Avoid using full equality (==) to compare float, avoid assert_array_equal compare float array

src/pymatgen/alchemy/filters.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import abc
+import math
 from collections import defaultdict
 from typing import TYPE_CHECKING
 
@@ -285,7 +286,7 @@ def __init__(self):
 
     def test(self, structure: Structure):
         """True if structure is neutral."""
-        return structure.charge == 0.0
+        return math.isclose(structure.charge, 0.0)
 
 
 class SpeciesMaxDistFilter(AbstractStructureFilter):

src/pymatgen/core/bonds.py

@@ -134,7 +134,10 @@ def obtain_all_bond_lengths(
             If None, a ValueError will be thrown.
 
     Returns:
-        A dict mapping bond order to bond length in angstrom
+        dict[float, float]: mapping bond order to bond length in Angstrom.
+
+    Todo:
+        it's better to avoid using float as dict keys.
     """
     if isinstance(sp1, Element):
         sp1 = sp1.symbol

src/pymatgen/electronic_structure/plotter.py

@@ -1245,7 +1245,7 @@ def get_elt_projected_plots_color(
                                 proj[b][str(spin)][band_idx][j][str(el)][o]
                                 for o in proj[b][str(spin)][band_idx][j][str(el)]
                             )
-                        if sum_e == 0.0:
+                        if math.isclose(sum_e, 0.0):
                             color = [0.0] * len(elt_ordered)
                         else:
                             color = [

src/pymatgen/io/aims/inputs.py

@@ -560,7 +560,7 @@ def get_content(
         magmom = structure.site_properties.get("magmom", spins)
         if (
             parameters.get("spin", "") == "collinear"
-            and np.all(magmom == 0.0)
+            and np.allclose(magmom, 0.0)
             and ("default_initial_moment" not in parameters)
         ):
             warn(

src/pymatgen/io/cp2k/outputs.py

@@ -1320,10 +1320,16 @@ def parse_bandstructure(self, bandstructure_filename=None) -> None:
         else:
             eigenvals = {Spin.up: bands_data.reshape((nbands, nkpts))}
 
-        occ = bands_data[:, 1][bands_data[:, -1] != 0.0]
+        # Filter out occupied and unoccupied states
+        occupied_mask = ~np.isclose(bands_data[:, -1], 0.0)
+        unoccupied_mask = np.isclose(bands_data[:, -1], 0.0)
+
+        occ = bands_data[:, 1][occupied_mask]
         homo = np.max(occ)
-        unocc = bands_data[:, 1][bands_data[:, -1] == 0.0]
+
+        unocc = bands_data[:, 1][unoccupied_mask]
         lumo = np.min(unocc)
+
         efermi = (lumo + homo) / 2
         self.efermi = efermi
 

src/pymatgen/io/vasp/outputs.py

@@ -779,13 +779,13 @@ def run_type(self) -> str:
             4: "dDsC",
         }
 
-        if self.parameters.get("AEXX", 1.00) == 1.00:
+        if math.isclose(self.parameters.get("AEXX", 1.00), 1.00):
             run_type = "HF"
-        elif self.parameters.get("HFSCREEN", 0.30) == 0.30:
+        elif math.isclose(self.parameters.get("HFSCREEN", 0.30), 0.30):
             run_type = "HSE03"
-        elif self.parameters.get("HFSCREEN", 0.20) == 0.20:
+        elif math.isclose(self.parameters.get("HFSCREEN", 0.20), 0.20):
             run_type = "HSE06"
-        elif self.parameters.get("AEXX", 0.20) == 0.20:
+        elif math.isclose(self.parameters.get("AEXX", 0.20), 0.20):
             run_type = "B3LYP"
         elif self.parameters.get("LHFCALC", True):
             run_type = "PBEO or other Hybrid Functional"
@@ -1021,7 +1021,7 @@ def get_band_structure(
             if (hybrid_band or force_hybrid_mode) and not use_kpoints_opt:
                 start_bs_index = 0
                 for i in range(len(self.actual_kpoints)):
-                    if self.actual_kpoints_weights[i] == 0.0:
+                    if math.isclose(self.actual_kpoints_weights[i], 0.0):
                         start_bs_index = i
                         break
                 for i in range(start_bs_index, len(kpoint_file.kpts)):
@@ -5274,8 +5274,11 @@ def get_parchg(
         Returns:
             A Chgcar object.
         """
-        if phase and not np.all(self.kpoints[kpoint] == 0.0):
-            warnings.warn("phase is True should only be used for the Gamma kpoint! I hope you know what you're doing!")
+        if phase and not np.allclose(self.kpoints[kpoint], 0.0):
+            warnings.warn(
+                "phase is True should only be used for the Gamma kpoint! I hope you know what you're doing!",
+                stacklevel=2,
+            )
 
