[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

gbasis/contractions.py

@@ -519,14 +519,17 @@ def coord_type(self, coord_type):
                 - 'spherical'
         """
 
-
         if not isinstance(coord_type, str):
             raise TypeError("Coordinate type must be given as a string.")
         if coord_type not in ["c", "cartesian", "p", "spherical"]:
-            raise ValueError("`coord_type` is incorrectly specified. It must be either 'c' "
-                             "or 'cartesian' for Cartesian coordinates, or 'p' or 'spherical' "
-                             "for spherical coordinates.")
-        self._coord_type = {"c": "cartesian",
-                            "cartesian": "cartesian",
-                            "spherical": "spherical",
-                            "p": "spherical"}[coord_type]
+            raise ValueError(
+                "`coord_type` is incorrectly specified. It must be either 'c' "
+                "or 'cartesian' for Cartesian coordinates, or 'p' or 'spherical' "
+                "for spherical coordinates."
+            )
+        self._coord_type = {
+            "c": "cartesian",
+            "cartesian": "cartesian",
+            "spherical": "spherical",
+            "p": "spherical",
+        }[coord_type]

gbasis/evals/stress_tensor.py

@@ -9,9 +9,7 @@
 
 
 # TODO: need to be tested against reference
-def evaluate_stress_tensor(
-    one_density_matrix, basis, points, alpha=1, beta=0, transform=None
-):
+def evaluate_stress_tensor(one_density_matrix, basis, points, alpha=1, beta=0, transform=None):
     r"""Return the stress tensor evaluated at the given coordinates.
 
     Stress tensor is defined here as:
@@ -129,9 +127,7 @@ def evaluate_stress_tensor(
 
 
 # TODO: need to be tested against reference
-def evaluate_ehrenfest_force(
-    one_density_matrix, basis, points, alpha=1, beta=0, transform=None
-):
+def evaluate_ehrenfest_force(one_density_matrix, basis, points, alpha=1, beta=0, transform=None):
     r"""Return the Ehrenfest force.
 
     Ehrenfest force is the negative of the divergence of the stress tensor:

gbasis/integrals/electron_repulsion.py

@@ -204,9 +204,7 @@ def construct_array_contraction(cls, cont_one, cont_two, cont_three, cont_four):
         return integrals
 
 
-def electron_repulsion_integral(
-    basis, transform=None, notation="physicist"
-):
+def electron_repulsion_integral(basis, transform=None, notation="physicist"):
     """Return the electron repulsion integrals fo the given basis set.
 
     Parameters

gbasis/integrals/nuclear_electron_attraction.py

@@ -4,9 +4,7 @@
 from gbasis.integrals.point_charge import point_charge_integral
 
 
-def nuclear_electron_attraction_integral(
-    basis, nuclear_coords, nuclear_charges, transform=None
-):
+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.
 
     Parameters
@@ -33,8 +31,6 @@ def nuclear_electron_attraction_integral(
 
     """
     return np.sum(
-        point_charge_integral(
-            basis, nuclear_coords, nuclear_charges, transform=transform
-        ),
+        point_charge_integral(basis, nuclear_coords, nuclear_charges, transform=transform),
         axis=2,
     )

gbasis/integrals/point_charge.py

@@ -269,9 +269,7 @@ def construct_array_contraction(
         return output
 
 
-def point_charge_integral(
-    basis, points_coords, points_charge, transform=None
-):
+def point_charge_integral(basis, points_coords, points_charge, transform=None):
     r"""Return the point-charge interaction integrals of basis set in the given coordinate systems.
 
     Parameters

tests/test_angular_momentum.py

@@ -15,10 +15,10 @@
 def test_angular_momentum_construct_array_contraction():
     """Test integrals.angular_momentum.angular_momentumIntegral.construct_array_contraction."""
     test_one = GeneralizedContractionShell(
-        1, np.array([0.5, 1, 1.5]), np.array([1.0, 2.0]), np.array([0.1, 0.01]), 'spherical'
+        1, np.array([0.5, 1, 1.5]), np.array([1.0, 2.0]), np.array([0.1, 0.01]), "spherical"
     )
     test_two = GeneralizedContractionShell(
-        2, np.array([1.5, 2, 3]), np.array([3.0, 4.0]), np.array([0.2, 0.02]), 'spherical'
+        2, np.array([1.5, 2, 3]), np.array([3.0, 4.0]), np.array([0.2, 0.02]), "spherical"
     )
 
