pre-commit autoupdate & fix typos (#3371)

* pre-commit autoupdate

updates:
- [github.com/codespell-project/codespell: v2.2.5 → v2.2.6](codespell-project/codespell@v2.2.5...v2.2.6)
- [github.com/igorshubovych/markdownlint-cli: v0.36.0 → v0.37.0](igorshubovych/markdownlint-cli@v0.36.0...v0.37.0)

* fix typos

---------

Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>

.pre-commit-config.yaml

@@ -31,7 +31,7 @@ repos:
       - id: mypy
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.2.6
     hooks:
       - id: codespell
         stages: [commit, commit-msg]
@@ -51,7 +51,7 @@ repos:
       - id: blacken-docs
 
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.36.0
+    rev: v0.37.0
     hooks:
       - id: markdownlint
         # MD013: line too long

CHANGES.md

@@ -2653,7 +2653,7 @@ package <https://pypi.python.org/pypi/monty>`\_, which is now a dependency
   Previously, the parsing was done incorrectly because VASP actually provides
   data by running through the x-axis first, followed by y, then z.
 - Bug fix for reverse_readline so that it works for gzipped and bzipped
-  strucutures (courtesy of Anubhav Jain).
+  structures (courtesy of Anubhav Jain).
 - Fix "lossy" composition to_dict method. Now composition.to_dict properly
   returns a correct species string as a key for compositions using species,
   instead of just the element symbols.

pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py

@@ -620,32 +620,32 @@ def compute_structure_environments(
         else:
             self.valences = valences
 
-        # Get a list of indices of unequivalent sites from the initial structure
+        # Get a list of indices of nonequivalent sites from the initial structure
         self.equivalent_sites = [[site] for site in self.structure]
         self.struct_sites_to_irreducible_site_list_map = list(range(len(self.structure)))
         self.sites_map = list(range(len(self.structure)))
         indices = list(range(len(self.structure)))
 
-        # Get list of unequivalent sites with valence >= 0
+        # Get list of nonequivalent sites with valence >= 0
         if only_cations and self.valences != "undefined":
-            sites_indices = [isite for isite in indices if self.valences[isite] >= 0]
+            sites_indices = [idx for idx in indices if self.valences[idx] >= 0]
         else:
             sites_indices = list(indices)
 
         # Include atoms that are in the list of "only_atoms" if it is provided
         if only_atoms is not None:
             sites_indices = [
-                isite
-                for isite in sites_indices
-                if any(at in [sp.symbol for sp in self.structure[isite].species] for at in only_atoms)
+                idx
+                for idx in sites_indices
+                if any(at in [sp.symbol for sp in self.structure[idx].species] for at in only_atoms)
             ]
 
         # Exclude atoms that are in the list of excluded atoms
         if excluded_atoms:
             sites_indices = [
-                isite
-                for isite in sites_indices
-                if not any(at in [sp.symbol for sp in self.structure[isite].species] for at in excluded_atoms)
+                idx
+                for idx in sites_indices
+                if not any(at in [sp.symbol for sp in self.structure[idx].species] for at in excluded_atoms)
             ]
 
         if only_indices is not None:

pymatgen/analysis/chemenv/coordination_environments/structure_environments.py

@@ -411,7 +411,7 @@ def __init__(
         Args:
             voronoi: VoronoiContainer object for the structure.
             valences: Valences provided.
-            sites_map: Mapping of equivalent sites to the unequivalent sites that have been computed.
+            sites_map: Mapping of equivalent sites to the nonequivalent sites that have been computed.
             equivalent_sites: List of list of equivalent sites of the structure.
             ce_list: List of chemical environments.
             structure: Structure object.

pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py

@@ -450,7 +450,7 @@ def changebasis(uu, vv, nn, pps):
     expressed in the basis (uu, vv, nn), which is supposed to be orthonormal.
     :param uu: First vector of the basis
     :param vv: Second vector of the basis
-    :param nn: Third vector of the bais
+    :param nn: Third vector of the basis
     :param pps: List of points in basis (e1, e2, e3)
     Returns:
         List of points in basis (uu, vv, nn).
@@ -473,7 +473,7 @@ def collinear(p1, p2, p3=None, tolerance=0.25):
     checked by computing the area of the triangle defined by the three points p1, p2 and p3. If the area of this
     triangle is less than (tolerance x largest_triangle), then the three points are considered collinear. The
     largest_triangle is defined as the right triangle whose legs are the two smallest distances between the three
-     points ie, its area is : 0.5 x (min(|p2-p1|,|p3-p1|,|p3-p2|) x secondmin(|p2-p1|,|p3-p1|,|p3-p2|))
+     points ie, its area is : 0.5 x (min(|p2-p1|,|p3-p1|,|p3-p2|) x second_min(|p2-p1|,|p3-p1|,|p3-p2|))
     :param p1: First point
     :param p2: Second point
     :param p3: Third point (origin [0.0, 0.0, 0.0 if not given])

pymatgen/analysis/diffraction/tem.py

@@ -444,7 +444,7 @@ def get_plot_coeffs(
         Args:
             p1 (3-tuple): The first point. Fixed.
             p2 (3-tuple): The second point. Fixed.
-            p3 (3-tuple): The point whose coefficients are to be calculted.
+            p3 (3-tuple): The point whose coefficients are to be calculated.
 
