scipy 1.14 update

GreshamLab · Jul 8, 2024 · 7e6bf5f · 7e6bf5f
1 parent 54ec546
commit 7e6bf5f
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Showing 5 changed files with 8 additions and 7 deletions.
diff --git a/supirfactor_dynamical/_io/load_data.py b/supirfactor_dynamical/_io/load_data.py
@@ -156,7 +156,7 @@ def _get_data_from_ad(
 
     if densify:
         try:
-            _output = _output.A
+            _output = _output.toarray()
         except AttributeError:
             pass
 

diff --git a/supirfactor_dynamical/_utils/_adata_load.py b/supirfactor_dynamical/_utils/_adata_load.py
@@ -1,6 +1,6 @@
 import anndata as ad
 import numpy as np
-
+import scipy.sparse as sps
 
 from pandas.api.types import is_float_dtype
 
@@ -112,7 +112,7 @@ def load_data_files_jtb_2023(
             count_data = count_scaling.fit_transform(count_data)
 
             try:
-                count_data = count_data.A
+                count_data = count_data.toarray()
             except AttributeError:
                 pass
 
@@ -226,7 +226,7 @@ def _shuffle_data(
         return _sim_ints(
             pvec / pvec.sum(),
             np.full(pvec.shape, 3099, dtype=int),
-            sparse=hasattr(x, 'A')
+            sparse=sps.issparse(x)
         )
 
     elif sim_velo:

diff --git a/supirfactor_dynamical/datasets/time_dataset.py b/supirfactor_dynamical/datasets/time_dataset.py
@@ -380,8 +380,9 @@ def _get_data(data, idx, keep_sparse=False):
 
         if issparse(_data) and not keep_sparse:
 
+            _data = _data.toarray()
             _data = torch.Tensor(
-                _data.A.reshape(-1) if _data.shape[0] == 1 else _data.A
+                _data.reshape(-1) if _data.shape[0] == 1 else _data
             )
 
         return _data

diff --git a/supirfactor_dynamical/tests/test_loader.py b/supirfactor_dynamical/tests/test_loader.py
@@ -96,7 +96,7 @@ def test_bulk_sampling(self):
         self.assertIsNone(td.strat_idxes)
 
         try:
-            x = self.adata.X.A
+            x = self.adata.X.toarray()
         except AttributeError:
             x = self.adata.X
 

diff --git a/supirfactor_dynamical/tests/test_serialize.py b/supirfactor_dynamical/tests/test_serialize.py
@@ -172,7 +172,7 @@ def test_h5ad_sparse(self):
 
         adata2 = _read_ad(self.temp_file_name, "adata")
 
-        npt.assert_almost_equal(adata.X.A, adata2.X.A)
+        npt.assert_almost_equal(adata.X.toarray(), adata2.X.toarray())
         pdt.assert_index_equal(adata.obs_names, adata2.obs_names)
         pdt.assert_index_equal(adata.var_names, adata2.var_names)