Linting

Former-commit-id: 3014ae2

.gitignore

@@ -150,4 +150,4 @@ snb_test.ipynb
 conda_packaging.md
 .pytest_cache/
 shakenbreak/__pycache__/
-tests/__pycache__/
+tests/__pycache__/

.pytest_cache/v/cache/lastfailed

@@ -29,5 +29,6 @@
   "tests/test_input.py::InputTestCase::test_write_vasp_files": true,
   "tests/test_input.py::InputTestCase::test_write_vasp_files_from_doped_defect_gen": true,
   "tests/test_input.py::InputTestCase::test_write_vasp_files_from_doped_dict": true,
-  "tests/test_input.py::InputTestCase::test_write_vasp_files_from_list": true
-}
+  "tests/test_input.py::InputTestCase::test_write_vasp_files_from_list": true,
+  "tests/test_cli.py": true
+}

.pytest_cache/v/cache/nodeids

@@ -1,4 +1,15 @@
 [
+  "tests/test_cli.py::CLITestCase::test_analyse",
+  "tests/test_cli.py::CLITestCase::test_groundstate",
+  "tests/test_cli.py::CLITestCase::test_mag",
+  "tests/test_cli.py::CLITestCase::test_parse",
+  "tests/test_cli.py::CLITestCase::test_parse_codes",
+  "tests/test_cli.py::CLITestCase::test_plot",
+  "tests/test_cli.py::CLITestCase::test_regenerate",
+  "tests/test_cli.py::CLITestCase::test_run",
+  "tests/test_cli.py::CLITestCase::test_snb_generate",
+  "tests/test_cli.py::CLITestCase::test_snb_generate_all",
+  "tests/test_cli.py::CLITestCase::test_snb_generate_config",
   "tests/test_input.py::InputTestCase::test_apply_rattle_bond_distortions_V_Cd_dimer",
   "tests/test_input.py::InputTestCase::test_apply_snb_distortions_V_Cd_Dimer",
   "tests/test_input.py::InputTestCase::test_apply_snb_distortions_V_Cd_dimer",
@@ -37,4 +48,4 @@
   "tests/test_plotting.py::PlottingDefectsTestCase::test_remove_high_energy_points",
   "tests/test_plotting.py::PlottingDefectsTestCase::test_save_plot",
   "tests/test_plotting.py::PlottingDefectsTestCase::test_verify_data_directories_exist"
-]
+]

.pytest_cache/v/cache/stepwise

@@ -1 +1 @@
-[]
+[]