         Returns:
             Numpy array

pymatgen/analysis/gb/grain.py

@@ -642,7 +642,7 @@ def gb_from_parameters(
         # top grain
         top_grain = fix_pbc(parent_structure * t1)
 
-        # obtain the smallest oriended cell
+        # obtain the smallest oriented cell
         if normal and not quick_gen:
             t_temp = self.get_trans_mat(
                 r_axis=rotation_axis,

pymatgen/apps/battery/plotter.py

@@ -23,7 +23,7 @@ def __init__(self, xaxis="capacity", hide_negative=False):
         """
         Args:
             xaxis: The quantity to use as the xaxis. Can be either
-            - capacity_grav: the graviometric capcity
+            - capacity_grav: the gravimetric capacity
             - capacity_vol: the volumetric capacity
             - x_form: the number of working ions per formula unit of the host
             - frac_x: the atomic fraction of the working ion

pymatgen/core/lattice.py

@@ -1386,7 +1386,7 @@ def get_points_in_sphere_py(
         Algorithm:
 
         1. place sphere of radius r in crystal and determine minimum supercell
-           (parallelpiped) which would contain a sphere of radius r. for this
+           (parallelepiped) which would contain a sphere of radius r. for this
            we need the projection of a_1 on a unit vector perpendicular
            to a_2 & a_3 (i.e. the unit vector in the direction b_1) to
            determine how many a_1"s it will take to contain the sphere.
@@ -1443,7 +1443,7 @@ def get_points_in_sphere_old(
         Algorithm:
 
         1. place sphere of radius r in crystal and determine minimum supercell
-           (parallelpiped) which would contain a sphere of radius r. for this
+           (parallelepiped) which would contain a sphere of radius r. for this
            we need the projection of a_1 on a unit vector perpendicular
            to a_2 & a_3 (i.e. the unit vector in the direction b_1) to
            determine how many a_1"s it will take to contain the sphere.

pymatgen/electronic_structure/boltztrap2.py

@@ -775,7 +775,7 @@ def compute_properties_doping(self, doping, temp_r=None):
             cond_Effective_mass_doping are dictionaries with 'n' and 'p' keys and
             arrays of dim (len(temp_r),len(doping),3,3) as values.
             Carriers_conc_doping: carriers concentration for each doping level and T.
-            mu_doping_eV: the chemical potential corrispondent to each doping level.
+            mu_doping_eV: the chemical potential correspondent to each doping level.
         """
         if temp_r is None:
             temp_r = self.temp_r

pymatgen/io/abinit/abitimer.py

@@ -495,7 +495,7 @@ class ParallelEfficiency(dict):
     def __init__(self, filenames, ref_idx, *args, **kwargs):
         """
         Args:
-            filennames: List of filenames
+            filenames: List of filenames
             ref_idx: Index of the Reference time (calculation done with the smallest number of cpus).
         """
         self.update(*args, **kwargs)

pymatgen/io/abinit/inputs.py

@@ -422,7 +422,7 @@ def ion_ioncell_relax_input(
     shift_mode="Monkhorst-pack",
 ):
     """
-    Returns a |BasicMultiDataset| for a structural relaxation. The first dataset optmizes the
+    Returns a |BasicMultiDataset| for a structural relaxation. The first dataset optimizes the
     atomic positions at fixed unit cell. The second datasets optimizes both ions and unit cell parameters.
 
     Args:

pymatgen/io/lammps/inputs.py

@@ -1,5 +1,5 @@
 """
-This module implements methods for reading/manupilating/writing LAMMPS input files.
+This module implements methods for reading/manipulating/writing LAMMPS input files.
 It does not implement methods for automatically creating inputs based on a structure
 and computation type. For this, see the InputSet and InputGenerator in sets.py, or
 https://github.com/Matgenix/atomate2-lammps.

pymatgen/io/lobster/lobsterenv.py

@@ -106,7 +106,7 @@ def __init__(
             additional condition
             add_additional_data_sg: (bool) will add the information from filename_add_bondinglist_sg1,
             filename_blist_sg1: (str) Path to additional ICOOP, ICOBI data for structure graphs
-            filename_blist_sg2: (str) Path to dditional ICOOP, ICOBI data for structure graphs
+            filename_blist_sg2: (str) Path to additional ICOOP, ICOBI data for structure graphs
             id_blist_sg1: (str) Identity of data in filename_blist_sg1,
                 e.g., "icoop" or "icobi"
             id_blist_sg2: (str) Identity of data in filename_blist_sg2,
@@ -695,7 +695,7 @@ def _evaluate_ce(
             only_bonds_to: restricts the types of bonds that will be considered
             additional_condition: Additional condition for the evaluation
             perc_strength_ICOHP: will be used to determine how strong the ICOHPs (percentage*strongest ICOHP) will be
-            that are still considered for the evalulation
+            that are still considered for the evaluation
             adapt_extremum_to_add_cond: will recalculate the limit based on the bonding type and not on the overall
             extremum.
 

pymatgen/io/vasp/outputs.py

@@ -4953,7 +4953,7 @@ class WSWQ(MSONable):
     r"""
     Class for reading a WSWQ file.
     The WSWQ file is used to calculation the wave function overlaps between
-        - W: Wavefunctions in the currenct directory's WAVECAR file
+        - W: Wavefunctions in the current directory's WAVECAR file
         - WQ: Wavefunctions stored in a filed named the WAVECAR.qqq.
 
