support anndata 0.13 layers unification

closes #148, closes #149, closes #150

(cherry picked from commit 19baeff)

Author: ilia-kats

src/mudata/_core/file_backing.py

@@ -62,7 +62,7 @@ def is_open(self) -> bool:
 
     @AnnDataFileManager.filename.setter
     def filename(self, filename: PathLike | None):
-        self._filename = None if filename is None else filename
+        self._filename = filename
 
 
 class AnnDataFileManager(ad._core.file_backing.AnnDataFileManager):
@@ -97,9 +97,13 @@ def close(self):
         self._parent._close()
 
     def _to_memory_mode(self):
-        self._adata._X = self._adata.X[()]
+        X = self._adata.X[()]
         self.close()
         self.filename = None
+        if hasattr(self._adata, "_X"):  # anndata < 0.13
+            self._adata._X = X
+        else:
+            self._adata.X = X  # anndata >= 0.13
 
     @property
     def is_open(self) -> bool:

src/mudata/_core/io.py

@@ -95,7 +95,7 @@ def _write_h5mu(file: h5py.File, mdata: MuData, write_data=True, **kwargs):
         write_elem(group, "varm", dict(adata.varm), dataset_kwargs=kwargs)
         write_elem(group, "obsp", dict(adata.obsp), dataset_kwargs=kwargs)
         write_elem(group, "varp", dict(adata.varp), dataset_kwargs=kwargs)
-        write_elem(group, "layers", dict(adata.layers), dataset_kwargs=kwargs)
+        write_elem(group, "layers", {k: v for k, v in adata.layers.items() if k is not None}, dataset_kwargs=kwargs)
         write_elem(group, "uns", dict(adata.uns), dataset_kwargs=kwargs)
 
         attrs = group.attrs
@@ -219,7 +219,7 @@ def write_zarr(
             write_elem(group, "varm", dict(adata.varm), dataset_kwargs=kwargs)
             write_elem(group, "obsp", dict(adata.obsp), dataset_kwargs=kwargs)
             write_elem(group, "varp", dict(adata.varp), dataset_kwargs=kwargs)
-            write_elem(group, "layers", dict(adata.layers), dataset_kwargs=kwargs)
+            write_elem(group, "layers", {k: v for k, v in adata.layers.items() if k is not None}, dataset_kwargs=kwargs)
             write_elem(group, "uns", dict(adata.uns), dataset_kwargs=kwargs)
 
             attrs = group.attrs
@@ -321,7 +321,7 @@ def write_h5ad(filename: str | PathLike, mod: str, data: MuData | AnnData):
         write_elem(fmd, "varm", dict(adata.varm))
         write_elem(fmd, "obsp", dict(adata.obsp))
         write_elem(fmd, "varp", dict(adata.varp))
-        write_elem(fmd, "layers", dict(adata.layers))
+        write_elem(fmd, "layers", {k: v for k, v in adata.layers.items() if k is not None})
         write_elem(fmd, "uns", dict(adata.uns))
 
         attrs = fmd.attrs

src/mudata/_core/mudata.py

@@ -24,7 +24,7 @@
 
 from .compat import AlignedView, AxisArrays, PairwiseArrays
 from .config import OPTIONS
-from .file_backing import MuDataFileManager
+from .file_backing import AnnDataFileManager, MuDataFileManager
 from .repr import MUDATA_CSS, block_matrix, details_block_table
 from .utils import (
     MetadataColumn,
@@ -1214,8 +1214,10 @@ def filename(self, filename: str | PathLike | None):
         elif filename is not None:
             self.write(filename)
             self.file.open(filename, "r+")
-            for ad in self._mod.values():
-                ad._X = None
+            for modname, mod in self._mod.items():
+                mod.X = None
+                if not isinstance(mod.file, AnnDataFileManager):
+                    mod.file = AnnDataFileManager(mod, modname, self.file)
 
     @property
     def obs(self) -> pd.DataFrame:

tests/test_io.py

@@ -55,6 +55,8 @@ def test_set_filename(mdata: md.MuData, filepath_h5mu: str | Path):
     mdata.filename = filepath_h5mu
     assert mdata.isbacked
     assert mdata.filename == filepath_h5mu
+    for mod in mdata.mod.values():
+        assert mod.isbacked
 
 
 def test_write_read_zarr_adata(mdata: md.MuData, filepath_zarr: str | Path):