Module-scoped imports

pymatgen/analysis/diffraction/neutron.py

@@ -44,7 +44,6 @@ class NDCalculator(AbstractDiffractionPatternCalculator):
     Reference:
     Marc De Graef and Michael E. McHenry, Structure of Materials 2nd ed,
     Chapter13, Cambridge University Press 2003.
-
     """
 
     def __init__(self, wavelength=1.54184, symprec: float = 0, debye_waller_factors=None):

pymatgen/analysis/ewald.py

@@ -496,12 +496,9 @@ class EwaldMinimizer:
     ALGO_FAST = 0
     ALGO_COMPLETE = 1
     ALGO_BEST_FIRST = 2
-
-    """
-    ALGO_TIME_LIMIT: Slowly increases the speed (with the cost of decreasing
-    accuracy) as the minimizer runs. Attempts to limit the run time to
-    approximately 30 minutes.
-    """
+    # ALGO_TIME_LIMIT: Slowly increases the speed (with the cost of decreasing
+    # accuracy) as the minimizer runs. Attempts to limit the run time to
+    # approximately 30 minutes.
     ALGO_TIME_LIMIT = 3
 
     def __init__(self, matrix, m_list, num_to_return=1, algo=ALGO_FAST):

pymatgen/analysis/ferroelectricity/polarization.py

@@ -47,6 +47,7 @@
 from __future__ import annotations
 
 import numpy as np
+from scipy.interpolate import UnivariateSpline
 
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
@@ -131,19 +132,16 @@ def get_nearest_site(self, coords, site, r=None):
 
 class Polarization:
     """
-    Class for recovering the same branch polarization for a set of
-    polarization calculations along the nonpolar - polar distortion
-    path of a ferroelectric.
+    Class for recovering the same branch polarization for a set of polarization
+    calculations along the nonpolar - polar distortion path of a ferroelectric.
 
     p_elecs, p_ions, and structures lists should be given in order
     of nonpolar to polar! For example, the structures returned from:
         nonpolar.interpolate(polar,interpolate_lattices=True)
     if nonpolar is the nonpolar Structure and polar is the polar structure.
 
-    It is assumed that the electronic and ionic dipole moment values
-    are given in electron Angstroms along the three lattice directions
-    (a,b,c).
-
+    It is assumed that the electronic and ionic dipole moment values are given in
+    electron Angstroms along the three lattice directions (a,b,c).
     """
 
     def __init__(
@@ -371,10 +369,8 @@ def get_polarization_change_norm(self, convert_to_muC_per_cm2=True, all_in_polar
     def same_branch_splines(self, convert_to_muC_per_cm2=True, all_in_polar=True):
         """
         Fit splines to same branch polarization. This is used to assess any jumps
-        in the same branch polarizaiton.
+        in the same branch polarization.
         """
-        from scipy.interpolate import UnivariateSpline
-
         tot = self.get_same_branch_polarization_data(
             convert_to_muC_per_cm2=convert_to_muC_per_cm2, all_in_polar=all_in_polar
         )
@@ -430,8 +426,6 @@ def __init__(self, energies):
 
     def spline(self):
         """Fit spline to energy trend data."""
-        from scipy.interpolate import UnivariateSpline
-
         return UnivariateSpline(range(len(self.energies)), self.energies, k=4)
 
     def smoothness(self):

pymatgen/analysis/local_env.py

@@ -4310,9 +4310,8 @@ def get_bonded_structure(self, structure: Structure, decorate: bool = False) ->
         Returns:
             StructureGraph: Bonded structure
         """
-        # not a top-level import because critic2 is an optional
-        # dependency, only want to raise an import error if
-        # Critic2NN() is used
+        # not a top-level import because critic2 is an optional dependency, only want
+        # to raise an import error if Critic2NN() is used
         from pymatgen.command_line.critic2_caller import Critic2Caller
 
         if structure == self.__last_structure:
@@ -4337,13 +4336,11 @@ def get_nn_info(self, structure: Structure, n: int):
 
         Args:
             structure (Structure): input structure.
-            n (int): index of site for which to determine near-neighbor
-                sites.
+            n (int): index of site for which to determine near-neighbor sites.
 
