Autotidying

bin/update_cff.py

@@ -1,5 +1,7 @@
 import sys
+
 import yaml
+
 if sys.version_info >= (3, 8):
     from importlib import metadata
 else:

src/koopmans/calculators/_koopmans_ham.py

@@ -52,7 +52,7 @@ def write_alphas(self):
     def _pre_calculate(self):
         super()._pre_calculate()
         self.write_alphas()
-    
+
     def _post_calculate(self):
         super()._post_calculate()
         if isinstance(self.parameters.kpts, BandPath) and len(self.parameters.kpts.kpts) > 1:

src/koopmans/calculators/_ph.py

@@ -14,7 +14,7 @@
 from ase import Atoms
 from ase.calculators.espresso import EspressoPh
 
-from koopmans.commands import ParallelCommand, Command
+from koopmans.commands import Command, ParallelCommand
 from koopmans.settings import PhSettingsDict
 
 from ._utils import CalculatorABC, CalculatorExt

src/koopmans/calculators/_projwfc.py

@@ -55,7 +55,7 @@ def _pre_calculate(self):
             if not hasattr(self, attr):
                 raise ValueError(f'Please set {self.__class__.__name__}.{attr} before calling '
                                  f'{self.__class__.__name__.calculate()}')
-    
+
     def _post_calculate(self):
         super()._post_calculate()
         self.generate_dos()

src/koopmans/calculators/_pw.py

@@ -50,7 +50,7 @@ def _pre_calculate(self):
             if not isinstance(self.parameters.kpts, BandPath):
                 raise KeyError('You are running a calculation that requires a kpoint path; please provide a BandPath '
                                'as the kpts parameter')
-            
+
         super()._pre_calculate()
 
         return
@@ -62,7 +62,7 @@ def _post_calculate(self):
         if isinstance(self.parameters.kpts, BandPath):
             # Add the bandstructure to the results. This is very un-ASE-y and might eventually be replaced
             self.generate_band_structure()
-        
+
         return
 
     def is_complete(self):

src/koopmans/calculators/_utils.py

@@ -162,7 +162,7 @@ def _pre_calculate(self):
 
     def _calculate(self):
         """Run the calculation using the ASE calculator's calculate() method
-        
+
         This method should NOT be overwritten by child classes. Child classes should only modify _pre_calculate() and
         _post_calculate() to perform any necessary pre- and post-calculation steps."""
 

src/koopmans/cli/main.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
-import sys
 import argparse
+import sys
 import textwrap
 
 import koopmans.mpl_config
@@ -28,7 +28,6 @@ def main():
     # Set traceback behaviour
     if not args.traceback:
         sys.tracebacklimit = 0
-
 
     # Run workflow
     workflow.run()

src/koopmans/settings/_ph.py

@@ -5,7 +5,7 @@ class PhSettingsDict(SettingsDict):
     def __init__(self, **kwargs) -> None:
         super().__init__(valid=['outdir', 'prefix', 'epsil', 'amass',
                                 'fildyn', 'tr2_ph', 'trans'],
-                            defaults={'outdir': 'TMP', 'prefix': 'kc', 'epsil': True, 'trans' : False
+                         defaults={'outdir': 'TMP', 'prefix': 'kc', 'epsil': True, 'trans': False
                                    },
                          are_paths=['outdir'],
                          **kwargs)

src/koopmans/settings/_wannier90.py

@@ -2,7 +2,8 @@
 
 import numpy as np
 from ase.dft.kpoints import BandPath, monkhorst_pack
-from ase.io.wannier90 import construct_kpoint_path, proj_string_to_dict, formatted_str_to_list
+from ase.io.wannier90 import (construct_kpoint_path, formatted_str_to_list,
+                              proj_string_to_dict)
 
 from ._utils import SettingsDict
 
@@ -55,8 +56,8 @@ def __setitem__(self, key: str, value: Any):
             self.kpoints = kpts
         elif key == 'koffset':
             if self.mp_grid is None:
-                raise ValueError('Cannot offset the list of k-points if "kpoints" has not been defined yet. ' + \
-                    'Check that "kgrid" is provided before "koffset"')
+                raise ValueError('Cannot offset the list of k-points if "kpoints" has not been defined yet. ' +
+                                 'Check that "kgrid" is provided before "koffset"')
             if isinstance(value, int) or isinstance(value, list) and all([isinstance(k, int) for k in value]):
                 # For koffset = [1, 1, 1], PW shifts the k-grid by half a grid step
                 self.kpoints += np.array(value) / self.mp_grid / 2

