Mechanical lint cleanup across the package

ThermoScreening/__init__.py

@@ -1,3 +1,5 @@
+"""ThermoScreening: DFTB+ thermochemistry screening package."""
+
 import logging
 import os
 import time

ThermoScreening/calculator/__init__.py

@@ -1 +1,3 @@
-from .dftbplus import Geoopt, Hessian, Modes
+"""Calculator backends for ThermoScreening."""
+
+from .dftbplus import Geoopt, Hessian, Modes

ThermoScreening/calculator/dftbplus.py

@@ -1,3 +1,5 @@
+"""DFTB+ calculators: geometry optimisation, Hessian, and vibrational modes."""
+
 import os
 import shutil
 import subprocess
@@ -121,7 +123,6 @@ def __init__(
 
         self.calculate(atoms)
 
-        return None
 
     def potential_energy(self):
         """
@@ -221,7 +222,6 @@ def __init__(
 
         self.calculate(atoms)
 
-        return None
 
     def read(self):
         """
@@ -278,7 +278,6 @@ def __init__(self, geometry="geo_opt.gen", hessian="hessian.out"):
         # read the vibrational modes
         self.wave_numbers = self.read()
 
-        return None
 
     def write(self):
         """
@@ -304,7 +303,6 @@ def write(self):
         with open("modes_in.hsd", "w") as f:
             f.write(string)
 
-        return None
 
     def calculate(self):
         """
@@ -328,7 +326,6 @@ def calculate(self):
         with open("modes.out", "w") as output:
             subprocess.run(["modes"], stdout=output, check=True)
 
-        return None
 
     def read(self):
         """

ThermoScreening/cli/__init__.py

@@ -1,4 +1,6 @@
+"""Command-line interface for ThermoScreening."""
+
 from .thermo import main
 from ..utils import print_header
 
-print_header()
+print_header()

ThermoScreening/cli/thermo.py

@@ -1,3 +1,5 @@
+"""The ``thermo`` command-line entry point."""
+
 from argparse import ArgumentParser
 import sys
 import time

ThermoScreening/exceptions.py

@@ -4,9 +4,9 @@
 
 class ThermoScreeningException(Exception):
     """Base class for exceptions in this package."""
-    
+
 class TSValueError(ThermoScreeningException):
     """Exception raised for errors in the input value."""
-    
+
 class TSNotImplementedError(ThermoScreeningException):
     """Exception raised for not implemented methods."""

ThermoScreening/thermo/__init__.py

@@ -1,7 +1,9 @@
+"""Thermochemistry API for ThermoScreening."""
+
 from .api import read_xyz, read_gen, read_vib_file, read_coord, read_vibrational, unit_length, unit_energy, unit_mass, run_thermo, execute
 from .atoms import Atom
 from .cell import Cell
 from .inputFileReader import InputFileReader
 from .system import System
 from .thermo import Thermo
-from .screening import screen
+from .screening import screen

ThermoScreening/thermo/api.py

@@ -1,3 +1,5 @@
+"""High-level thermochemistry functions: coordinate/frequency I/O and run helpers."""
+
 import logging
 import os
 from contextlib import contextmanager
@@ -181,14 +183,13 @@ def read_coord(coord_file: str, engine: str):
         if coord_file.endswith(".xyz"):
             data_N, data_atoms, data_xyz, cell, pbc = read_xyz(coord_file)
             return data_N, data_atoms, data_xyz, cell, pbc
-        elif coord_file.endswith(".gen"):
+        if coord_file.endswith(".gen"):
             data_N, data_atoms, data_xyz, cell_vectors, pbc = read_gen(coord_file)
             return data_N, data_atoms, data_xyz, cell_vectors, pbc
-        else:
-            logger.error(
-                "The input file is not supported.",
-                exception=TSNotImplementedError
-            )
+        logger.error(
+            "The input file is not supported.",
+            exception=TSNotImplementedError
+        )
 
     else:
         logger.error(
@@ -251,11 +252,10 @@ def unit_length(engine: str):
     """
     if engine == "dftb+":
         return "Angstrom"
-    else:
-        logger.error(
-            "The engine is not supported.",
-            exception=TSNotImplementedError
-        )
+    logger.error(
+        "The engine is not supported.",
+        exception=TSNotImplementedError
+    )
 
 
 def unit_energy(engine: str):
@@ -279,11 +279,10 @@ def unit_energy(engine: str):
     """
     if engine == "dftb+":
         return "Hartree"
-    else:
-        logger.error(
-            "The engine is not supported.",
-            exception=TSNotImplementedError
-        )
+    logger.error(
+        "The engine is not supported.",
+        exception=TSNotImplementedError
+    )
 
