Fix linting errors.

pymatgen/alchemy/tests/test_materials.py

@@ -33,7 +33,7 @@ def test_append_transformation(self):
         self.trans.append_transformation(t)
         self.assertEqual("NaMnPO4", self.trans.final_structure.composition.reduced_formula)
         self.assertEqual(len(self.trans.structures), 3)
-        coords = list()
+        coords = []
         coords.append([0, 0, 0])
         coords.append([0.75, 0.5, 0.75])
         lattice = [

pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py

@@ -977,7 +977,7 @@ def __init__(self, permutations_safe_override=False, only_symbols=None):
             only_symbols: Whether to restrict the list of environments to be identified.
         """
         dict.__init__(self)
-        self.cg_list = list()
+        self.cg_list = []
         if only_symbols is None:
             with open("{}/coordination_geometries_files/allcg.txt".format(module_dir), "r") as f:
                 data = f.readlines()
@@ -1075,7 +1075,7 @@ def get_geometries(self, coordination=None, returned="cg"):
             coordination: The coordination number of which the list of coordination geometries are returned.
             returned: Type of objects in the list.
         """
-        geom = list()
+        geom = []
         if coordination is None:
             for gg in self.cg_list:
                 if returned == "cg":
@@ -1139,7 +1139,7 @@ def get_implemented_geometries(self, coordination=None, returned="cg", include_d
             returned: Type of objects in the list.
             include_deactivated: Whether to include CoordinationGeometry that are deactivated.
         """
-        geom = list()
+        geom = []
         if coordination is None:
             for gg in self.cg_list:
                 if gg.points is not None and ((not gg.deactivate) or include_deactivated):
@@ -1169,7 +1169,7 @@ def get_not_implemented_geometries(self, coordination=None, returned="mp_symbol"
                 are returned.
             returned: Type of objects in the list.
         """
-        geom = list()
+        geom = []
         if coordination is None:
             for gg in self.cg_list:
                 if gg.points is None:

pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py

@@ -1094,7 +1094,7 @@ def setup_random_structure(self, coordination):
         """
         aa = 0.4
         bb = -0.2
-        coords = list()
+        coords = []
         for ii in range(coordination + 1):
             coords.append(
                 aa
@@ -1419,10 +1419,10 @@ def coordination_geometry_symmetry_measures_standard(
         #                                           np.float_)
         if optimization == 2:
             permutations_symmetry_measures = [None] * len(algo.permutations)
-            permutations = list()
-            algos = list()
-            local2perfect_maps = list()
-            perfect2local_maps = list()
+            permutations = []
+            algos = []
+            local2perfect_maps = []
+            perfect2local_maps = []
             for iperm, perm in enumerate(algo.permutations):
 
                 local2perfect_map = {}
@@ -1450,10 +1450,10 @@ def coordination_geometry_symmetry_measures_standard(
             )
 
         permutations_symmetry_measures = [None] * len(algo.permutations)
-        permutations = list()
-        algos = list()
-        local2perfect_maps = list()
-        perfect2local_maps = list()
+        permutations = []
+        algos = []
+        local2perfect_maps = []
+        perfect2local_maps = []
         for iperm, perm in enumerate(algo.permutations):
             local2perfect_map = {}
             perfect2local_map = {}
@@ -1493,14 +1493,14 @@ def coordination_geometry_symmetry_measures_separation_plane(
         :param coordination_geometry: The coordination geometry to be investigated
         :return: The symmetry measures for the given coordination geometry for each plane and permutation investigated
         """
-        permutations = list()
-        permutations_symmetry_measures = list()
-        plane_separations = list()
-        algos = list()
-        perfect2local_maps = list()
-        local2perfect_maps = list()
+        permutations = []
+        permutations_symmetry_measures = []
+        plane_separations = []
+        algos = []
+        perfect2local_maps = []
+        local2perfect_maps = []
         if testing:
-            separation_permutations = list()
+            separation_permutations = []
         nplanes = 0
         for npoints in range(
             separation_plane_algo.minimum_number_of_points,
@@ -1613,11 +1613,11 @@ def coordination_geometry_symmetry_measures_separation_plane_optim(
             raise ValueError("Optimization should be 1 or 2")
         cn = len(self.local_geometry.coords)
 
