anndata 0.12.0rc4__py3-none-any.whl → 0.12.1__py3-none-any.whl

anndata/_core/aligned_df.py

@@ -59,7 +59,7 @@ def _gen_dataframe_mapping(
         df = pd.DataFrame(
             anno,
             index=None if length is None else mk_index(length),
-            columns=None if len(anno) else [],
+            columns=None if anno else [],
         )
 
     if length is None:

anndata/_core/anndata.py

@@ -62,7 +62,7 @@ if TYPE_CHECKING:
     from .index import Index
 
 
-class AnnData(metaclass=utils.DeprecationMixinMeta):
+class AnnData(metaclass=utils.DeprecationMixinMeta):  # noqa: PLW1641
     """\
     An annotated data matrix.
 

anndata/_core/merge.py

@@ -904,12 +904,6 @@ def concat_arrays(  # noqa: PLR0911, PLR0912
             ],
             format="csr",
         )
-        scipy_version = Version(scipy.__version__)
-        # Bug where xstack produces a matrix not an array in 1.11.*
-        if use_sparse_array and (scipy_version.major, scipy_version.minor) == (1, 11):
-            if mat.format == "csc":
-                return sparse.csc_array(mat)
-            return sparse.csr_array(mat)
         return mat
     else:
         return np.concatenate(

anndata/_core/sparse_dataset.py

@@ -165,7 +165,11 @@ class BackedSparseMatrix(_cs_matrix):
     def _get_contiguous_compressed_slice(
         self, s: slice
     ) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
-        new_indptr = self.indptr[s.start : s.stop + 1].copy()
+        new_indptr = self.indptr[s.start : s.stop + 1]
+        # If indptr is cached, we need to make a copy of the subset
+        # so as not to alter the underlying cached data.
+        if isinstance(self.indptr, np.ndarray):
+            new_indptr = new_indptr.copy()
 
         start = new_indptr[0]
         stop = new_indptr[-1]

anndata/_core/xarray.py

@@ -245,7 +245,7 @@ class Dataset2D:
         if df.index.name != index_key and index_key is not None:
             df = df.set_index(index_key)
         for col in set(self.columns) - non_nullable_string_cols:
-            df[col] = pd.array(self[col].data, dtype="string")
+            df[col] = df[col].astype(dtype="string")
         df.index.name = None  # matches old AnnData object
         return df
 
@@ -389,9 +389,12 @@ class Dataset2D:
         }
         el = self.ds.drop_vars(extension_arrays.keys())
         el = el.reindex({index_dim: index}, method=None, fill_value=fill_value)
-        for col in self.ds:
-            el[col] = pd.Series(self.ds[col], index=self.index).reindex(
-                index, fill_value=fill_value
+        for col, data in extension_arrays.items():
+            el[col] = XDataArray.from_series(
+                pd.Series(data.data, index=self.index).reindex(
+                    index.rename(self.index.name) if index is not None else index,
+                    fill_value=fill_value,
+                )
             )
         return Dataset2D(el)
 

anndata/_io/h5ad.py

@@ -176,7 +176,7 @@ def read_h5ad_backed(
 
 def read_h5ad(
     filename: PathLike[str] | str,
-    backed: Literal["r", "r+"] | bool | None = None,
+    backed: Literal["r", "r+"] | bool | None = None,  # noqa: FBT001
     *,
     as_sparse: Sequence[str] = (),
     as_sparse_fmt: type[CSMatrix] = sparse.csr_matrix,

anndata/_io/read.py

@@ -22,9 +22,11 @@ if TYPE_CHECKING:
     from collections.abc import Generator, Iterable, Iterator, Mapping
 
 
+@old_positionals("first_column_names", "dtype")
 def read_csv(
     filename: PathLike[str] | str | Iterator[str],
     delimiter: str | None = ",",
+    *,
     first_column_names: bool | None = None,
     dtype: str = "float32",
 ) -> AnnData:
@@ -331,9 +333,11 @@ def read_mtx(filename: PathLike[str] | str, dtype: str = "float32") -> AnnData:
     return AnnData(X)
 