     # copied the code it is testing
@@ -370,7 +370,7 @@ def test_angular_momentum_construct_array_contraction():
 def test_angular_momentum_integral_cartesian():
     """Test gbasis.integrals.angular_momentum.angular_momentum_integral_cartesian."""
     basis_dict = parse_nwchem(find_datafile("data_sto6g.nwchem"))
-    basis = make_contractions(basis_dict, ["Kr"], np.array([[0, 0, 0]]), 'cartesian')
+    basis = make_contractions(basis_dict, ["Kr"], np.array([[0, 0, 0]]), "cartesian")
     angular_momentum_integral_obj = AngularMomentumIntegral(basis)
     assert np.allclose(
         angular_momentum_integral_obj.construct_array_cartesian(),
@@ -382,7 +382,7 @@ def test_angular_momentum_integral_spherical():
     """Test gbasis.integrals.angular_momentum.angular_momentum_integral_spherical."""
     basis_dict = parse_nwchem(find_datafile("data_sto6g.nwchem"))
 
-    basis = make_contractions(basis_dict, ["Kr"], np.array([[0, 0, 0]]), 'spherical')
+    basis = make_contractions(basis_dict, ["Kr"], np.array([[0, 0, 0]]), "spherical")
     angular_momentum_integral_obj = AngularMomentumIntegral(basis)
     assert np.allclose(
         angular_momentum_integral_obj.construct_array_spherical(),
@@ -394,7 +394,7 @@ def test_angular_momentum_integral_mix():
     """Test gbasis.integrals.angular_momentum.angular_momentum_integral_mix."""
     basis_dict = parse_nwchem(find_datafile("data_sto6g.nwchem"))
 
-    basis = make_contractions(basis_dict, ["Kr"], np.array([[0, 0, 0]]), ['spherical'] * 8)
+    basis = make_contractions(basis_dict, ["Kr"], np.array([[0, 0, 0]]), ["spherical"] * 8)
     angular_momentum_integral_obj = AngularMomentumIntegral(basis)
     assert np.allclose(
         angular_momentum_integral_obj.construct_array_mix(["spherical"] * 8),
@@ -405,7 +405,7 @@ def test_angular_momentum_integral_mix():
 def test_angular_momentum_integral_lincomb():
     """Test gbasis.integrals.angular_momentum.angular_momentum_integral_lincomb."""
     basis_dict = parse_nwchem(find_datafile("data_sto6g.nwchem"))
-    basis = make_contractions(basis_dict, ["Kr"], np.array([[0, 0, 0]]), 'spherical')
+    basis = make_contractions(basis_dict, ["Kr"], np.array([[0, 0, 0]]), "spherical")
     angular_momentum_integral_obj = AngularMomentumIntegral(basis)
     transform = np.random.rand(14, 18)
     assert np.allclose(

tests/test_base.py

@@ -11,7 +11,9 @@ def test_init():
     """Test base.BaseGaussianRelatedArray."""
     Test = disable_abstract(BaseGaussianRelatedArray)
     test = skip_init(Test)
-    contractions = GeneralizedContractionShell(1, np.array([1, 2, 3]), np.ones(1), np.ones(1), 'spherical')
+    contractions = GeneralizedContractionShell(
+        1, np.array([1, 2, 3]), np.ones(1), np.ones(1), "spherical"
+    )
     assert not hasattr(test, "_axes_contractions")
     with pytest.raises(TypeError):
         Test.__init__(test, set([contractions]))
@@ -39,7 +41,9 @@ def test_contruct_array_contraction():
             "construct_array_contraction": BaseGaussianRelatedArray.construct_array_contraction
         },
     )
-    contractions = GeneralizedContractionShell(1, np.array([1, 2, 3]), np.ones(1), np.ones(1), 'spherical')
+    contractions = GeneralizedContractionShell(
+        1, np.array([1, 2, 3]), np.ones(1), np.ones(1), "spherical"
+    )
     with pytest.raises(TypeError):
         Test([contractions])
 
@@ -53,7 +57,9 @@ def test_contruct_array_cartesian():
             "construct_array_cartesian": BaseGaussianRelatedArray.construct_array_cartesian
         },
     )
-    contractions = GeneralizedContractionShell(1, np.array([1, 2, 3]), np.ones(1), np.ones(1), 'spherical')
+    contractions = GeneralizedContractionShell(
+        1, np.array([1, 2, 3]), np.ones(1), np.ones(1), "spherical"
+    )
     with pytest.raises(TypeError):
         Test([contractions])
 
@@ -67,7 +73,9 @@ def test_contruct_array_spherical():
             "construct_array_spherical": BaseGaussianRelatedArray.construct_array_spherical
         },
     )
-    contractions = GeneralizedContractionShell(1, np.array([1, 2, 3]), np.ones(1), np.ones(1), 'spherical')
+    contractions = GeneralizedContractionShell(
+        1, np.array([1, 2, 3]), np.ones(1), np.ones(1), "spherical"
+    )
     with pytest.raises(TypeError):
         Test([contractions])
 
