anndata 0.12.2__py3-none-any.whl → 0.12.3__py3-none-any.whl

anndata/__init__.py

@@ -12,7 +12,6 @@ from ._core.extensions import register_anndata_namespace
 from ._core.merge import concat
 from ._core.raw import Raw
 from ._settings import settings
-from ._version import __version__
 from ._warnings import (
     ExperimentalFeatureWarning,
     ImplicitModificationWarning,
@@ -28,22 +27,6 @@ from . import abc, experimental, typing, io, types  # isort: skip
 # We use these in tests by attribute access
 from . import logging  # noqa: F401  # isort: skip
 
-_DEPRECATED_IO = (
-    "read_loom",
-    "read_hdf",
-    "read_excel",
-    "read_umi_tools",
-    "read_csv",
-    "read_text",
-    "read_mtx",
-)
-_DEPRECATED = {method: f"io.{method}" for method in _DEPRECATED_IO}
-
-
-def __getattr__(attr_name: str) -> Any:
-    return module_get_attr_redirect(attr_name, deprecated_mapping=_DEPRECATED)
-
-
 __all__ = [
     "AnnData",
     "ExperimentalFeatureWarning",
@@ -51,7 +34,6 @@ __all__ = [
     "OldFormatWarning",
     "Raw",
     "WriteWarning",
-    "__version__",
     "abc",
     "concat",
     "experimental",
@@ -63,3 +45,26 @@ __all__ = [
     "types",
     "typing",
 ]
+
+_DEPRECATED_IO = (
+    "read_loom",
+    "read_hdf",
+    "read_excel",
+    "read_umi_tools",
+    "read_csv",
+    "read_text",
+    "read_mtx",
+)
+_DEPRECATED = {method: f"io.{method}" for method in _DEPRECATED_IO}
+
+
+def __getattr__(attr_name: str) -> Any:
+    if attr_name == "__version__":
+        import warnings
+        from importlib.metadata import version
+
+        msg = "`__version__` is deprecated, use `importlib.metadata.version('anndata')` instead."
+        warnings.warn(msg, FutureWarning, stacklevel=2)
+        return version("anndata")
+
+    return module_get_attr_redirect(attr_name, deprecated_mapping=_DEPRECATED)

anndata/_core/anndata.py

@@ -42,11 +42,7 @@ from .index import _normalize_indices, _subset, get_vector
 from .raw import Raw
 from .sparse_dataset import BaseCompressedSparseDataset, sparse_dataset
 from .storage import coerce_array
-from .views import (
-    DictView,
-    _resolve_idxs,
-    as_view,
-)
+from .views import DictView, _resolve_idxs, as_view
 from .xarray import Dataset2D
 
 if TYPE_CHECKING:
@@ -940,22 +936,27 @@ class AnnData(metaclass=utils.DeprecationMixinMeta):  # noqa: PLW1641
     Is sliced with `data` and `var` but behaves otherwise like a :term:`mapping`.
     """
 
+    @deprecated("obs (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)")
     def obs_keys(self) -> list[str]:
         """List keys of observation annotation :attr:`obs`."""
         return self._obs.keys().tolist()
 
+    @deprecated("var (e.g. `k in adata.var` or `str(adata.var.columns.tolist())`)")
     def var_keys(self) -> list[str]:
         """List keys of variable annotation :attr:`var`."""
         return self._var.keys().tolist()
 
+    @deprecated("obsm (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`)")
     def obsm_keys(self) -> list[str]:
         """List keys of observation annotation :attr:`obsm`."""
         return list(self.obsm.keys())
 
+    @deprecated("varm (e.g. `k in adata.varm` or `adata.varm.keys() | {'u'}`)")
     def varm_keys(self) -> list[str]:
         """List keys of variable annotation :attr:`varm`."""
         return list(self.varm.keys())
 
+    @deprecated("uns (e.g. `k in adata.uns` or `sorted(adata.uns)`)")
     def uns_keys(self) -> list[str]:
         """List keys of unstructured annotation."""
         return sorted(self._uns.keys())
@@ -1907,8 +1908,8 @@ class AnnData(metaclass=utils.DeprecationMixinMeta):  # noqa: PLW1641
             compression_opts=compression_opts,
             as_dense=as_dense,
         )
-
-        if self.isbacked:
+        # Only reset the filename if the AnnData object now points to a complete new copy
+        if self.isbacked and not self.is_view:
             self.file.filename = filename
 
     write = write_h5ad  # a shortcut and backwards compat

anndata/_core/merge.py

@@ -14,9 +14,7 @@ from warnings import warn
 
 import numpy as np
 import pandas as pd
-import scipy
 from natsort import natsorted
-from packaging.version import Version
 from scipy import sparse
 
 from anndata._core.file_backing import to_memory
@@ -30,7 +28,6 @@ from ..compat import (
     CupyCSRMatrix,
     CupySparseMatrix,
     DaskArray,
-    _map_cat_to_str,
 )
 from ..utils import asarray, axis_len, warn_once
 from .anndata import AnnData
@@ -146,11 +143,16 @@ def equal_dask_array(a, b) -> bool:
         return False
     if isinstance(b, DaskArray) and tokenize(a) == tokenize(b):
         return True
-    if isinstance(a._meta, CSMatrix):
+    if isinstance(a._meta, np.ndarray):
+        return da.equal(a, b, where=~(da.isnan(a) & da.isnan(b))).all().compute()
+    if a.chunksize == b.chunksize and isinstance(
+        a._meta, CupySparseMatrix | CSMatrix | CSArray
+    ):
         # TODO: Maybe also do this in the other case?
         return da.map_blocks(equal, a, b, drop_axis=(0, 1)).all()
-    else:
-        return da.equal(a, b, where=~(da.isnan(a) == da.isnan(b))).all()
+    msg = "Misaligned chunks detected when checking for merge equality of dask arrays.  Reading full arrays into memory."
+    warn(msg, UserWarning, stacklevel=3)
+    return equal(a.compute(), b.compute())
 
 
 @equal.register(np.ndarray)
@@ -185,15 +187,6 @@ def equal_sparse(a, b) -> bool:
             # Comparison broken for CSC matrices
             # https://github.com/cupy/cupy/issues/7757
             a, b = CupyCSRMatrix(a), CupyCSRMatrix(b)
-        if Version(scipy.__version__) >= Version("1.16.0rc1"):
-            # TODO: https://github.com/scipy/scipy/issues/23068
-            return bool(
-                a.format == b.format
-                and (a.shape == b.shape)
-                and np.all(a.indptr == b.indptr)
-                and np.all(a.indices == b.indices)
-                and np.all((a.data == b.data) | (np.isnan(a.data) & np.isnan(b.data)))
-            )
         comp = a != b
         if isinstance(comp, bool):
             return not comp
@@ -617,6 +610,9 @@ class Reindexer:
         sub_el = _subset(el, make_slice(indexer, axis, len(shape)))
 
         if any(indexer == -1):
+            # TODO: Remove this condition once https://github.com/dask/dask/pull/12078 is released
+            if isinstance(sub_el._meta, CSArray | CSMatrix) and np.isscalar(fill_value):
+                fill_value = np.array([[fill_value]])
             sub_el[make_slice(indexer == -1, axis, len(shape))] = fill_value
 
         return sub_el
@@ -1643,7 +1639,7 @@ def concat(  # noqa: PLR0912, PLR0913, PLR0915
     )
     if index_unique is not None:
         concat_indices = concat_indices.str.cat(
-            _map_cat_to_str(label_col), sep=index_unique
+            label_col.map(str, na_action="ignore"), sep=index_unique
         )
     concat_indices = pd.Index(concat_indices)
 