     The overlap is computed using the overlap operator S

pymatgen/io/zeopp.py

@@ -253,9 +253,9 @@ def get_voronoi_nodes(structure, rad_dict=None, probe_rad=0.1):
                 for el in rad_dict:
                     fp.write(f"{el} {rad_dict[el].real}\n")
 
-        atmnet = AtomNetwork.read_from_CSSR(zeo_inp_filename, rad_flag=rad_flag, rad_file=rad_file)
-        vornet, vor_edge_centers, vor_face_centers = atmnet.perform_voronoi_decomposition()
-        vornet.analyze_writeto_XYZ(name, probe_rad, atmnet)
+        atom_net = AtomNetwork.read_from_CSSR(zeo_inp_filename, rad_flag=rad_flag, rad_file=rad_file)
+        vor_net, vor_edge_centers, vor_face_centers = atom_net.perform_voronoi_decomposition()
+        vor_net.analyze_writeto_XYZ(name, probe_rad, atom_net)
         voro_out_filename = name + "_voro.xyz"
         voro_node_mol = ZeoVoronoiXYZ.from_file(voro_out_filename).molecule
 
@@ -276,12 +276,12 @@ def get_voronoi_nodes(structure, rad_dict=None, probe_rad=0.1):
         site_properties={"voronoi_radius": prop},
     )
 
-    # PMG-Zeo c<->a transformation for voronoi face centers
+    # PMG-Zeo c<->a transformation for Voronoi face centers
     rot_face_centers = [(center[1], center[2], center[0]) for center in vor_face_centers]
     rot_edge_centers = [(center[1], center[2], center[0]) for center in vor_edge_centers]
 
     species = ["X"] * len(rot_face_centers)
-    prop = [0.0] * len(rot_face_centers)  # Vor radius not evaluated for fc
+    prop = [0.0] * len(rot_face_centers)  # Voronoi radius not evaluated for fc
     vor_facecenter_struct = Structure(
         lattice,
         species,
@@ -292,7 +292,7 @@ def get_voronoi_nodes(structure, rad_dict=None, probe_rad=0.1):
     )
 
     species = ["X"] * len(rot_edge_centers)
-    prop = [0.0] * len(rot_edge_centers)  # Vor radius not evaluated for fc
+    prop = [0.0] * len(rot_edge_centers)  # Voronoi radius not evaluated for fc
     vor_edgecenter_struct = Structure(
         lattice,
         species,

pymatgen/symmetry/settings.py

@@ -37,7 +37,7 @@ def __init__(self, P, p):
           hexagonal setting)
         * `a,b,c;-1/4,-1/4,-1/4` is Pnnn:1 to Pnnn:2 (change in origin
           choice)
-        * `b,c,a;-1/2,-1/2,-1/2` is Bbab:1 to Ccca:2 (change settin
+        * `b,c,a;-1/2,-1/2,-1/2` is Bbab:1 to Ccca:2 (change setting
           and origin)
 
         Can transform points (coords), lattices and symmetry operations.

pyproject.toml

@@ -134,8 +134,8 @@ ignore_missing_imports = true
 
 [tool.codespell]
 ignore-words-list = """
-titel,alls,ans,nd,mater,nwo,te,hart,ontop,ist,ot,fo,nax,coo,coul,ser,leary,thre,
-fase,rute,reson,titels,ges,scalr,strat,struc,hda,nin,ons,pres,kno,loos,lamda,lew
+titel,alls,ans,nd,mater,nwo,te,hart,ontop,ist,ot,fo,nax,coo,coul,ser,leary,thre,fase,
+rute,reson,titels,ges,scalr,strat,struc,hda,nin,ons,pres,kno,loos,lamda,lew,atomate
 """
 skip = "pymatgen/analysis/aflow_prototypes.json"
 check-filenames = true

tests/io/test_zeopp.py

@@ -146,8 +146,8 @@ def test_str(self):
 
     def test_from_file(self):
         filename = f"{TEST_FILES_DIR}/EDI_voro.xyz"
-        vor = ZeoVoronoiXYZ.from_file(filename)
-        assert isinstance(vor.molecule, Molecule)
+        voronoi = ZeoVoronoiXYZ.from_file(filename)
+        assert isinstance(voronoi.molecule, Molecule)
 
 
 @unittest.skipIf(not zeo, "zeo not present.")