Fix linters and installation using editable mode

gbasis/base_four_symm.py

@@ -2,9 +2,10 @@
 import abc
 import itertools as it
 
+import numpy as np
+
 from gbasis.base import BaseGaussianRelatedArray
 from gbasis.spherical import generate_transformation
-import numpy as np
 
 
 # pylint: disable=W0235

gbasis/base_one.py

@@ -1,9 +1,10 @@
 """Base class for arrays that depend on one contracted Gaussian."""
 import abc
 
+import numpy as np
+
 from gbasis.base import BaseGaussianRelatedArray
 from gbasis.spherical import generate_transformation
-import numpy as np
 
 
 # pylint: disable=W0235

gbasis/base_two_asymm.py

@@ -1,9 +1,10 @@
 """Base class for arrays that depend on two contracted Gaussians."""
 import abc
 
+import numpy as np
+
 from gbasis.base import BaseGaussianRelatedArray
 from gbasis.spherical import generate_transformation
-import numpy as np
 
 
 # pylint: disable=W0235

gbasis/base_two_symm.py

@@ -1,9 +1,10 @@
 """Base class for arrays that depend on two contracted Gaussians."""
 import abc
 
+import numpy as np
+
 from gbasis.base import BaseGaussianRelatedArray
 from gbasis.spherical import generate_transformation
-import numpy as np
 
 
 # pylint: disable=W0235

gbasis/contractions.py

@@ -1,7 +1,8 @@
 """Data class for contractions of Gaussian-type primitives."""
-from gbasis.utils import factorial2
 import numpy as np
 
+from gbasis.utils import factorial2
+
 
 class GeneralizedContractionShell:
     r"""Data class for generalized contractions.
@@ -384,8 +385,8 @@ def angmom_components_sph(self):
 
         """
         return tuple(
-            ["s{}".format(m) for m in range(self.angmom, 0, -1)]
-            + ["c{}".format(m) for m in range(self.angmom + 1)]
+            [f"s{m}" for m in range(self.angmom, 0, -1)]
+            + [f"c{m}" for m in range(self.angmom + 1)]
         )
 
     @property

gbasis/evals/density.py

@@ -1,9 +1,10 @@
 """Density Evaluation."""
-from gbasis.evals.eval import evaluate_basis
-from gbasis.evals.eval_deriv import evaluate_deriv_basis
 import numpy as np
 from scipy.special import comb
 
+from gbasis.evals.eval import evaluate_basis
+from gbasis.evals.eval_deriv import evaluate_deriv_basis
+
 
 def evaluate_density_using_evaluated_orbs(one_density_matrix, orb_eval):
     """Return the evaluation of the density given the evaluated orbitals.

gbasis/evals/electrostatic_potential.py

@@ -1,7 +1,8 @@
 """Module for computing electrostatic potential integrals."""
-from gbasis.integrals.point_charge import point_charge_integral
 import numpy as np
 
+from gbasis.integrals.point_charge import point_charge_integral
+
 
 def electrostatic_potential(
     basis,

gbasis/evals/eval.py

@@ -1,8 +1,9 @@
 """Functions for evaluating Gaussian contractions."""
+import numpy as np
+
 from gbasis.base_one import BaseOneIndex
 from gbasis.contractions import GeneralizedContractionShell
 from gbasis.evals._deriv import _eval_deriv_contractions
-import numpy as np
 
 
 class Eval(BaseOneIndex):

gbasis/evals/eval_deriv.py

@@ -1,8 +1,9 @@
 """Functions for evaluating Gaussian primitives."""
+import numpy as np
+
 from gbasis.base_one import BaseOneIndex
 from gbasis.contractions import GeneralizedContractionShell
 from gbasis.evals._deriv import _eval_deriv_contractions
-import numpy as np
 
 
 class EvalDeriv(BaseOneIndex):

gbasis/evals/stress_tensor.py

@@ -1,10 +1,11 @@
 """Module for computing properties related to the stress tensor."""
+import numpy as np
+
 from gbasis.evals.density import (
     evaluate_density_laplacian,
     evaluate_deriv_density,
     evaluate_deriv_reduced_density_matrix,
 )
-import numpy as np
 
