Migrate from attr to attrs

iodata/basis.py

@@ -28,8 +28,9 @@
 from numbers import Integral
 from typing import Union
 
-import attr
+import attrs
 import numpy as np
+from numpy.typing import NDArray
 
 from .attrutils import validate_shape
 
@@ -100,7 +101,7 @@ def angmom_its(angmom: Union[int, list[int]]) -> Union[str, list[str]]:
     return ANGMOM_CHARS[angmom]
 
 
-@attr.s(auto_attribs=True, slots=True, on_setattr=[attr.setters.validate, attr.setters.convert])
+@attrs.define
 class Shell:
     """A shell in a molecular basis representing (generalized) contractions with the same exponents.
 
@@ -126,11 +127,11 @@ class Shell:
 
     """
 
-    icenter: int
-    angmoms: list[int] = attr.ib(validator=validate_shape(("coeffs", 1)))
-    kinds: list[str] = attr.ib(validator=validate_shape(("coeffs", 1)))
-    exponents: np.ndarray = attr.ib(validator=validate_shape(("coeffs", 0)))
-    coeffs: np.ndarray = attr.ib(validator=validate_shape(("exponents", 0), ("kinds", 0)))
+    icenter: int = attrs.field()
+    angmoms: list[int] = attrs.field(validator=validate_shape(("coeffs", 1)))
+    kinds: list[str] = attrs.field(validator=validate_shape(("coeffs", 1)))
+    exponents: NDArray = attrs.field(validator=validate_shape(("coeffs", 0)))
+    coeffs: NDArray = attrs.field(validator=validate_shape(("exponents", 0), ("kinds", 0)))
 
     @property
     def nbasis(self) -> int:
@@ -156,7 +157,7 @@ def ncon(self) -> int:
         return len(self.angmoms)
 
 
-@attr.s(auto_attribs=True, slots=True, on_setattr=[attr.setters.validate, attr.setters.convert])
+@attrs.define
 class MolecularBasis:
     """A complete molecular orbital or density basis set.
 
@@ -205,9 +206,9 @@ class MolecularBasis:
 
     """
 
-    shells: list[Shell]
-    conventions: dict[str, str]
-    primitive_normalization: str
+    shells: list[Shell] = attrs.field()
+    conventions: dict[str, str] = attrs.field()
+    primitive_normalization: str = attrs.field()
 
     @property
     def nbasis(self) -> int:
@@ -222,12 +223,12 @@ def get_segmented(self):
                 shells.append(
                     Shell(shell.icenter, [angmom], [kind], shell.exponents, coeffs.reshape(-1, 1))
                 )
-        return attr.evolve(self, shells=shells)
+        return attrs.evolve(self, shells=shells)
 
 
 def convert_convention_shell(
     conv1: list[str], conv2: list[str], reverse=False
-) -> tuple[np.ndarray, np.ndarray]:
+) -> tuple[NDArray, NDArray]:
     """Return a permutation vector and sign changes to convert from 1 to 2.
 
     The transformation from convention 1 to convention 2 can be done applying
@@ -289,7 +290,7 @@ def convert_convention_shell(
 
 def convert_conventions(
     molbasis: MolecularBasis, new_conventions: dict[str, list[str]], reverse=False
-) -> tuple[np.ndarray, np.ndarray]:
+) -> tuple[NDArray, NDArray]:
     """Return a permutation vector and sign changes to convert from 1 to 2.
 
     The transformation from molbasis.convention to the new convention can be done
@@ -339,7 +340,7 @@ def convert_conventions(
     return np.array(permutation), np.array(signs)
 
 
-def iter_cart_alphabet(n: int) -> np.ndarray:
+def iter_cart_alphabet(n: int) -> NDArray:
     """Loop over powers of Cartesian basis functions in alphabetical order.
 