@@ -1748,15 +1744,10 @@ def concat(  # noqa: PLR0912, PLR0913, PLR0915
             for r, a in zip(reindexers, adatas, strict=True)
         ],
     )
-    alt_pairwise = merge(
-        [
-            {
-                k: r(r(v, axis=0), axis=1)
-                for k, v in getattr(a, f"{alt_axis_name}p").items()
-            }
-            for r, a in zip(reindexers, adatas, strict=True)
-        ]
-    )
+    alt_pairwise = merge([
+        {k: r(r(v, axis=0), axis=1) for k, v in getattr(a, f"{alt_axis_name}p").items()}
+        for r, a in zip(reindexers, adatas, strict=True)
+    ])
     uns = uns_merge([a.uns for a in adatas])
 
     raw = None
@@ -1785,17 +1776,15 @@ def concat(  # noqa: PLR0912, PLR0913, PLR0915
             "not concatenating `.raw` attributes."
         )
         warn(msg, UserWarning, stacklevel=2)
-    return AnnData(
-        **{
-            "X": X,
-            "layers": layers,
-            axis_name: concat_annot,
-            alt_axis_name: alt_annot,
-            f"{axis_name}m": concat_mapping,
-            f"{alt_axis_name}m": alt_mapping,
-            f"{axis_name}p": concat_pairwise,
-            f"{alt_axis_name}p": alt_pairwise,
-            "uns": uns,
-            "raw": raw,
-        }
-    )
+    return AnnData(**{
+        "X": X,
+        "layers": layers,
+        axis_name: concat_annot,
+        alt_axis_name: alt_annot,
+        f"{axis_name}m": concat_mapping,
+        f"{alt_axis_name}m": alt_mapping,
+        f"{axis_name}p": concat_pairwise,
+        f"{alt_axis_name}p": alt_pairwise,
+        "uns": uns,
+        "raw": raw,
+    })

anndata/_core/sparse_dataset.py

@@ -16,6 +16,7 @@ import warnings
 from abc import ABC
 from collections.abc import Iterable
 from functools import cached_property
+from importlib.metadata import version
 from itertools import accumulate, chain, pairwise
 from math import floor
 from pathlib import Path
@@ -23,7 +24,6 @@ from typing import TYPE_CHECKING, NamedTuple
 
 import h5py
 import numpy as np
-import scipy
 import scipy.sparse as ss
 from packaging.version import Version
 from scipy.sparse import _sparsetools
@@ -54,7 +54,7 @@ else:
     from scipy.sparse import spmatrix as _cs_matrix
 
 
-SCIPY_1_15 = Version(scipy.__version__) >= Version("1.15rc0")
+SCIPY_1_15 = Version(version("scipy")) >= Version("1.15rc0")
 
 
 class BackedFormat(NamedTuple):
@@ -278,9 +278,9 @@ def get_compressed_vectors(
     indptr_slices = [slice(*(x.indptr[i : i + 2])) for i in row_idxs]
     # HDF5 cannot handle out-of-order integer indexing
     if isinstance(x.data, ZarrArray):
-        as_np_indptr = np.concatenate(
-            [np.arange(s.start, s.stop) for s in indptr_slices]
-        )
+        as_np_indptr = np.concatenate([
+            np.arange(s.start, s.stop) for s in indptr_slices
+        ])
         data = x.data[as_np_indptr]
         indices = x.indices[as_np_indptr]
     else:
@@ -309,9 +309,9 @@ def get_compressed_vectors_for_slices(
     start_indptr = indptr_indices[0] - next(offsets)
     if len(slices) < 2:  # there is only one slice so no need to concatenate
         return data, indices, start_indptr
-    end_indptr = np.concatenate(
-        [s[1:] - o for s, o in zip(indptr_indices[1:], offsets, strict=True)]
-    )
+    end_indptr = np.concatenate([
+        s[1:] - o for s, o in zip(indptr_indices[1:], offsets, strict=True)
+    ])
     indptr = np.concatenate([start_indptr, end_indptr])
     return data, indices, indptr
 

anndata/_core/views.py

@@ -100,7 +100,7 @@ class _ViewMixin(_SetItemMixin):
 
     # TODO: This makes `deepcopy(obj)` return `obj._view_args.parent._adata_ref`, fix it
     def __deepcopy__(self, memo):
-        parent, attrname, keys = self._view_args
+        parent, attrname, _keys = self._view_args
         return deepcopy(getattr(parent._adata_ref, attrname))
 
 

anndata/_io/h5ad.py

@@ -27,7 +27,6 @@ from ..experimental import read_dispatched
 from .specs import read_elem, write_elem
 from .specs.registry import IOSpec, write_spec
 from .utils import (
-    H5PY_V3,
     _read_legacy_raw,
     idx_chunks_along_axis,
     no_write_dataset_2d,
@@ -264,15 +263,13 @@ def read_h5ad(
 
         def callback(func, elem_name: str, elem, iospec):
             if iospec.encoding_type == "anndata" or elem_name.endswith("/"):
-                return AnnData(
-                    **{
-                        # This is covering up backwards compat in the anndata initializer
-                        # In most cases we should be able to call `func(elen[k])` instead
-                        k: read_dispatched(elem[k], callback)
-                        for k in elem
-                        if not k.startswith("raw.")
-                    }
-                )
+                return AnnData(**{
+                    # This is covering up backwards compat in the anndata initializer
+                    # In most cases we should be able to call `func(elen[k])` instead
+                    k: read_dispatched(elem[k], callback)
+                    for k in elem
+                    if not k.startswith("raw.")
+                })
             elif elem_name.startswith("/raw."):
                 return None
             elif elem_name == "/X" and "X" in as_sparse:
@@ -326,16 +323,12 @@ def read_dataframe_legacy(dataset: h5py.Dataset) -> pd.DataFrame:
         "Consider rewriting it."
     )
     warn(msg, OldFormatWarning, stacklevel=2)
-    if H5PY_V3:
-        df = pd.DataFrame(
-            _decode_structured_array(
-                _from_fixed_length_strings(dataset[()]), dtype=dataset.dtype
-            )
+    df = pd.DataFrame(
+        _decode_structured_array(
+            _from_fixed_length_strings(dataset[()]), dtype=dataset.dtype
         )
-    else:
-        df = pd.DataFrame(_from_fixed_length_strings(dataset[()]))
-    df.set_index(df.columns[0], inplace=True)
-    return df
+    )
+    return df.set_index(df.columns[0])
 
 
 def read_dataframe(group: h5py.Group | h5py.Dataset) -> pd.DataFrame:
@@ -348,10 +341,9 @@ def read_dataframe(group: h5py.Group | h5py.Dataset) -> pd.DataFrame:
 
