO) -> None:
 
         self.level = level
         self.console = self.get_console()
-        self.handlers: Dict[str, logging.Handler] = {}
+        self.handlers: dict[str, logging.Handler] = {}
 
         self._setup_handlers()