 
+@old_positionals("first_column_names", "dtype")
 def read_text(
     filename: PathLike[str] | str | Iterator[str],
     delimiter: str | None = None,
+    *,
     first_column_names: bool | None = None,
     dtype: str = "float32",
 ) -> AnnData:
@@ -381,7 +385,7 @@ def _iter_lines(file_like: Iterable[str]) -> Generator[str, None, None]:
 def _read_text(  # noqa: PLR0912, PLR0915
     f: Iterator[str],
     delimiter: str | None,
-    first_column_names: bool | None,
+    first_column_names: bool | None,  # noqa: FBT001
     dtype: str,
 ) -> AnnData:
     comments = []

anndata/_io/specs/lazy_methods.py

@@ -132,7 +132,7 @@ def read_sparse_as_dask(
     path_or_sparse_dataset = (
         Path(filename(elem))
         if isinstance(elem, H5Group)
-        else ad.io.sparse_dataset(elem)
+        else ad.io.sparse_dataset(elem, should_cache_indptr=False)
     )
     elem_name = get_elem_name(elem)
     shape: tuple[int, int] = tuple(elem.attrs["shape"])
@@ -177,21 +177,37 @@ def read_sparse_as_dask(
     return da_mtx
 
 
+def resolve_chunks(
+    elem: H5Array | ZarrArray,
+    chunks_arg: tuple[int, ...] | None,
+    shape: tuple[int, ...],
+) -> tuple[int, ...]:
+    shape = tuple(elem.shape)
+    if chunks_arg is not None:
+        # None and -1 on a given axis indicate that one should use the shape
+        # in `dask`'s semantics.
+        return tuple(
+            c if c not in {None, -1} else s
+            for c, s in zip(chunks_arg, shape, strict=True)
+        )
+    elif elem.chunks is None:  # h5 unchunked
+        return tuple(min(_DEFAULT_STRIDE, s) for s in shape)
+    return elem.chunks
+
+
 @_LAZY_REGISTRY.register_read(H5Array, IOSpec("string-array", "0.2.0"))
 def read_h5_string_array(
     elem: H5Array,
     *,
     _reader: LazyReader,
-    chunks: tuple[int, int] | None = None,
+    chunks: tuple[int] | None = None,
 ) -> DaskArray:
     import dask.array as da
 
     from anndata._io.h5ad import read_dataset
 
-    return da.from_array(
-        read_dataset(elem),
-        chunks=chunks if chunks is not None else (_DEFAULT_STRIDE,) * len(elem.shape),
-    )
+    chunks = resolve_chunks(elem, chunks, tuple(elem.shape))
+    return da.from_array(read_dataset(elem), chunks=chunks)
 
 
 @_LAZY_REGISTRY.register_read(H5Array, IOSpec("array", "0.2.0"))
@@ -204,13 +220,7 @@ def read_h5_array(
     elem_name: str = elem.name
     shape = tuple(elem.shape)
     dtype = elem.dtype
-    chunks = (
-        tuple(
-            c if c not in {None, -1} else s for c, s in zip(chunks, shape, strict=True)
-        )
-        if chunks is not None
-        else tuple(min(_DEFAULT_STRIDE, s) for s in shape)
-    )
+    chunks = resolve_chunks(elem, chunks, shape)
 
     chunk_layout = tuple(
         compute_chunk_layout_for_axis_size(chunks[i], shape[i])
@@ -228,7 +238,6 @@ def read_h5_array(
 def read_zarr_array(
     elem: ZarrArray, *, _reader: LazyReader, chunks: tuple[int, ...] | None = None
 ) -> DaskArray:
-    chunks: tuple[int, ...] = chunks if chunks is not None else elem.chunks
     import dask.array as da
 