 @report_read_key_on_error
 def read_dataset(dataset: h5py.Dataset):
-    if H5PY_V3:
-        string_dtype = h5py.check_string_dtype(dataset.dtype)
-        if (string_dtype is not None) and (string_dtype.encoding == "utf-8"):
-            dataset = dataset.asstr()
+    string_dtype = h5py.check_string_dtype(dataset.dtype)
+    if (string_dtype is not None) and (string_dtype.encoding == "utf-8"):
+        dataset = dataset.asstr()
     value = dataset[()]
     if not hasattr(value, "dtype"):
         return value
@@ -364,10 +356,9 @@ def read_dataset(dataset: h5py.Dataset):
             return value[0]
     elif len(value.dtype.descr) > 1:  # Compound dtype
         # For backwards compat, now strings are written as variable length
-        dtype = value.dtype
-        value = _from_fixed_length_strings(value)
-        if H5PY_V3:
-            value = _decode_structured_array(value, dtype=dtype)
+        value = _decode_structured_array(
+            _from_fixed_length_strings(value), dtype=value.dtype
+        )
     if value.shape == ():
         value = value[()]
     return value

anndata/_io/specs/lazy_methods.py

@@ -37,7 +37,7 @@ if TYPE_CHECKING:
     from .registry import LazyDataStructures, LazyReader
 
     BlockInfo = Mapping[
-        Literal[None],
+        None,
         dict[str, Sequence[tuple[int, int]]],
     ]
 

anndata/_io/specs/methods.py

@@ -4,6 +4,7 @@ import warnings
 from collections.abc import Mapping
 from copy import copy
 from functools import partial
+from importlib.metadata import version
 from itertools import product
 from types import MappingProxyType
 from typing import TYPE_CHECKING
@@ -21,7 +22,7 @@ from anndata._core import views
 from anndata._core.index import _normalize_indices
 from anndata._core.merge import intersect_keys
 from anndata._core.sparse_dataset import _CSCDataset, _CSRDataset, sparse_dataset
-from anndata._io.utils import H5PY_V3, check_key, zero_dim_array_as_scalar
+from anndata._io.utils import check_key, zero_dim_array_as_scalar
 from anndata._warnings import OldFormatWarning
 from anndata.compat import (
     NULLABLE_NUMPY_STRING_TYPE,
@@ -492,6 +493,7 @@ _REGISTRY.register_write(ZarrGroup, CupyArray, IOSpec("array", "0.2.0"))(
 )
 
 
+@_REGISTRY.register_write(ZarrGroup, views.DaskArrayView, IOSpec("array", "0.2.0"))
 @_REGISTRY.register_write(ZarrGroup, DaskArray, IOSpec("array", "0.2.0"))
 def write_basic_dask_zarr(
     f: ZarrGroup,
@@ -514,6 +516,7 @@ def write_basic_dask_zarr(
 
 # Adding this separately because h5py isn't serializable
 # https://github.com/pydata/xarray/issues/4242
+@_REGISTRY.register_write(H5Group, views.DaskArrayView, IOSpec("array", "0.2.0"))
 @_REGISTRY.register_write(H5Group, DaskArray, IOSpec("array", "0.2.0"))
 def write_basic_dask_h5(
     f: H5Group,
@@ -607,7 +610,7 @@ def write_vlen_string_array_zarr(
     if is_zarr_v2():
         import numcodecs
 
-        if Version(numcodecs.__version__) < Version("0.13"):
+        if Version(version("numcodecs")) < Version("0.13"):
             msg = "Old numcodecs version detected. Please update for improved performance and stability."
             warnings.warn(msg, UserWarning, stacklevel=2)
             # Workaround for https://github.com/zarr-developers/numcodecs/issues/514
@@ -663,10 +666,9 @@ def _to_hdf5_vlen_strings(value: np.ndarray) -> np.ndarray:
 @_REGISTRY.register_read(ZarrArray, IOSpec("rec-array", "0.2.0"))
 def read_recarray(d: ArrayStorageType, *, _reader: Reader) -> np.recarray | npt.NDArray:
     value = d[()]
-    dtype = value.dtype
-    value = _from_fixed_length_strings(value)
-    if H5PY_V3:
-        value = _decode_structured_array(value, dtype=dtype)
+    value = _decode_structured_array(
+        _from_fixed_length_strings(value), dtype=value.dtype
+    )
     return value
 
 
@@ -778,10 +780,10 @@ for store_type, (cls, spec, func) in product(
     _REGISTRY.register_write(store_type, cls, spec)(func)
 
 
-@_REGISTRY.register_write(H5Group, _CSRDataset, IOSpec("", "0.1.0"))
-@_REGISTRY.register_write(H5Group, _CSCDataset, IOSpec("", "0.1.0"))
-@_REGISTRY.register_write(ZarrGroup, _CSRDataset, IOSpec("", "0.1.0"))
-@_REGISTRY.register_write(ZarrGroup, _CSCDataset, IOSpec("", "0.1.0"))
+@_REGISTRY.register_write(H5Group, _CSRDataset, IOSpec("csr_matrix", "0.1.0"))
+@_REGISTRY.register_write(H5Group, _CSCDataset, IOSpec("csc_matrix", "0.1.0"))
+@_REGISTRY.register_write(ZarrGroup, _CSRDataset, IOSpec("csr_matrix", "0.1.0"))
+@_REGISTRY.register_write(ZarrGroup, _CSCDataset, IOSpec("csc_matrix", "0.1.0"))
 def write_sparse_dataset(
     f: GroupStorageType,
     k: str,
@@ -798,26 +800,9 @@ def write_sparse_dataset(
         fmt=elem.format,
         dataset_kwargs=dataset_kwargs,
     )
-    # TODO: Cleaner way to do this
-    f[k].attrs["encoding-type"] = f"{elem.format}_matrix"
-    f[k].attrs["encoding-version"] = "0.1.0"
 
 
-@_REGISTRY.register_write(H5Group, (DaskArray, CupyArray), IOSpec("array", "0.2.0"))
-@_REGISTRY.register_write(ZarrGroup, (DaskArray, CupyArray), IOSpec("array", "0.2.0"))
-@_REGISTRY.register_write(
-    H5Group, (DaskArray, CupyCSRMatrix), IOSpec("csr_matrix", "0.1.0")
-)
-@_REGISTRY.register_write(
-    H5Group, (DaskArray, CupyCSCMatrix), IOSpec("csc_matrix", "0.1.0")
-)
-@_REGISTRY.register_write(
-    ZarrGroup, (DaskArray, CupyCSRMatrix), IOSpec("csr_matrix", "0.1.0")
-)
-@_REGISTRY.register_write(
-    ZarrGroup, (DaskArray, CupyCSCMatrix), IOSpec("csc_matrix", "0.1.0")
-)
-def write_cupy_dask_sparse(f, k, elem, _writer, dataset_kwargs=MappingProxyType({})):
+def write_cupy_dask(f, k, elem, _writer, dataset_kwargs=MappingProxyType({})):
     _writer.write_elem(
         f,
         k,
@@ -826,18 +811,6 @@ def write_cupy_dask_sparse(f, k, elem, _writer, dataset_kwargs=MappingProxyType(
     )
 
 
-@_REGISTRY.register_write(
-    H5Group, (DaskArray, sparse.csr_matrix), IOSpec("csr_matrix", "0.1.0")
-)
-@_REGISTRY.register_write(
-    H5Group, (DaskArray, sparse.csc_matrix), IOSpec("csc_matrix", "0.1.0")
-)
-@_REGISTRY.register_write(
-    ZarrGroup, (DaskArray, sparse.csr_matrix), IOSpec("csr_matrix", "0.1.0")
-)
-@_REGISTRY.register_write(
-    ZarrGroup, (DaskArray, sparse.csc_matrix), IOSpec("csc_matrix", "0.1.0")
-)
 def write_dask_sparse(
     f: GroupStorageType,
     k: str,
@@ -886,6 +859,26 @@ def write_dask_sparse(
         disk_mtx.append(elem[chunk_slice(chunk_start, chunk_stop)].compute())
 
