Apply suggestions from code review

Co-authored-by: Jacob Wilkins <46597752+oerc0122@users.noreply.github.com>
Signed-off-by: Maciej Bartkowiak <108934199+MBartkowiakSTFC@users.noreply.github.com>

Author: MBartkowiakSTFC

MDANSE/Src/MDANSE/Framework/Configurators/HDFTrajectoryConfigurator.py

@@ -98,10 +98,10 @@ def next_prime(nchunks: int) -> int:
     int
         A prime number larger than the input number.
     """
-    for prime in PRIMES:
-        if prime > nchunks:
-            return prime
-    return nchunks
+    import bisect
+
+    ip = bisect.bisect_right(nchunks, PRIMES)
+    return nchunks if ip == len(PRIMES) else PRIMES[ip]
 
 
 def guess_hdf5_trajectory_parameters(
@@ -154,17 +154,18 @@ def configure(self, value):
         self.error_status = "OK"
         self.warning_status = ""
 
-        if isinstance(value, (str, Path)):
-            file_name = value
-            driver = None
-            rdcc_nbytes, rdcc_nslots = guess_hdf5_trajectory_parameters(value)
-            rdcc_w0 = None
-        else:
-            file_name = value[0]
-            driver = value[1] if value[1] in HDF5_DRIVERS else None
-            rdcc_nbytes = value[2]
-            rdcc_nslots = value[3]
-            rdcc_w0 = value[4]
+        match value:
+            case str() | Path():
+                file_name = value
+                driver = None
+                rdcc_nbytes, rdcc_nslots = guess_hdf5_trajectory_parameters(value)
+                rdcc_w0 = None
+            case (str(), str(), int(), int(), int()):
+                file_name, driver, rdcc_nbytes, rdcc_nslots, rdcc_w0 = value
+                driver = driver if driver in HDF5_DRIVERS else None
+            case _:
+                self.error_status = f"Invalid value {value!r}"
+                return 
 
         self["driver"] = driver
         self["rdcc_nbytes"] = rdcc_nbytes

MDANSE/Src/MDANSE/Framework/Jobs/ScatteringLengthDensityProfile.py

@@ -184,7 +184,7 @@ def run_step(self, index: int):
         conf = self.trajectory.configuration(frame_index)
 
         box_coords = conf.to_fractional_coordinates()
-        box_coords = box_coords - np.floor(box_coords)
+        box_coords -= np.floor(box_coords)
 
         axis_index = self.configuration["axis"]["index"]
         self._extent += np.linalg.norm(conf.unit_cell.direct[axis_index])

MDANSE/Src/MDANSE/Framework/Jobs/TrajectoryEditor.py

@@ -160,9 +160,7 @@ def initialize(self):
                 com_conf = AbsoluteConfiguration(
                     coords,
                 )
-            self.grouped_indices = reduce(
-                list.__add__, new_chemical_system.clusters.values(), []
-            )
+            self.grouped_indices = list(more_itertools.flatten(new_chemical_system.clusters.values()))
             coords = com_conf.contiguous_configuration(self.grouped_indices).coordinates
         else:
             assign_molecules_after_atom_selection(

MDANSE/Src/MDANSE/MolecularDynamics/Configuration.py

@@ -423,7 +423,7 @@ def clone(self) -> _PeriodicConfiguration:
         variables = copy.deepcopy(self.variables)
         coords = variables.pop("coordinates")
 
-        return self.__class__(coords, unit_cell, **variables)
+        return type(self)(coords, unit_cell, **variables)
 
     def fold_coordinates(self):
         """Fold the coordinates into simulation box."""

MDANSE/Src/MDANSE/MolecularDynamics/Trajectory.py

@@ -651,7 +651,7 @@ def to_absolute_coordinates(
         Returns
         -------
         ndarray
-            2D array containing the real coordinates converted from box coordinates.
+            2D array containing the absolute coordinates converted from fractionals.
 
         """
         return self._trajectory.to_absolute_coordinates(box_coordinates, first, last, step)

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/OutputTrajectoryWidget.py

@@ -68,13 +68,16 @@ def __init__(self, *args, **kwargs):
         self.dtype_box.setCurrentText("float64")
         self.chunk_atom_box = QSpinBox(self._base)
         self.chunk_frame_box = QSpinBox(self._base)
-        for index, chunk_box in enumerate((self.chunk_atom_box, self.chunk_frame_box)):
+        for typ, chunk_box in zip(
+           ("atoms", "frames"),
+           (self.chunk_atom_box, self.chunk_frame_box)
+        ):
             chunk_box.setMinimum(1)
             chunk_box.setMaximum(0xFFFF)
-            chunk_box.setValue(1 if index else 128)
-            chunk_box.setSingleStep(1 if index else 32)
+            chunk_box.setValue(1 if typ == "frames" else 128)
+            chunk_box.setSingleStep(1 if typ == "frames" else 32)
             chunk_box.setToolTip(
-                f"Specifies the number of {'frames' if index else 'atoms'} in a single chunk of the HDF5 file."
+                f"Specifies the number of {typ} in a single chunk of the HDF5 file."
                 "Affects the performance of reading and writing the trajectory."
             )
         self.compression_box = QComboBox(self._base)