     See https://theochem.github.io/horton/2.1.1/tech_ref_gaussian_basis.html

iodata/formats/chgcar.py

@@ -26,6 +26,7 @@
 """
 
 import numpy as np
+from numpy.typing import NDArray
 
 from ..docstrings import document_load_one
 from ..periodic import sym2num
@@ -37,7 +38,7 @@
 PATTERNS = ["CHGCAR*", "AECCAR*"]
 
 
-def _load_vasp_header(lit: LineIterator) -> tuple[str, np.ndarray, np.ndarray, np.ndarray]:
+def _load_vasp_header(lit: LineIterator) -> tuple[str, NDArray, NDArray, NDArray]:
     """Load the cell and atoms from a VASP file format.
 
     Parameters

iodata/formats/cp2klog.py

@@ -21,6 +21,7 @@
 from typing import Union
 
 import numpy as np
+from numpy.typing import NDArray
 from scipy.special import factorialk
 
 from ..basis import HORTON2_CONVENTIONS, MolecularBasis, Shell, angmom_sti
@@ -42,9 +43,7 @@
 }
 
 
-def _get_cp2k_norm_corrections(
-    ell: int, alphas: Union[float, np.ndarray]
-) -> Union[float, np.ndarray]:
+def _get_cp2k_norm_corrections(ell: int, alphas: Union[float, NDArray]) -> Union[float, NDArray]:
     """Compute the corrections for the normalization of the basis functions.
 
     This correction is needed because the CP2K atom code works with a different
@@ -236,7 +235,7 @@ def _read_cp2k_occupations_energies(
 
 def _read_cp2k_orbital_coeffs(
     lit: LineIterator, oe: list[tuple[int, int, float, float]]
-) -> dict[tuple[int, int], np.ndarray]:
+) -> dict[tuple[int, int], NDArray]:
     """Read the expansion coefficients of the orbital from an open CP2K ATOM output.
 
     Parameters
@@ -294,11 +293,11 @@ def _get_norb_nel(oe: list[tuple[int, int, float, float]]) -> tuple[int, float]:
 
 
 def _fill_orbitals(
-    orb_coeffs: np.ndarray,
-    orb_energies: np.ndarray,
-    orb_occupations: np.ndarray,
+    orb_coeffs: NDArray,
+    orb_energies: NDArray,
+    orb_occupations: NDArray,
     oe: list[tuple[int, int, float, float]],
-    coeffs: dict[tuple[int, int], np.ndarray],
+    coeffs: dict[tuple[int, int], NDArray],
     obasis: MolecularBasis,
     restricted: bool,
 ):

iodata/formats/cube.py

@@ -29,6 +29,7 @@
 from typing import TextIO
 
 import numpy as np
+from numpy.typing import NDArray
 
 from ..docstrings import document_dump_one, document_load_one
 from ..iodata import IOData
@@ -42,7 +43,7 @@
 
 def _read_cube_header(
     lit: LineIterator,
-) -> tuple[str, np.ndarray, np.ndarray, np.ndarray, dict[str, np.ndarray], np.ndarray]:
+) -> tuple[str, NDArray, NDArray, NDArray, dict[str, NDArray], NDArray]:
     """Load header data from a CUBE file object.
 
     Parameters
@@ -62,7 +63,7 @@ def _read_cube_header(
     # skip the second line
     next(lit)
 
-    def read_grid_line(line: str) -> tuple[int, np.ndarray]:
+    def read_grid_line(line: str) -> tuple[int, NDArray]:
         """Read a grid line from the cube file."""
         words = line.split()
         return (
@@ -83,7 +84,7 @@ def read_grid_line(line: str) -> tuple[int, np.ndarray]:
     cellvecs = axes * shape.reshape(-1, 1)
     cube = {"origin": origin, "axes": axes, "shape": shape}
 
-    def read_atom_line(line: str) -> tuple[int, float, np.ndarray]:
+    def read_atom_line(line: str) -> tuple[int, float, NDArray]:
         """Read an atomic number and coordinate from the cube file."""
         words = line.split()
         return (
@@ -106,7 +107,7 @@ def read_atom_line(line: str) -> tuple[int, float, np.ndarray]:
     return title, atcoords, atnums, cellvecs, cube, atcorenums
 
 
-def _read_cube_data(lit: LineIterator, cube: dict[str, np.ndarray]):
+def _read_cube_data(lit: LineIterator, cube: dict[str, NDArray]):
     """Load cube data from a CUBE file object.
 