         # Scaling of ng for the fft grid, need to restore value at the end
         temp_ng = self.ng

src/pymatgen/transformations/advanced_transformations.py

@@ -7,7 +7,6 @@
 import warnings
 from fractions import Fraction
 from itertools import groupby, product
-from math import gcd
 from string import ascii_lowercase
 from typing import TYPE_CHECKING
 
@@ -49,6 +48,8 @@
     from collections.abc import Callable, Iterable, Sequence
     from typing import Any, Literal
 
+    from numpy.typing import NDArray
+
 
 __author__ = "Shyue Ping Ong, Stephen Dacek, Anubhav Jain, Matthew Horton, Alex Ganose"
 
@@ -68,6 +69,9 @@ def __init__(self, charge_balance_sp):
         """
         self.charge_balance_sp = str(charge_balance_sp)
 
+    def __repr__(self):
+        return f"Charge Balance Transformation : Species to remove = {self.charge_balance_sp}"
+
     def apply_transformation(self, structure: Structure):
         """Apply the transformation.
 
@@ -87,9 +91,6 @@ def apply_transformation(self, structure: Structure):
         trans = SubstitutionTransformation({self.charge_balance_sp: {self.charge_balance_sp: 1 - removal_fraction}})
         return trans.apply_transformation(structure)
 
-    def __repr__(self):
-        return f"Charge Balance Transformation : Species to remove = {self.charge_balance_sp}"
-
 
 class SuperTransformation(AbstractTransformation):
     """This is a transformation that is inherently one-to-many. It is constructed
@@ -111,6 +112,9 @@ def __init__(self, transformations, nstructures_per_trans=1):
         self._transformations = transformations
         self.nstructures_per_trans = nstructures_per_trans
 
+    def __repr__(self):
+        return f"Super Transformation : Transformations = {' '.join(map(str, self._transformations))}"
+
     def apply_transformation(self, structure: Structure, return_ranked_list: bool | int = False):
         """Apply the transformation.
 
@@ -140,11 +144,8 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool |
                 )
         return structures
 
-    def __repr__(self):
-        return f"Super Transformation : Transformations = {' '.join(map(str, self._transformations))}"
-
     @property
-    def is_one_to_many(self) -> bool:
+    def is_one_to_many(self) -> Literal[True]:
         """Transform one structure to many."""
         return True
 
@@ -192,6 +193,9 @@ def __init__(
         self.charge_balance_species = charge_balance_species
         self.order = order
 
+    def __repr__(self):
+        return f"Multiple Substitution Transformation : Substitution on {self.sp_to_replace}"
+
     def apply_transformation(self, structure: Structure, return_ranked_list: bool | int = False):
         """Apply the transformation.
 
@@ -235,11 +239,8 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool |
                 outputs.append({"structure": new_structure})
         return outputs
 
-    def __repr__(self):
-        return f"Multiple Substitution Transformation : Substitution on {self.sp_to_replace}"
-
     @property
-    def is_one_to_many(self) -> bool:
+    def is_one_to_many(self) -> Literal[True]:
         """Transform one structure to many."""
         return True
 
@@ -324,6 +325,9 @@ def __init__(
         if max_cell_size and max_disordered_sites:
             raise ValueError("Cannot set both max_cell_size and max_disordered_sites!")
 
+    def __repr__(self):
+        return "EnumerateStructureTransformation"
+
     def apply_transformation(
         self, structure: Structure, return_ranked_list: bool | int = False
     ) -> Structure | list[dict]:
@@ -469,11 +473,8 @@ def sort_func(struct):
             return self._all_structures[:num_to_return]
         return self._all_structures[0]["structure"]
 
-    def __repr__(self):
-        return "EnumerateStructureTransformation"
-
     @property
-    def is_one_to_many(self) -> bool:
+    def is_one_to_many(self) -> Literal[True]:
         """Transform one structure to many."""
         return True
 
@@ -495,6 +496,9 @@ def __init__(self, threshold=1e-2, scale_volumes=True, **kwargs):
         self.scale_volumes = scale_volumes
         self._substitutor = SubstitutionPredictor(threshold=threshold, **kwargs)
 
+    def __repr__(self):
+        return "SubstitutionPredictorTransformation"
+
     def apply_transformation(self, structure: Structure, return_ranked_list: bool | int = False):
         """Apply the transformation.
 
