Merge 756013e into 0a66334

materialsproject · Feb 1, 2023 · 5fdebc9 · 5fdebc9
2 parents 0a66334 + 756013e
commit 5fdebc9
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ ci:
 
 repos:
   - repo: https://github.com/PyCQA/autoflake
-    rev: v2.0.0
+    rev: v2.0.1
     hooks:
       - id: autoflake
 
@@ -25,13 +25,13 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/PyCQA/isort
-    rev: 5.11.4
+    rev: 5.12.0
     hooks:
       - id: isort
         args: [--profile, black]
 
   - repo: https://github.com/psf/black
-    rev: 22.12.0
+    rev: 23.1.0
     hooks:
       - id: black
 
@@ -65,13 +65,13 @@ repos:
         args: [--ignore-words-list, 'titel,titels,reson,rute,pres,kno,coo']
 
   - repo: https://github.com/PyCQA/pydocstyle
-    rev: 6.1.1
+    rev: 6.3.0
     hooks:
       - id: pydocstyle
         exclude: tests
 
   - repo: https://github.com/MarcoGorelli/cython-lint
-    rev: v0.10.1
+    rev: v0.11.1
     hooks:
       - id: cython-lint
         args: [--no-pycodestyle]

diff --git a/dev_scripts/chemenv/equivalent_indices.py b/dev_scripts/chemenv/equivalent_indices.py
@@ -17,7 +17,6 @@
 __date__ = "Feb 20, 2016"
 
 if __name__ == "__main__":
-
     cg_symbol = "O:6"
     equiv_list = []
 

diff --git a/dev_scripts/chemenv/explicit_permutations.py b/dev_scripts/chemenv/explicit_permutations.py
@@ -36,7 +36,6 @@ class Algo:
 
 
 if __name__ == "__main__":
-
     # Choose the geometry
     allcg = AllCoordinationGeometries()
     while True:

diff --git a/dev_scripts/chemenv/explicit_permutations_plane_algorithm.py b/dev_scripts/chemenv/explicit_permutations_plane_algorithm.py
@@ -23,7 +23,6 @@
 from pymatgen.analysis.chemenv.utils.coordination_geometry_utils import Plane, collinear
 
 if __name__ == "__main__":
-
     # Choose the geometry
     allcg = AllCoordinationGeometries()
     while True:

diff --git a/dev_scripts/chemenv/get_plane_permutations_optimized.py b/dev_scripts/chemenv/get_plane_permutations_optimized.py
@@ -343,7 +343,6 @@ def random_permutations_iterator(initial_permutation, n_permutations):
             t0 = time.process_time()
             timeleft = "Unknown"
             for indices_perm in perms_iterator:
-
                 prt1(
                     string=f"Perm # {iperm:d}/{npermutations:d} : "
                     f"{'-'.join(map(str, indices_perm))} "

diff --git a/dev_scripts/chemenv/plane_multiplicity.py b/dev_scripts/chemenv/plane_multiplicity.py
@@ -19,7 +19,6 @@
 __date__ = "Feb 20, 2016"
 
 if __name__ == "__main__":
-
     allcg = AllCoordinationGeometries()
 
     cg_symbol = "I:12"

diff --git a/dev_scripts/chemenv/test_algos.py b/dev_scripts/chemenv/test_algos.py
@@ -30,7 +30,6 @@
 __date__ = "Feb 20, 2016"
 
 if __name__ == "__main__":
-
     allcg = AllCoordinationGeometries()
 
     while True:
@@ -68,7 +67,6 @@
     iperm = 1
     t1 = time.clock()
     for indices_perm in perms_iterator:
-
         lgf.setup_test_perfect_environment(cg_symbol, indices=indices_perm)
 
         lgf.perfect_geometry = AbstractGeometry.from_cg(cg=cg)

diff --git a/dev_scripts/chemenv/test_algos_all_geoms.py b/dev_scripts/chemenv/test_algos_all_geoms.py
@@ -27,7 +27,6 @@
 __date__ = "Feb 20, 2016"
 
 if __name__ == "__main__":
-
     allcg = AllCoordinationGeometries()
 
     test = input('Standard ("s", all permutations for cn <= 6, 500 random permutations for cn > 6) or on demand')
@@ -96,7 +95,6 @@
             # Loop on the permutations
             iperm = 1
             for indices_perm in perms_iterator:
-
                 lgf.setup_test_perfect_environment(
                     cg_symbol,
                     indices=indices_perm,

diff --git a/pymatgen/analysis/adsorption.py b/pymatgen/analysis/adsorption.py
@@ -496,7 +496,6 @@ def adsorb_both_surfaces(
 
         new_ad_slabss = []
         for ad_slabs in ad_slabss:
-
             # Find the adsorbate sites and indices in each slab
             _, adsorbates, indices = False, [], []
             for i, site in enumerate(ad_slabs.sites):