 
 def unit_mass(engine: str):
@@ -307,11 +306,10 @@ def unit_mass(engine: str):
     """
     if engine == "dftb+":
         return "amu"
-    else:
-        logger.error(
-            "The engine is not supported.",
-            exception=TSNotImplementedError
-        )
+    logger.error(
+        "The engine is not supported.",
+        exception=TSNotImplementedError
+    )
 
 
 def unit_frequency(engine: str):
@@ -335,11 +333,10 @@ def unit_frequency(engine: str):
     """
     if engine == "dftb+":
         return "cm^-1"
-    else:
-        logger.error(
-            "The engine is not supported.",
-            exception=TSNotImplementedError
-        )
+    logger.error(
+        "The engine is not supported.",
+        exception=TSNotImplementedError
+    )
 
 
 def _atoms_from_ase(atoms):

ThermoScreening/thermo/atoms.py

@@ -1,3 +1,5 @@
+"""Atom representation and element reference data."""
+
 import logging
 
 import numpy as np
@@ -45,7 +47,7 @@ class Atom:
     >>> atom.position
     array([0., 0., 0.])
     """
-    
+
     logger = logging.getLogger(__package_name__).getChild(__qualname__)
     logger = setup_logger(logger)
 
@@ -96,7 +98,7 @@ def __init__(
                 self._symbol = atomic_Symbol[int(number)].capitalize()
             except:
                 self.logger.error(
-                    "The atomic number %s is not known." % number,
+                    f"The atomic number {number} is not known.",
                     exception=TSValueError
                 )
             self._mass = atomicMasses[self._symbol.lower()]
@@ -107,7 +109,7 @@ def __init__(
                 self._number = atomicNumbers[symbol.lower()]
             except:
                 self.logger.error(
-                    "The chemical symbol %s is not known." % symbol,
+                    f"The chemical symbol {symbol} is not known.",
                     exception=TSValueError
                 )
             self._mass = atomicMasses[symbol.lower()]
@@ -225,7 +227,7 @@ def change_atom(
                 self._number = atomicNumbers[self._symbol.lower()]
             except:
                 self.logger.error(
-                    "The chemical symbol %s is not known." % symbol,
+                    f"The chemical symbol {symbol} is not known.",
                     exception=TSValueError
                 )
 
@@ -238,14 +240,14 @@ def change_atom(
                 self._symbol = atomic_Symbol[int(number)].capitalize()
             except:
                 self.logger.error(
-                    "The atomic number %s is not known." % number,
+                    f"The atomic number {number} is not known.",
                     exception=TSValueError
                 )
             self._mass = atomicMasses[self._symbol.lower()]
             self._configuration = atomicElectronConfigurations[self._symbol.lower()]
         if position is not None:
-            
-            self.position = position        
+
+            self.position = position
 
 
 atomic_Symbol = atomicNumbersReverse

ThermoScreening/thermo/cell.py

@@ -1,3 +1,5 @@
+"""Periodic cell helpers."""
+
 import numpy as np
 
 

ThermoScreening/thermo/inputFileReader.py

@@ -1,3 +1,5 @@
+"""Reader for ThermoScreening key=value input files."""
+
 import logging
 
 from ThermoScreening.exceptions import TSValueError
@@ -14,7 +16,7 @@ class InputFileReader:
         The input file.
 
     """
-    
+
     logger = logging.getLogger(__package_name__).getChild(__qualname__)
     logger = setup_logger(logger)
 
@@ -58,7 +60,6 @@ def __init__(
         self._read()
         self._check()
 
-        return None
 
     def _read(self):
         """
@@ -84,7 +85,6 @@ def _read(self):
             key, value = line.split("=", maxsplit=1)
             self._dictionary[key.strip()] = value.strip()
 
-        return None
 
     def _check(self):
         """
@@ -101,8 +101,7 @@ def _check(self):
         """
         self._check_required_keys()
         self._check_known_keys()
-
-        return None
+
 
     def _check_required_keys(self):
         """
@@ -120,11 +119,10 @@ def _check_required_keys(self):
         for key in self.required_keys:
             if key not in self._dictionary.keys():
                 self.logger.error(
-                    "The key {} is not set in the input file.".format(key),
+                    f"The key {key} is not set in the input file.",
                     exception=TSValueError
                 )
-
-        return None
+
 
     def _check_known_keys(self):
         """
@@ -142,8 +140,7 @@ def _check_known_keys(self):
         for key in self._dictionary.keys():
             if key not in self.required_keys:
                 self.logger.error(
-                    "The key {} is not known.".format(key),
+                    f"The key {key} is not known.",
                     exception=TSValueError
                 )
 
-        return None