     return da.from_zarr(elem, chunks=chunks)
@@ -284,9 +293,10 @@ def read_dataframe(
     *,
     _reader: LazyReader,
     use_range_index: bool = False,
+    chunks: tuple[int] | None = None,
 ) -> Dataset2D:
     elem_dict = {
-        k: _reader.read_elem(elem[k])
+        k: _reader.read_elem(elem[k], chunks=chunks)
         for k in [*elem.attrs["column-order"], elem.attrs["_index"]]
     }
     # If we use a range index, the coord axis needs to have the special dim name

anndata/_io/specs/methods.py

@@ -24,6 +24,7 @@ from anndata._core.sparse_dataset import _CSCDataset, _CSRDataset, sparse_datase
 from anndata._io.utils import H5PY_V3, check_key, zero_dim_array_as_scalar
 from anndata._warnings import OldFormatWarning
 from anndata.compat import (
+    NULLABLE_NUMPY_STRING_TYPE,
     AwkArray,
     CupyArray,
     CupyCSCMatrix,
@@ -431,7 +432,7 @@ def write_basic(
         dataset_kwargs = zarr_v3_compressor_compat(dataset_kwargs)
         f.create_array(k, shape=elem.shape, dtype=dtype, **dataset_kwargs)
         # see https://github.com/zarr-developers/zarr-python/discussions/2712
-        if isinstance(elem, ZarrArray):
+        if isinstance(elem, ZarrArray | H5Array):
             f[k][...] = elem[...]
         else:
             f[k][...] = elem
@@ -622,24 +623,20 @@ def write_vlen_string_array_zarr(
         f[k][:] = elem
     else:
         from numcodecs import VLenUTF8
+        from zarr.core.dtype import VariableLengthUTF8
 
         dataset_kwargs = dataset_kwargs.copy()
         dataset_kwargs = zarr_v3_compressor_compat(dataset_kwargs)
-        match (
-            ad.settings.zarr_write_format,
-            Version(np.__version__) >= Version("2.0.0"),
-        ):
-            case 2, _:
-                filters, dtype = [VLenUTF8()], object
-            case 3, True:
-                filters, dtype = None, np.dtypes.StringDType()
-            case 3, False:
-                filters, dtype = None, np.dtypes.ObjectDType()
+        dtype = VariableLengthUTF8()
+        filters, fill_value = None, None
+        if ad.settings.zarr_write_format == 2:
+            filters, fill_value = [VLenUTF8()], ""
         f.create_array(
             k,
             shape=elem.shape,
             dtype=dtype,
             filters=filters,
+            fill_value=fill_value,
             **dataset_kwargs,
         )
         f[k][:] = elem
@@ -1041,7 +1038,7 @@ def read_dataframe_partial(
     df = pd.DataFrame(
         {k: read_elem_partial(elem[k], indices=indices[0]) for k in columns},
         index=read_elem_partial(elem[idx_key], indices=indices[0]),
-        columns=columns if len(columns) else None,
+        columns=columns if columns else None,
     )
     if idx_key != "_index":
         df.index.name = idx_key
@@ -1210,7 +1207,10 @@ def _string_array(
     values: np.ndarray, mask: np.ndarray
 ) -> pd.api.extensions.ExtensionArray:
     """Construct a string array from values and mask."""
-    arr = pd.array(values, dtype=pd.StringDtype())
+    arr = pd.array(
+        values.astype(NULLABLE_NUMPY_STRING_TYPE),
+        dtype=pd.StringDtype(),
+    )
     arr[mask] = pd.NA
     return arr
 
@@ -1281,19 +1281,21 @@ def write_scalar_zarr(
         return f.create_dataset(key, data=np.array(value), shape=(), **dataset_kwargs)
     else:
         from numcodecs import VLenUTF8
+        from zarr.core.dtype import VariableLengthUTF8
 
         match ad.settings.zarr_write_format, value:
             case 2, str():
-                filters, dtype = [VLenUTF8()], object
+                filters, dtype, fill_value = [VLenUTF8()], VariableLengthUTF8(), ""
             case 3, str():
-                filters, dtype = None, np.dtypes.StringDType()
+                filters, dtype, fill_value = None, VariableLengthUTF8(), None
             case _, _:
-                filters, dtype = None, np.array(value).dtype
+                filters, dtype, fill_value = None, np.array(value).dtype, None
         a = f.create_array(
             key,
             shape=(),
             dtype=dtype,
             filters=filters,
+            fill_value=fill_value,
             **dataset_kwargs,
         )
         a[...] = np.array(value)

anndata/_io/specs/registry.py

@@ -360,11 +360,22 @@ class Writer:
         dest_type = type(store)
 