 
+for array_type, group_type in product(
+    [DaskArray, views.DaskArrayView], [H5Group, ZarrGroup]
+):
+    for cupy_array_type, spec in [
+        (CupyArray, IOSpec("array", "0.2.0")),
+        (CupyCSCMatrix, IOSpec("csc_matrix", "0.1.0")),
+        (CupyCSRMatrix, IOSpec("csr_matrix", "0.1.0")),
+    ]:
+        _REGISTRY.register_write(group_type, (array_type, cupy_array_type), spec)(
+            write_cupy_dask
+        )
+    for scipy_sparse_type, spec in [
+        (sparse.csr_matrix, IOSpec("csr_matrix", "0.1.0")),
+        (sparse.csc_matrix, IOSpec("csc_matrix", "0.1.0")),
+    ]:
+        _REGISTRY.register_write(group_type, (array_type, scipy_sparse_type), spec)(
+            write_dask_sparse
+        )
+
+
 @_REGISTRY.register_read(H5Group, IOSpec("csc_matrix", "0.1.0"))
 @_REGISTRY.register_read(H5Group, IOSpec("csr_matrix", "0.1.0"))
 @_REGISTRY.register_read(ZarrGroup, IOSpec("csc_matrix", "0.1.0"))

anndata/_io/specs/registry.py

@@ -9,6 +9,7 @@ from types import MappingProxyType
 from typing import TYPE_CHECKING, Generic, TypeVar
 
 from anndata._io.utils import report_read_key_on_error, report_write_key_on_error
+from anndata._settings import settings
 from anndata._types import Read, ReadLazy, _ReadInternal, _ReadLazyInternal
 from anndata.compat import DaskArray, ZarrGroup, _read_attr, is_zarr_v2
 
@@ -240,12 +241,9 @@ def proc_spec_mapping(spec: Mapping[str, str]) -> IOSpec:
 def get_spec(
     elem: StorageType,
 ) -> IOSpec:
-    return proc_spec(
-        {
-            k: _read_attr(elem.attrs, k, "")
-            for k in ["encoding-type", "encoding-version"]
-        }
-    )
+    return proc_spec({
+        k: _read_attr(elem.attrs, k, "") for k in ["encoding-type", "encoding-version"]
+    })
 
 
 def _iter_patterns(
@@ -349,10 +347,17 @@ class Writer:
 
         import h5py
 
+        from anndata._io.zarr import is_group_consolidated
+
         # we allow stores to have a prefix like /uns which are then written to with keys like /uns/foo
+        is_zarr_group = isinstance(store, ZarrGroup)
         if "/" in k.split(store.name)[-1][1:]:
-            msg = "Forward slashes are not allowed in keys."
-            raise ValueError(msg)
+            if is_zarr_group or settings.disallow_forward_slash_in_h5ad:
+                msg = f"Forward slashes are not allowed in keys in {type(store)}"
+                raise ValueError(msg)
+            else:
+                msg = "Forward slashes will be disallowed in h5 stores in the next minor release"
+                warnings.warn(msg, FutureWarning, stacklevel=2)
 
         if isinstance(store, h5py.File):
             store = store["/"]
@@ -360,19 +365,11 @@ class Writer:
         dest_type = type(store)
 
         # Normalize k to absolute path
-        if (
-            is_zarr_v2_store := (
-                (is_zarr_store := isinstance(store, ZarrGroup)) and is_zarr_v2()
-            )
-        ) or (isinstance(store, h5py.Group) and not PurePosixPath(k).is_absolute()):
+        if (is_zarr_group and is_zarr_v2()) or (
+            isinstance(store, h5py.Group) and not PurePosixPath(k).is_absolute()
+        ):
             k = str(PurePosixPath(store.name) / k)
-        is_consolidated = False
-        if is_zarr_v2_store:
-            from zarr.storage import ConsolidatedMetadataStore
-
-            is_consolidated = isinstance(store.store, ConsolidatedMetadataStore)
-        elif is_zarr_store:
-            is_consolidated = store.metadata.consolidated_metadata is not None
+        is_consolidated = is_group_consolidated(store) if is_zarr_group else False
         if is_consolidated:
             msg = "Cannot overwrite/edit a store with consolidated metadata"
             raise ValueError(msg)

anndata/_io/utils.py

@@ -1,13 +1,11 @@
 from __future__ import annotations
 
+from collections.abc import Callable
 from functools import WRAPPER_ASSIGNMENTS, wraps
 from itertools import pairwise
-from typing import TYPE_CHECKING, cast
+from typing import TYPE_CHECKING, Literal, cast
 from warnings import warn
 
-import h5py
-from packaging.version import Version
-
 from .._core.sparse_dataset import BaseCompressedSparseDataset
 
 if TYPE_CHECKING:
@@ -21,9 +19,6 @@ if TYPE_CHECKING:
 
     Storage = StorageType | BaseCompressedSparseDataset
 
-# For allowing h5py v3
-# https://github.com/scverse/anndata/issues/442
-H5PY_V3 = Version(h5py.__version__).major >= 3
 
 # -------------------------------------------------------------------------------
 # Type conversion

anndata/_io/zarr.py

@@ -77,13 +77,11 @@ def read_zarr(store: PathLike[str] | str | MutableMapping | zarr.Group) -> AnnDa
     # Read with handling for backwards compat
     def callback(func, elem_name: str, elem, iospec):
         if iospec.encoding_type == "anndata" or elem_name.endswith("/"):
-            return AnnData(
-                **{
-                    k: read_dispatched(v, callback)
-                    for k, v in dict(elem).items()
-                    if not k.startswith("raw.")
-                }
-            )
+            return AnnData(**{
+                k: read_dispatched(v, callback)
+                for k, v in dict(elem).items()
+                if not k.startswith("raw.")
+            })
         elif elem_name.startswith("/raw."):
             return None
         elif elem_name in {"/obs", "/var"}:
@@ -155,3 +153,14 @@ def open_write_group(
     if not is_zarr_v2() and "zarr_format" not in kwargs:
         kwargs["zarr_format"] = settings.zarr_write_format
     return zarr.open_group(store, mode=mode, **kwargs)
+
+
+def is_group_consolidated(group: zarr.Group) -> bool:
+    if not isinstance(group, zarr.Group):
+        msg = f"Expected zarr.Group, got {type(group)}"
+        raise TypeError(msg)
+    if is_zarr_v2():
+        from zarr.storage import ConsolidatedMetadataStore
+
+        return isinstance(group.store, ConsolidatedMetadataStore)
+    return group.metadata.consolidated_metadata is not None

anndata/_settings.py

@@ -478,6 +478,14 @@ settings.register(
     get_from_env=check_and_get_int,
 )
 
+settings.register(
+    "disallow_forward_slash_in_h5ad",
+    default_value=False,
+    description="Whether or not to disallow the `/` character in keys for h5ad files",
+    validate=validate_bool,
+    get_from_env=check_and_get_bool,
+)
+
 