 
 # TODO: need to be tested against reference
@@ -163,7 +164,8 @@ def evaluate_ehrenfest_force(
             - (1 - 2\alpha)
             \sum_i
             \left.
-              \frac{\partial^3}{\partial r_i \partial r_j \partial r'_i} \gamma(\mathbf{r}, \mathbf{r})
+            \frac{\partial^3}{\partial r_i \partial r_j \partial r'_i} \gamma(\mathbf{r},
+            \mathbf{r})
             \right|_{\mathbf{r} = \mathbf{r}' = \mathbf{r}_n}\\
             &+ \frac{1}{2} \beta
             \left.

gbasis/integrals/_diff_operator_int.py

@@ -1,9 +1,10 @@
 """Integrals over differential operator involving contracted Cartesian Gaussians."""
+import numpy as np
+
 from gbasis.integrals._moment_int import (
     _cleanup_intermediate_integrals,
     _compute_multipole_moment_integrals_intermediate,
 )
-import numpy as np
 
 
 # FIXME: returns nan when exponent is zero

gbasis/integrals/_one_elec_int.py

@@ -1,5 +1,6 @@
 """One-electron integrals involving Contracted Cartesian Gaussians."""
 import numpy as np
+
 from gbasis.utils import factorial2
 
 

gbasis/integrals/_two_elec_int.py

@@ -1,5 +1,6 @@
 """Two-electron integrals involving Contracted Cartesian Gaussians."""
 import numpy as np
+
 from gbasis.utils import factorial2
 
 # pylint: disable=C0103,R0914,R0915

gbasis/integrals/angular_momentum.py

@@ -1,11 +1,12 @@
 """Module for evaluating the integral over the angular momentum operator."""
+import numpy as np
+
 from gbasis.base_two_symm import BaseTwoIndexSymmetric
 from gbasis.contractions import GeneralizedContractionShell
 from gbasis.integrals._diff_operator_int import (
     _compute_differential_operator_integrals_intermediate,
 )
 from gbasis.integrals._moment_int import _compute_multipole_moment_integrals_intermediate
-import numpy as np
 
 
 # TODO: need to test against reference

gbasis/integrals/electron_repulsion.py

@@ -1,12 +1,13 @@
 """Electron-electron repulsion integral."""
+import numpy as np
+
 from gbasis.base_four_symm import BaseFourIndexSymmetric
 from gbasis.contractions import GeneralizedContractionShell
 from gbasis.integrals._two_elec_int import (
     _compute_two_elec_integrals,
     _compute_two_elec_integrals_angmom_zero,
 )
 from gbasis.integrals.point_charge import PointChargeIntegral
-import numpy as np
 
 
 class ElectronRepulsionIntegral(BaseFourIndexSymmetric):

gbasis/integrals/kinetic_energy.py

@@ -1,8 +1,9 @@
 """Module for evaluating the kinetic energy integral."""
+import numpy as np
+
 from gbasis.base_two_symm import BaseTwoIndexSymmetric
 from gbasis.contractions import GeneralizedContractionShell
 from gbasis.integrals._diff_operator_int import _compute_differential_operator_integrals
-import numpy as np
 
 
 class KineticEnergyIntegral(BaseTwoIndexSymmetric):

gbasis/integrals/moment.py

@@ -1,8 +1,9 @@
 """Module for computing the moments of a basis set."""
+import numpy as np
+
 from gbasis.base_two_symm import BaseTwoIndexSymmetric
 from gbasis.contractions import GeneralizedContractionShell
 from gbasis.integrals._moment_int import _compute_multipole_moment_integrals
-import numpy as np
 
 
 class Moment(BaseTwoIndexSymmetric):

gbasis/integrals/momentum.py

@@ -1,8 +1,9 @@
 """Module for evaluating the integral over the momentum operator."""
+import numpy as np
+
 from gbasis.base_two_symm import BaseTwoIndexSymmetric
 from gbasis.contractions import GeneralizedContractionShell
 from gbasis.integrals._diff_operator_int import _compute_differential_operator_integrals
-import numpy as np
 
