use anndata's read_zarr instead of our custom implementation

MuData/AnnData read from Zarr cannot be backed, so there is no need for
custom handling

Author: ilia-kats

src/mudata/_core/io.py

@@ -21,11 +21,11 @@
 from anndata import AnnData
 from anndata._io.h5ad import _read_raw
 from anndata._io.h5ad import read_dataframe as read_h5ad_dataframe
-from anndata._io.zarr import _read_legacy_raw
 from anndata._io.zarr import read_dataframe as read_zarr_dataframe
-from anndata._io.zarr import write_zarr as anndata_write_zarr
 from anndata.compat import _read_attr
 from anndata.io import read_elem, write_elem
+from anndata.io import read_zarr as anndata_read_zarr
+from anndata.io import write_zarr as anndata_write_zarr
 from scipy import sparse
 
 from .config import OPTIONS
@@ -197,7 +197,7 @@ def write_zarr(
             if adata.raw is not None:
                 adata.strings_to_categoricals(adata.raw.var)
 
-            if write_data or not adata.isbacked:
+            if write_data:
                 if chunks is not None and not isinstance(adata.X, sparse.spmatrix):
                     write_elem(group, "X", adata.X, dataset_kwargs=dict(chunks=chunks, **kwargs))
                 else:
@@ -479,23 +479,19 @@ def read_zarr(store: str | PathLike | MutableMapping | zarr.Group | zarr.abc.sto
     """
     import zarr
 
-    if isinstance(store, Path):
-        store = str(store)
-
     f = zarr.open(store, mode="r")
     d = {}
     if "mod" not in f.keys():
         return ad.read_zarr(store)
 
-    manager = MuDataFileManager()
     for k in f.keys():
         if k in {"obs", "var"}:
             d[k] = read_zarr_dataframe(f[k])
         if k == "mod":
             mods = {}
             gmods = f[k]
             for m in gmods.keys():
-                mods[m] = _read_zarr_mod(gmods[m], manager)
+                mods[m] = anndata_read_zarr(gmods[m])
 
             mod_order = None
             if "mod-order" in gmods.attrs:
@@ -508,35 +504,11 @@ def read_zarr(store: str | PathLike | MutableMapping | zarr.Group | zarr.abc.sto
             d[k] = read_elem(f[k])
 
     mu = MuData._init_from_dict_(**d)
-    mu.file = manager
+    mu.file = MuDataFileManager()
 
     return mu
 
 
-def _read_zarr_mod(g: zarr.Group, manager: MuDataFileManager = None, backed: bool = False) -> dict:
-    d = {}
-
-    for k in g.keys():
-        if k in ("obs", "var"):
-            d[k] = read_zarr_dataframe(g[k])
-        elif k == "X":
-            X = g["X"]
-            if not backed:
-                d["X"] = read_elem(X)
-        elif k != "raw":
-            d[k] = read_elem(g[k])
-    ad = AnnData(**d)
-    if manager is not None:
-        ad.file = AnnDataFileManager(ad, Path(g.name).name, manager)
-
-    raw = _read_legacy_raw(
-        g, d.get("raw"), read_zarr_dataframe, read_elem, attrs=("var", "varm") if backed else ("var", "varm", "X")
-    )
-    if raw:
-        ad._raw = ad.Raw(ad, **raw)
-    return ad
-
-
 def _read_h5mu_mod(g: h5py.Group, manager: MuDataFileManager = None, backed: bool = False) -> dict:
     d = {}