src/koopmans/utils/_xml.py

@@ -36,18 +36,18 @@ def read_xml_nr(xml_file: Path, string: str = 'EFFECTIVE-POTENTIAL') -> List[int
 
 
 def read_xml_array(
-    xml_file: Path, norm_const: float, string: str = 'EFFECTIVE-POTENTIAL', retain_final_element: bool=False
-    ) -> np.ndarray:
+    xml_file: Path, norm_const: float, string: str = 'EFFECTIVE-POTENTIAL', retain_final_element: bool = False
+) -> np.ndarray:
     """
     Loads an array from an xml file.
-    
+
     :param xml_file: The xml file to read from
     :param norm_const: The normalization constant to multiply the array with (in our case 1/((Bohr radii)^3)
-    :param string: The name of the field in the xml file that contains the array, in our case either 
+    :param string: The name of the field in the xml file that contains the array, in our case either
     'EFFECTIVE-POTENTIAL' or 'CHARGE-DENSITY'
-    :param retain_final_element: If True, the array is returned in with periodic boundary conditions, i.e. the last 
+    :param retain_final_element: If True, the array is returned in with periodic boundary conditions, i.e. the last
     element in each dimension is equal to the first element in each dimension. This is required for the xsf format.
-    
+
     :return: The array
     """
 
@@ -71,7 +71,7 @@ def read_xml_array(
                 array_xml[k, j, i] = rho_tmp[(j % (nr_xml[1]-1))*(nr_xml[0]-1)+(i % (nr_xml[0]-1))]
     array_xml *= norm_const
 
-    if retain_final_element: 
+    if retain_final_element:
         # the xsf format requires an array where the last element is equal to the first element in each dimension
         return array_xml
     else:

src/koopmans/utils/_xsf.py

@@ -28,7 +28,7 @@ def write_xsf(filename: Path, atoms: Atoms, arrays: List[np.ndarray], nr_xml: Tu
         out.write('CRYSTAL\n\n')
         out.write('PRIMVEC\n\n')
         for vec in cell_parameters:
-            out.write("\t" + " ".join([f"{x:13.10f}" for x in vec])+ " \n")
+            out.write("\t" + " ".join([f"{x:13.10f}" for x in vec]) + " \n")
         out.write('PRIMCOORD\n')
         out.write(f"\t{len(symbols)}\t1\n")
         for symbol, pos in zip(symbols, positions):

src/koopmans/workflows/_convergence_ml.py

@@ -134,9 +134,9 @@ def convert_to_list(param, type):
                 return [param]
             else:
                 # If param is not an int or a float check that it is a list of ints / floats
-                assert(isinstance(param, list))
+                assert (isinstance(param, list))
                 for value in param:
-                    assert(isinstance(value, type))
+                    assert (isinstance(value, type))
                 return param
 
         n_maxs = convert_to_list(self.ml.n_max, int)

src/koopmans/workflows/_koopmans_dfpt.py

@@ -10,7 +10,7 @@
 from pathlib import Path
 from typing import Dict
 
-from koopmans import utils, pseudopotentials
+from koopmans import pseudopotentials, utils
 from koopmans.bands import Bands
 from koopmans.calculators import (KoopmansHamCalculator, PWCalculator,
                                   Wann2KCCalculator)
@@ -144,7 +144,7 @@ def _run(self):
                 if key.startswith('w90'):
                     self.calculator_parameters[key].write_u_matrices = True
                     self.calculator_parameters[key].write_xyz = True
-            wf_workflow = WannierizeWorkflow.fromparent(self, force_nspin2=True, scf_kgrid = self._scf_kgrid)
+            wf_workflow = WannierizeWorkflow.fromparent(self, force_nspin2=True, scf_kgrid=self._scf_kgrid)
             wf_workflow.run()
 
         else:

src/koopmans/workflows/_koopmans_dscf.py

@@ -642,13 +642,13 @@ def perform_alpha_calculations(self) -> None:
 