 ##################################################################################
 ##################################################################################

anndata/_settings.pyi

@@ -45,5 +45,6 @@ class _AnnDataSettingsManager(SettingsManager):
     zarr_write_format: Literal[2, 3] = 2
     use_sparse_array_on_read: bool = False
     min_rows_for_chunked_h5_copy: int = 1000
+    disallow_forward_slash_in_h5ad: bool = False
 
 settings: _AnnDataSettingsManager

anndata/compat/__init__.py

@@ -3,6 +3,7 @@ from __future__ import annotations
 from codecs import decode
 from collections.abc import Mapping, Sequence
 from functools import cache, partial, singledispatch
+from importlib.metadata import version
 from importlib.util import find_spec
 from types import EllipsisType
 from typing import TYPE_CHECKING, TypeVar
@@ -75,10 +76,9 @@ H5File = h5py.File
 #############################
 @cache
 def is_zarr_v2() -> bool:
-    import zarr
     from packaging.version import Version
 
-    return Version(zarr.__version__) < Version("3.0.0")
+    return Version(version("zarr")) < Version("3.0.0")
 
 
 if is_zarr_v2():
@@ -213,7 +213,7 @@ else:
 
 NULLABLE_NUMPY_STRING_TYPE = (
     np.dtype("O")
-    if Version(np.__version__) < Version("2")
+    if Version(version("numpy")) < Version("2")
     else np.dtypes.StringDType(na_object=pd.NA)
 )
 
@@ -428,11 +428,3 @@ def _safe_transpose(x):
         return _transpose_by_block(x)
     else:
         return x.T
-
-
-def _map_cat_to_str(cat: pd.Categorical) -> pd.Categorical:
-    if Version(pd.__version__) >= Version("2.1"):
-        # Argument added in pandas 2.1
-        return cat.map(str, na_action="ignore")
-    else:
-        return cat.map(str)

anndata/experimental/merge.py

@@ -26,8 +26,8 @@ from .._core.merge import (
 )
 from .._core.sparse_dataset import BaseCompressedSparseDataset, sparse_dataset
 from .._io.specs import read_elem, write_elem
-from ..compat import H5Array, H5Group, ZarrArray, ZarrGroup, _map_cat_to_str
-from . import read_dispatched
+from ..compat import H5Array, H5Group, ZarrArray, ZarrGroup
+from . import read_dispatched, read_elem_lazy
 
 if TYPE_CHECKING:
     from collections.abc import Callable, Collection, Iterable, Sequence
@@ -173,7 +173,7 @@ def write_concat_dense(  # noqa: PLR0917
     output_path: ZarrGroup | H5Group,
     axis: Literal[0, 1] = 0,
     reindexers: Reindexer | None = None,
-    fill_value=None,
+    fill_value: Any = None,
 ):
     """
     Writes the concatenation of given dense arrays to disk using dask.
@@ -193,9 +193,10 @@ def write_concat_dense(  # noqa: PLR0917
         axis=axis,
     )
     write_elem(output_group, output_path, res)
-    output_group[output_path].attrs.update(
-        {"encoding-type": "array", "encoding-version": "0.2.0"}
-    )
+    output_group[output_path].attrs.update({
+        "encoding-type": "array",
+        "encoding-version": "0.2.0",
+    })
 
 
 def write_concat_sparse(  # noqa: PLR0917
@@ -205,7 +206,7 @@ def write_concat_sparse(  # noqa: PLR0917
     max_loaded_elems: int,
     axis: Literal[0, 1] = 0,
     reindexers: Reindexer | None = None,
-    fill_value=None,
+    fill_value: Any = None,
 ):
     """
     Writes and concatenates sparse datasets into a single output dataset.
@@ -245,26 +246,24 @@ def write_concat_sparse(  # noqa: PLR0917
 
 
 def _write_concat_mappings(  # noqa: PLR0913, PLR0917
-    mappings,
+    mappings: Collection[dict],
     output_group: ZarrGroup | H5Group,
-    keys,
-    path,
-    max_loaded_elems,
-    axis=0,
-    index=None,
-    reindexers=None,
-    fill_value=None,
+    keys: Collection[str],
+    output_path: str | Path,
+    max_loaded_elems: int,
+    axis: Literal[0, 1] = 0,
+    index: pd.Index = None,
+    reindexers: list[Reindexer] | None = None,
+    fill_value: Any = None,
 ):
     """
     Write a list of mappings to a zarr/h5 group.
     """
-    mapping_group = output_group.create_group(path)
-    mapping_group.attrs.update(
-        {
-            "encoding-type": "dict",
-            "encoding-version": "0.1.0",
-        }
-    )
+    mapping_group = output_group.create_group(output_path)
+    mapping_group.attrs.update({
+        "encoding-type": "dict",
+        "encoding-version": "0.1.0",
+    })
     for k in keys:
         elems = [m[k] for m in mappings]
         _write_concat_sequence(
@@ -281,13 +280,13 @@ def _write_concat_mappings(  # noqa: PLR0913, PLR0917
 
 def _write_concat_arrays(  # noqa: PLR0913, PLR0917
     arrays: Sequence[ZarrArray | H5Array | BaseCompressedSparseDataset],
-    output_group,
-    output_path,
-    max_loaded_elems,
-    axis=0,
-    reindexers=None,
-    fill_value=None,
-    join="inner",
+    output_group: ZarrGroup | H5Group,
+    output_path: str | Path,
+    max_loaded_elems: int,
+    axis: Literal[0, 1] = 0,
+    reindexers: list[Reindexer] | None = None,
+    fill_value: Any = None,
+    join: Literal["inner", "outer"] = "inner",
 ):
     init_elem = arrays[0]
     init_type = type(init_elem)
@@ -325,14 +324,14 @@ def _write_concat_arrays(  # noqa: PLR0913, PLR0917
 
 def _write_concat_sequence(  # noqa: PLR0913, PLR0917
     arrays: Sequence[pd.DataFrame | BaseCompressedSparseDataset | H5Array | ZarrArray],
-    output_group,
-    output_path,
-    max_loaded_elems,
-    axis=0,
-    index=None,
-    reindexers=None,
-    fill_value=None,
-    join="inner",
+    output_group: ZarrGroup | H5Group,
+    output_path: str | Path,
+    max_loaded_elems: int,
+    axis: Literal[0, 1] = 0,
+    index: pd.Index = None,
+    reindexers: list[Reindexer] | None = None,
+    fill_value: Any = None,
+    join: Literal["inner", "outer"] = "inner",
 ):
     """
     array, dataframe, csc_matrix, csc_matrix
@@ -377,17 +376,27 @@ def _write_concat_sequence(  # noqa: PLR0913, PLR0917
         raise NotImplementedError(msg)
 
 
-def _write_alt_mapping(groups, output_group, alt_axis_name, alt_indices, merge):
-    alt_mapping = merge([read_as_backed(g[alt_axis_name]) for g in groups])
-    # If its empty, we need to write an empty dataframe with the correct index
-    if not alt_mapping:
-        alt_df = pd.DataFrame(index=alt_indices)
-        write_elem(output_group, alt_axis_name, alt_df)
-    else:
-        write_elem(output_group, alt_axis_name, alt_mapping)
+def _write_alt_mapping(
+    groups: Collection[H5Group, ZarrGroup],
+    output_group: ZarrGroup | H5Group,
+    alt_axis_name: Literal["obs", "var"],
+    merge: Callable,
+    reindexers: list[Reindexer],
+):
+    alt_mapping = merge([
+        {k: r(read_elem(v), axis=0) for k, v in dict(g[f"{alt_axis_name}m"]).items()}
+        for r, g in zip(reindexers, groups, strict=True)
+    ])
+    write_elem(output_group, f"{alt_axis_name}m", alt_mapping)
 