     Parameters
@@ -150,10 +151,10 @@ def load_one(lit: LineIterator) -> dict:
 def _write_cube_header(
     f: TextIO,
     title: str,
-    atcoords: np.ndarray,
-    atnums: np.ndarray,
-    cube: dict[str, np.ndarray],
-    atcorenums: np.ndarray,
+    atcoords: NDArray,
+    atnums: NDArray,
+    cube: dict[str, NDArray],
+    atcorenums: NDArray,
 ):
     print(title, file=f)
     print("OUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z", file=f)
@@ -169,7 +170,7 @@ def _write_cube_header(
         print(f"{atnums[i]:5d} {q: 11.6f} {x: 11.6f} {y: 11.6f} {z: 11.6f}", file=f)
 
 
-def _write_cube_data(f: TextIO, cube_data: np.ndarray, block_size: int):
+def _write_cube_data(f: TextIO, cube_data: NDArray, block_size: int):
     counter = 0
     for value in cube_data.flat:
         f.write(f" {value: 12.5E}")

iodata/formats/fchk.py

@@ -23,6 +23,7 @@
 from typing import Optional, TextIO
 
 import numpy as np
+from numpy.typing import NDArray
 
 from ..basis import HORTON2_CONVENTIONS, MolecularBasis, Shell, convert_conventions
 from ..docstrings import document_dump_one, document_load_many, document_load_one
@@ -473,7 +474,7 @@ def _load_dm(label: str, fchk: dict, result: dict, key: str):
         result[key] = _triangle_to_dense(fchk[label])
 
 
-def _triangle_to_dense(triangle: np.ndarray) -> np.ndarray:
+def _triangle_to_dense(triangle: NDArray) -> NDArray:
     """Convert a symmetric matrix in triangular storage to a dense square matrix.
 
     Parameters
@@ -512,7 +513,7 @@ def _dump_real_scalars(name: str, val: float, f: TextIO):
     print(f"{name:40}   R     {float(val): 16.8E}", file=f)
 
 
-def _dump_integer_arrays(name: str, val: np.ndarray, f: TextIO):
+def _dump_integer_arrays(name: str, val: NDArray, f: TextIO):
     """Dumper for a array of integers."""
     nval = val.size
     if nval != 0:
@@ -527,7 +528,7 @@ def _dump_integer_arrays(name: str, val: np.ndarray, f: TextIO):
                 k = 0
 
 
-def _dump_real_arrays(name: str, val: np.ndarray, f: TextIO):
+def _dump_real_arrays(name: str, val: NDArray, f: TextIO):
     """Dumper for a array of float."""
     nval = val.size
     if nval != 0:

iodata/formats/gamess.py

@@ -19,6 +19,7 @@
 """GAMESS punch file format."""
 
 import numpy as np
+from numpy.typing import NDArray
 
 from ..docstrings import document_load_one
 from ..utils import LineIterator, angstrom
@@ -29,7 +30,7 @@
 PATTERNS = ["*.dat"]
 
 
-def _read_data(lit: LineIterator) -> tuple:
+def _read_data(lit: LineIterator) -> tuple[str, str, list[str]]:
     """Extract ``title``, ``symmetry`` and ``symbols`` from the punch file."""
     title = next(lit).strip()
     symmetry = next(lit).split()[0]
@@ -46,7 +47,7 @@ def _read_data(lit: LineIterator) -> tuple:
     return title, symmetry, symbols
 
 
-def _read_coordinates(lit: LineIterator, result: dict) -> tuple:
+def _read_coordinates(lit: LineIterator, result: dict[str]) -> tuple[NDArray, NDArray]:
     """Extract ``numbers`` and ``coordinates`` from the punch file."""
     for _ in range(2):
         next(lit)
@@ -67,7 +68,7 @@ def _read_coordinates(lit: LineIterator, result: dict) -> tuple:
     return numbers, coordinates
 
