(fix): fix index on obs.to_df()

scverse · Mar 9, 2023 · f4f5c7c · f4f5c7c
1 parent 515a6d2
commit f4f5c7c
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Showing 2 changed files with 23 additions and 10 deletions.
diff --git a/anndata/experimental/read_remote/read_remote.py b/anndata/experimental/read_remote/read_remote.py
@@ -66,16 +66,17 @@ def to_df(self) -> pd.DataFrame:
         """Convert to pandas dataframe."""
         df = pd.DataFrame(index=self.dim_names)
         for key in self.keys():
-            z = self[key]
-            if isinstance(z, zarr.Group) and "codes" in z:  # catrgoricql
-                value = pd.Categorical.from_codes(
-                    codes=read_elem(z["codes"]),
-                    categories=read_elem(z["categories"]),
-                    ordered=bool(_read_attr(z.attrs, "ordered")),
-                )
-            else:
-                value = z[()]
-            df[key] = value
+            if "index" not in key:
+                z = self[key]
+                if isinstance(z, zarr.Group) and "codes" in z:  # catrgoricql
+                    value = pd.Categorical.from_codes(
+                        codes=read_elem(z["codes"]),
+                        categories=read_elem(z["categories"]),
+                        ordered=bool(_read_attr(z.attrs, "ordered")),
+                    )
+                else:
+                    value = z[()]
+                df[key] = value
         return df
 
     @property

diff --git a/anndata/tests/test_read_remote.py b/anndata/tests/test_read_remote.py
@@ -77,3 +77,15 @@ def test_read_write_X(tmp_path, mtx_format):
     # remote.write_zarr(remote_pth) # need to implement writing!
 
     assert np.all(asarray(orig.X) == asarray(remote.X))
+    assert (orig.obs == remote.obs.to_df()).all().all()
+    assert (orig.var == remote.var.to_df()).all().all()
+
+
+def test_read_write_full(adata, tmp_path):
+    base_pth = Path(tmp_path)
+    orig_pth = base_pth / "orig.zarr"
+    adata.write_zarr(orig_pth)
+    remote = read_remote(orig_pth)
+    assert np.all(asarray(adata.X) == asarray(remote.X))
+    assert (adata.obs == remote.obs.to_df()).all().all()
+    assert (adata.var == remote.var.to_df()).all().all()