Finalize scipy sparse fixes

flatironinstitute · Jul 8, 2024 · 23848c9 · 23848c9
1 parent 5fdaa8b
commit 23848c9
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Showing 2 changed files with 8 additions and 12 deletions.
diff --git a/inferelator/preprocessing/velocity.py b/inferelator/preprocessing/velocity.py
@@ -312,6 +312,6 @@ def _sparse_safe_add(x, y):
     """
 
     if sparse.issparse(x) or sparse.issparse(y):
-        return todense(x + y).A
+        return todense(x + y)
     else:
         return np.add(x, y)
diff --git a/inferelator/tfa/ridge_tfa.py b/inferelator/tfa/ridge_tfa.py
@@ -1,6 +1,7 @@
 from .tfa_base import ActivityOnlyTFA
 from sklearn.linear_model import Ridge
-from scipy.sparse import issparse
+from inferelator.utils.sparse import todense
+
 
 class _Ridge_TFA_mixin:
     """
@@ -23,18 +24,13 @@ def _calculate_activity(
             positive=True
         )
 
-        if issparse(expression_data):
-            ridge_regressor.fit(
-                prior,
-                expression_data.A.T
-            )
-        else:
-            ridge_regressor.fit(
-                prior,
-                expression_data.T
-            )
+        ridge_regressor.fit(
+            prior,
+            todense(expression_data).T
+        )
 
         return ridge_regressor.coef_.copy()
 
+
 class RidgeTFA(_Ridge_TFA_mixin, ActivityOnlyTFA):
     pass