diff --git a/pymatgen/analysis/bond_valence.py b/pymatgen/analysis/bond_valence.py
@@ -286,7 +286,7 @@ def get_valences(self, structure):
                 all_prob.append(prob)
                 full_all_prob.extend(prob.values())
                 vals = []
-                for (elsp, _) in get_z_ordered_elmap(test_site.species):
+                for elsp, _ in get_z_ordered_elmap(test_site.species):
                     val = list(prob[elsp.symbol])
                     # Sort valences in order of decreasing probability.
                     val = sorted(val, key=lambda v: -prob[elsp.symbol][v])

diff --git a/pymatgen/analysis/chemenv/connectivity/connected_components.py b/pymatgen/analysis/chemenv/connectivity/connected_components.py
@@ -41,7 +41,7 @@ def draw_network(env_graph, pos, ax, sg=None, periodicity_vectors=None):
         ax.annotate(str(n), pos[n], ha="center", va="center", xycoords="data")
     seen = {}
     e = None
-    for (u, v, d) in env_graph.edges(data=True):
+    for u, v, d in env_graph.edges(data=True):
         n1 = env_graph.node[u]["patch"]
         n2 = env_graph.node[v]["patch"]
         rad = 0.1
@@ -147,7 +147,7 @@ def make_supergraph(graph, multiplicity, periodicity_vectors):
         edges = graph.edges(data=True, keys=True)
         connecting_edges = []
         other_edges = []
-        for (n1, n2, key, data) in edges:
+        for n1, n2, key, data in edges:
             print(n1, n2, key, data)
             if np.all(np.array(data["delta"]) == np.array(periodicity_vectors[0])):
                 connecting_edges.append((n1, n2, key, data))
@@ -457,7 +457,7 @@ def compute_periodicity_all_simple_paths_algorithm(self):
                     # TODO: there are some paths that appears twice for cycles, and there are some paths that should
                     # probably not be considered
                     this_path_deltas = [np.zeros(3, int)]
-                    for (node1, node2) in [(node1, path[inode1 + 1]) for inode1, node1 in enumerate(path[:-1])]:
+                    for node1, node2 in [(node1, path[inode1 + 1]) for inode1, node1 in enumerate(path[:-1])]:
                         this_path_deltas_new = []
                         for edge_data in self._connected_subgraph[node1][node2].values():
                             delta = get_delta(node1, node2, edge_data)
@@ -496,7 +496,7 @@ def compute_periodicity_cycle_basis(self):
             mycyc = list(cyc)
             mycyc.append(cyc[0])
             this_cycle_deltas = [np.zeros(3, int)]
-            for (node1, node2) in [(node1, mycyc[inode1 + 1]) for inode1, node1 in enumerate(mycyc[:-1])]:
+            for node1, node2 in [(node1, mycyc[inode1 + 1]) for inode1, node1 in enumerate(mycyc[:-1])]:
                 this_cycle_deltas_new = []
                 for edge_data in self._connected_subgraph[node1][node2].values():
                     delta = get_delta(node1, node2, edge_data)

diff --git a/pymatgen/analysis/chemenv/connectivity/structure_connectivity.py b/pymatgen/analysis/chemenv/connectivity/structure_connectivity.py
@@ -122,7 +122,7 @@ def add_bonds(self, isite, site_neighbors_set):
                         break
             else:
                 if isite == nb_index_unitcell:
-                    for (isite1, ineighb1, data1) in existing_edges:
+                    for isite1, ineighb1, data1 in existing_edges:
                         if isite1 == ineighb1:
                             if np.allclose(data1["delta"], nb_image_cell) or np.allclose(
                                 data1["delta"], -nb_image_cell
@@ -316,7 +316,7 @@ def print_links(self):
         print("Links in graph :")
         for node in nodes:
             print(node.isite, " is connected with : ")
-            for (n1, n2, data) in self.environment_subgraph().edges(node, data=True):
+            for n1, n2, data in self.environment_subgraph().edges(node, data=True):
                 if n1.isite == data["start"]:
                     print(
                         f"  - {n2.isite} by {len(data['ligands'])} ligands ({data['delta'][0]} "

diff --git a/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py b/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py
@@ -1427,7 +1427,6 @@ def coordination_geometry_symmetry_measures_standard(
             local2perfect_maps = []
             perfect2local_maps = []
             for iperm, perm in enumerate(algo.permutations):
-
                 local2perfect_map = {}
                 perfect2local_map = {}
                 permutations.append(perm)

diff --git a/pymatgen/analysis/chemenv/coordination_environments/structure_environments.py b/pymatgen/analysis/chemenv/coordination_environments/structure_environments.py
@@ -1266,7 +1266,6 @@ def differences_wrt(self, other):
         return differences
 
     def __eq__(self, other: object) -> bool:
-
         if not isinstance(other, StructureEnvironments):
             return NotImplemented
 

