build: changed black lint strategy and versions + code formatting

Author: m-rauen

overreact/_misc.py

@@ -139,7 +139,9 @@ def _derivative(func, x0, dx=1.0, n=1, args=(), order=3):
         msg = "'order' (the number of points used to compute the derivative), must be at least the derivative order 'n' + 1."
         raise ValueError(msg)
     if order % 2 == 0:
-        msg = "'order' (the number of points used to compute the derivative) must be odd."
+        msg = (
+            "'order' (the number of points used to compute the derivative) must be odd."
+        )
         raise ValueError(msg)
 
     # pre-computed for n=1 and 2 and low-order for speed.
@@ -175,6 +177,7 @@ def _derivative(func, x0, dx=1.0, n=1, args=(), order=3):
         val += weights[k] * func(x0 + (k - ho) * dx, *args)
     return val / prod((dx,) * n, axis=0)
 
+
 def make_hashable(obj):
     """
     Given an array, list or set make it immutable by transforming it into a tuple.
@@ -194,10 +197,11 @@ def make_hashable(obj):
     if isinstance(obj, np.ndarray):
         return (tuple(obj.shape), tuple(obj.ravel()))
     elif isinstance(obj, (list, set)):
-            return tuple(make_hashable(item) for item in obj)
+        return tuple(make_hashable(item) for item in obj)
     else:
         return obj
 
+
 def copy_unhashable(maxsize=128, typed=False):
     """
     Cache resultant tuples while handling the received unhashable types (array, list, dictionaries).
@@ -218,6 +222,7 @@ def copy_unhashable(maxsize=128, typed=False):
     function
         A wrapper version of the original function that is cacheable now
     """
+
     def decorator(func):
         @cache(maxsize=maxsize, typed=typed)
         @wraps(func)
@@ -242,7 +247,6 @@ def convert_back(arg):
                             raise ValueError(msg)
                 return arg
 
-
             args = [convert_back(arg) for arg in hashable_args]
             for k, v in hashable_kwargs.items():
                 kwargs[k] = convert_back(v)
@@ -254,14 +258,18 @@ def wrapper(*args, **kwargs):
             wrapper_hashable_kwargs = {}
 
             wrapper_hashable_args = [make_hashable(arg) for arg in args]
-            for k,v in kwargs.items():
+            for k, v in kwargs.items():
                 wrapper_hashable_kwargs[k] = make_hashable(v)
             wrapper_hashable_args = tuple(wrapper_hashable_args)
-            return deepcopy(cached_func(*wrapper_hashable_args, **wrapper_hashable_kwargs))
+            return deepcopy(
+                cached_func(*wrapper_hashable_args, **wrapper_hashable_kwargs),
+            )
 
         return wrapper
+
     return decorator
 
+
 def _find_package(package):
     """Check if a package exists without importing it.
 

overreact/coords.py

@@ -1680,6 +1680,7 @@ def gyradius(atommasses, atomcoords, method="iupac"):
         msg = f"unavailable method: '{method}'"
         raise ValueError(msg)
 
+
 @misc.copy_unhashable()
 def inertia(atommasses, atomcoords, align=True):
     r"""Calculate primary moments and axes from the inertia tensor.

tests/test_rates.py

@@ -1,4 +1,4 @@
-#ruff: noqa: ERA001
+# ruff: noqa: ERA001
 """Tests for rates module."""
 
 from __future__ import annotations
@@ -77,37 +77,38 @@ def test_eyring_calculates_reaction_barrier() -> None:
         temperature=[298.15, 1074.0],
     ) == pytest.approx([1.38, 3.2513e9], 4e-3)
 
+
 # TODO(mrauen): this piece of code tests the old implementation for diffusion controlled reactions. I will implement the new test and change it here.
-#def test_smoluchowski_calculates_diffusion_limited_reaction_rates() -> None:
-    # """Ensure Smoluchowski rates are correct."""
-    # radii = np.array([2.59, 2.71]) * constants.angstrom
-    # assert rx.rates.collins_kimball(
-    #     radii,
-    #     reactive_radius=2.6 * constants.angstrom,
-    #     viscosity=[
-    #         8.90e-4,
-    #         8.54e-4,
-    #         6.94e-4,
-    #         5.77e-4,
-    #         4.90e-4,
-    #         4.22e-4,
-    #         3.69e-4,
-    #     ],
-    #     temperature=[298.15, 300.00, 310.00, 320.00, 330.00, 340.00, 350.00],
-    # ) / constants.liter == pytest.approx(
-    #     [3.6e9, 3.8e9, 4.9e9, 6.0e9, 7.3e9, 8.8e9, 1.0e10],
-    #     4e-2,
-    # )
-
-    # assert rx.rates.collins_kimball(
-    #     radii,
-    #     reactive_radius=2.6 * constants.angstrom,
-    #     viscosity="water",
-    #     temperature=[298.15, 300.00, 310.00, 320.00, 330.00, 340.00, 350.00],
-    # ) / constants.liter == pytest.approx(
-    #     [3.6e9, 3.8e9, 4.9e9, 6.0e9, 7.3e9, 8.8e9, 1.0e10],
-    #     4e-2,
-    # )
+# def test_smoluchowski_calculates_diffusion_limited_reaction_rates() -> None:
+# """Ensure Smoluchowski rates are correct."""
+# radii = np.array([2.59, 2.71]) * constants.angstrom
+# assert rx.rates.collins_kimball(
+#     radii,
+#     reactive_radius=2.6 * constants.angstrom,
+#     viscosity=[
+#         8.90e-4,
+#         8.54e-4,
+#         6.94e-4,
+#         5.77e-4,
+#         4.90e-4,
+#         4.22e-4,
+#         3.69e-4,
+#     ],
+#     temperature=[298.15, 300.00, 310.00, 320.00, 330.00, 340.00, 350.00],
+# ) / constants.liter == pytest.approx(
+#     [3.6e9, 3.8e9, 4.9e9, 6.0e9, 7.3e9, 8.8e9, 1.0e10],
+#     4e-2,
+# )
+
+# assert rx.rates.collins_kimball(
+#     radii,
+#     reactive_radius=2.6 * constants.angstrom,
+#     viscosity="water",
+#     temperature=[298.15, 300.00, 310.00, 320.00, 330.00, 340.00, 350.00],
+# ) / constants.liter == pytest.approx(
+#     [3.6e9, 3.8e9, 4.9e9, 6.0e9, 7.3e9, 8.8e9, 1.0e10],
+#     4e-2,
+# )
 
 
 def test_liquid_viscosities_are_correct() -> None: