Compatibility with anndata 0.13

CHANGELOG.md

@@ -16,12 +16,15 @@ and this project adheres to [Semantic Versioning][].
 
 ### Fixed
 
-## [0.3.0] - 2026-07-07
+
+## [0.3.0] - 2026-07-08
 
 ### Added
 
 ### Changed
 
+- Require `anndata>=0.13` (and consequently Python `>=3.12`, which anndata 0.13 requires) (#88)
+- Require `zarr>=3` (anndata 0.13 no longer supports zarr <3). Removed the dead `zarr<3` (`ZARR_V2`) code branches and the dead `anndata<0.11` (`USE_EXPERIMENTAL`) code branches now that the supported floors exceed them  (#88)
 - Zarr writes now store `obst`/`vart` in a columnar layout (one array per node/edge attribute key) instead of a single JSON scalar. Dense numeric/boolean columns use native dtypes; ragged or complex columns fall back to per-element JSON. This fixes a `TypeError: string too large to store inside array` crash when writing large trees to zarr v3 (#86)
 - `dtype` parameter in `TreeData.__init__` is now deprecated; passing it raises a `FutureWarning` and has no effect, matching anndata's removal of this argument
 - `obsm`, `varm`, `layers`, `raw`, `shape`, `filename`, `filemode`, `asview`, and related parameters in `TreeData.__init__` are now keyword-only, matching the anndata 0.13.x API
@@ -30,6 +33,7 @@ and this project adheres to [Semantic Versioning][].
 
 ### Fixed
 
+- `TreeData.__getitem__` now delegates `anndata.acc` accessor indexers (`AdRef`, `MapAcc`, `RefAcc`) to `AnnData.__getitem__` instead of routing them through `_normalize_indices`. This fixes an `IndexError: Unknown indexer` from `obs_vector`/`var_vector` (and any `var_names`/layer column lookup) under anndata ≥ 0.13 (#88)
 - Fixed `UserWarning: Duplicate name: 'zarr.json'` spam when writing to a zarr `ZipStore` by staging the write in a `MemoryStore` and copying to the `ZipStore` once (#86)
 - `read_zarr` now auto-detects `.zip` paths and opens them as a `ZipStore` (#86)
 - Node/edge attributes explicitly set to `None` are now preserved through a zarr round-trip and kept distinct from absent attributes (#86)

pyproject.toml

@@ -14,24 +14,23 @@ maintainers = [
 authors = [
   { name = "William Colgan" },
 ]
-requires-python = ">=3.11"
+requires-python = ">=3.12"
 classifiers = [
   "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
   "Programming Language :: Python :: 3.14",
 ]
 dependencies = [
-  "anndata>=0.11",
+  "anndata>=0.13",
   "h5py",
   "networkx",
   "numpy",
   "packaging",
   "pandas",
   "pyarrow",
   "session-info2",
-  "zarr>=2",
+  "zarr>=3",
 ]
 urls.Documentation = "https://treedata.readthedocs.io/"
 urls.Homepage = "https://github.com/colganwi/treedata"
@@ -76,7 +75,7 @@ envs.docs.scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
 envs.docs.dependency-groups = [ "doc" ]
 envs.hatch-test.matrix = [
   # Test the lowest and highest supported Python versions with normal deps
-  { deps = [ "stable" ], python = [ "3.11", "3.14" ] },
+  { deps = [ "stable" ], python = [ "3.12", "3.14" ] },
   # Test the newest supported Python version also with pre-release deps
   { deps = [ "pre" ], python = [ "3.14" ] },
 ]

src/treedata/_core/read.py

@@ -3,31 +3,23 @@
 import json
 import warnings
 from collections.abc import MutableMapping
-from importlib.metadata import version as get_version
 from os import PathLike
 from typing import Literal
 
 import anndata as ad
 import h5py
 import networkx as nx
 import zarr
-from packaging import version
 
 from treedata._core.treedata import TreeData
 
-ANNDATA_VERSION = version.parse(get_version("anndata"))
-USE_EXPERIMENTAL = ANNDATA_VERSION < version.parse("0.11.0")
-
 # Sentinel distinguishing an absent attribute from an attribute explicitly set to ``None``.
 _MISSING = object()
 
 
 def _read_elem(elem):
     """Read an element from a store."""
-    if USE_EXPERIMENTAL:
-        return ad.experimental.read_elem(elem)
-    else:
-        return ad.io.read_elem(elem)
+    return ad.io.read_elem(elem)
 
 
 def _dict_to_digraph(graph_dict: dict) -> nx.DiGraph:

src/treedata/_core/treedata.py

@@ -397,6 +397,11 @@ def __repr__(self) -> str:
 
     def __getitem__(self, index: Any) -> TreeData:
         """Returns a sliced view of the object."""
+        from anndata.acc import AdRef, MapAcc, RefAcc
+
+        if isinstance(index, AdRef | MapAcc | RefAcc):
+            # Accessor indexers retrieve an array/vector, not a TreeData view.
+            return super().__getitem__(index)
         oidx, vidx = self._normalize_indices(index)
         return TreeData(self, oidx=oidx, vidx=vidx, asview=True)
 

src/treedata/_core/write.py

@@ -3,7 +3,6 @@
 import json
 import warnings
 from collections.abc import MutableMapping
-from importlib.metadata import version as get_version
 from os import PathLike
 from pathlib import Path
 from typing import Any, Literal
@@ -14,15 +13,10 @@
 import numpy as np
 import pandas as pd
 import zarr
-from packaging import version
 
 from treedata._core.aligned_mapping import AxisTrees
 from treedata._core.treedata import TreeData
 
-ANNDATA_VERSION = version.parse(get_version("anndata"))
-USE_EXPERIMENTAL = ANNDATA_VERSION < version.parse("0.11.0")
-ZARR_V2 = version.parse(get_version("zarr")) < version.parse("3.0.0")
-
 # Sentinel distinguishing an absent attribute from an attribute explicitly set to ``None``.
 _MISSING = object()
 
@@ -45,10 +39,7 @@ def _make_serializable(data: Any) -> Any:
 
 def _write_elem(f, k, elem, *, dataset_kwargs) -> None:
     """Write an element to a storage group using anndata encoding."""
-    if USE_EXPERIMENTAL:
-        ad.experimental.write_elem(f, k, elem, dataset_kwargs=dataset_kwargs)
-    else:
-        ad.io.write_elem(f, k, elem, dataset_kwargs=dataset_kwargs)
+    ad.io.write_elem(f, k, elem, dataset_kwargs=dataset_kwargs)
 
 
 def _digraph_to_dict(G: nx.DiGraph) -> dict:
@@ -229,10 +220,7 @@ def _open_zarr_group(
     """Open a Zarr group for writing and indicate ownership."""
     if isinstance(store, zarr.Group):
         return store, False
-    group_kwargs: dict[str, int] = {}
-    if not ZARR_V2:
-        group_kwargs["zarr_format"] = 3
-    return zarr.open_group(store, mode=mode, **group_kwargs), True
+    return zarr.open_group(store, mode=mode, zarr_format=3), True
 
 
 def _close_zarr_group(group: zarr.Group) -> None:
@@ -246,8 +234,6 @@ def _close_zarr_group(group: zarr.Group) -> None:
 
 def _is_zip_store(store: Any) -> bool:
     """Return True if store is or resolves to a zarr ZipStore."""
-    if ZARR_V2:
-        return False
     return isinstance(store, zarr.storage.ZipStore) or (
         isinstance(store, (str, PathLike)) and str(store).endswith(".zip")
     )