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

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

Author: pre-commit-ci[bot]

src/squidpy/gr/_ppatterns.py

@@ -41,7 +41,6 @@
 
 from squidpy.gr._spagft import _spagft
 
-
 it = nt.int32
 ft = nt.float32
 tt = nt.UniTuple

src/squidpy/gr/_spagft.py

@@ -1,7 +1,11 @@
+from __future__ import annotations
+
 import numpy as np
 from scipy.sparse import spmatrix
+
 from squidpy._utils import NDArrayA
 
+
 def _spagft(g: spmatrix, vals: NDArrayA) -> NDArrayA:
     """
     SpaGFT: Identify spatially variable genes using graph Fourier transform.
@@ -25,6 +29,7 @@ def _spagft(g: spmatrix, vals: NDArrayA) -> NDArrayA:
     n_eig = min(20, lap.shape[0] - 2)
     if n_eig <= 0:
         from scipy.sparse.linalg import ArpackError
+
         raise ArpackError("Number of eigenvectors requested must be positive.")
     eigvals, eigvecs = eigsh(lap, k=n_eig, which="SM")
 

tests/graph/test_spagft.py

@@ -2,26 +2,31 @@
 
 import pytest
 
-from squidpy.gr import spatial_autocorr
 from squidpy._constants._constants import SpatialAutocorr
+from squidpy.gr import spatial_autocorr
+
 
 def test_spagft_incompatible_shapes():
-    from squidpy.gr._spagft import _spagft
     import numpy as np
     from scipy.sparse import lil_matrix
+
+    from squidpy.gr._spagft import _spagft
+
     n = 10
     g = lil_matrix((n, n))
     for i in range(n):
         g[i, (i + 1) % n] = 1
         g[i, (i - 1) % n] = 1
     g = g.tocsr()
     vals = np.random.rand(5, 7)
-    with pytest.raises((ValueError)):
+    with pytest.raises(ValueError):
         _spagft(g, vals)
 
+
 def test_spagft_svg_identification():
     import numpy as np
     from anndata import AnnData
+
     from squidpy.gr import spatial_autocorr
 
     n_cells = 50
@@ -31,6 +36,7 @@ def test_spagft_svg_identification():
     X = np.vstack([spatial_pattern, random_gene])
     adata = AnnData(X=X.T)
     from scipy.sparse import lil_matrix
+
     g = lil_matrix((n_cells, n_cells))
     for i in range(n_cells):
         g[i, (i + 1) % n_cells] = 1
@@ -40,22 +46,25 @@ def test_spagft_svg_identification():
     assert "GFT" in df.columns
     assert df["GFT"].iloc[0] > df["GFT"].iloc[1]
 
+
 def test_spagft_enum_recognition():
     # Check that the enum contains "spagft"
     assert hasattr(SpatialAutocorr, "SPAGFT")
     # Check that spatial_autocorr accepts the enum member
     import numpy as np
     from anndata import AnnData
+
     n_cells = 10
     np.random.seed(0)
     X = np.random.normal(size=(n_cells, 2))
     adata = AnnData(X=X)
     from scipy.sparse import lil_matrix
+
     g = lil_matrix((n_cells, n_cells))
     for i in range(n_cells):
         g[i, (i + 1) % n_cells] = 1
         g[i, (i - 1) % n_cells] = 1
     adata.obsp["spatial_connectivities"] = g.tocsr()
     # Should not raise
     df = spatial_autocorr(adata, mode=SpatialAutocorr.SPAGFT, copy=True)
-    assert "GFT" in df.columns
+    assert "GFT" in df.columns