Merge branch master into kpoints-tuple-type

.github/CODEOWNERS

@@ -2,3 +2,5 @@
 pymatgen/io/ase.py @Andrew-S-Rosen
 pymatgen/io/abinit/* @gmatteo
 pymatgen/io/lobster/* @JaGeo
+pymatgen/ext/* @ml-evs
+tests/ext/* @ml-evs

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.5
+    rev: v0.3.7
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]

dev_scripts/chemenv/equivalent_indices.py

@@ -99,9 +99,9 @@
         # 0. any point
         for i0 in range(8):
             # 1. point opposite to point 0. in the square face
-            if i0 in [0, 2]:
+            if i0 in {0, 2}:
                 i1 = i0 + 1
-            elif i0 in [1, 3]:
+            elif i0 in {1, 3}:
                 i1 = i0 - 1
             elif i0 == 4:
                 i1 = 7
@@ -111,10 +111,14 @@
                 i1 = 5
             elif i0 == 7:
                 i1 = 4
+            else:
+                raise RuntimeError("Cannot determine point.")
+
             # 2. one of the two last points in the square face
             sfleft = list(sf1) if i0 in sf1 else list(sf2)
             sfleft.remove(i0)
             sfleft.remove(i1)
+            i2 = 0
             for i2 in sfleft:
                 sfleft2 = list(sfleft)
                 sfleft2.remove(i2)

dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py

@@ -151,17 +151,18 @@ def get_structure(self, morphing_factor):
 
         coords = copy.deepcopy(self.abstract_geometry.points_wcs_ctwcc())
         bare_points = self.abstract_geometry.bare_points_with_centre
+        origin = None
 
         for morphing in self.morphing_description:
-            if morphing["site_type"] == "neighbor":
-                i_site = morphing["ineighbor"] + 1
-                if morphing["expansion_origin"] == "central_site":
-                    origin = bare_points[0]
-                vector = bare_points[i_site] - origin
-                coords[i_site] += vector * (morphing_factor - 1.0)
-            else:
+            if morphing["site_type"] != "neighbor":
                 raise ValueError(f"Key \"site_type\" is {morphing['site_type']} while it can only be neighbor")
 
+            i_site = morphing["ineighbor"] + 1
+            if morphing["expansion_origin"] == "central_site":
+                origin = bare_points[0]
+            vector = bare_points[i_site] - origin
+            coords[i_site] += vector * (morphing_factor - 1.0)
+
         return Structure(lattice=lattice, species=species, coords=coords, coords_are_cartesian=True)
 
     def estimate_parameters(self, dist_factor_min, dist_factor_max, symmetry_measure_type="csm_wcs_ctwcc"):
@@ -269,7 +270,7 @@ def get_weights(self, weights_options):
         "+-------------------------------------------------------------+\n"
     )
 
-    with open("ce_pairs.json") as file:
+    with open("ce_pairs.json", encoding="utf-8") as file:
         ce_pairs = json.load(file)
     self_weight_max_csms: dict[str, list[float]] = {}
     self_weight_max_csms_per_cn: dict[str, list[float]] = {}

dev_scripts/chemenv/view_environment.py

@@ -52,6 +52,7 @@
             print()
         # Visualize the separation plane of a given algorithm
         sep_plane = False
+        algo = None
         if any(algo.algorithm_type == SEPARATION_PLANE for algo in cg.algorithms):
             test = input("Enter index of the algorithm for which you want to visualize the plane : ")
             if test != "":

dev_scripts/update_pt_data.py

@@ -150,9 +150,10 @@ def parse_shannon_radii():
     from openpyxl import load_workbook
 
     wb = load_workbook("Shannon Radii.xlsx")
-    print(wb.get_sheet_names())
+    print(wb.sheetnames())
     sheet = wb["Sheet1"]
     i = 2
+    el = charge = cn = None
     radii = collections.defaultdict(dict)
     while sheet[f"E{i}"].value:
         if sheet[f"A{i}"].value:
@@ -235,6 +236,7 @@ def add_electron_affinities():
 