-        permutations = list()
-        permutations_symmetry_measures = list()
-        algos = list()
-        perfect2local_maps = list()
-        local2perfect_maps = list()
+        permutations = []
+        permutations_symmetry_measures = []
+        algos = []
+        perfect2local_maps = []
+        local2perfect_maps = []
 
         if separation_plane_algo.separation in nb_set.separations:
             for sep_indices, (local_plane, npsep) in nb_set.separations[separation_plane_algo.separation].items():
@@ -2016,10 +2016,10 @@ def coordination_geometry_symmetry_measures_fallback_random(
         :return: The symmetry measures for the given coordination geometry for each permutation investigated
         """
         permutations_symmetry_measures = [None] * NRANDOM
-        permutations = list()
-        algos = list()
-        perfect2local_maps = list()
-        local2perfect_maps = list()
+        permutations = []
+        algos = []
+        perfect2local_maps = []
+        local2perfect_maps = []
         for iperm in range(NRANDOM):
             perm = np.random.permutation(coordination_geometry.coordination_number)
             permutations.append(perm)

pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py

@@ -433,7 +433,7 @@ def rotateCoords(coords, R):
     :param R: Rotation matrix
     :return: List of rotated points
     """
-    newlist = list()
+    newlist = []
     for pp in coords:
         rpp = matrixTimesVector(R, pp)
         newlist.append(rpp)
@@ -466,7 +466,7 @@ def changebasis(uu, vv, nn, pps):
         MM[ii, 1] = vv[ii]
         MM[ii, 2] = nn[ii]
     PP = np.linalg.inv(MM)
-    newpps = list()
+    newpps = []
     for pp in pps:
         newpps.append(matrixTimesVector(PP, pp))
     return newpps
@@ -501,7 +501,7 @@ def anticlockwise_sort(pps):
     :param pps: List of points to be sorted
     :return: Sorted list of points
     """
-    newpps = list()
+    newpps = []
     angles = np.zeros(len(pps), np.float_)
     for ipp, pp in enumerate(pps):
         angles[ipp] = np.arctan2(pp[1], pp[0])
@@ -724,9 +724,9 @@ def indices_separate(self, points, dist_tolerance):
         :return: The lists of indices of the points on one side of the plane, on the plane and
             on the other side of the plane
         """
-        side1 = list()
-        inplane = list()
-        side2 = list()
+        side1 = []
+        inplane = []
+        side2 = []
         for ip, pp in enumerate(points):
             if self.is_in_plane(pp, dist_tolerance):
                 inplane.append(ip)
@@ -862,7 +862,7 @@ def project_and_to2dim(self, pps, plane_center):
         proj = self.projectionpoints(pps)
         [u1, u2, u3] = self.orthonormal_vectors()
         PP = np.array([[u1[0], u2[0], u3[0]], [u1[1], u2[1], u3[1]], [u1[2], u2[2], u3[2]]])
-        xypps = list()
+        xypps = []
         for pp in proj:
             xyzpp = np.dot(pp, PP)
             xypps.append(xyzpp[0:2])

pymatgen/analysis/chemenv/utils/graph_utils.py

@@ -498,7 +498,7 @@ def get_all_elementary_cycles(graph):
             cycles_matrix[icycle, iedge] = True
 
     # print(cycles_matrix)
-    elementary_cycles_list = list()
+    elementary_cycles_list = []
 
     for ncycles in range(1, len(cycle_basis) + 1):
         for cycles_combination in itertools.combinations(cycles_matrix, ncycles):

pymatgen/analysis/graphs.py

@@ -2067,7 +2067,7 @@ def get_disconnected_fragments(self):
             return [copy.deepcopy(self)]
 
         original = copy.deepcopy(self)
-        sub_mols = list()
+        sub_mols = []
 