         Returns:
             siw (list of tuples (Site, array, float)): tuples, each one
-                of which represents a coordinated site, its image location,
-                and its weight.
+                of which represents a coordinated site, its image location, and its weight.
         """
         sg = self.get_bonded_structure(structure)
 
@@ -4411,7 +4408,6 @@ def metal_edge_extender(
     Returns:
         mol_graph: pymatgen.analysis.graphs.MoleculeGraph object with additional
             metal bonds (if any found) added
-
     """
     if metals is None:
         metals = []

pymatgen/analysis/pourbaix_diagram.py

@@ -12,17 +12,12 @@
 from copy import deepcopy
 from functools import cmp_to_key, partial
 from multiprocessing import Pool
+from typing import TYPE_CHECKING, Any, no_type_check
 
 import numpy as np
 from monty.json import MontyDecoder, MSONable
 from scipy.spatial import ConvexHull, HalfspaceIntersection
-
-try:
-    from scipy.special import comb
-except ImportError:
-    from scipy.misc import comb
-
-from typing import TYPE_CHECKING, Any, no_type_check
+from scipy.special import comb
 
 from pymatgen.analysis.phase_diagram import PDEntry, PhaseDiagram
 from pymatgen.analysis.reaction_calculator import Reaction, ReactionError

pymatgen/analysis/quasirrho.py

@@ -92,7 +92,6 @@ class QuasiRRHO:
         free_energy_ho (float): Free energy calculated without the Quasi-RRHO
             method, i.e. with a harmonic oscillator approximation for the
             vibrational entropy [Ha]
-
     """
 
     def __init__(

pymatgen/analysis/solar/slme.py

@@ -155,7 +155,6 @@ def slme(
 
     Returns:
         The calculated maximum efficiency.
-
     """
     # Defining constants for tidy equations
     c = constants.c  # speed of light, m/s

pymatgen/core/lattice.py

@@ -15,6 +15,7 @@
 from monty.json import MSONable
 from numpy import dot, pi, transpose
 from numpy.linalg import inv
+from scipy.spatial import Voronoi
 
 from pymatgen.util.coord import pbc_shortest_vectors
 from pymatgen.util.due import Doi, due
@@ -1222,8 +1223,6 @@ def get_wigner_seitz_cell(self) -> list[list[np.ndarray]]:
         for ii, jj, kk in itertools.product([-1, 0, 1], [-1, 0, 1], [-1, 0, 1]):
             list_k_points.append(ii * vec1 + jj * vec2 + kk * vec3)
 
-        from scipy.spatial import Voronoi
-
         tess = Voronoi(list_k_points)
         out = []
         for r in tess.ridge_dict:

pymatgen/core/structure.py

@@ -31,7 +31,9 @@
 from numpy import cross, eye
 from numpy.linalg import norm
 from ruamel.yaml import YAML
-from scipy.linalg import expm
+from scipy.cluster.hierarchy import fcluster, linkage
+from scipy.linalg import expm, polar
+from scipy.spatial.distance import squareform
 from tabulate import tabulate
 
 from pymatgen.core.bonds import CovalentBond, get_bond_length
@@ -2218,8 +2220,6 @@ def interpolate(
 
         if interpolate_lattices:
             # interpolate lattice matrices using polar decomposition
-            from scipy.linalg import polar
-
             # u is a unitary rotation, p is stretch
             u, p = polar(np.dot(end_structure.lattice.matrix.T, np.linalg.inv(self.lattice.matrix.T)))
             lvec = p - np.identity(3)
@@ -4235,9 +4235,6 @@ def merge_sites(self, tol: float = 0.01, mode: Literal["sum", "delete", "average
                 "average" means that the site is deleted but the properties are averaged
                 Only first letter is considered.
         """
-        from scipy.cluster.hierarchy import fcluster, linkage
-        from scipy.spatial.distance import squareform
-
         dist_mat = self.distance_matrix
         np.fill_diagonal(dist_mat, 0)
         clusters = fcluster(linkage(squareform((dist_mat + dist_mat.T) / 2)), tol, "distance")
@@ -4632,10 +4629,6 @@ def rotate_sites(
             axis (3x1 array): Rotation axis vector.
             anchor (3x1 array): Point of rotation.
         """
-        from numpy import cross, eye
-        from numpy.linalg import norm
-        from scipy.linalg import expm
-
         if indices is None:
             indices = range(len(self))
 

pymatgen/core/units.py

@@ -735,12 +735,10 @@ def unitized(unit):
     Args:
         unit: Specific unit (eV, Ha, m, ang, etc.).
 