shakenbreak/analysis.py

@@ -117,15 +117,15 @@ def _get_distortion_filename(distortion) -> str:
             distortion_label = f"Bond_Distortion_{distortion:.1f}%"
     elif isinstance(distortion, str):
         if "_from_" in distortion and (
-            "Rattled" not in distortion
-            and "Dimer" not in distortion
+            "Rattled" not in distortion and "Dimer" not in distortion
         ):
             distortion_label = f"Bond_Distortion_{distortion}"
             # runs from other charge states
         elif (
             "Rattled_from_" in distortion
             or "Dimer_from" in distortion
-            or distortion in [
+            or distortion
+            in [
                 "Unperturbed",
                 "Rattled",
                 "Dimer",
@@ -194,9 +194,8 @@ def _format_distortion_names(
     ):
         return float(distortion_label.split("Bond_Distortion_")[-1].split("%")[0]) / 100
     elif (
-        ("Dimer" in distortion_label or "Rattled" in distortion_label)
-        and "High_Energy" in distortion_label
-    ):
+        "Dimer" in distortion_label or "Rattled" in distortion_label
+    ) and "High_Energy" in distortion_label:
         return distortion_label
     else:
         return "Label_not_recognized"
@@ -505,7 +504,10 @@ def get_structures(
         distortion_subdirectories = [
             i
             for i in next(os.walk(f"{output_path}/{defect_species}"))[1]
-            if ("Bond_Distortion" in i) or ("Unperturbed" in i) or ("Rattled" in i) or ("Dimer" in i)
+            if ("Bond_Distortion" in i)
+            or ("Unperturbed" in i)
+            or ("Rattled" in i)
+            or ("Dimer" in i)
         ]  # distortion subdirectories
         if not distortion_subdirectories:
             raise FileNotFoundError(
@@ -1000,8 +1002,10 @@ def get_homoionic_bonds(
             homoionic neighbours and distances (A) (e.g.
             {'O(1)': {'O(2)': '2.0 A', 'O(3)': '2.0 A'}})
     """
-    if isinstance(elements, str): # For backward compatibility
-        elements = [elements,]
+    if isinstance(elements, str):  # For backward compatibility
+        elements = [
+            elements,
+        ]
     structure = structure.copy()
     structure.remove_oxidation_states()
     for element in elements:
@@ -1012,11 +1016,13 @@ def get_homoionic_bonds(
     # Search for homoionic bonds in the whole structure
     sites = []
     for element in elements:
-        sites.extend([
-            (site_index, site)
-            for site_index, site in enumerate(structure)
-            if site.species_string == element
-        ])
+        sites.extend(
+            [
+                (site_index, site)
+                for site_index, site in enumerate(structure)
+                if site.species_string == element
+            ]
+        )
     homoionic_bonds = {}
     for site_index, site in sites:
         neighbours = structure.get_neighbors(site, r=radius)
@@ -1040,9 +1046,9 @@ def get_homoionic_bonds(
                         if neighbour[0] == element
                     }
                     if f"{site.species_string}({site_index})" in homoionic_bonds:
-                        homoionic_bonds[
-                            f"{site.species_string}({site_index})"
-                        ].update(homoionic_neighbours)
+                        homoionic_bonds[f"{site.species_string}({site_index})"].update(
+                            homoionic_neighbours
+                        )
                     else:
                         homoionic_bonds[
                             f"{site.species_string}({site_index})"

shakenbreak/cli.py

@@ -10,8 +10,8 @@
 
 import click
 from doped.generation import get_defect_name_from_entry
-from doped.utils.plotting import _format_defect_name
 from doped.utils.parsing import get_outcar
+from doped.utils.plotting import _format_defect_name
 
 # Monty and pymatgen
 from monty.serialization import dumpfn, loadfn

shakenbreak/distortions.py

@@ -10,10 +10,10 @@
     _probability_mc_rattle,
     generate_mc_rattled_structures,
 )
-from pymatgen.analysis.local_env import MinimumDistanceNN
+from pymatgen.analysis.local_env import CrystalNN, MinimumDistanceNN
 from pymatgen.core.structure import Structure
 from pymatgen.io.ase import AseAtomsAdaptor
-from pymatgen.analysis.local_env import CrystalNN
+
 
 def _warning_on_one_line(message, category, filename, lineno, file=None, line=None):
     """Format warnings output"""
@@ -89,7 +89,9 @@ def distort(
     if distorted_atoms and len(distorted_atoms) >= num_nearest_neighbours:
         nearest = [
             (
-                round(input_structure_ase.get_distance(atom_number, index, mic=True), 4),
+                round(
+                    input_structure_ase.get_distance(atom_number, index, mic=True), 4
+                ),
                 index + 1,
                 input_structure_ase.get_chemical_symbols()[index],
             )
@@ -106,7 +108,9 @@ def distort(
             )
         distances = [  # Get all distances between the selected atom and all other atoms
             (
-                round(input_structure_ase.get_distance(atom_number, index, mic=True), 4),
+                round(
+                    input_structure_ase.get_distance(atom_number, index, mic=True), 4
+                ),
                 index + 1,  # Indices start from 1
                 symbol,
             )
@@ -124,7 +128,9 @@ def distort(
         ):  # filter the neighbours that match the element criteria and are
             # closer than 4.5 Angstroms
             nearest = []  # list of nearest neighbours
-            for dist, index, element in distances[1:]: # starting from 1 to exclude defect atom
+            for dist, index, element in distances[
+                1:
+            ]:  # starting from 1 to exclude defect atom
                 if (
                     element == distorted_element
                     and dist < 4.5
@@ -228,7 +234,7 @@ def apply_dimer_distortion(
 