diff --git a/pymatgen/analysis/chemenv/coordination_environments/tests/test_weights.py b/pymatgen/analysis/chemenv/coordination_environments/tests/test_weights.py
@@ -545,7 +545,6 @@ def test_delta_csms_weight(self):
         assert abs(delta_w - 1.0) < 1e-8
 
     def test_dist_angle_area_weight(self):
-
         surface_definition = {
             "type": "standard_elliptic",
             "distance_bounds": {"lower": 1.2, "upper": 1.8},
@@ -589,7 +588,6 @@ def test_dist_angle_area_weight(self):
         assert da_area_weight.rectangle_crosses_area(d1=d1, d2=d2, a1=a1, a2=a2)
 
     def test_dist_nb_set_weight(self):
-
         dnbset_weight = DistanceNbSetWeight()
         dnbset_weight2 = DistanceNbSetWeight(
             weight_function={

diff --git a/pymatgen/analysis/chemenv/coordination_environments/voronoi.py b/pymatgen/analysis/chemenv/coordination_environments/voronoi.py
@@ -583,7 +583,7 @@ def maps_and_surfaces(
         for cn, value in self._unique_coordinated_neighbors_parameters_indices[isite].items():  # pylint: disable=E1101
             for imap, list_parameters_indices in enumerate(value):
                 thissurf = 0.0
-                for (idp, iap, iacb) in list_parameters_indices:
+                for idp, iap, iacb in list_parameters_indices:
                     if iacb in additional_conditions:
                         thissurf += surfaces[idp, iap]
                 maps_and_surfaces.append(
@@ -617,7 +617,7 @@ def maps_and_surfaces_bounded(self, isite, surface_calculation_options=None, add
         for cn, value in self._unique_coordinated_neighbors_parameters_indices[isite].items():  # pylint: disable=E1101
             for imap, list_parameters_indices in enumerate(value):
                 thissurf = 0.0
-                for (idp, iap, iacb) in list_parameters_indices:
+                for idp, iap, iacb in list_parameters_indices:
                     if iacb in additional_conditions:
                         thissurf += surfaces[idp, iap]
                 maps_and_surfaces.append(

diff --git a/pymatgen/analysis/chemenv/utils/graph_utils.py b/pymatgen/analysis/chemenv/utils/graph_utils.py
@@ -56,7 +56,7 @@ def get_all_simple_paths_edges(graph, source, target, cutoff=None, data=True):
             continue
         node_paths.append(path)
         current_edge_paths = [[]]
-        for (node1, node2) in [(node1, path[inode1 + 1]) for inode1, node1 in enumerate(path[:-1])]:
+        for node1, node2 in [(node1, path[inode1 + 1]) for inode1, node1 in enumerate(path[:-1])]:
             new_edge_paths = []
             for key, edge_data in graph[node1][node2].items():
                 for tmp_edge_path in current_edge_paths:

diff --git a/pymatgen/analysis/diffraction/core.py b/pymatgen/analysis/diffraction/core.py
@@ -224,6 +224,7 @@ def get_unique_families(hkls):
     Returns:
         {hkl: multiplicity}: A dict with unique hkl and multiplicity.
     """
+
     # TODO: Definitely can be sped up.
     def is_perm(hkl1, hkl2) -> bool:
         h1 = np.abs(hkl1)

diff --git a/pymatgen/analysis/diffraction/neutron.py b/pymatgen/analysis/diffraction/neutron.py
@@ -140,7 +140,6 @@ def get_pattern(self, structure: Structure, scaled=True, two_theta_range=(0, 90)
             # Force miller indices to be integers.
             hkl = [int(round(i)) for i in hkl]
             if g_hkl != 0:
-
                 d_hkl = 1 / g_hkl
 
                 # Bragg condition

diff --git a/pymatgen/analysis/diffraction/xrd.py b/pymatgen/analysis/diffraction/xrd.py
@@ -214,7 +214,6 @@ def get_pattern(self, structure: Structure, scaled=True, two_theta_range=(0, 90)
             # Force miller indices to be integers.
             hkl = [int(round(i)) for i in hkl]
             if g_hkl != 0:
-
                 # Bragg condition
                 theta = asin(wavelength * g_hkl / 2)
 

diff --git a/pymatgen/analysis/dimensionality.py b/pymatgen/analysis/dimensionality.py
@@ -229,7 +229,6 @@ def rank_increase(seen, candidate):
         seen_comp_vertices[comp_i].add(image_i)
 
         for comp_j, image_j in connected_sites[comp_i]:
-
             image_j = tuple(np.add(image_j, image_i))
 
             if (comp_j, image_j) in seen_vertices:
@@ -280,7 +279,6 @@ def zero_d_graph_to_molecule_graph(bonded_structure, graph):
         sites.append(site_i)
 
         for site_j in bonded_structure.get_connected_sites(comp_i, jimage=image_i):
-
             if (site_j.index, site_j.jimage) not in seen_indices and (
                 site_j.index,
                 site_j.jimage,