chore: switches from black and isort to ruff

diceplayer/shared/environment/molecule.py

@@ -2,6 +2,7 @@ from __future__ import annotations
 
 from typing_extensions import TYPE_CHECKING
 
+
 if TYPE_CHECKING:
     from nptyping import Float, NDArray, Shape
 
@@ -319,7 +320,7 @@ class Molecule:
                 self.com[0], self.com[1], self.com[2]
             )
         )
-        inertia = self.inertia_tensor()
+        self.inertia_tensor()
         evals, evecs = self.principal_axes()
 
         logger.info(

diceplayer/shared/environment/system.py

@@ -1,11 +1,10 @@
 from diceplayer import logger
 from diceplayer.shared.environment.molecule import Molecule
 from diceplayer.shared.utils.misc import BOHR2ANG
-from diceplayer.shared.utils.ptable import atomsymb
 
 import numpy as np
 from numpy import linalg
-from typing_extensions import List, TextIO, Tuple
+from typing_extensions import List, Tuple
 
 import math
 from copy import deepcopy
@@ -92,8 +91,10 @@ class System:
 
         try:
             evals, evecs = linalg.eigh(rr)
-        except:
-            raise RuntimeError("Error: diagonalization of RR matrix did not converge")
+        except Exception as err:
+            raise RuntimeError(
+                "Error: diagonalization of RR matrix did not converge"
+            ) from err
 
         a1 = evecs[:, 2].T
         a2 = evecs[:, 1].T

diceplayer/shared/interface/__init__.py

@@ -1 +1,4 @@
 from .__interface import Interface
+
+
+__all__ = ["Interface"]

diceplayer/shared/interface/dice_interface.py

@@ -17,6 +17,7 @@ import time
 from multiprocessing import Process, connection
 from pathlib import Path
 
+
 DICE_END_FLAG: Final[str] = "End of simulation"
 DICE_FLAG_LINE: Final[int] = -2
 UMAANG3_TO_GCM3: Final[float] = 1.6605
@@ -206,10 +207,10 @@ class DiceInterface(Interface):
             f.write(f"temp = {self.step.dice.temp}\n")
 
             if self.step.dice.randominit == "first" and cycle > 1:
-                f.write(f"init = yesreadxyz\n")
+                f.write("init = yesreadxyz\n")
                 f.write(f"nstep = {self.step.altsteps}\n")
             else:
-                f.write(f"init = yes\n")
+                f.write("init = yes\n")
                 f.write(f"nstep = {self.step.dice.nstep[0]}\n")
 
             f.write("vstep = 0\n")
@@ -301,7 +302,7 @@ class DiceInterface(Interface):
             f.write(f"press = {self.step.dice.press}\n")
             f.write(f"temp = {self.step.dice.temp}\n")
 
-            f.write(f"nstep = 5\n")
+            f.write("nstep = 5\n")
 
             f.write(f"vstep = {int(self.step.dice.nstep[2] / 5)}\n")
             f.write("init = no\n")

diceplayer/shared/interface/gaussian_interface.py

@@ -60,13 +60,13 @@ class GaussianInterface(Interface):
 
     def _copy_chk_file_from_previous_step(self, cycle: int):
         current_chk_file_path = Path(
-            self.step.simulation_dir, f"step{cycle:02d}", "qm", f"asec.chk"
+            self.step.simulation_dir, f"step{cycle:02d}", "qm", "asec.chk"
         )
         if current_chk_file_path.exists():
             raise FileExistsError(f"File {current_chk_file_path} already exists.")
 
         previous_chk_file_path = Path(
-            self.step.simulation_dir, f"step{(cycle - 1):02d}", "qm", f"asec.chk"
+            self.step.simulation_dir, f"step{(cycle - 1):02d}", "qm", "asec.chk"
         )
         if not previous_chk_file_path.exists():
             raise FileNotFoundError(f"File {previous_chk_file_path} does not exist.")
@@ -139,7 +139,7 @@ class GaussianInterface(Interface):
             charges_nsites = int(charges.pop(0))
             if int(charges_nsites) != total_nsites:
                 raise ValueError(
-                    f"Number of sites does not match total number of sites."
+                    "Number of sites does not match total number of sites."
                 )
 
             thickness.append(self._calculate_proc_thickness(charges))
@@ -166,7 +166,7 @@ class GaussianInterface(Interface):
                             ].strip()
                         ):
                             raise SyntaxError(
-                                f"Error: Invalid Dice Output. Atom type does not match."
+                                "Error: Invalid Dice Output. Atom type does not match."
                             )
 
                         new_molecule.add_atom(
@@ -216,7 +216,7 @@ class GaussianInterface(Interface):
 
     def _make_gaussian_input_file(self, cycle: int, asec_charges: list[dict]) -> None:
         gaussian_input_file_path = Path(
-            self.step.simulation_dir, f"step{cycle:02d}", "qm", f"asec.gjf"
+            self.step.simulation_dir, f"step{cycle:02d}", "qm", "asec.gjf"
         )
 
         with open(gaussian_input_file_path, "w") as gaussian_input_file:

diceplayer/shared/utils/misc.py

@@ -6,6 +6,7 @@ import shutil
 import sys
 import time
 
+
 #######################################  constants  ######################################
 
 
@@ -36,7 +37,7 @@ def compress_files_1mb(path):
                 with open(file, "rb") as f_in:
                     with gzip.open(filegz, "wb") as f_out:
                         shutil.copyfileobj(f_in, f_out)
-            except:
+            except Exception as _:
                 sys.exit("Error: cannot compress file {}".format(file))
 
     os.chdir(working_dir)
@@ -52,7 +53,7 @@ def make_step_dir(cycle):
         sys.exit("Error: a file or directory {} already exists".format(step_dir))
     try:
         os.makedirs(path)
-    except:
+    except Exception as _:
         sys.exit("Error: cannot make directory {}".format(step_dir))
 
 
@@ -62,5 +63,5 @@ def make_qm_dir(cycle):
     path = sim_dir + os.sep + step_dir + os.sep + "qm"
     try:
         os.makedirs(path)
-    except:
+    except Exception as _:
         sys.exit("Error: cannot make directory {}".format(path))