 
-def _read_energy(lit: LineIterator, result: dict) -> tuple:
+def _read_energy(lit: LineIterator, result: dict[str]) -> tuple[float, NDArray]:
     """Extract ``energy`` and ``gradient`` from the punch file."""
     energy = float(next(lit).split()[1])
     natom = len(result["symbols"])
@@ -81,7 +82,7 @@ def _read_energy(lit: LineIterator, result: dict) -> tuple:
     return energy, gradient
 
 
-def _read_hessian(lit: LineIterator, result: dict) -> np.ndarray:
+def _read_hessian(lit: LineIterator, result: dict[str]) -> NDArray:
     """Extract ``hessian`` from the punch file."""
     # check that $HESS is not already parsed
     if "athessian" in result:
@@ -102,7 +103,7 @@ def _read_hessian(lit: LineIterator, result: dict) -> np.ndarray:
     return hessian
 
 
-def _read_masses(lit: LineIterator, result: dict) -> np.ndarray:
+def _read_masses(lit: LineIterator, result: dict[str]) -> NDArray:
     """Extract ``masses`` from the punch file."""
     natom = len(result["symbols"])
     masses = np.zeros(natom, float)
@@ -119,7 +120,7 @@ def _read_masses(lit: LineIterator, result: dict) -> np.ndarray:
     "PUNCH",
     ["title", "energy", "grot", "atgradient", "athessian", "atmasses", "atnums", "atcoords"],
 )
-def load_one(lit: LineIterator) -> dict:
+def load_one(lit: LineIterator) -> dict[str]:
     """Do not edit this docstring. It will be overwritten."""
     result = {}
     while True:

iodata/formats/gaussianlog.py

@@ -28,6 +28,7 @@
 """
 
 import numpy as np
+from numpy.typing import NDArray
 
 from ..docstrings import document_load_one
 from ..utils import LineIterator, set_four_index_element
@@ -73,7 +74,7 @@ def load_one(lit: LineIterator) -> dict:
     return result
 
 
-def _load_twoindex_g09(lit: LineIterator, nbasis: int) -> np.ndarray:
+def _load_twoindex_g09(lit: LineIterator, nbasis: int) -> NDArray:
     """Load a two-index operator from a GAUSSIAN LOG file format.
 
     Parameters
@@ -106,7 +107,7 @@ def _load_twoindex_g09(lit: LineIterator, nbasis: int) -> np.ndarray:
     return result
 
 
-def _load_fourindex_g09(lit: LineIterator, nbasis: int) -> np.ndarray:
+def _load_fourindex_g09(lit: LineIterator, nbasis: int) -> NDArray:
     """Load a four-index operator from a GAUSSIAN LOG file.
 
     Parameters

iodata/formats/mol2.py

@@ -26,6 +26,7 @@
 from typing import TextIO
 
 import numpy as np
+from numpy.typing import NDArray
 
 from ..docstrings import (
     document_dump_many,
@@ -83,9 +84,7 @@ def load_one(lit: LineIterator) -> dict:
     return result
 
 
-def _load_helper_atoms(
-    lit: LineIterator, natoms: int
-) -> tuple[np.ndarray, np.ndarray, np.ndarray, tuple]:
+def _load_helper_atoms(lit: LineIterator, natoms: int) -> tuple[NDArray, NDArray, NDArray, tuple]:
     """Load element numbers, coordinates and atomic charges."""
     atnums = np.empty(natoms)
     atcoords = np.empty((natoms, 3))
@@ -112,7 +111,7 @@ def _load_helper_atoms(
     return atnums, atcoords, atchgs, attypes
 
 
-def _load_helper_bonds(lit: LineIterator, nbonds: int) -> tuple[np.ndarray]:
+def _load_helper_bonds(lit: LineIterator, nbonds: int) -> NDArray:
     """Load bond information.
 
     Each line in a bond definition has the following structure