 
-def _write_alt_annot(groups, output_group, alt_axis_name, alt_indices, merge):
+def _write_alt_annot(
+    groups: Collection[H5Group, ZarrGroup],
+    output_group: ZarrGroup | H5Group,
+    alt_axis_name: Literal["obs", "var"],
+    alt_indices: pd.Index,
+    merge: Callable,
+):
     # Annotation for other axis
     alt_annot = merge_dataframes(
         [read_elem(g[alt_axis_name]) for g in groups], alt_indices, merge
@@ -396,7 +405,13 @@ def _write_alt_annot(groups, output_group, alt_axis_name, alt_indices, merge):
 
 
 def _write_axis_annot(  # noqa: PLR0917
-    groups, output_group, axis_name, concat_indices, label, label_col, join
+    groups: Collection[H5Group, ZarrGroup],
+    output_group: ZarrGroup | H5Group,
+    axis_name: Literal["obs", "var"],
+    concat_indices: pd.Index,
+    label: str,
+    label_col: str,
+    join: Literal["inner", "outer"],
 ):
     concat_annot = pd.concat(
         unify_dtypes(read_elem(g[axis_name]) for g in groups),
@@ -409,6 +424,23 @@ def _write_axis_annot(  # noqa: PLR0917
     write_elem(output_group, axis_name, concat_annot)
 
 
+def _write_alt_pairwise(
+    groups: Collection[H5Group, ZarrGroup],
+    output_group: ZarrGroup | H5Group,
+    alt_axis_name: Literal["obs", "var"],
+    merge: Callable,
+    reindexers: list[Reindexer],
+):
+    alt_pairwise = merge([
+        {
+            k: r(r(read_elem_lazy(v), axis=0), axis=1)
+            for k, v in dict(g[f"{alt_axis_name}p"]).items()
+        }
+        for r, g in zip(reindexers, groups, strict=True)
+    ])
+    write_elem(output_group, f"{alt_axis_name}p", alt_pairwise)
+
+
 def concat_on_disk(  # noqa: PLR0912, PLR0913, PLR0915
     in_files: Collection[PathLike[str] | str] | Mapping[str, PathLike[str] | str],
     out_file: PathLike[str] | str,
@@ -491,7 +523,8 @@ def concat_on_disk(  # noqa: PLR0912, PLR0913, PLR0915
         DataFrames are padded with missing values.
     pairwise
         Whether pairwise elements along the concatenated dimension should be included.
-        This is False by default, since the resulting arrays are often not meaningful.
+        This is False by default, since the resulting arrays are often not meaningful, and raises {class}`NotImplementedError` when True.
+        If you are interested in this feature, please open an issue.
 
     Notes
     -----
@@ -610,7 +643,7 @@ def concat_on_disk(  # noqa: PLR0912, PLR0913, PLR0915
     )
     if index_unique is not None:
         concat_indices = concat_indices.str.cat(
-            _map_cat_to_str(label_col), sep=index_unique
+            label_col.map(str, na_action="ignore"), sep=index_unique
         )
 
     # Resulting indices for {axis_name} and {alt_axis_name}
@@ -635,7 +668,10 @@ def concat_on_disk(  # noqa: PLR0912, PLR0913, PLR0915
     _write_alt_annot(groups, output_group, alt_axis_name, alt_index, merge)
 
     # Write {alt_axis_name}m
-    _write_alt_mapping(groups, output_group, alt_axis_name, alt_index, merge)
+    _write_alt_mapping(groups, output_group, alt_axis_name, merge, reindexers)
+
+    # Write {alt_axis_name}p
+    _write_alt_pairwise(groups, output_group, alt_axis_name, merge, reindexers)
 
     # Write X
 

anndata/experimental/multi_files/_anncollection.py

@@ -16,7 +16,7 @@ from ..._core.index import _normalize_index, _normalize_indices
 from ..._core.merge import concat_arrays, inner_concat_aligned_mapping
 from ..._core.sparse_dataset import BaseCompressedSparseDataset
 from ..._core.views import _resolve_idx
-from ...compat import _map_cat_to_str, old_positionals
+from ...compat import old_positionals
 
 if TYPE_CHECKING:
     from collections.abc import Iterable, Sequence
@@ -731,7 +731,7 @@ class AnnCollection(_ConcatViewMixin, _IterateViewMixin):
         )
         if index_unique is not None:
             concat_indices = concat_indices.str.cat(
-                _map_cat_to_str(label_col), sep=index_unique
+                label_col.map(str, na_action="ignore"), sep=index_unique
             )
         self.obs_names = pd.Index(concat_indices)
 

{anndata-0.12.2.dist-info → anndata-0.12.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: anndata
-Version: 0.12.2
+Version: 0.12.3
 Summary: Annotated data.
 Project-URL: Documentation, https://anndata.readthedocs.io/
 Project-URL: Source, https://github.com/scverse/anndata
@@ -38,15 +38,14 @@ Requires-Dist: cupy-cuda11x; extra == 'cu11'
 Provides-Extra: cu12
 Requires-Dist: cupy-cuda12x; extra == 'cu12'
 Provides-Extra: dask
-Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,<2025.2.0,>=2023.5.1; extra == 'dask'
+Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,!=2025.2.*,!=2025.3.*,!=2025.4.*,!=2025.5.*,!=2025.6.*,!=2025.7.*,!=2025.8.*,>=2023.5.1; extra == 'dask'
 Provides-Extra: dev
-Requires-Dist: hatch-vcs; extra == 'dev'
 Requires-Dist: towncrier>=24.8.0; extra == 'dev'
 Provides-Extra: dev-doc
 Requires-Dist: towncrier>=24.8.0; extra == 'dev-doc'
 Provides-Extra: doc
 Requires-Dist: awkward>=2.3; extra == 'doc'
-Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,<2025.2.0,>=2023.5.1; extra == 'doc'
+Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,!=2025.2.*,!=2025.3.*,!=2025.4.*,!=2025.5.*,!=2025.6.*,!=2025.7.*,!=2025.8.*,>=2023.5.1; extra == 'doc'
 Requires-Dist: ipython; extra == 'doc'
 Requires-Dist: myst-nb; extra == 'doc'
 Requires-Dist: myst-parser; extra == 'doc'
@@ -64,14 +63,14 @@ Provides-Extra: gpu
 Requires-Dist: cupy; extra == 'gpu'
 Provides-Extra: lazy
 Requires-Dist: aiohttp; extra == 'lazy'
-Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,<2025.2.0,>=2023.5.1; extra == 'lazy'
+Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,!=2025.2.*,!=2025.3.*,!=2025.4.*,!=2025.5.*,!=2025.6.*,!=2025.7.*,!=2025.8.*,>=2023.5.1; extra == 'lazy'
 Requires-Dist: requests; extra == 'lazy'
 Requires-Dist: xarray>=2025.06.1; extra == 'lazy'
 Provides-Extra: test
 Requires-Dist: aiohttp; extra == 'test'
 Requires-Dist: awkward>=2.3.2; extra == 'test'
 Requires-Dist: boltons; extra == 'test'
-Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,<2025.2.0,>=2023.5.1; extra == 'test'
+Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,!=2025.2.*,!=2025.3.*,!=2025.4.*,!=2025.5.*,!=2025.6.*,!=2025.7.*,!=2025.8.*,>=2023.5.1; extra == 'test'
 Requires-Dist: dask[distributed]; extra == 'test'
 Requires-Dist: filelock; extra == 'test'
 Requires-Dist: httpx<1.0; extra == 'test'
@@ -93,7 +92,7 @@ Requires-Dist: xarray>=2025.06.1; extra == 'test'
 Provides-Extra: test-min
 Requires-Dist: awkward>=2.3.2; extra == 'test-min'
 Requires-Dist: boltons; extra == 'test-min'
-Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,<2025.2.0,>=2023.5.1; extra == 'test-min'
+Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,!=2025.2.*,!=2025.3.*,!=2025.4.*,!=2025.5.*,!=2025.6.*,!=2025.7.*,!=2025.8.*,>=2023.5.1; extra == 'test-min'
 Requires-Dist: dask[distributed]; extra == 'test-min'
 Requires-Dist: filelock; extra == 'test-min'
 Requires-Dist: httpx<1.0; extra == 'test-min'