@@ -81,6 +89,8 @@ def test_contruct_array_lincomb():
             "construct_array_lincomb": BaseGaussianRelatedArray.construct_array_lincomb
         },
     )
-    contractions = GeneralizedContractionShell(1, np.array([1, 2, 3]), np.ones(1), np.ones(1), 'spherical')
+    contractions = GeneralizedContractionShell(
+        1, np.array([1, 2, 3]), np.ones(1), np.ones(1), "spherical"
+    )
     with pytest.raises(TypeError):
         Test([contractions])

tests/test_base_four_symm.py

@@ -12,7 +12,9 @@ def test_init():
     """Test BaseFourIndexSymmetric.__init__."""
     Test = disable_abstract(BaseFourIndexSymmetric)
     test = skip_init(Test)
-    contractions = GeneralizedContractionShell(1, np.array([1, 2, 3]), np.ones(1), np.ones(1), 'spherical')
+    contractions = GeneralizedContractionShell(
+        1, np.array([1, 2, 3]), np.ones(1), np.ones(1), "spherical"
+    )
     Test.__init__(test, [contractions])
     assert test._axes_contractions[0][0] == contractions
     with pytest.raises(TypeError):
@@ -22,7 +24,7 @@ def test_init():
 def test_contractions():
     """Test BaseFourIndexSymmetric.contractions."""
     Test = disable_abstract(BaseFourIndexSymmetric)
-    cont = GeneralizedContractionShell(1, np.array([1, 2, 3]), np.ones(1), np.ones(1), 'spherical')
+    cont = GeneralizedContractionShell(1, np.array([1, 2, 3]), np.ones(1), np.ones(1), "spherical")
     test = Test([cont])
     assert test.contractions[0] == cont
 
@@ -36,15 +38,21 @@ def test_construct_array_contraction():
             "construct_array_contraction": BaseFourIndexSymmetric.construct_array_contraction
         },
     )
-    contractions = GeneralizedContractionShell(1, np.array([1, 2, 3]), np.ones(1), np.ones(1), 'spherical')
+    contractions = GeneralizedContractionShell(
+        1, np.array([1, 2, 3]), np.ones(1), np.ones(1), "spherical"
+    )
     with pytest.raises(TypeError):
         Test([contractions])
 
 
 def test_construct_array_cartesian():
     """Test BaseFourIndexSymmetric.construct_array_cartesian."""
-    cont_one = GeneralizedContractionShell(1, np.array([1, 2, 3]), np.ones((1, 1)), np.ones(1), 'spherical')
-    cont_two = GeneralizedContractionShell(2, np.array([2, 3, 4]), np.ones((1, 1)), 2 * np.ones(1), 'spherical')
+    cont_one = GeneralizedContractionShell(
+        1, np.array([1, 2, 3]), np.ones((1, 1)), np.ones(1), "spherical"
+    )
+    cont_two = GeneralizedContractionShell(
+        2, np.array([2, 3, 4]), np.ones((1, 1)), 2 * np.ones(1), "spherical"
+    )
     Test = disable_abstract(
         BaseFourIndexSymmetric,
         dict_overwrite={
@@ -92,7 +100,9 @@ def test_construct_array_cartesian():
 
 def test_construct_array_spherical():
     """Test BaseFourIndexSymmetric.construct_array_spherical."""
-    contractions = GeneralizedContractionShell(1, np.array([1, 2, 3]), np.ones(1), np.ones(1), 'spherical')
+    contractions = GeneralizedContractionShell(
+        1, np.array([1, 2, 3]), np.ones(1), np.ones(1), "spherical"
+    )
     transform = generate_transformation(
         1, contractions.angmom_components_cart, contractions.angmom_components_sph, "left"
     )
@@ -128,8 +138,12 @@ def test_construct_array_spherical():
     with pytest.raises(TypeError):
         test.construct_array_spherical(bad_keyword=3)
 