         # Had to use nx.weakly_connected_components because of deprecation
         # of nx.weakly_connected_component_subgraphs
@@ -2443,7 +2443,7 @@ def replace_group(
                 )
 
             to_remove = set()
-            sizes = dict()
+            sizes = {}
             disconnected = self.graph.to_undirected()
             disconnected.remove_node(index)
             for neighbor in neighbors:

pymatgen/analysis/local_env.py

@@ -486,7 +486,7 @@ def _get_nn_shell_info(
         # Each allowed step results in many terminal neighbors
         #  And, different first steps might results in the same neighbor
         #  Now, we condense those neighbors into a single entry per neighbor
-        all_sites = dict()
+        all_sites = {}
         for first_site, term_sites in zip(allowed_steps, terminal_neighbors):
             for term_site in term_sites:
                 key = (term_site["site_index"], tuple(term_site["image"]))

pymatgen/analysis/phase_diagram.py

@@ -1696,7 +1696,7 @@ def pd_plot_data(self):
 
         all_entries = pd.all_entries
         all_data = np.array(pd.all_entries_hulldata)
-        unstable_entries = dict()
+        unstable_entries = {}
         stable = pd.stable_entries
         for i, entry in enumerate(all_entries):
             if entry not in stable:
@@ -2071,7 +2071,7 @@ def _get_3d_plot(self, label_stable=True):
         font = FontProperties(weight="bold", size=13)
         (lines, labels, unstable) = self.pd_plot_data
         count = 1
-        newlabels = list()
+        newlabels = []
         for x, y, z in lines:
             ax.plot(
                 x,
@@ -2472,7 +2472,7 @@ def _create_plotly_figure_layout(self, label_stable=True):
         :return: Dictionary with Plotly figure layout settings.
         """
         annotations_list = None
-        layout = dict()
+        layout = {}
 
         if label_stable:
             annotations_list = self._create_plotly_element_annotations()
@@ -2563,7 +2563,7 @@ def get_marker_props(coords, entries, stable=True):
 
         unstable_props = get_marker_props(unstable_coords, unstable_entries, stable=False)
 
-        stable_markers, unstable_markers = dict(), dict()
+        stable_markers, unstable_markers = {}, {}
 
         if self._dim == 2:
             stable_markers = plotly_layouts["default_binary_marker_settings"].copy()

pymatgen/analysis/pourbaix_diagram.py

@@ -661,7 +661,7 @@ def _preprocess_pourbaix_entries(self, entries, nproc=None):
         combos = []
         for facet in valid_facets:
             for i in range(1, self.dim + 2):
-                these_combos = list()
+                these_combos = []
                 for combo in itertools.combinations(facet, i):
                     these_entries = [min_entries[i] for i in combo]
                     these_combos.append(frozenset(these_entries))

pymatgen/analysis/tests/test_structure_analyzer.py

@@ -132,7 +132,7 @@ def test_oxide_type(self):
         el_o = Element("O")
         latt = Lattice([[3.985034, 0.0, 0.0], [0.0, 4.881506, 0.0], [0.0, 0.0, 2.959824]])
         elts = [el_li, el_li, el_o, el_o, el_o, el_o]
-        coords = list()
+        coords = []
         coords.append([0.500000, 0.500000, 0.500000])
         coords.append([0.0, 0.0, 0.0])
         coords.append([0.632568, 0.085090, 0.500000])

pymatgen/command_line/gulp_caller.py

@@ -899,7 +899,7 @@ def __init__(self):
         """
         module_dir = os.path.dirname(os.path.abspath(__file__))
         with open(os.path.join(module_dir, "OxideTersoffPotentials"), "r") as f:
-            data = dict()
+            data = {}
             for row in f:
                 metaloxi = row.split()[0]
                 line = row.split(")")

pymatgen/core/composition.py

@@ -97,7 +97,7 @@ def __init__(self, *args, strict: bool = False, **kwargs):
         dict(). Also extended to allow simple string init.
 
         Args:
-            Any form supported by the Python built-in dict() function.
+            Any form supported by the Python built-in {} function.
 
             1. A dict of either {Element/Species: amount},
 
@@ -119,7 +119,7 @@ def __init__(self, *args, strict: bool = False, **kwargs):
         """
         self.allow_negative = kwargs.pop("allow_negative", False)
         # it's much faster to recognize a composition and use the elmap than
-        # to pass the composition to dict()
+        # to pass the composition to {}
         if len(args) == 1 and isinstance(args[0], Composition):
             elmap = args[0]
         elif len(args) == 1 and isinstance(args[0], str):

pymatgen/core/tests/test_ion.py

@@ -13,7 +13,7 @@
 
 class IonTest(unittest.TestCase):
     def setUp(self):
-        self.comp = list()
+        self.comp = []
         self.comp.append(Ion.from_formula("Li+"))
         self.comp.append(Ion.from_formula("MnO4-"))
         self.comp.append(Ion.from_formula("Mn++"))