{anndata-0.12.2.dist-info → anndata-0.12.3.dist-info}/RECORD

@@ -1,8 +1,7 @@
-anndata/__init__.py,sha256=GdrXtUOgciN34rNOl3CxpzvoBgl0yERqrDLWjlwF3RI,1468
-anndata/_settings.py,sha256=UR6tHlWmEEgoaC3e4LuYavveeHICgaC7XOZOyEgNX-0,15712
-anndata/_settings.pyi,sha256=KUJEheJy1zvCBN2NvNEXAGcjLPUQcdhk0STIcU4mM4I,1545
+anndata/__init__.py,sha256=daAzY8GGouJxCe30Lcr2pl9Jwo2dcGXHPi7WxnHpuOE,1710
+anndata/_settings.py,sha256=Y6d28jAF7qnZLfDdg-0L_-Z7zXZR8zjSYlmvWRU_HO4,15949
+anndata/_settings.pyi,sha256=88wa1EG5Bz3ZKIJ68iw41nwGPA8asnpqYsnATsC5mpc,1594
 anndata/_types.py,sha256=c71REP9wS7Vz2cYrNxuNjPYdnq8MJ5g04MNrSi85ATA,5427
-anndata/_version.py,sha256=qsRPKvJAzUrnf49DHZk-FYfXKOASg5nJV2qomuOttX0,2160
 anndata/_warnings.py,sha256=iFXa9EzPyuPbzRAzoG04oTXAyjnXhQa5zxAMZdsGLwM,702
 anndata/abc.py,sha256=jG64k59ZZ9Hfn-QWt_btZLuF7eGv_YNYwH91WdbR240,1645
 anndata/io.py,sha256=DrIo-FU6qbrdk5aVKoUIBoMttZaO5QWP4bowS9xaebI,698
@@ -14,45 +13,45 @@ anndata/_core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 anndata/_core/access.py,sha256=pts7fGUKgGZANSsu_qAA7L10qHM-jT1zIehbl3441OY,873
 anndata/_core/aligned_df.py,sha256=MrGdi1zNZZlkkv4IeS2yY-R5ldXpchTlMlJK7PKRa7A,3833
 anndata/_core/aligned_mapping.py,sha256=BYU1jslMWIhtFTtUMaXY8ZCyt0J4_ZsJTmj6J2yAXTQ,14257
-anndata/_core/anndata.py,sha256=ZQF9L5Zt4k1Bg0npd9iL-PS_pYx62MfQzW1llN4QcRA,78291
+anndata/_core/anndata.py,sha256=e9ISy2CI7QaG6mievs8Aw33sho8ZN1CMgqPQZ-ZfbSw,78782
 anndata/_core/extensions.py,sha256=9Rsho6qnr3PJHULrYGiZHCBinBZYJK6zyf3cFsl_gBY,10425
 anndata/_core/file_backing.py,sha256=kT71R_kZp_CiHImBK8IaZXsvYVtbX2Mg-7L2ldAWojM,5113
 anndata/_core/index.py,sha256=6oED8kjTFKXnZSJXbkGFwscRtqV346h05Dx_Spd68WY,9298
-anndata/_core/merge.py,sha256=v0PxVs49KUZx6X252EtGt7XUHbO3mytTPK_o3Vd1nuo,60302
+anndata/_core/merge.py,sha256=q9eDTQNdqvEJhnkft2UP9gXrmYLQf6CzWgj4YXHIn-s,60242
 anndata/_core/raw.py,sha256=x_PwwaDQscVQOFJ38kF7sNQ47LxowpS38h2RQfU5Zwo,7925
-anndata/_core/sparse_dataset.py,sha256=syXVDdQsEPSBvEi4eyBiAxPiq2TSk7qGStP8QSBTwBg,26801
+anndata/_core/sparse_dataset.py,sha256=9ZVzH7cPdom-bsWEYgbqQvCucc3erhEIeqK2Z_wzDwA,26826
 anndata/_core/storage.py,sha256=mHzqp7YBJ-rGQFulMAx__D-Z7y4omHPyb1cP7YxfbFE,2555
-anndata/_core/views.py,sha256=eOFSV9pKhgcfPvK-c9nxfYdD6o0EVSxE7eSJissojwU,15018
+anndata/_core/views.py,sha256=DIJgnqPvh07wbLousjZbGBsMC55oyBsMbSeybQC5sIY,15019
 anndata/_core/xarray.py,sha256=JeQjTuSQEiZF8cryKDYf9d7yt-ufQEVo9x94YaczuPQ,16078
 anndata/_io/__init__.py,sha256=GTNeUZ8d8aA3sK4P33tyljIc60KapLbkqBC6J1y3l9U,346
-anndata/_io/h5ad.py,sha256=gABV7M7YjThZ7X9VAsHWs7baqQ4L0Zp90dBz4Kle7ys,14191
+anndata/_io/h5ad.py,sha256=BwBEYU_SZWn3KDD3RuxltDSkyqHxE3xXUfkiPh8OG-Y,13908
 anndata/_io/read.py,sha256=MuTR6dR2WItV2y0sKYvxSO2fu7OlDjaCRYJuT5UbuBo,15933
-anndata/_io/utils.py,sha256=dB2RRaWm9V-CMGI46KhqpmzBGA6LLBnsJc83Q85OcgM,9613
+anndata/_io/utils.py,sha256=3Lg27Q0Uo3HYlz980bG2Y02_VFIt0PiXMNIj_o-mgC4,9490
 anndata/_io/write.py,sha256=r55w6yPIIuUSLW9wyYL8GnkzHHQdAxy6xiCEw9cAC38,4811
-anndata/_io/zarr.py,sha256=hLi7nkgTiqe0ftgVaVSpwlU0Y7VurSTf_C3DfILdfAo,5117
+anndata/_io/zarr.py,sha256=Z996SZ8LV1Fpa_q8o70vHnBzNLOLlVjhf_Rs5EM_Slo,5461
 anndata/_io/specs/__init__.py,sha256=Z6l8xqa7B480U3pqrNIg4-fhUvpBW85w4xA3i3maAUM,427
-anndata/_io/specs/lazy_methods.py,sha256=64rr1C83aaiN-iO7m1R03dqd6TbiJQbhzOQI5lXHD0o,12270
-anndata/_io/specs/methods.py,sha256=dz-lfDjoLRpnRXdKjzDaA9_DBbOdys5BIL5ivMCHqvs,46405
-anndata/_io/specs/registry.py,sha256=hno-mvefhcDHmACrBjcKmlf5T87FPoe-N1Gd3i9otYo,17459
-anndata/compat/__init__.py,sha256=zCh9_7FcePbTTvXceZYY6mPemlKFgiYCy3x7srFQum4,12915
+anndata/_io/specs/lazy_methods.py,sha256=k-s-YwOtwXpdjsyrM0IAsGSadPFxDsVDA3d_Nbpb7Ak,12261
+anndata/_io/specs/methods.py,sha256=rAxRyMphd7DOI7gf2jpUloRFFYA5XgBxQ4mvX4Wcsk0,46171
+anndata/_io/specs/registry.py,sha256=6Z_ffk3uOIagzRPcDCvEoszcgD-U3n8wYnGiPA71ZeI,17539
+anndata/compat/__init__.py,sha256=lsLHB7je0SHSePi9noY3p7kRbOAHhZzmMT1hs_ZSXys,12702
 anndata/experimental/__init__.py,sha256=polIxriEkby0iEqw-IXkUzp8k0wp92BpYY4zl4BsHH0,1648
 anndata/experimental/_dispatch_io.py,sha256=JzH8Uvewabc1gIF3L16RZnM9m2NAG28bQIQ57uP097k,1869
-anndata/experimental/merge.py,sha256=Y18C1AT9R1IF60Y7YxyprJ1hz-ySNb2okXHA6IR6fCU,21914
+anndata/experimental/merge.py,sha256=pl4MtDs_M76cTEqrJ_YJ8zyB6ID7QGzjntlAL7vp_qk,23303
 anndata/experimental/backed/__init__.py,sha256=4dc9M_-_SlfUidDrbWt8PRyD_8bYjypHJ86IpdThHus,230
 anndata/experimental/backed/_compat.py,sha256=rM7CnSJEZCko5wPBFRfvZA9ZKUSpaOVcWFy5u09p1go,519
 anndata/experimental/backed/_io.py,sha256=7bFzn3h8ut49NzppUvsqAX1gjXxAVCFK55Ln0XWzZdY,5965
 anndata/experimental/backed/_lazy_arrays.py,sha256=FR-ZPCOhjPaha278KkhMuYYPYx4T_5IOxtjX3XYjDC4,7424
 anndata/experimental/multi_files/__init__.py,sha256=T7iNLlRbe-KnLT3o7Tb7_nE4Iy_hLkG66UjBOvj2Bj8,107
-anndata/experimental/multi_files/_anncollection.py,sha256=RQ79_7r8sdV_kx66UJUuY9ZgcdM92NxplMEDQUrZXvM,35259
+anndata/experimental/multi_files/_anncollection.py,sha256=d_d-v8X2WJTGNjAJoo2Mdykd-woSTM_oXEf2PUIqS6A,35254
 anndata/experimental/pytorch/__init__.py,sha256=4CkgrahLO8Kc-s2bmv6lVQfDxbO3IUyV0v4ygBDkttY,95
 anndata/experimental/pytorch/_annloader.py,sha256=7mpsFV5vBfxKIje1cPjahtDZ5afkU-H663XB4FJhmok,8075
 anndata/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 anndata/tests/helpers.py,sha256=27p_Nc5vFIiW-7EhV85g3QiE0dStMnUg0uFBRyroZUg,36072
 testing/anndata/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 testing/anndata/_doctest.py,sha256=Qew0N0zLLNiPKN1CLunqY5cTinFLaEhY5GagiYfm6KI,344
-testing/anndata/_pytest.py,sha256=a1Qn5KR5mjCcQI05negkMEv0e2aJX2P_teyl0UMfoeQ,4160
+testing/anndata/_pytest.py,sha256=cg4oWbtH9J1sRNul0n2oOraU1h7cprugr27EUPGDaN0,3997
 testing/anndata/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-anndata-0.12.2.dist-info/METADATA,sha256=M4Jcewb7LkN2pgT41Trw2y3YvZ4Z1EzZAzcQ78K03SE,9643
-anndata-0.12.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-anndata-0.12.2.dist-info/licenses/LICENSE,sha256=VcrXoEVMhtNuvMvKYGP-I5lMT8qZ_6dFf22fsL180qA,1575
-anndata-0.12.2.dist-info/RECORD,,
+anndata-0.12.3.dist-info/METADATA,sha256=6MqCFe54oaFQd9YKcXv8ctz2irw1mLOhFBnq9YgDA3s,9937
+anndata-0.12.3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+anndata-0.12.3.dist-info/licenses/LICENSE,sha256=VcrXoEVMhtNuvMvKYGP-I5lMT8qZ_6dFf22fsL180qA,1575
+anndata-0.12.3.dist-info/RECORD,,