     req = requests.get("https://wikipedia.org/wiki/Electron_affinity_(data_page)")
     soup = BeautifulSoup(req.text, "html.parser")
+    table = None
     for table in soup.find_all("table"):
         if "Hydrogen" in table.text:
             break
@@ -271,6 +273,7 @@ def add_ionization_energies():
 
     with open("NIST Atomic Ionization Energies Output.html") as file:
         soup = BeautifulSoup(file.read(), "html.parser")
+    table = None
     for table in soup.find_all("table"):
         if "Hydrogen" in table.text:
             break

pymatgen/analysis/chemenv/connectivity/connected_components.py

@@ -241,17 +241,16 @@ def __init__(
                 if links_data is None:
                     edge_data = None
 
+                elif (env_node1, env_node2, key) in links_data:
+                    edge_data = links_data[(env_node1, env_node2, key)]
+                elif (env_node2, env_node1, key) in links_data:
+                    edge_data = links_data[(env_node2, env_node1, key)]
+                elif (env_node1, env_node2) in links_data:
+                    edge_data = links_data[(env_node1, env_node2)]
+                elif (env_node2, env_node1) in links_data:
+                    edge_data = links_data[(env_node2, env_node1)]
                 else:
-                    if (env_node1, env_node2, key) in links_data:
-                        edge_data = links_data[(env_node1, env_node2, key)]
-                    elif (env_node2, env_node1, key) in links_data:
-                        edge_data = links_data[(env_node2, env_node1, key)]
-                    elif (env_node1, env_node2) in links_data:
-                        edge_data = links_data[(env_node1, env_node2)]
-                    elif (env_node2, env_node1) in links_data:
-                        edge_data = links_data[(env_node2, env_node1)]
-                    else:
-                        edge_data = None
+                    edge_data = None
 
                 if edge_data:
                     self._connected_subgraph.add_edge(env_node1, env_node2, key, **edge_data)

pymatgen/analysis/elasticity/stress.py

@@ -6,12 +6,15 @@
 from __future__ import annotations
 
 import math
+from typing import TYPE_CHECKING
 
 import numpy as np
-from typing_extensions import Self
 
 from pymatgen.core.tensors import SquareTensor
 
+if TYPE_CHECKING:
+    from typing_extensions import Self
+
 __author__ = "Joseph Montoya"
 __copyright__ = "Copyright 2012, The Materials Project"
 __credits__ = "Maarten de Jong, Mark Asta, Anubhav Jain"

pymatgen/analysis/ewald.py

@@ -344,8 +344,7 @@ def _calc_recip(self):
 
         for g, g2, gr, exp_val, s_real, s_imag in zip(gs, g2s, grs, exp_vals, s_reals, s_imags):
             # Uses the identity sin(x)+cos(x) = 2**0.5 sin(x + pi/4)
-            m = (gr[None, :] + pi / 4) - gr[:, None]
-            np.sin(m, m)
+            m = np.sin((gr[None, :] + pi / 4) - gr[:, None])
             m *= exp_val / g2
 
             e_recip += m

pymatgen/analysis/local_env.py

@@ -4164,10 +4164,10 @@ def _get_radius(site):
             return el.ionic_radii[oxi]
 
         # e.g., oxi = 2.667, average together 2+ and 3+ radii
-        if int(math.floor(oxi)) in el.ionic_radii and int(math.ceil(oxi)) in el.ionic_radii:
-            oxi_low = el.ionic_radii[int(math.floor(oxi))]
-            oxi_high = el.ionic_radii[int(math.ceil(oxi))]
-            x = oxi - int(math.floor(oxi))
+        if math.floor(oxi) in el.ionic_radii and math.ceil(oxi) in el.ionic_radii:
+            oxi_low = el.ionic_radii[math.floor(oxi)]
+            oxi_high = el.ionic_radii[math.ceil(oxi)]
+            x = oxi - math.floor(oxi)
             return (1 - x) * oxi_low + x * oxi_high
 
         if oxi > 0 and el.average_cationic_radius > 0:

pymatgen/command_line/enumlib_caller.py

@@ -256,7 +256,7 @@ def get_sg_info(ss):
         # enumeration. See Cu7Te5.cif test file.
         base *= 10
 