                         alpha, error = self.calculate_alpha_from_list_of_calcs(
                             calcs, trial_calc, band, filled=band.filled)
-                        
+
                         # Mixing
                         alpha = self.parameters.alpha_mixing * alpha + (1 - self.parameters.alpha_mixing) * band.alpha
 
                     warning_message = 'The computed screening parameter is {0}. Proceed with caution.'
                     failure_message = 'The computed screening parameter is significantly {0}. This should not ' \
-                         'happen. Decrease alpha_mixing and/or change alpha_guess.'
+                        'happen. Decrease alpha_mixing and/or change alpha_guess.'
 
                     if alpha < -0.1:
                         raise ValueError(failure_message.format('less than 0'))

src/koopmans/workflows/_singlepoint.py

@@ -14,9 +14,9 @@
 import numpy as np
 
 from koopmans import utils
+from koopmans.calculators import ProjwfcCalculator
 
 from ._workflow import Workflow
-from koopmans.calculators import ProjwfcCalculator
 
 load_results_from_output = True
 

src/koopmans/workflows/_trajectory.py

@@ -97,7 +97,7 @@ def _run(self):
             snapshot = self.snapshots[i]
             self.ml.current_snapshot = i
             self.atoms.set_positions(snapshot.positions)
-            
+
             # after each snapshot we want to set the from_scratch_parameter to its original value
             # To do so, we save it here since it might get set from False to True during the calculation
             # of the snapshot

src/koopmans/workflows/_wannierize.py

@@ -11,7 +11,7 @@
 import math
 import shutil
 from pathlib import Path
-from typing import List, TypeVar, Optional
+from typing import List, Optional, TypeVar
 
 # isort: off
 import koopmans.mpl_config

src/koopmans/workflows/_workflow.py

@@ -568,9 +568,9 @@ def convert_to_list(param, type):
                 if isinstance(param, type):  # if param is an int or a float convert it for the checks to a list
                     return [param]
                 else:  # if param is not an int or a float check that it is a list of ints / floats
-                    assert(isinstance(param, list))
+                    assert (isinstance(param, list))
                     for value in param:
-                        assert(isinstance(value, type))
+                        assert (isinstance(value, type))
                     return param
 
             n_maxs = convert_to_list(self.ml.n_max, int)
@@ -718,7 +718,7 @@ def supercell_to_primitive(self, matrix: Optional[npt.NDArray[np.int_]] = None):
 
     def run_calculator(self, master_calc: calculators.Calc, enforce_spin_symmetry: bool = False):
         ''' Run a calculator.
-        
+
         If enforce_spin_symmetry is True, the calculation will be run with spin symmetry enforced.
         Ultimately this wraps self.run_calculators
 
@@ -800,7 +800,7 @@ def _pre_run_calculator(self, qe_calc: calculators.Calc) -> bool:
                 qe_calc.command.postfix = f'-npool {self.parameters.npool}'
 
         return True
-    
+
     def _run_calculators(self, calcs: List[calculators.Calc]) -> None:
         """Run a list of calculators, without doing anything else (other than printing messages.)
 
@@ -842,7 +842,7 @@ def _post_run_calculator(self, calc: calculators.Calc) -> None:
         self.parameters.from_scratch = True
 
         return
-    
+
     def run_calculators(self, calcs: List[calculators.Calc]):
         '''
         Run a list of *independent* calculators (default implementation is to run them in sequence)
@@ -855,7 +855,7 @@ def run_calculators(self, calcs: List[calculators.Calc]):
                 calcs_to_run.append(calc)
 
         self._run_calculators(calcs_to_run)
-        
+
         for calc in calcs_to_run:
             self._post_run_calculator(calc)
 

tests/calculators/test_ph.py

@@ -6,8 +6,6 @@
 from koopmans import utils, workflows
 from koopmans.io import read_kwf as read_encoded_json
 from koopmans.io import write_kwf as write_encoded_json
-
-
 from tests.helpers.patches import benchmark_filename
 
 

tests/calculators/test_projwfc.py

@@ -7,8 +7,6 @@
 from koopmans import utils, workflows
 from koopmans.io import read_kwf as read_encoded_json
 from koopmans.io import write_kwf as write_encoded_json
-
-
 from tests.helpers.patches import benchmark_filename
 