testing/anndata/_pytest.py

@@ -35,14 +35,10 @@ def _anndata_test_env(request: pytest.FixtureRequest) -> None:
 def _doctest_env(
     request: pytest.FixtureRequest, cache: pytest.Cache, tmp_path: Path
 ) -> Generator[None, None, None]:
-    with warnings.catch_warnings():
-        warnings.filterwarnings(
-            "ignore", message=r"Importing read_.* from `anndata` is deprecated"
-        )
-        from scanpy import settings
-
     from contextlib import chdir
 
+    from scanpy import settings
+
     from anndata.utils import import_name
 
     assert isinstance(request.node.parent, pytest.Module)

anndata/_version.py

@@ -1,62 +0,0 @@
-"""Get version from VCS in a dev environment or from package metadata in production.
-
-See <https://github.com/maresb/hatch-vcs-footgun-example>.
-"""
-
-from __future__ import annotations
-
-import warnings
-from pathlib import Path
-
-__all__ = ["__version__"]
-
-_PROJECT_NAME = "anndata"
-
-
-class GetVersionError(Exception):
-    pass
-
-
-def _get_version_from_vcs(project_name: str) -> str:  # pragma: no cover
-    from hatchling.metadata.core import ProjectMetadata
-    from hatchling.plugin.exceptions import UnknownPluginError
-    from hatchling.plugin.manager import PluginManager
-    from hatchling.utils.fs import locate_file
-
-    if (pyproject_toml := locate_file(__file__, "pyproject.toml")) is None:
-        msg = "pyproject.toml not found although hatchling is installed"
-        raise LookupError(msg)
-    root = Path(pyproject_toml).parent
-    metadata = ProjectMetadata(root=str(root), plugin_manager=PluginManager())
-    try:
-        # Version can be either statically set in pyproject.toml or computed dynamically:
-        version = metadata.core.version or metadata.hatch.version.cached
-    except UnknownPluginError as e:
-        msg = "Unable to import hatch plugin."
-        raise ImportError(msg) from e
-    except ValueError as e:
-        msg = f"Could not find hatchling project data in TOML file, {pyproject_toml}"
-        raise GetVersionError(msg) from e
-    except TypeError as e:
-        msg = "Could not parse build configuration."
-        raise GetVersionError(msg) from e
-    except Exception as e:
-        msg = (
-            f"Unknown error getting version from hatchling config for '{project_name}'."
-        )
-        warnings.warn(f"{msg}: {e}", stacklevel=1)
-        raise GetVersionError(msg) from e
-
-    # We found a hatchling environment, but is it ours?
-    if metadata.core.name != project_name:
-        msg = f"Data in pyproject.toml is not related to {project_name}."
-        raise GetVersionError(msg)
-    return version
-
-
-try:
-    __version__ = _get_version_from_vcs(_PROJECT_NAME)
-except (ImportError, LookupError, GetVersionError):
-    import importlib.metadata
-
-    __version__ = importlib.metadata.version(_PROJECT_NAME)