 
 # TODO: need to test against reference

gbasis/integrals/nuclear_electron_attraction.py

@@ -1,7 +1,8 @@
 """Module for computing the nuclear electron attraction."""
-from gbasis.integrals.point_charge import point_charge_integral
 import numpy as np
 
+from gbasis.integrals.point_charge import point_charge_integral
+
 
 def nuclear_electron_attraction_integral(
     basis, nuclear_coords, nuclear_charges, transform=None, coord_type="spherical"

gbasis/integrals/overlap.py

@@ -1,8 +1,9 @@
 """Functions for computing overlap of a basis set."""
+import numpy as np
+
 from gbasis.base_two_symm import BaseTwoIndexSymmetric
 from gbasis.contractions import GeneralizedContractionShell
 from gbasis.integrals._moment_int import _compute_multipole_moment_integrals
-import numpy as np
 
 
 class Overlap(BaseTwoIndexSymmetric):

gbasis/integrals/point_charge.py

@@ -1,9 +1,10 @@
 """Module for computing point charge integrals."""
+import numpy as np
+from scipy.special import hyp1f1  # pylint: disable=E0611
+
 from gbasis.base_two_symm import BaseTwoIndexSymmetric
 from gbasis.contractions import GeneralizedContractionShell
 from gbasis.integrals._one_elec_int import _compute_one_elec_integrals
-import numpy as np
-from scipy.special import hyp1f1  # pylint: disable=E0611
 
 
 class PointChargeIntegral(BaseTwoIndexSymmetric):
@@ -37,7 +38,9 @@ class PointChargeIntegral(BaseTwoIndexSymmetric):
         Boys function used to evaluate the one-electron integral.
         `M` is the number of orders that will be evaluated.
         `K_a` and `K_b` are the number of primitives on the left and right side, respectively.
-    construct_array_contraction(self, contractions_one, contractions_two, points_coords, points_charge)
+    construct_array_contraction(self, contractions_one, contractions_two, points_coords,
+        **points_charge)**
+
         Return the point charge integrals for the given `GeneralizedContractionShell` instances.
         `M_1` is the number of segmented contractions with the same exponents (and angular
         momentum) associated with the first index.

gbasis/parsers.py

@@ -1,9 +1,10 @@
 """Parsers for reading basis set files."""
 import re
 
-from gbasis.contractions import GeneralizedContractionShell
 import numpy as np
 
+from gbasis.contractions import GeneralizedContractionShell
+
 
 def parse_nwchem(nwchem_basis_file):
     """Parse nwchem basis set file.
@@ -26,7 +27,7 @@ def parse_nwchem(nwchem_basis_file):
 
     """
     # pylint: disable=R0914
-    with open(nwchem_basis_file, "r") as basis_fh:
+    with open(nwchem_basis_file) as basis_fh:
         nwchem_basis = basis_fh.read()
 
     data = re.split(r"\n\s*(\w[\w]?)[ ]+(\w+)\s*\n", nwchem_basis)
@@ -97,7 +98,7 @@ def parse_gbs(gbs_basis_file):
 
     """
     # pylint: disable=R0914
-    with open(gbs_basis_file, "r") as basis_fh:
+    with open(gbs_basis_file) as basis_fh:
         gbs_basis = basis_fh.read()
     # splits file into 'element', 'basis stuff', 'element',' basis stuff'
     # e.g., ['H','stuff with exponents & coefficients\n', 'C', 'stuff with etc\n']

gbasis/spherical.py

@@ -4,6 +4,7 @@
 
 import numpy as np
 from scipy.special import comb, factorial
+
 from gbasis.utils import factorial2
 
