[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

aiida_gaussian/calculations/cubegen.py

@@ -107,7 +107,6 @@ def define(cls, spec):
 
     # --------------------------------------------------------------------------
     def prepare_for_submission(self, folder):
-
         # create calculation info
         calcinfo = CalcInfo()
         calcinfo.uuid = self.uuid
@@ -124,7 +123,6 @@ def prepare_for_submission(self, folder):
             )
 
         for key, params in self.inputs.parameters.get_dict().items():
-
             cube_name = key + ".cube"
             kind_str = params["kind"]
             npts = params["npts"]

aiida_gaussian/calculations/formchk.py

@@ -44,7 +44,6 @@ def define(cls, spec):
 
     # --------------------------------------------------------------------------
     def prepare_for_submission(self, folder):
-
         # create code info
         codeinfo = CodeInfo()
         codeinfo.code_uuid = self.inputs.code.uuid

aiida_gaussian/parsers/cubegen.py

@@ -48,7 +48,6 @@ def parse(self, **kwargs):
         return ExitCode(0)
 
     def _parse_folders(self, retrieved_folders, parser_params):
-
         if "heights" in parser_params:
             heights = parser_params["heights"]
         else:
@@ -66,7 +65,6 @@ def _parse_folders(self, retrieved_folders, parser_params):
         for retrieved_fd in retrieved_folders:
             for filename in retrieved_fd.list_object_names():
                 if filename.endswith(".cube"):
-
                     with retrieved_fd.open(filename) as handle:
                         cube = Cube.from_file_handle(handle)
 

aiida_gaussian/parsers/gaussian.py

@@ -45,7 +45,6 @@ def parse(self, **kwargs):
         return ExitCode(0)
 
     def _parse_log(self, log_file_string, inputs):
-
         # parse with cclib
         property_dict = self._parse_log_cclib(log_file_string)
 
@@ -69,7 +68,6 @@ def _parse_log(self, log_file_string, inputs):
         return None
 
     def _parse_electron_numbers(self, log_file_string):
-
         find_el = re.search(
             r"({0})\s*alpha electrons\s*({0}) beta".format(NUM_RE), log_file_string
         )
@@ -80,7 +78,6 @@ def _parse_electron_numbers(self, log_file_string):
             return {}
 
     def _parse_log_cclib(self, log_file_string):
-
         data = cclib.io.ccread(io.StringIO(log_file_string))
 
         if data is None:
@@ -122,7 +119,6 @@ def _set_output_structure(self, inputs, property_dict):
                 "opt" in inputs.parameters["route_parameters"]
                 or len(property_dict["atomcoords"]) > 1
             ):
-
                 opt_coords = property_dict["atomcoords"][-1]
 
                 # The StructureData output node needs a cell,
@@ -140,7 +136,6 @@ def _set_output_structure(self, inputs, property_dict):
                 self.out("output_structure", structure)
 
     def _final_checks_on_log(self, log_file_string, property_dict):
-
         # Error related to the symmetry identification (?).
         if "Logic error in ASyTop." in log_file_string:
             return self.exit_codes.ERROR_ASYTOP

aiida_gaussian/utils/cube.py

@@ -105,7 +105,6 @@ def from_file(cls, filepath, read_data=True):
         return c
 
     def write_cube_file(self, filename):
-
         natoms = len(self.ase_atoms)
 
         f = open(filename, "w")
@@ -134,7 +133,6 @@ def write_cube_file(self, filename):
             )
 
         if natoms > 0:
-
             positions = self.ase_atoms.positions * ANG_TO_BOHR
             numbers = self.ase_atoms.get_atomic_numbers()
             for i in range(natoms):
@@ -149,7 +147,6 @@ def write_cube_file(self, filename):
         f.close()
 
     def swapaxes(self, ax1, ax2):
-
         p = self.ase_atoms.positions
         p[:, ax1], p[:, ax2] = p[:, ax2], p[:, ax1].copy()
 

aiida_gaussian/workchains/base.py

@@ -21,7 +21,6 @@ class GaussianBaseWorkChain(BaseRestartWorkChain):
 
     @classmethod
     def define(cls, spec):
-
         super().define(spec)
         spec.expose_inputs(GaussianCalculation, namespace="gaussian")
 

aiida_gaussian/workchains/cubes.py

@@ -150,7 +150,6 @@ def check_input(self):
         return ExitCode(0)
 
     def formchk_step(self):
-
         self.report("Running FormChk")
 
         builder = FormchkCalculation.get_builder()
@@ -177,7 +176,6 @@ def _get_orbital_label(self, i_orb_wrt_homo):
         return label
 
     def cubegen_step(self):
-
         if not self._check_if_previous_calc_ok(self.ctx.formchk_node):
             return self.exit_codes.ERROR_TERMINATION  # pylint: disable=no-member
 
@@ -221,7 +219,6 @@ def cubegen_step(self):
         abs_orb_indexes = []
 
         if self.inputs.orbital_index_ref == "half_num_el":
-
             total_num_electrons = sum(gout_params["num_electrons"])
             ref_index = total_num_electrons // 2
 
@@ -235,7 +232,6 @@ def cubegen_step(self):
         abs_orb_indexes = [i for i in abs_orb_indexes if i >= 1]
 
         for i_orb in abs_orb_indexes:
-
             if self.inputs.natural_orbitals:
                 params_dict[f"{i_orb}_no"] = {
                     "kind": "MO=%d" % i_orb,

examples/example_cubes_workchain.py

@@ -20,7 +20,6 @@
 
 
 def example(gaussian_code, formchk_code, cubegen_code):
-
     # geometry
     ase_geom = ase.io.read("./p-quinodimethane.xyz")
     ase_geom.cell = np.diag([10.0, 10.0, 10.0])