     if site_index is not None:  # site_index can be 0
         atom_number = site_index - 1  # Align atom number with python 0-indexing
-    elif type(frac_coords) in  [list, tuple, np.ndarray]:  # Only for vacancies!
+    elif type(frac_coords) in [list, tuple, np.ndarray]:  # Only for vacancies!
         input_structure_ase.append("V")  # fake "V" at vacancy
         input_structure_ase.positions[-1] = np.dot(
             frac_coords, input_structure_ase.cell
@@ -243,20 +249,20 @@ def apply_dimer_distortion(
     # Get defect nn
     struct = aaa.get_structure(input_structure_ase)
     cnn = CrystalNN()
-    sites = [d['site'] for d in cnn.get_nn_info(struct, atom_number)]
+    sites = [d["site"] for d in cnn.get_nn_info(struct, atom_number)]
 
     # Get distances between NN
     distances = {}
     for i, site in enumerate(sites):
-        for other_site in sites[i+1:]:
+        for other_site in sites[i + 1 :]:
             distances[(site.index, other_site.index)] = site.distance(other_site)
     # Get defect NN with smallest distance
     site_indexes = min(distances, key=distances.get)
     # Set their distance to 2 A
     input_structure_ase.set_distance(
         a0=site_indexes[0], a1=site_indexes[1], distance=2.0, fix=0.5, mic=True
     )
-    if type(frac_coords) in  [list, tuple, np.ndarray]:
+    if type(frac_coords) in [list, tuple, np.ndarray]:
         input_structure_ase.pop(-1)  # remove fake V from vacancy structure
 
     distorted_structure = aaa.get_structure(input_structure_ase)

shakenbreak/input.py

@@ -1360,7 +1360,10 @@ def _apply_rattle_bond_distortions(
         # unit cell is conserved in the supercell
         frac_coords = None  # only for vacancies
         if defect_site_index is not None:
-            if isinstance(distortion_factor, str) and distortion_factor.lower() == "dimer":
+            if (
+                isinstance(distortion_factor, str)
+                and distortion_factor.lower() == "dimer"
+            ):
                 bond_distorted_defect = distortions.apply_dimer_distortion(
                     structure=defect_structure,
                     site_index=defect_site_index,
@@ -1568,14 +1571,18 @@ def apply_snb_distortions(
                     seed=seed,
                     **mc_rattle_kwargs,
                 )
-                distorted_defect_dict["distortions"]["Dimer"] = (
-                    bond_distorted_defect["distorted_structure"]
+                distorted_defect_dict["distortions"]["Dimer"] = bond_distorted_defect[
+                    "distorted_structure"
+                ]
+                distorted_defect_dict["distortion_parameters"].update(
+                    {
+                        "unique_site": bulk_supercell_site.frac_coords,
+                        "num_distorted_neighbours_in_dimer": 2,  # Dimer distortion only affects 2 atoms
+                        "distorted_atoms_in_dimer": bond_distorted_defect[
+                            "distorted_atoms"
+                        ],
+                    }
                 )
-                distorted_defect_dict["distortion_parameters"].update({
-                    "unique_site": bulk_supercell_site.frac_coords,
-                    "num_distorted_neighbours_in_dimer": 2,  # Dimer distortion only affects 2 atoms
-                    "distorted_atoms_in_dimer": bond_distorted_defect["distorted_atoms"],
-                })
                 if defect_site_index:  # only add site index if not vacancy
                     distorted_defect_dict["distortion_parameters"][
                         "defect_site_index"
@@ -1635,11 +1642,15 @@ def apply_snb_distortions(
             distorted_defect_dict["distortions"]["Dimer"] = bond_distorted_defect[
                 "distorted_structure"
             ]
-            distorted_defect_dict["distortion_parameters"].update({
-                "unique_site": bulk_supercell_site.frac_coords,
-                "num_distorted_neighbours_in_dimer": 2,  # Dimer distortion only affects 2 atoms
-                "distorted_atoms_in_dimer": bond_distorted_defect["distorted_atoms"],
-            })
+            distorted_defect_dict["distortion_parameters"].update(
+                {
+                    "unique_site": bulk_supercell_site.frac_coords,
+                    "num_distorted_neighbours_in_dimer": 2,  # Dimer distortion only affects 2 atoms
+                    "distorted_atoms_in_dimer": bond_distorted_defect[
+                        "distorted_atoms"
+                    ],
+                }
+            )
     return distorted_defect_dict
 