         # Normalize k to absolute path
-        if (isinstance(store, ZarrGroup) and is_zarr_v2()) or (
-            isinstance(store, h5py.Group) and not PurePosixPath(k).is_absolute()
-        ):
+        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()):
             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
+        if is_consolidated:
+            msg = "Cannot overwrite/edit a store with consolidated metadata"
+            raise ValueError(msg)
         if k == "/":
             if isinstance(store, ZarrGroup) and not is_zarr_v2():
                 from zarr.core.sync import sync

anndata/_io/zarr.py

@@ -27,19 +27,6 @@ if TYPE_CHECKING:
 T = TypeVar("T")
 
 
-def _check_rec_array(adata: AnnData) -> None:
-    if settings.zarr_write_format == 3 and (
-        structured_dtype_keys := {
-            k
-            for k, v in adata.uns.items()
-            if isinstance(v, np.recarray)
-            or (isinstance(v, np.ndarray) and v.dtype.fields)
-        }
-    ):
-        msg = f"zarr v3 does not support structured dtypes.  Found keys {structured_dtype_keys}"
-        raise NotImplementedError(msg)
-
-
 @no_write_dataset_2d
 def write_zarr(
     store: StoreLike,
@@ -50,7 +37,6 @@ def write_zarr(
     **ds_kwargs,
 ) -> None:
     """See :meth:`~anndata.AnnData.write_zarr`."""
-    _check_rec_array(adata)
     if isinstance(store, Path):
         store = str(store)
     if convert_strings_to_categoricals:

anndata/_settings.py

@@ -13,7 +13,7 @@ from inspect import Parameter, signature
 from types import GenericAlias
 from typing import TYPE_CHECKING, Generic, NamedTuple, TypeVar, cast
 
-from .compat import old_positionals
+from .compat import is_zarr_v2, old_positionals
 
 if TYPE_CHECKING:
     from collections.abc import Callable, Sequence
@@ -333,7 +333,7 @@ class SettingsManager:
         raise AttributeError(msg)
 
     def __dir__(self) -> Iterable[str]:
-        return sorted((*dir(super()), *self._config.keys()))
+        return sorted((*super().__dir__(), *self._config.keys()))
 
     def reset(self, option: Iterable[str] | str) -> None:
         """
@@ -439,6 +439,9 @@ def validate_zarr_write_format(format: int):
     if format not in {2, 3}:
         msg = "non-v2 zarr on-disk format not supported"
         raise ValueError(msg)
+    if format == 3 and is_zarr_v2():
+        msg = "Cannot write v3 format against v2 package"
+        raise ValueError(msg)
 