@@ -529,11 +533,8 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool |
             outputs.append(output)
         return outputs
 
-    def __repr__(self):
-        return "SubstitutionPredictorTransformation"
-
     @property
-    def is_one_to_many(self) -> bool:
+    def is_one_to_many(self) -> Literal[True]:
         """Transform one structure to many."""
         return True
 
@@ -660,7 +661,7 @@ def determine_min_cell(disordered_structure):
 
         def lcm(n1, n2):
             """Find least common multiple of two numbers."""
-            return n1 * n2 / gcd(n1, n2)
+            return n1 * n2 / math.gcd(n1, n2)
 
         # assumes all order parameters for a given species are the same
         mag_species_order_parameter = {}
@@ -683,7 +684,7 @@ def lcm(n1, n2):
         for sp, order_parameter in mag_species_order_parameter.items():
             denom = Fraction(order_parameter).limit_denominator(100).denominator
             num_atom_per_specie = mag_species_occurrences[sp]
-            n_gcd = gcd(denom, num_atom_per_specie)
+            n_gcd = math.gcd(denom, num_atom_per_specie)
             smallest_n.append(lcm(int(n_gcd), denom) / n_gcd)
 
         return max(smallest_n)
@@ -894,7 +895,7 @@ def key(struct: Structure) -> int:
         return self._all_structures[:num_to_return]  # type: ignore[return-value]
 
     @property
-    def is_one_to_many(self) -> bool:
+    def is_one_to_many(self) -> Literal[True]:
         """Transform one structure to many."""
         return True
 
@@ -983,15 +984,19 @@ def __init__(
         self.allowed_doping_species = allowed_doping_species
         self.kwargs = kwargs
 
-    def apply_transformation(self, structure: Structure, return_ranked_list: bool | int = False):
+    def apply_transformation(
+        self,
+        structure: Structure,
+        return_ranked_list: bool | int = False,
+    ) -> list[dict[Literal["structure", "energy"], Structure | float]] | Structure:
         """
         Args:
-            structure (Structure): Input structure to dope
-            return_ranked_list (bool | int, optional): If return_ranked_list is int, that number of structures.
-                is returned. If False, only the single lowest energy structure is returned. Defaults to False.
+            structure (Structure): Input structure to dope.
+            return_ranked_list (bool | int, optional): If is int, that number of structures is returned.
+                If False, only the single lowest energy structure is returned. Defaults to False.
 
         Returns:
-            list[dict] | Structure: each dict has shape {"structure": Structure, "energy": float}.
+            list[dict] | Structure: each dict as {"structure": Structure, "energy": float}.
         """
         comp = structure.composition
         logger.info(f"Composition: {comp}")
@@ -1124,7 +1129,7 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool |
         return all_structures[0]["structure"]
 
     @property
-    def is_one_to_many(self) -> bool:
+    def is_one_to_many(self) -> Literal[True]:
         """Transform one structure to many."""
         return True
 
@@ -1252,7 +1257,7 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool |
         return disordered_structures
 
     @property
-    def is_one_to_many(self) -> bool:
+    def is_one_to_many(self) -> Literal[True]:
         """Transform one structure to many."""
         return True
 
@@ -1713,7 +1718,7 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool |
         return [{"structure": structure} for structure in structures[:return_ranked_list]]
 
     @property
-    def is_one_to_many(self) -> bool:
+    def is_one_to_many(self) -> Literal[True]:
         """Transform one structure to many."""
         return True
 
@@ -1867,16 +1872,25 @@ def apply_transformation(
         return [{"structure": structure} for structure in structures[:return_ranked_list]]
 
     @property
-    def is_one_to_many(self) -> bool:
+    def is_one_to_many(self) -> Literal[True]:
         """Transform one structure to many."""
         return True
 
 
-def _proj(b, a):
-    """Get vector projection (np.ndarray) of vector b (np.ndarray)
-    onto vector a (np.ndarray).
+def _proj(b: NDArray, a: NDArray) -> NDArray:
+    """Get vector projection of vector b onto vector a.
+
+    Args:
+        b (NDArray): Vector to be projected.
+        a (NDArray): Vector onto which `b` is projected.
+
+    Returns:
+        NDArray: Projection of `b` onto `a`.
     """
-    return (b.T @ (a / np.linalg.norm(a))) * (a / np.linalg.norm(a))
+    a = np.asarray(a)
+    b = np.asarray(b)
+
+    return (np.dot(b, a) / np.dot(a, a)) * a
 
 
 class SQSTransformation(AbstractTransformation):
@@ -2145,7 +2159,7 @@ def _get_unique_best_sqs_structs(sqs, best_only, return_ranked_list, remove_dupl
         return to_return
 
     @property
-    def is_one_to_many(self) -> bool:
+    def is_one_to_many(self) -> Literal[True]:
         """Transform one structure to many."""
         return True
 
@@ -2194,6 +2208,9 @@ def __init__(self, rattle_std: float, min_distance: float, seed: int | None = No
         self.random_state = np.random.RandomState(seed)
         self.kwargs = kwargs
 
+    def __repr__(self):
+        return f"{__name__} : rattle_std = {self.rattle_std}"
+
     def apply_transformation(self, structure: Structure) -> Structure:
         """Apply the transformation.
 
@@ -2215,6 +2232,3 @@ def apply_transformation(self, structure: Structure) -> Structure:
             structure.cart_coords + displacements,
             coords_are_cartesian=True,
         )
-
-    def __repr__(self):
-        return f"{__name__} : rattle_std = {self.rattle_std}"