-    Example usage::
-
+    Example:
         @unitized(unit="kg")
         def get_mass():
             return 123.45
-
     """
 
     def wrap(func):

pymatgen/electronic_structure/boltztrap.py

@@ -32,6 +32,7 @@
 from monty.json import MSONable, jsanitize
 from monty.os import cd
 from scipy import constants
+from scipy.optimize import fsolve
 from scipy.spatial import distance
 
 from pymatgen.core.lattice import Lattice
@@ -2264,8 +2265,6 @@ def eta_from_seebeck(seeb, Lambda):
     Returns:
         float: eta where the two seebeck coefficients are equal (reduced chemical potential).
     """
-    from scipy.optimize import fsolve
-
     out = fsolve(lambda x: (seebeck_spb(x, Lambda) - abs(seeb)) ** 2, 1.0, full_output=True)
     return out[0][0]
 

pymatgen/electronic_structure/dos.py

@@ -10,6 +10,7 @@
 import numpy as np
 from monty.json import MSONable
 from scipy.constants import value as _cd
+from scipy.ndimage import gaussian_filter1d
 from scipy.signal import hilbert
 
 from pymatgen.core import Structure, get_el_sp
@@ -220,13 +221,11 @@ def get_smeared_densities(self, sigma: float):
         Returns:
             Dict of Gaussian-smeared densities.
         """
-        from scipy.ndimage import gaussian_filter1d
-
         smeared_dens = {}
         diff = [self.energies[i + 1] - self.energies[i] for i in range(len(self.energies) - 1)]
-        avgdiff = sum(diff) / len(diff)
+        avg_diff = sum(diff) / len(diff)
         for spin, dens in self.densities.items():
-            smeared_dens[spin] = gaussian_filter1d(dens, sigma / avgdiff)
+            smeared_dens[spin] = gaussian_filter1d(dens, sigma / avg_diff)
         return smeared_dens
 
     def __add__(self, other):
@@ -343,14 +342,14 @@ def get_gap(self, tol: float = 0.001, abs_tol: bool = False, spin: Spin | None =
     def __str__(self):
         """Returns a string which can be easily plotted (using gnuplot)."""
         if Spin.down in self.densities:
-            stringarray = [f"#{'Energy':30s} {'DensityUp':30s} {'DensityDown':30s}"]
+            str_arr = [f"#{'Energy':30s} {'DensityUp':30s} {'DensityDown':30s}"]
             for i, energy in enumerate(self.energies):
-                stringarray.append(f"{energy:.5f} {self.densities[Spin.up][i]:.5f} {self.densities[Spin.down][i]:.5f}")
+                str_arr.append(f"{energy:.5f} {self.densities[Spin.up][i]:.5f} {self.densities[Spin.down][i]:.5f}")
         else:
-            stringarray = [f"#{'Energy':30s} {'DensityUp':30s}"]
+            str_arr = [f"#{'Energy':30s} {'DensityUp':30s}"]
             for i, energy in enumerate(self.energies):
-                stringarray.append(f"{energy:.5f} {self.densities[Spin.up][i]:.5f}")
-        return "\n".join(stringarray)
+                str_arr.append(f"{energy:.5f} {self.densities[Spin.up][i]:.5f}")
+        return "\n".join(str_arr)
 
     @classmethod
     def from_dict(cls, d) -> Dos:

pymatgen/electronic_structure/plotter.py

@@ -4217,7 +4217,7 @@ def plot_points(points, lattice=None, coords_are_cartesian=False, fold=False, ax
 
 
 @add_fig_kwargs
-def plot_brillouin_zone_from_kpath(kpath, ax: plt.Axes = None, **kwargs):
+def plot_brillouin_zone_from_kpath(kpath, ax: plt.Axes = None, **kwargs) -> plt.Axes:
     """Gives the plot (as a matplotlib object) of the symmetry line path in
         the Brillouin Zone.
 