 
 settings.register(

anndata/_settings.pyi

@@ -0,0 +1,49 @@
+from collections.abc import Callable as Callable
+from collections.abc import Generator, Iterable
+from contextlib import contextmanager
+from dataclasses import dataclass
+from typing import Literal, TypeVar
+
+_T = TypeVar("_T")
+
+@dataclass
+class SettingsManager:
+    __doc_tmpl__: str = ...
+    def describe(
+        self,
+        option: str | Iterable[str] | None = None,
+        *,
+        should_print_description: bool = True,
+        as_rst: bool = False,
+    ) -> str: ...
+    def deprecate(
+        self, option: str, removal_version: str, message: str | None = None
+    ) -> None: ...
+    def register(
+        self,
+        option: str,
+        *,
+        default_value: _T,
+        description: str,
+        validate: Callable[[_T], None],
+        option_type: object | None = None,
+        get_from_env: Callable[[str, _T], _T] = ...,
+    ) -> None: ...
+    def __setattr__(self, option: str, val: object) -> None: ...
+    def __getattr__(self, option: str) -> object: ...
+    def __dir__(self) -> Iterable[str]: ...
+    def reset(self, option: Iterable[str] | str) -> None: ...
+    @contextmanager
+    def override(self, **overrides) -> Generator[None]: ...
+    @property
+    def __doc__(self): ...
+
+class _AnnDataSettingsManager(SettingsManager):
+    remove_unused_categories: bool = True
+    check_uniqueness: bool = True
+    allow_write_nullable_strings: bool = False
+    zarr_write_format: Literal[2, 3] = 2
+    use_sparse_array_on_read: bool = False
+    min_rows_for_chunked_h5_copy: int = 1000
+
+settings: _AnnDataSettingsManager

anndata/compat/__init__.py

@@ -190,6 +190,13 @@ else:
 #############################
 
 
+NULLABLE_NUMPY_STRING_TYPE = (
+    np.dtype("O")
+    if Version(np.__version__) < Version("2")
+    else np.dtypes.StringDType(na_object=pd.NA)
+)
+
+
 @singledispatch
 def _read_attr(attrs: Mapping, name: str, default: Any | None = Empty):
     if default is Empty:
@@ -404,10 +411,3 @@ def _map_cat_to_str(cat: pd.Categorical) -> pd.Categorical:
         return cat.map(str, na_action="ignore")
     else:
         return cat.map(str)
-
-
-NULLABLE_NUMPY_STRING_TYPE = (
-    np.dtype("O")
-    if Version(np.__version__) < Version("2")
-    else np.dtypes.StringDType(na_object=pd.NA)
-)

anndata/experimental/backed/_lazy_arrays.py

@@ -3,19 +3,21 @@ from __future__ import annotations
 from functools import cached_property
 from typing import TYPE_CHECKING, Generic, TypeVar
 
+import numpy as np
 import pandas as pd
 
 from anndata._core.index import _subset
 from anndata._core.views import as_view
 from anndata._io.specs.lazy_methods import get_chunksize
-from anndata.compat import H5Array, ZarrArray
 
 from ..._settings import settings
 from ...compat import (
     NULLABLE_NUMPY_STRING_TYPE,
+    H5Array,
     XBackendArray,
     XDataArray,
     XZarrArrayWrapper,
+    ZarrArray,
 )
 from ...compat import xarray as xr
 
@@ -23,8 +25,6 @@ if TYPE_CHECKING:
     from pathlib import Path
     from typing import Literal
 
-    import numpy as np
-
     from anndata._core.index import Index
     from anndata.compat import ZarrGroup
 
@@ -45,12 +45,34 @@ class ZarrOrHDF5Wrapper(XZarrArrayWrapper, Generic[K]):
     def __getitem__(self, key: xr.core.indexing.ExplicitIndexer):
         if isinstance(self._array, ZarrArray):
             return super().__getitem__(key)
-        return xr.core.indexing.explicit_indexing_adapter(
+        res = xr.core.indexing.explicit_indexing_adapter(
             key,
             self.shape,
             xr.core.indexing.IndexingSupport.OUTER_1VECTOR,
-            lambda key: self._array[key],
+            self._getitem,
         )
+        return res
+
+    def _getitem(self, key: tuple[int | np.integer | slice | np.ndarray]):
+        if not isinstance(key, tuple):
+            msg = f"`xr.core.indexing.explicit_indexing_adapter` should have produced a tuple, got {type(key)} instead"
+            raise ValueError(msg)
+        if (n_key_dims := len(key)) != 1:
+            msg = f"Backed arrays currently only supported in 1d, got {n_key_dims} dims"
+            raise ValueError(msg)
+        key = key[0]
+        # See https://github.com/h5py/h5py/issues/293 for why we need to convert.
+        # See https://github.com/pydata/xarray/blob/fa03b5b4ae95a366f6de5b60f5cc4eb801cd51ec/xarray/core/indexing.py#L1259-L1263
+        # for why we can expect sorted/deduped indexers (which are needed for hdf5).
+        if (
+            isinstance(key, np.ndarray)
+            and np.issubdtype(key.dtype, np.integer)
+            and isinstance(self._array, H5Array)
+        ):
+            key_mask = np.zeros(self._array.shape).astype("bool")
+            key_mask[key] = True
+            return self._array[key_mask]
+        return self._array[key]
 
