Merge branch 'main' into enhancement/issue-822

ehrapy/anndata/anndata_ext.py

@@ -252,13 +252,13 @@ def delete_from_obs(adata: AnnData, to_delete: list[str]) -> AnnData:
     return adata
 
 
-def move_to_x(adata: AnnData, to_x: list[str] | str) -> AnnData:
+def move_to_x(adata: AnnData, to_x: list[str] | str, copy_x: bool = False) -> AnnData:
     """Move features from obs to X inplace.
 
     Args:
         adata: The AnnData object
         to_x: The columns to move to X
-        copy: Whether to return a copy or not
+        copy_x: The values are copied to X (and therefore kept in obs) instead of moved completely
 
     Returns:
         A new AnnData object with moved columns from obs to X. This should not be used for datetime columns currently.
@@ -292,7 +292,10 @@ def move_to_x(adata: AnnData, to_x: list[str] | str) -> AnnData:
 
     if cols_not_in_x:
         new_adata = concat([adata, AnnData(adata.obs[cols_not_in_x])], axis=1)
-        new_adata.obs = adata.obs[adata.obs.columns[~adata.obs.columns.isin(cols_not_in_x)]]
+        if copy_x:
+            new_adata.obs = adata.obs
+        else:
+            new_adata.obs = adata.obs[adata.obs.columns[~adata.obs.columns.isin(cols_not_in_x)]]
 
         # AnnData's concat discards var if they don't match in their keys, so we need to create a new var
         created_var = pd.DataFrame(index=cols_not_in_x)

tests/anndata/test_anndata_ext.py

@@ -164,6 +164,13 @@ def test_move_to_x(adata_move_obs_mix):
     )
 
 
+def test_move_to_x_copy_x(adata_move_obs_mix):
+    move_to_obs(adata_move_obs_mix, ["name"], copy_obs=False)
+    obs_df = adata_move_obs_mix.obs.copy()
+    new_adata = move_to_x(adata_move_obs_mix, ["name"], copy_x=True)
+    assert_frame_equal(new_adata.obs, obs_df)
+
+
 def test_move_to_x_invalid_column_names(adata_move_obs_mix):
     move_to_obs(adata_move_obs_mix, ["name"], copy_obs=True)
     move_to_obs(adata_move_obs_mix, ["clinic_id"], copy_obs=False)