 

tests/conftest.py

@@ -1,10 +1,12 @@
 from pathlib import Path
+
 import pytest
 
-from .helpers.systems import gaas, ozone, silicon, tio2, water
 from .helpers.os import datadir, sys2file
-from .helpers.patches import tutorial_patch, workflow_patch, ui_patch, espresso_patch
+from .helpers.patches import (espresso_patch, tutorial_patch, ui_patch,
+                              workflow_patch)
 from .helpers.strategies import ase_cells, bandpaths, kpoints
+from .helpers.systems import gaas, ozone, silicon, tio2, water
 
 
 def pytest_addoption(parser):

tests/helpers/os.py

@@ -1,4 +1,5 @@
 from pathlib import Path
+
 import pytest
 
 

tests/helpers/patches/__init__.py

@@ -1,25 +1,22 @@
 import pytest
 
-from ._check import (CheckEnvironCalculator, CheckKoopmansCPCalculator,
-                     CheckKoopmansHamCalculator, CheckKoopmansScreenCalculator,
-                     CheckMLFittingWorkflow, CheckPhCalculator,
-                     CheckProjwfcCalculator, CheckPW2WannierCalculator,
-                     CheckPWCalculator, CheckUnfoldAndInterpolateCalculator,
-                     CheckWann2KCCalculator, CheckWann2KCPCalculator,
-                     CheckWannier90Calculator)
 from ._benchmark import (BenchGenEnvironCalculator,
                          BenchGenKoopmansCPCalculator,
                          BenchGenKoopmansHamCalculator,
                          BenchGenKoopmansScreenCalculator,
-                         BenchGenMLFittingWorkflow,
-                         BenchGenPhCalculator,
+                         BenchGenMLFittingWorkflow, BenchGenPhCalculator,
                          BenchGenProjwfcCalculator,
-                         BenchGenPW2WannierCalculator,
-                         BenchGenPWCalculator,
+                         BenchGenPW2WannierCalculator, BenchGenPWCalculator,
                          BenchGenUnfoldAndInterpolateCalculator,
-                         BenchGenWann2KCCalculator,
-                         BenchGenWann2KCPCalculator,
+                         BenchGenWann2KCCalculator, BenchGenWann2KCPCalculator,
                          BenchGenWannier90Calculator)
+from ._check import (CheckEnvironCalculator, CheckKoopmansCPCalculator,
+                     CheckKoopmansHamCalculator, CheckKoopmansScreenCalculator,
+                     CheckMLFittingWorkflow, CheckPhCalculator,
+                     CheckProjwfcCalculator, CheckPW2WannierCalculator,
+                     CheckPWCalculator, CheckUnfoldAndInterpolateCalculator,
+                     CheckWann2KCCalculator, CheckWann2KCPCalculator,
+                     CheckWannier90Calculator)
 from ._mock import (MockEnvironCalculator, MockKoopmansCPCalculator,
                     MockKoopmansDSCFWorkflow, MockKoopmansHamCalculator,
                     MockKoopmansScreenCalculator, MockMLFittingWorkflow,
@@ -39,7 +36,6 @@
                        StumblingTrajectoryWorkflow,
                        StumblingUnfoldAndInterpolateWorkflow,
                        StumblingWannierizeWorkflow)
-
 from ._utils import benchmark_filename
 
 

tests/helpers/patches/_check.py

@@ -166,7 +166,7 @@ def _print_messages(self, messages: List[Dict[str, str]]) -> None:
                 message = message.replace('disagreements', 'disagreement')
 
             raise CalculationFailed(message)
-        
+
     def _load_benchmark(self) -> Calc:
         with utils.chdir(self.directory):  # type: ignore[attr-defined]
             # By moving into the directory where the calculation was run, we ensure when we read in the settings that
@@ -177,7 +177,7 @@ def _load_benchmark(self) -> Calc:
 
     def _pre_calculate(self):
         """Before running the calculation, check the settings are the same"""
-        
+
         # Perform the pre_calculate first, as sometimes this function modifies the input parameters
         super()._pre_calculate()
 

tests/io/test_io_json.py

@@ -5,6 +5,7 @@
 '''
 
 from ase.build import molecule
+
 from koopmans import utils
 from koopmans.io import read, write
 from koopmans.workflows import (ConvergenceMLWorkflow, SinglepointWorkflow,

tests/test_cell.py

@@ -6,7 +6,6 @@
 from hypothesis import given, settings, strategies
 
 from koopmans.cell import cell_to_parameters, parameters_to_cell
-
 from tests.helpers import strategies as kst
 
 # Reference list of ASE Bravais lattice classes