making copy of lists inside functions likely to have side effects

requirements.txt

@@ -1,9 +1,13 @@
 anndata>=0.7.6
 scanpy>=1.7.2
 POT==0.9.0
-numpy
-scipy
+numpy~=1.24.4
+scipy~=1.10.1
 scikit-learn>=0.24.0
 IPython>=7.18.1
-pytest
-
+pytest~=8.3.2
+seaborn~=0.13.2
+matplotlib~=3.7.5
+pandas~=2.0.3
+statsmodels~=0.14.1
+networkx~=3.1

tests/conftest.py

@@ -3,8 +3,6 @@
 import scanpy as sc
 import pytest
 from paste.helper import intersect
-from pandas.testing import assert_frame_equal
-
 
 test_dir = Path(__file__).parent
 input_dir = test_dir / "data/input"
@@ -29,6 +27,9 @@ def slices():
 
 @pytest.fixture(scope="session")
 def intersecting_slices(slices):
+    # Make a copy of the list
+    slices = list(slices)
+
     common_genes = slices[0].var.index
     for slice in slices[1:]:
         common_genes = intersect(common_genes, slice.var.index)

tests/test_paste.py

@@ -60,6 +60,8 @@ def test_pairwise_alignment(slices):
 def test_center_alignment(slices):
     temp_dir = Path(tempfile.mkdtemp())
 
+    # Make a copy of the list
+    slices = list(slices)
     n_slices = len(slices)
     center_slice, pairwise_info = center_align(
         slices[0],
@@ -255,4 +257,4 @@ def test_gromov_linesearch(slices):
     )
     assert alpha == 1.0
     assert fc == 1
-    assert round(cost_G, 6) == -11.419226
+    assert round(cost_G, 6) == -11.205454

tests/test_paste_helpers.py

@@ -17,15 +17,14 @@
 
 def test_intersect(slices):
     common_genes = intersect(slices[1].var.index, slices[2].var.index)
-
     assert np.all(
         np.equal(
             common_genes, np.genfromtxt(output_dir / "common_genes.csv", dtype=str)
         )
     )
 
 
-def test_kl_divergence_bakcend(slices):
+def test_kl_divergence_backend(slices):
     nx = ot.backend.NumpyBackend()
 
     common_genes = intersect(slices[1].var.index, slices[2].var.index)
@@ -43,4 +42,3 @@ def test_kl_divergence_bakcend(slices):
         rtol=1e-05,
         atol=1e-08,
     )
-