Fix linters and installation using editable mode

.editorconfig

@@ -1,4 +1,4 @@
-# EditorConfig is awesome: https://EditorConfig.org
+# EditorConfig: https://EditorConfig.org
 
 root = true
 

.github/workflows/pytest.yaml

@@ -9,14 +9,17 @@ on:
   pull_request:
 
 jobs:
-  tests:
+  pytest:
     name: "Python ${{ matrix.py }} on OS ${{ matrix.os }}"
     runs-on: ${{ matrix.os }}
+    env:
+      COVERAGE_SINGLE: 80
+      COVERAGE_TOTAL: 90
 
     strategy:
       matrix:
         os: ["ubuntu-latest", "windows-latest"]
-        py: ["3.7", "3.9", "3.10", "3.11"]
+        py: ["3.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
       - uses: "actions/checkout@v3"
@@ -36,18 +39,6 @@ jobs:
           # Need editable mode in order to include the test files
           pip install -e .
 
-      - name: Run pytest
-        uses: pavelzw/pytest-action@v2
-        with:
-          verbose: true
-          emoji: true
-          job-summary: true
-          click-to-expand: true
-          custom-arguments: "--junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=gbasis"
-          report-title: 'Test Report'
-
-      - name: Pytest coverage comment
-        uses: MishaKav/pytest-coverage-comment@main
-        with:
-          pytest-coverage-path: ./pytest-coverage.txt
-          junitxml-path: ./pytest.xml
+      - name: Run Pytest
+        run: |
+          pytest --cov=./gbasis/ --cov-fail-under=90 --cov-report term .

.pre-commit-config.yaml

@@ -1,3 +1,5 @@
+files: "gbasis/|tests/"
+exclude: "website/"
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.5.0

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

@@ -3,6 +3,8 @@
 import numpy as np
 from gbasis.utils import factorial2
 
+from gbasis.utils import factorial2
+
 
 class GeneralizedContractionShell:
     r"""Data class for generalized contractions.
@@ -496,8 +498,7 @@ 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.
@@ -696,6 +697,10 @@ def evaluate_general_kinetic_energy_density(
     )
     if alpha != 0:
         general_kinetic_energy_density += alpha * evaluate_density_laplacian(
-            one_density_matrix, basis, points, transform=transform, deriv_type=deriv_type
+            one_density_matrix,
+            basis,
+            points,
+            transform=transform,
+            deriv_type=deriv_type,
         )
     return general_kinetic_energy_density

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

@@ -1,9 +1,12 @@
 """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
-from gbasis.evals._deriv import _eval_first_second_order_deriv_contractions
-import numpy as np
+from gbasis.evals._deriv import (
+    _eval_deriv_contractions,
+    _eval_first_second_order_deriv_contractions,
+)
 
 
 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
@@ -149,7 +150,8 @@ def evaluate_ehrenfest_force(one_density_matrix, basis, points, alpha=1, beta=0,
             - (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):
     """Return the nuclear electron attraction integrals of the basis set in the Cartesian form.

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)
@@ -176,12 +177,12 @@ def make_contractions(basis_dict, atoms, coords, coord_types, tol=1e-20, overlap
         Atoms at which the contractions are centered.
     coords : np.ndarray(N, 3)
         Coordinates of each atom.
-    coord_types : {"cartesian"/"c", list/tuple of "cartesian"/"c" or "spherical"/"p", "spherical"/"p"}
+    coord_types: {"cartesian"/"c", list/tuple of "cartesian"/"c", "spherical"/"p", "spherical"/"p"}
         Types of the coordinate system for the contractions.
         If "cartesian" or "c", then all of the contractions are treated as Cartesian contractions.
         If "spherical" or "p", then all of the contractions are treated as spherical contractions.
-        If list/tuple, then each entry must be a "cartesian" (or "c") or "spherical" (or "p") to specify the
-        coordinate type of each `GeneralizedContractionShell` instance.
+        If list/tuple, then each entry must be a "cartesian" (or "c") or "spherical" (or "p") to
+        specify the coordinate type of each `GeneralizedContractionShell` instance.
         Default value is "spherical".
     ovr : bool
         Flag for performing overlap screening between contractions.
@@ -233,8 +234,8 @@ def make_contractions(basis_dict, atoms, coords, coord_types, tol=1e-20, overlap
 
     if len(coord_types) != num_coord_types:
         raise ValueError(
-            f"If coord_types is a list, it must be the same length as the total number of contractions."
-            f"got {len(coord_types)}"
+            f"If coord_types is a list, it must be the same length "
+            f"as the total number of contractions. got {len(coord_types)}"
         )
 
     # make shells