IO refactor

pyproject.toml

@@ -14,22 +14,20 @@ maintainers = [
 authors = [
   { name = "Danila Bredikhin" },
 ]
-requires-python = ">=3.10"
+requires-python = ">=3.12"
 classifiers = [
   "Intended Audience :: Science/Research",
   "License :: OSI Approved :: BSD License",
   "Operating System :: OS Independent",
   "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.10",
-  "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
   "Programming Language :: Python :: 3.14",
   "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
 dynamic = [ "version" ]
 dependencies = [
-  "anndata>=0.10.8",
+  "anndata>=0.11",
   "h5py",
   "numpy",
   "pandas>=1.4",
@@ -78,7 +76,7 @@ envs.docs.scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
 envs.docs.scripts.clean = "git clean -fdX -- {args:docs}"
 envs.hatch-test.dependency-groups = [ "dev", "test" ]
 envs.hatch-test.matrix = [
-  { deps = [ "stable" ], python = [ "3.11", "3.14" ] },
+  { deps = [ "stable" ], python = [ "3.12", "3.14" ] },
   { deps = [ "pre" ], python = [ "3.14" ] }
 ]
 # If the matrix variable `deps` is set to "pre",

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.specs.registry import read_elem, write_elem
-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 = {}
 

src/mudata/_core/mudata.py

@@ -17,11 +17,10 @@
 import numpy as np
 import pandas as pd
 from anndata import AnnData
-from anndata._core.aligned_mapping import AxisArraysBase
+from anndata._core.aligned_mapping import AlignedView, AxisArrays, AxisArraysBase, PairwiseArrays
 from anndata._core.views import DataFrameView
 from anndata.utils import convert_to_dict
 
-from .compat import AlignedView, AxisArrays, PairwiseArrays
 from .config import OPTIONS
 from .file_backing import MuDataFileManager
 from .repr import MUDATA_CSS, block_matrix, details_block_table

tests/test_pull_push.py

@@ -1,5 +1,5 @@
 from collections.abc import Callable
-from typing import Literal, TypeAlias
+from typing import Literal
 
 import numpy as np
 import pandas as pd
@@ -8,8 +8,8 @@
 
 from mudata import MuData, set_options
 
-Axis: TypeAlias = Literal[0, 1]
-AxisAttr: TypeAlias = Literal["obs", "var"]
+type Axis = Literal[0, 1]
+type AxisAttr = Literal["obs", "var"]
 
 
 @pytest.fixture(params=(0, 1))

tests/test_update.py

@@ -1,6 +1,6 @@
 from collections.abc import Mapping, Sequence
 from functools import reduce
-from typing import Literal, TypeAlias
+from typing import Literal
 
 import numpy as np
 import pandas as pd
@@ -10,7 +10,7 @@
 
 from mudata import MuData, set_options
 
-Axis: TypeAlias = Literal[0, 1]
+type Axis = Literal[0, 1]
 
 
 @pytest.fixture