 
 class CategoricalArray(XBackendArray, Generic[K]):

anndata/tests/helpers.py

@@ -17,7 +17,6 @@ import pytest
 from pandas.api.types import is_numeric_dtype
 from scipy import sparse
 
-import anndata
 from anndata import AnnData, ExperimentalFeatureWarning, Raw
 from anndata._core.aligned_mapping import AlignedMappingBase
 from anndata._core.sparse_dataset import BaseCompressedSparseDataset
@@ -413,10 +412,6 @@ def gen_adata(  # noqa: PLR0913
         awkward_ragged=gen_awkward((12, None, None)),
         # U_recarray=gen_vstr_recarray(N, 5, "U4")
     )
-    # https://github.com/zarr-developers/zarr-python/issues/2134
-    # zarr v3 on-disk does not write structured dtypes
-    if anndata.settings.zarr_write_format == 3:
-        del uns["O_recarray"]
     with warnings.catch_warnings():
         warnings.simplefilter("ignore", ExperimentalFeatureWarning)
         adata = AnnData(
@@ -1088,11 +1083,17 @@ class AccessTrackingStoreBase(LocalStore):
     _accessed_keys: defaultdict[str, list[str]]
 
     def __init__(self, *args, **kwargs):
+        # Needed for zarr v3 to prevent a read-only copy being made
+        # https://github.com/zarr-developers/zarr-python/pull/3156
+        if not is_zarr_v2() and "read_only" not in kwargs:
+            kwargs["read_only"] = True
         super().__init__(*args, **kwargs)
         self._access_count = Counter()
         self._accessed = defaultdict(set)
         self._accessed_keys = defaultdict(list)
 
+        self._read_only = True
+
     def _check_and_track_key(self, key: str):
         for tracked in self._access_count:
             if tracked in key:
@@ -1147,26 +1148,9 @@ if is_zarr_v2():
 else:
 
     class AccessTrackingStore(AccessTrackingStoreBase):
-        async def get(
-            self,
-            key: str,
-            prototype: BufferPrototype | None = None,
-            byte_range: ByteRequest | None = None,
-        ) -> object:
-            self._check_and_track_key(key)
-            return await super().get(key, prototype=prototype, byte_range=byte_range)
-
-
-if is_zarr_v2():
-
-    class AccessTrackingStore(AccessTrackingStoreBase):
-        def __getitem__(self, key: str) -> bytes:
-            self._check_and_track_key(key)
-            return super().__getitem__(key)
+        def __init__(self, *args, **kwargs):
+            super().__init__(*args, **kwargs, read_only=True)
 
-else:
-
-    class AccessTrackingStore(AccessTrackingStoreBase):
         async def get(
             self,
             key: str,

anndata/utils.py

@@ -266,10 +266,9 @@ def make_index_unique(index: pd.Index, join: str = "-"):
 
     if issue_interpretation_warning:
         msg = (
-            f"Suffix used ({join}[0-9]+) to deduplicate index values may make index "
-            "values difficult to interpret. There values with a similar suffixes in "
-            "the index. Consider using a different delimiter by passing "
-            "`join={delimiter}`"
+            f"Suffix used ({join}[0-9]+) to deduplicate index values may make index values difficult to interpret. "
+            "There values with a similar suffixes in the index. "
+            "Consider using a different delimiter by passing `join={delimiter}`. "
             "Example key collisions generated by the make_index_unique algorithm: "
             f"{example_colliding_values}"
         )

