Fix for pandas 3 CoW policy (#1106)

Author: selmanozleyen

src/squidpy/gr/_niche.py

@@ -456,7 +456,9 @@ def _get_nhood_profile_niches(
         nhood_profile = weighted_profile
 
     # create AnnData object from neighborhood profile to perform scanpy functions
-    adata_neighborhood = ad.AnnData(X=nhood_profile)
+    # Use .to_numpy(copy=True) to ensure the array is writeable (required for pandas CoW compatibility)
+    # Preserve the DataFrame index for later matching with adata_masked
+    adata_neighborhood = ad.AnnData(X=nhood_profile.to_numpy(copy=True), obs=pd.DataFrame(index=nhood_profile.index))
 
     # reason for scaling see https://monkeybread.readthedocs.io/en/latest/notebooks/tutorial.html#niche-analysis
     if scale:

src/squidpy/tl/_sliding_window.py

@@ -152,7 +152,8 @@ def sliding_window(
             else:
                 col_name = f"{sliding_window_key}_{lib_key}window_{idx}"
                 sliding_window_df.loc[obs_indices, col_name] = True
-                sliding_window_df.loc[:, col_name].fillna(False, inplace=True)
+                # Avoid chained assignment for pandas CoW compatibility
+                sliding_window_df[col_name] = sliding_window_df[col_name].fillna(False)
 
     if overlap == 0:
         # create categorical variable for ordered windows