Merge branch 'main' of https://github.com/CCPBioSim/CodeEntropy into 110-improve-test-coverage-for-main

Author: harryswift01

CodeEntropy/entropy.py

@@ -822,7 +822,7 @@ def orientational_entropy_calculation(self, neighbours_dict):
         # Replaced molecule with neighbour as this is what the for loop uses
         S_or_total = 0
         for neighbour in neighbours_dict:  # we are going through neighbours
-            if neighbour in []:  # water molecules - call POSEIDON functions
+            if neighbour in ["H2O"]:  # water molecules - call POSEIDON functions
                 pass  # TODO temporary until function is written
             else:
                 # the bound ligand is always going to be a neighbour
@@ -835,16 +835,16 @@ def orientational_entropy_calculation(self, neighbours_dict):
                     f"S_or_component (log(omega)) for neighbour {neighbour}: "
                     f"{S_or_component}"
                 )
-                S_or_component *= self.GAS_CONST
+                S_or_component *= self._GAS_CONST
                 logger.debug(
                     f"S_or_component after multiplying by GAS_CONST for neighbour "
                     f"{neighbour}: {S_or_component}"
                 )
-            S_or_total += S_or_component
-            logger.debug(
-                f"S_or_total after adding component for neighbour {neighbour}: "
-                f"{S_or_total}"
-            )
+                S_or_total += S_or_component
+                logger.debug(
+                    f"S_or_total after adding component for neighbour {neighbour}: "
+                    f"{S_or_total}"
+                )
         # TODO for future releases
         # implement a case for molecules with hydrogen bonds but to a lesser
         # extent than water

CodeEntropy/levels.py

@@ -441,14 +441,17 @@ def get_sphCoord_axes(self, arg_r):
         if x2y2 == 0.0:
             raise ValueError("x2y2 is zero, cannot compute sin_phi and cos_phi.")
 
+        # These conditions are mathematically unreachable for real-valued vectors.
+        # Marked as no cover to avoid false negatives in coverage reports.
+
         # Check for non-negative values inside the square root
-        if x2y2 / r2 < 0:
+        if x2y2 / r2 < 0:  # pragma: no cover
             raise ValueError(
                 f"Negative value encountered for sin_theta calculation: {x2y2 / r2}. "
                 f"Cannot take square root."
             )
 
-        if x2y2 < 0:
+        if x2y2 < 0:  # pragma: no cover
             raise ValueError(
                 f"Negative value encountered for sin_phi and cos_phi "
                 f"calculation: {x2y2}. "
@@ -462,7 +465,7 @@ def get_sphCoord_axes(self, arg_r):
             sin_phi = arg_r[1] / np.sqrt(x2y2)
             cos_phi = arg_r[0] / np.sqrt(x2y2)
 
-        else:
+        else:  # pragma: no cover
             sin_theta = 0.0
             cos_theta = 1