 
@@ -1961,9 +1972,9 @@ def guess_oxidation_states(bulk_comp):
                 self.bond_distortions.append("Dimer")
                 bond_distortions.remove("Dimer")
 
-            self.bond_distortions.extend(list(
-                np.around(bond_distortions, 3)
-            ))  # round to 3 decimal places
+            self.bond_distortions.extend(
+                list(np.around(bond_distortions, 3))
+            )  # round to 3 decimal places
         else:
             # If the user does not specify bond_distortions, use
             # distortion_increment:
@@ -2123,7 +2134,7 @@ def _print_distortion_info(
     ) -> None:
         """Print applied bond distortions and rattle standard deviation."""
         rounded_distortions = [
-            f'{round(i,3)+0}' if isinstance(i, float) else i for i in bond_distortions
+            f"{round(i,3)+0}" if isinstance(i, float) else i for i in bond_distortions
         ]
         print(
             "Applying ShakeNBreak...",

shakenbreak/io.py

@@ -368,7 +368,7 @@ def parse_fhi_aims_energy(defect_dir, dist, energy, aims_out):
                         "Bond_Distortion",
                         "Rattled",
                         "Unperturbed",
-                                    "Dimer",
+                        "Dimer",
                     ]
                 )
                 and "High_Energy" in dir

shakenbreak/plotting.py

@@ -412,7 +412,7 @@ def _format_datapoints_from_other_chargestates(
         elif entry == "Rattled":  # add 0.0 for Rattled
             # (to avoid problems when sorting distortions)
             keys.append(0.0)
-        elif entry == "Dimer": # add 0.0 for Dimer
+        elif entry == "Dimer":  # add 0.0 for Dimer
             # (to avoid problems when sorting distortions)
             keys.append(0.0)
         else:
@@ -1340,7 +1340,7 @@ def plot_colorbar(
                 energies_dict["distortions"]["Dimer"],
                 c=disp_dict["Dimer"],
                 s=50,
-                marker="s", #default_style_settings["marker"],
+                marker="s",  # default_style_settings["marker"],
                 label="Dimer",
                 cmap=colormap,
                 norm=norm,
@@ -1728,15 +1728,14 @@ def plot_datasets(
                     dataset["distortions"]["Dimer"],
                     c=colors[dataset_number],
                     s=50,
-                    marker="s", #default_style_settings["marker"],
+                    marker="s",  # default_style_settings["marker"],
                     label="Dimer",
                 )
 
             if len(sorted_distortions) > 0 and [
-
-                    key for key in dataset["distortions"]
-                    if (key != "Rattled" and key != "Dimer")
-
+                key
+                for key in dataset["distortions"]
+                if (key != "Rattled" and key != "Dimer")
             ]:  # more than just Rattled
                 if imported_indices:  # Exclude datapoints from other charge states
                     non_imported_sorted_indices = [