fix: don’t double-open h5ad files in backed mode (#2274)

Author: flying-sheep

docs/release-notes/2274.fix.md

@@ -0,0 +1 @@
+Only open HDF5 file once in backed mode {user}`flying-sheep`

src/anndata/_core/anndata.py

@@ -364,7 +364,12 @@ def _init_as_actual(  # noqa: PLR0912, PLR0913, PLR0915
 
         # init from file
         if filename is not None:
-            self.file = AnnDataFileManager(self, filename, filemode)
+            fileobj, filename = (
+                (filename, None)
+                if isinstance(filename, h5py.File)
+                else (None, filename)
+            )
+            self.file = AnnDataFileManager(self, filename, filemode, fileobj)
         else:
             self.file = AnnDataFileManager(self, None)
 

src/anndata/_io/h5ad.py

@@ -170,9 +170,8 @@ def write_sparse_as_dense(
 def read_h5ad_backed(
     filename: str | PathLike[str], mode: Literal["r", "r+"]
 ) -> AnnData:
-    d = dict(filename=filename, filemode=mode)
-
     f = h5py.File(filename, mode)
+    d = dict(filename=f)
 
     attributes = ["obsm", "varm", "obsp", "varp", "uns", "layers"]
     df_attributes = ["obs", "var"]
@@ -189,6 +188,7 @@ def read_h5ad_backed(
     d["raw"] = _read_raw(f, attrs={"var", "varm"})
 
     adata = AnnData(**d)
+    assert adata.file._file is f
 
     # Backwards compat to <0.7
     if isinstance(f["obs"], h5py.Dataset):