@@ -4227,8 +4227,7 @@ def plot_brillouin_zone_from_kpath(kpath, ax: plt.Axes = None, **kwargs):
         **kwargs: provided by add_fig_kwargs decorator
 
     Returns:
-        matplotlib figure
-
+        plt.Axes: matplotlib Axes
     """
     lines = [[kpath.kpath["kpoints"][k] for k in p] for p in kpath.kpath["path"]]
     return plot_brillouin_zone(

pymatgen/entries/__init__.py

@@ -33,7 +33,6 @@ class Entry(MSONable, metaclass=ABCMeta):
     a specific chemical composition. This base class is not
     intended to be instantiated directly. Note that classes
     which inherit from Entry must define a .energy property.
-
     """
 
     def __init__(self, composition: Composition | str | dict[str, float], energy: float) -> None:

pymatgen/entries/compatibility.py

@@ -206,7 +206,7 @@ def get_correction(self, entry) -> ufloat:
         # set error to 0 because old MPCompatibility doesn't have errors
 
         # only correct GGA or GGA+U entries
-        if entry.parameters.get("run_type") not in ["GGA", "GGA+U"]:
+        if entry.parameters.get("run_type") not in ("GGA", "GGA+U"):
             return ufloat(0.0, 0.0)
 
         rform = entry.composition.reduced_formula
@@ -253,7 +253,7 @@ def get_correction(self, entry) -> ufloat:
         correction = ufloat(0.0, 0.0)
 
         # only correct GGA or GGA+U entries
-        if entry.parameters.get("run_type") not in ["GGA", "GGA+U"]:
+        if entry.parameters.get("run_type") not in ("GGA", "GGA+U"):
             return ufloat(0.0, 0.0)
 
         # Check for sulfide corrections
@@ -347,14 +347,12 @@ def get_correction(self, entry) -> ufloat:
         Returns:
             Correction, Uncertainty.
         """
-        from pymatgen.analysis.pourbaix_diagram import MU_H2O
-
         comp = entry.composition
         rform = comp.reduced_formula
         cpd_energies = self.cpd_energies
 
         # only correct GGA or GGA+U entries
-        if entry.parameters.get("run_type") not in ["GGA", "GGA+U"]:
+        if entry.parameters.get("run_type") not in ("GGA", "GGA+U"):
             return ufloat(0.0, 0.0)
 
         correction = ufloat(0.0, 0.0)
@@ -467,21 +465,20 @@ def get_correction(self, entry) -> ufloat:
         Returns:
             Correction, Uncertainty.
         """
-        if entry.parameters.get("run_type") not in ["GGA", "GGA+U"]:
+        if entry.parameters.get("run_type") not in ("GGA", "GGA+U"):
             raise CompatibilityError(
                 f"Entry {entry.entry_id} has invalid run type {entry.parameters.get('run_type')}. Discarding."
             )
 
-        calc_u = entry.parameters.get("hubbards")
-        calc_u = defaultdict(int) if calc_u is None else calc_u
+        calc_u = entry.parameters.get("hubbards") or defaultdict(int)
         comp = entry.composition
 
         elements = sorted((el for el in comp.elements if comp[el] > 0), key=lambda el: el.X)
         most_electroneg = elements[-1].symbol
         correction = ufloat(0.0, 0.0)
 
         # only correct GGA or GGA+U entries
-        if entry.parameters.get("run_type") not in ["GGA", "GGA+U"]:
+        if entry.parameters.get("run_type") not in ("GGA", "GGA+U"):
             return ufloat(0.0, 0.0)
 
         u_corr = self.u_corrections.get(most_electroneg, {})
@@ -934,7 +931,7 @@ def get_adjustments(self, entry: AnyComputedEntry) -> list[EnergyAdjustment]:
         Raises:
             CompatibilityError if the entry is not compatible
         """
-        if entry.parameters.get("run_type") not in ["GGA", "GGA+U"]:
+        if entry.parameters.get("run_type") not in ("GGA", "GGA+U"):
             raise CompatibilityError(
                 f"Entry {entry.entry_id} has invalid run type {entry.parameters.get('run_type')}. "
                 f"Must be GGA or GGA+U. Discarding."

pymatgen/ext/matproj_legacy.py

@@ -26,6 +26,7 @@
 from pymatgen.core import SETTINGS, Composition, Element, Structure
 from pymatgen.core import __version__ as PMG_VERSION
 from pymatgen.core.surface import get_symmetrically_equivalent_miller_indices
+from pymatgen.entries.compatibility import MaterialsProject2020Compatibility
 from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
 from pymatgen.entries.exp_entries import ExpEntry
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
@@ -557,8 +558,6 @@ def get_entries(
                 )
             entries.append(e)
         if compatible_only:
-            from pymatgen.entries.compatibility import MaterialsProject2020Compatibility
-
             # suppress the warning about missing oxidation states
             with warnings.catch_warnings():
                 warnings.filterwarnings("ignore", message="Failed to guess oxidation states.*")