{anndata-0.12.0rc4.dist-info → anndata-0.12.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: anndata
-Version: 0.12.0rc4
+Version: 0.12.1
 Summary: Annotated data.
 Project-URL: Documentation, https://anndata.readthedocs.io/
 Project-URL: Source, https://github.com/scverse/anndata
@@ -28,11 +28,11 @@ Requires-Dist: array-api-compat>=1.7.1
 Requires-Dist: h5py>=3.8
 Requires-Dist: legacy-api-wrap
 Requires-Dist: natsort
-Requires-Dist: numpy>=1.25
+Requires-Dist: numpy>=1.26
 Requires-Dist: packaging>=24.2
-Requires-Dist: pandas!=2.1.0rc0,!=2.1.2,>=2.0.0
-Requires-Dist: scipy>=1.11
-Requires-Dist: zarr!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3,!=3.0.4,!=3.0.5,!=3.0.6,!=3.0.7,<3.1,>=2.18.7
+Requires-Dist: pandas!=2.1.2,>=2.1.0
+Requires-Dist: scipy>=1.12
+Requires-Dist: zarr!=3.0.*,>=2.18.7
 Provides-Extra: cu11
 Requires-Dist: cupy-cuda11x; extra == 'cu11'
 Provides-Extra: cu12
@@ -74,13 +74,12 @@ Requires-Dist: boltons; extra == 'test'
 Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,<2025.2.0,>=2023.5.1; extra == 'test'
 Requires-Dist: dask[distributed]; extra == 'test'
 Requires-Dist: filelock; extra == 'test'
-Requires-Dist: httpx; extra == 'test'
+Requires-Dist: httpx<1.0; extra == 'test'
 Requires-Dist: joblib; extra == 'test'
 Requires-Dist: loompy>=3.0.5; extra == 'test'
 Requires-Dist: matplotlib; extra == 'test'
 Requires-Dist: openpyxl; extra == 'test'
-Requires-Dist: pandas>=2.1.0; extra == 'test'
-Requires-Dist: pyarrow; extra == 'test'
+Requires-Dist: pyarrow<21; extra == 'test'
 Requires-Dist: pytest-cov; extra == 'test'
 Requires-Dist: pytest-memray; extra == 'test'
 Requires-Dist: pytest-mock; extra == 'test'
@@ -97,12 +96,12 @@ 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[distributed]; extra == 'test-min'
 Requires-Dist: filelock; extra == 'test-min'
-Requires-Dist: httpx; extra == 'test-min'
+Requires-Dist: httpx<1.0; extra == 'test-min'
 Requires-Dist: joblib; extra == 'test-min'
 Requires-Dist: loompy>=3.0.5; extra == 'test-min'
 Requires-Dist: matplotlib; extra == 'test-min'
 Requires-Dist: openpyxl; extra == 'test-min'
-Requires-Dist: pyarrow; extra == 'test-min'
+Requires-Dist: pyarrow<21; extra == 'test-min'
 Requires-Dist: pytest-cov; extra == 'test-min'
 Requires-Dist: pytest-memray; extra == 'test-min'
 Requires-Dist: pytest-mock; extra == 'test-min'