-    cont_one = GeneralizedContractionShell(1, np.array([1, 2, 3]), np.ones(1), np.ones(1), 'spherical')
-    cont_two = GeneralizedContractionShell(2, np.array([1, 2, 3]), np.ones(1), np.ones(1), 'spherical')
+    cont_one = GeneralizedContractionShell(
+        1, np.array([1, 2, 3]), np.ones(1), np.ones(1), "spherical"
+    )
+    cont_two = GeneralizedContractionShell(
+        2, np.array([1, 2, 3]), np.ones(1), np.ones(1), "spherical"
+    )
     transform_one = generate_transformation(
         1, cont_one.angmom_components_cart, cont_one.angmom_components_sph, "left"
     )
@@ -401,7 +415,9 @@ def test_construct_array_spherical():
 
 def test_construct_array_mix():
     """Test BaseFourIndex.construct_array_mix."""
-    contractions = GeneralizedContractionShell(1, np.array([1, 2, 3]), np.ones(1), np.ones(1), 'spherical')
+    contractions = GeneralizedContractionShell(
+        1, np.array([1, 2, 3]), np.ones(1), np.ones(1), "spherical"
+    )
 
     Test = disable_abstract(
         BaseFourIndexSymmetric,
@@ -424,8 +440,12 @@ def test_construct_array_mix():
         test.construct_array_cartesian(a=3), test.construct_array_mix(["cartesian"], a=3)
     )
 
-    cont_one = GeneralizedContractionShell(1, np.array([1, 2, 3]), np.ones(1), np.ones(1), 'spherical')
-    cont_two = GeneralizedContractionShell(2, np.array([1, 2, 3]), np.ones(1), np.ones(1), 'spherical')
+    cont_one = GeneralizedContractionShell(
+        1, np.array([1, 2, 3]), np.ones(1), np.ones(1), "spherical"
+    )
+    cont_two = GeneralizedContractionShell(
+        2, np.array([1, 2, 3]), np.ones(1), np.ones(1), "spherical"
+    )
 
     Test = disable_abstract(
         BaseFourIndexSymmetric,
@@ -567,8 +587,12 @@ def construct_array_cont(self, cont_one, cont_two, cont_three, cont_four):
         BaseFourIndexSymmetric,
         dict_overwrite={"construct_array_contraction": construct_array_cont},
     )
-    cont_one = GeneralizedContractionShell(1, np.array([1, 2, 3]), np.ones(1), np.ones(1), 'spherical')
-    cont_two = GeneralizedContractionShell(2, np.array([1, 2, 3]), np.ones(1), np.ones(1), 'spherical')
+    cont_one = GeneralizedContractionShell(
+        1, np.array([1, 2, 3]), np.ones(1), np.ones(1), "spherical"
+    )
+    cont_two = GeneralizedContractionShell(
+        2, np.array([1, 2, 3]), np.ones(1), np.ones(1), "spherical"
+    )
 
     # Remove the dependence on norm constants.
     cont_one.norm_cont = np.ones((1, cont_one.num_cart))
@@ -657,7 +681,9 @@ def construct_array_cont(self, cont_one, cont_two, cont_three, cont_four):
 
 def test_construct_array_lincomb():
     """Test BaseFourIndexSymmetric.construct_array_lincomb."""
-    contractions = GeneralizedContractionShell(1, np.array([1, 2, 3]), np.ones(1), np.ones(1), 'spherical')
+    contractions = GeneralizedContractionShell(
+        1, np.array([1, 2, 3]), np.ones(1), np.ones(1), "spherical"
+    )
     sph_transform = generate_transformation(
         1, contractions.angmom_components_cart, contractions.angmom_components_sph, "left"
     )
@@ -733,8 +759,12 @@ def test_construct_array_lincomb():
             )
         },
     )
-    cont_one = GeneralizedContractionShell(1, np.array([1, 2, 3]), np.ones(1), np.ones(1), 'spherical')
-    cont_two = GeneralizedContractionShell(2, np.array([1, 2, 3]), np.ones(1), np.ones(1), 'spherical')
+    cont_one = GeneralizedContractionShell(
+        1, np.array([1, 2, 3]), np.ones(1), np.ones(1), "spherical"
+    )
+    cont_two = GeneralizedContractionShell(
+        2, np.array([1, 2, 3]), np.ones(1), np.ones(1), "spherical"
+    )
     cont_one.norm_cont = np.ones((1, cont_one.num_cart))
     cont_two.norm_cont = np.ones((1, cont_two.num_cart))
     test = Test([cont_one, cont_two])
@@ -1251,8 +1281,8 @@ def angmom_components_sph(self):
             """Raise error in case undefined conventions are accessed."""
             raise NotImplementedError
 
-    contractions = SpecialShell(1, np.array([1, 2, 3]), np.ones((1, 2)), np.ones(1), 'spherical')
-    Test = disable_abstract( 
+    contractions = SpecialShell(1, np.array([1, 2, 3]), np.ones((1, 2)), np.ones(1), "spherical")
+    Test = disable_abstract(
         BaseFourIndexSymmetric,
         dict_overwrite={
             "construct_array_contraction": (