lint

mdgo/coordination.py

@@ -363,9 +363,7 @@ def check_contiguous_steps(
         An array of distance between the center atom and the neighbor atoms
         in the checkpoint +/- lag time range.
     """
-    coord_num: dict[str, list[list[int]] | np.ndarray] = {
-        x: [[] for _ in range(lag * 2 + 1)] for x in distance_dict
-    }
+    coord_num: dict[str, list[list[int]] | np.ndarray] = {x: [[] for _ in range(lag * 2 + 1)] for x in distance_dict}
     trj_analysis = nvt_run.trajectory[run_start:run_end:]
     has = False
     for i, _ts in enumerate(trj_analysis):
@@ -1092,9 +1090,7 @@ def write_out(center_pos: np.ndarray, center_name: str, neighbors: AtomGroup, pa
         xyz_file.write("\n".join(lines))
 
 
-def select_shell(
-    select: dict[str, str] | str, distance: dict[str, float] | str, center_atom: Atom, kw: str
-) -> str:
+def select_shell(select: dict[str, str] | str, distance: dict[str, float] | str, center_atom: Atom, kw: str) -> str:
     """
     Select a group of atoms that is within a distance of an ``center_atom``.
 

mdgo/msd.py

@@ -284,9 +284,7 @@ def parse_msd_type(msd_type: DIM) -> list[int]:
     try:
         dim = keys[msd_type_str]
     except KeyError:
-        raise ValueError(
-            f"invalid msd_type: {msd_type_str} specified, please specify one of xyz, xy, xz, yz, x, y, z"
-        )
+        raise ValueError(f"invalid msd_type: {msd_type_str} specified, please specify one of xyz, xy, xz, yz, x, y, z")
     return dim
 
 

mdgo/util/reformat.py

@@ -68,9 +68,7 @@
     },
 }
 
-BOX: Final[
-    str
-] = """{0:6f} {1:6f} xlo xhi
+BOX: Final[str] = """{0:6f} {1:6f} xlo xhi
 {0:6f} {1:6f} ylo yhi
 {0:6f} {1:6f} zlo zhi"""
 

setup.py

@@ -71,7 +71,7 @@
             "Topic :: Scientific/Engineering :: Physics",
             "Topic :: Scientific/Engineering :: Chemistry",
             "Topic :: Software Development :: Libraries :: Python Modules",
-            ],
+        ],
         packages=find_packages(),
         install_requires=INSTALL_REQUIRES,
         extras_require={

tests/test_msd.py

@@ -55,36 +55,36 @@ def test_msd_fft(self):
     def test_create_position_arrays(self):
         assert_allclose(
             np.array([21.53381769, 14.97501839, -3.87998785]),
-            create_position_arrays(self.gen2, 0, 100, select="type 3")[50][2]
+            create_position_arrays(self.gen2, 0, 100, select="type 3")[50][2],
         )
         assert_allclose(
             np.array([-2.78550047, -11.85487624, -17.1221954]),
-            create_position_arrays(self.gen2, 0, 100, select="type 3")[99][10]
+            create_position_arrays(self.gen2, 0, 100, select="type 3")[99][10],
         )
         assert_allclose(
-            np.array([41.1079216 , 34.95127106, 18.00482368]),
-            create_position_arrays(self.gen2, 0, 100, select="type 3", center_of_mass=False)[50][2]
+            np.array([41.1079216, 34.95127106, 18.00482368]),
+            create_position_arrays(self.gen2, 0, 100, select="type 3", center_of_mass=False)[50][2],
         )
         assert_allclose(
-            np.array([16.98478317,  8.27190208,  5.07116079]),
-            create_position_arrays(self.gen2, 0, 100, select="type 3", center_of_mass=False)[99][10]
+            np.array([16.98478317, 8.27190208, 5.07116079]),
+            create_position_arrays(self.gen2, 0, 100, select="type 3", center_of_mass=False)[99][10],
         )
 
     def test_parse_msd_type(self):
         xyz = parse_msd_type("xyz")
-        assert ["x", "y", "z"] == self.dims[xyz[0]:xyz[1]:xyz[2]]
+        assert ["x", "y", "z"] == self.dims[xyz[0] : xyz[1] : xyz[2]]
         xy = parse_msd_type("xy")
-        assert ["x", "y"] == self.dims[xy[0]:xy[1]:xy[2]]
+        assert ["x", "y"] == self.dims[xy[0] : xy[1] : xy[2]]
         yz = parse_msd_type("yz")
-        assert ["y", "z"] == self.dims[yz[0]:yz[1]:yz[2]]
+        assert ["y", "z"] == self.dims[yz[0] : yz[1] : yz[2]]
         xz = parse_msd_type("xz")
-        assert ["x", "z"] == self.dims[xz[0]:xz[1]:xz[2]]
+        assert ["x", "z"] == self.dims[xz[0] : xz[1] : xz[2]]
         x = parse_msd_type("x")
-        assert ["x"] == self.dims[x[0]:x[1]:x[2]]
+        assert ["x"] == self.dims[x[0] : x[1] : x[2]]
         y = parse_msd_type("y")
-        assert ["y"] == self.dims[y[0]:y[1]:y[2]]
+        assert ["y"] == self.dims[y[0] : y[1] : y[2]]
         z = parse_msd_type("z")
-        assert ["z"] == self.dims[z[0]:z[1]:z[2]]
+        assert ["z"] == self.dims[z[0] : z[1] : z[2]]
 
     def test_onsager_ii_self(self):
         onsager_ii_self_fft = onsager_ii_self(self.gen2, 0, 100, select="type 3")
@@ -155,9 +155,9 @@ def test_total_msd(self):
         assert_allclose(total_builtin_cation[50], 32.14254152556588)
         assert_allclose(total_mda_cation[50], 32.338364098424634)
         with pytest.raises(
-                ValueError,
-                match="Warning! MDAnalysis does not support subtracting center "
-                "of mass. Calculating without subtracting...",
+            ValueError,
+            match="Warning! MDAnalysis does not support subtracting center "
+            "of mass. Calculating without subtracting...",
         ):
             total_msd(self.gen2, 0, 100, select="type 3", fft=True, built_in=False, center_of_mass=True)
 

tests/test_volume.py

@@ -50,9 +50,7 @@ def test_molecular_volume(self) -> None:
         litfsi_volume_4 = molecular_volume(self.litfsi, radii_type="Lange")
         litfsi_volume_5 = molecular_volume(self.litfsi, radii_type="pymatgen")
         litfsi_volume_6 = molecular_volume(self.litfsi, molar_volume=False)
-        litfsi_volume_7 = molecular_volume(
-            self.litfsi, mode="act", x_size=8, y_size=8, z_size=8
-        )
+        litfsi_volume_7 = molecular_volume(self.litfsi, mode="act", x_size=8, y_size=8, z_size=8)
         assert litfsi_volume_1 == 100.16
         assert litfsi_volume_2 == 100.16
         assert litfsi_volume_3 == 99.37