-        # base = n_disordered # 10 ** int(math.ceil(math.log10(n_disordered)))
+        # base = n_disordered # 10 ** math.ceil(math.log10(n_disordered))
         # To get a reasonable number of structures, we fix concentrations to the
         # range expected in the original structure.
         total_amounts = sum(index_amounts)
@@ -266,7 +266,7 @@ def get_sg_info(ss):
             if abs(conc * base - round(conc * base)) < 1e-5:
                 output.append(f"{int(round(conc * base))} {int(round(conc * base))} {base}")
             else:
-                min_conc = int(math.floor(conc * base))
+                min_conc = math.floor(conc * base)
                 output.append(f"{min_conc - 1} {min_conc + 1} {base}")
         output.append("")
         logger.debug("Generated input file:\n" + "\n".join(output))

pymatgen/command_line/vampire_caller.py

@@ -135,9 +135,9 @@ def __init__(
             stdout: str = _stdout.decode()
 
         if stderr:
-            vanhelsing = stderr.decode()
-            if len(vanhelsing) > 27:  # Suppress blank warning msg
-                logging.warning(vanhelsing)
+            van_helsing = stderr.decode()
+            if len(van_helsing) > 27:  # Suppress blank warning msg
+                logging.warning(van_helsing)
 
         if process.returncode != 0:
             raise RuntimeError(f"Vampire exited with return code {process.returncode}.")
@@ -146,9 +146,9 @@ def __init__(
         self._stderr = stderr
 
         # Process output
-        nmats = max(self.mat_id_dict.values())
-        parsed_out, critical_temp = VampireCaller.parse_stdout("output", nmats)
-        self.output = VampireOutput(parsed_out, nmats, critical_temp)
+        n_mats = max(self.mat_id_dict.values())
+        parsed_out, critical_temp = VampireCaller.parse_stdout("output", n_mats)
+        self.output = VampireOutput(parsed_out, n_mats, critical_temp)
 
     def _create_mat(self):
         structure = self.structure
@@ -158,43 +158,41 @@ def _create_mat(self):
         # Maps sites to material id for vampire inputs
         mat_id_dict = {}
 
-        nmats = 0
+        n_mats = 0
         for key in self.unique_site_ids:
             spin_up, spin_down = False, False
-            nmats += 1  # at least 1 mat for each unique site
+            n_mats += 1  # at least 1 mat for each unique site
 
             # Check which spin sublattices exist for this site id
             for site in key:
-                m = magmoms[site]
-                if m > 0:
+                if magmoms[site] > 0:
                     spin_up = True
-                if m < 0:
+                if magmoms[site] < 0:
                     spin_down = True
 
             # Assign material id for each site
             for site in key:
-                m = magmoms[site]
                 if spin_up and not spin_down:
-                    mat_id_dict[site] = nmats
+                    mat_id_dict[site] = n_mats
                 if spin_down and not spin_up:
-                    mat_id_dict[site] = nmats
+                    mat_id_dict[site] = n_mats
                 if spin_up and spin_down:
                     # Check if spin up or down shows up first
                     m0 = magmoms[key[0]]
-                    if m > 0 and m0 > 0:
-                        mat_id_dict[site] = nmats
-                    if m < 0 and m0 < 0:
-                        mat_id_dict[site] = nmats
-                    if m > 0 > m0:
-                        mat_id_dict[site] = nmats + 1
-                    if m < 0 < m0:
-                        mat_id_dict[site] = nmats + 1
+                    if magmoms[site] > 0 and m0 > 0:
+                        mat_id_dict[site] = n_mats
+                    if magmoms[site] < 0 and m0 < 0:
+                        mat_id_dict[site] = n_mats
+                    if magmoms[site] > 0 > m0:
+                        mat_id_dict[site] = n_mats + 1
+                    if magmoms[site] < 0 < m0:
+                        mat_id_dict[site] = n_mats + 1
 
             # Increment index if two sublattices
             if spin_up and spin_down:
-                nmats += 1
+                n_mats += 1
 
-        mat_file = [f"material:num-materials={nmats}"]
+        mat_file = [f"material:num-materials={n_mats}"]
 
         for key in self.unique_site_ids:
             i = self.unique_site_ids[key]  # unique site id
@@ -230,7 +228,7 @@ def _create_mat(self):
 
     def _create_input(self):
         structure = self.structure
-        mcbs = self.mc_box_size
+        mc_box_size = self.mc_box_size
         equil_timesteps = self.equil_timesteps
         mc_timesteps = self.mc_timesteps
         mat_name = self.mat_name
@@ -255,9 +253,9 @@ def _create_input(self):
 
         # System size in nm
         input_script += [
-            f"dimensions:system-size-x = {mcbs:.1f} !nm",
-            f"dimensions:system-size-y = {mcbs:.1f} !nm",
-            f"dimensions:system-size-z = {mcbs:.1f} !nm",
+            f"dimensions:system-size-x = {mc_box_size:.1f} !nm",
+            f"dimensions:system-size-y = {mc_box_size:.1f} !nm",
+            f"dimensions:system-size-z = {mc_box_size:.1f} !nm",
         ]
 
         # Critical temperature Monte Carlo calculation

pymatgen/core/__init__.py

@@ -1,4 +1,3 @@
-# ruff: noqa: PLC0414
 """This package contains core modules and classes for representing structures and operations on them."""
 
 from __future__ import annotations
@@ -10,25 +9,13 @@
 
 from ruamel.yaml import YAML
 
-from pymatgen.core.composition import Composition as Composition
-from pymatgen.core.lattice import Lattice as Lattice
-from pymatgen.core.operations import SymmOp as SymmOp
-from pymatgen.core.periodic_table import DummySpecie as DummySpecie
-from pymatgen.core.periodic_table import DummySpecies as DummySpecies
-from pymatgen.core.periodic_table import Element as Element
-from pymatgen.core.periodic_table import Species as Species
-from pymatgen.core.periodic_table import get_el_sp as get_el_sp
-from pymatgen.core.sites import PeriodicSite as PeriodicSite
-from pymatgen.core.sites import Site as Site
-from pymatgen.core.structure import IMolecule as IMolecule
-from pymatgen.core.structure import IStructure as IStructure
-from pymatgen.core.structure import Molecule as Molecule
-from pymatgen.core.structure import PeriodicNeighbor as PeriodicNeighbor
-from pymatgen.core.structure import SiteCollection as SiteCollection
-from pymatgen.core.structure import Structure as Structure
-from pymatgen.core.units import ArrayWithUnit as ArrayWithUnit
-from pymatgen.core.units import FloatWithUnit as FloatWithUnit
-from pymatgen.core.units import Unit as Unit
+from pymatgen.core.composition import Composition
+from pymatgen.core.lattice import Lattice
+from pymatgen.core.operations import SymmOp
+from pymatgen.core.periodic_table import DummySpecie, DummySpecies, Element, Species, get_el_sp
+from pymatgen.core.sites import PeriodicSite, Site
+from pymatgen.core.structure import IMolecule, IStructure, Molecule, PeriodicNeighbor, SiteCollection, Structure
+from pymatgen.core.units import ArrayWithUnit, FloatWithUnit, Unit
 
 __author__ = "Pymatgen Development Team"
 __email__ = "pymatgen@googlegroups.com"