 
@@ -45,7 +46,8 @@ def expansion_coeff(angmom, mag, i, j, k):
         C^{angmom,mag,i,j,k} = -1^{i + k - \text{shift_factor}} * (1/4)^i * {angmom \choose i}
         * {(angmom - i) \choose (|mag| + i)} * {i \choose j} * {|mag| \choose 2 * k},
 
-    where :math:`shift_factor = 0` if :math:`mag >= 0` and :math:`shift_factor = 1/2` if :math:`mag < 0`    .
+    where :math:`shift_factor = 0` if :math:`mag >= 0` and :math:`shift_factor = 1/2`
+    if :math:`mag < 0`.
 
     Parameters
     ----------
@@ -122,7 +124,8 @@ def harmonic_norm(angmom, mag):
     Calculate the normalization constant of a real solid harmonic.
 
     .. math::
-        N^S_{angmom,m} = 1/(2^{|m|} * angmom!) * \sqrt{2 * (angmom + |{m}|)! * (angmom - |{m}|)! / 2^{\delta_0^m}},
+        N^S_{angmom,m} = 1/(2^{|m|} * angmom!) * \sqrt{2 * (angmom + |{m}|)! * (angmom - |{m}|)! /
+        2^{\delta_0^m}},
 
     where :math: `del{0, m}` is the Kronecker delta of 0 and m.
 
@@ -301,8 +304,8 @@ def generate_transformation(angmom, cartesian_order, spherical_order, apply_from
         # Strip out "-" from the ordering to make sure the right components are there
         and {x.replace("-", "") for x in spherical_order}
         == set(
-            ["s{}".format(m) for m in range(angmom, 0, -1)]
-            + ["c{}".format(m) for m in range(angmom + 1)]
+            [f"s{m}" for m in range(angmom, 0, -1)]
+            + [f"c{m}" for m in range(angmom + 1)]
         )
     ):
         raise ValueError(

gbasis/wrappers.py

@@ -1,7 +1,8 @@
 """Module for interfacing to other quantum chemistry packages."""
-from gbasis.contractions import GeneralizedContractionShell
 import numpy as np
 
+from gbasis.contractions import GeneralizedContractionShell
+
 
 def from_iodata(mol):
     """Return basis set stored within the `IOData` instance in `iodata`.
@@ -115,15 +116,15 @@ def angmom_components_sph(self):
             if self.angmom not in sph_conventions:
                 raise ValueError(
                     "Given convention does not support spherical contractions for the angular "
-                    "momentum {0}".format(self.angmom)
+                    f"momentum {self.angmom}"
                 )
 
             return tuple(sph_conventions[self.angmom])
 
     if molbasis.primitive_normalization != "L2":  # pragma: no cover
         raise ValueError(
             "Only L2 normalization scheme is supported in `gbasis`. Given `IOData` instance uses "
-            "primitive normalization scheme, {}".format(molbasis.primitive_normalization)
+            f"primitive normalization scheme, {molbasis.primitive_normalization}"
         )
 
     basis = []

pyproject.toml

@@ -38,6 +38,10 @@ dependencies = [
 ]
 dynamic = ["version"]
 
+[tool.setuptools.packages.find]
+where = ["."]  # list of folders that contain the packages (["."] by default)
+include = ["gbasis"]  # package names should match these glob patterns (["*"] by default)
+
 [project.urls]
 Documentation = "https://gbasis.qcdevs.org"
 Issues = "https://github.com/theochem/gbasis/issues"
@@ -76,7 +80,7 @@ line-length = 100
 # RUF is Ruff-specific rules
 select = ["E", "F", "UP", "B", "I", "PGH", "PL", "RUF"]
 line-length = 100
-ignore = ["PLR2004", "PLR0913", "PLR0912", "PLW2901", "PLR0915", "RUF013"]
+ignore = ["PLR2004", "PLR0913", "PLR0912", "PLW2901", "PLR0915", "RUF013", "E741"]
 extend-exclude = ["doc/*", "doc/*/*"]
 
 [tool.pytest.ini_options]