{anndata-0.12.0rc4.dist-info → anndata-0.12.1.dist-info}/RECORD

@@ -1,5 +1,6 @@
 anndata/__init__.py,sha256=GdrXtUOgciN34rNOl3CxpzvoBgl0yERqrDLWjlwF3RI,1468
-anndata/_settings.py,sha256=rLc-rwxLifFdTPQZyunGGOaY3R0p6dMaz8t4Yftd4AY,15512
+anndata/_settings.py,sha256=Le3ysSfuG0vuYCtnUN3DV4HOnyiGgC-k9Gv0JShosSs,15654
+anndata/_settings.pyi,sha256=KUJEheJy1zvCBN2NvNEXAGcjLPUQcdhk0STIcU4mM4I,1545
 anndata/_types.py,sha256=c71REP9wS7Vz2cYrNxuNjPYdnq8MJ5g04MNrSi85ATA,5427
 anndata/_version.py,sha256=qsRPKvJAzUrnf49DHZk-FYfXKOASg5nJV2qomuOttX0,2160
 anndata/_warnings.py,sha256=iFXa9EzPyuPbzRAzoG04oTXAyjnXhQa5zxAMZdsGLwM,702
@@ -8,50 +9,50 @@ anndata/io.py,sha256=DrIo-FU6qbrdk5aVKoUIBoMttZaO5QWP4bowS9xaebI,698
 anndata/logging.py,sha256=E6nlPl-Em0yBjL5p-EcQFmhHTIUirhnZbfXbQtSVSek,1662
 anndata/types.py,sha256=FF3wDkntl6Jq35l0r_kEET33ljj9L7pmIrUr5-MLAvE,698
 anndata/typing.py,sha256=sRiAg16asjnKyXk1L4BtKWggyHMPLoxXzxTDmX3i7MY,1555
-anndata/utils.py,sha256=IHct5lsDXsvwm3-_Z-Sm3dTDfGpgmmJyZVf-gQH941k,14771
+anndata/utils.py,sha256=D4t_iQdTPeHukN4H7no0QZTIzWzclMYsWAHSBpubvCg,14758
 anndata/_core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 anndata/_core/access.py,sha256=pts7fGUKgGZANSsu_qAA7L10qHM-jT1zIehbl3441OY,873
-anndata/_core/aligned_df.py,sha256=oZl2S2fQps4Uio6unXM-vdsi1SIU8tfVgfbNNhz9b08,3838
+anndata/_core/aligned_df.py,sha256=MrGdi1zNZZlkkv4IeS2yY-R5ldXpchTlMlJK7PKRa7A,3833
 anndata/_core/aligned_mapping.py,sha256=BYU1jslMWIhtFTtUMaXY8ZCyt0J4_ZsJTmj6J2yAXTQ,14257
-anndata/_core/anndata.py,sha256=L3w4QA6c5dqoUiNBLnEo03tuWRqPSvMB2z260KuY3xA,77730
+anndata/_core/anndata.py,sha256=BADYc8TpS6yc1-bw5sh5cPzB4v63O5ZH0YFFChKO7TY,77747
 anndata/_core/extensions.py,sha256=9Rsho6qnr3PJHULrYGiZHCBinBZYJK6zyf3cFsl_gBY,10425
 anndata/_core/file_backing.py,sha256=kT71R_kZp_CiHImBK8IaZXsvYVtbX2Mg-7L2ldAWojM,5113
 anndata/_core/index.py,sha256=lyVuDfKvEeQYpgKjDsnuZNt4k4wV3adFowO_RrcohpE,9353
-anndata/_core/merge.py,sha256=eIKxNmUSj7SopcKxs8GkjXoIKLSp8syIWQCTdw1GvDw,60630
+anndata/_core/merge.py,sha256=v0PxVs49KUZx6X252EtGt7XUHbO3mytTPK_o3Vd1nuo,60302
 anndata/_core/raw.py,sha256=EfTLoizP_mLtfYn0BR1Rpya0iZoGF4CupojWyeLGWpc,7797
-anndata/_core/sparse_dataset.py,sha256=Tx-3kHXV2cdE9gScaIDhQd-QtAmpx0turRS7Ad6yuJg,26592
+anndata/_core/sparse_dataset.py,sha256=syXVDdQsEPSBvEi4eyBiAxPiq2TSk7qGStP8QSBTwBg,26801
 anndata/_core/storage.py,sha256=mHzqp7YBJ-rGQFulMAx__D-Z7y4omHPyb1cP7YxfbFE,2555
 anndata/_core/views.py,sha256=rbmI7P4dEcefhjons2l42H9D509xhxyXKTeyWiIBdtw,14657
-anndata/_core/xarray.py,sha256=IprGtB6TY4__8khyLM9lMkukEHVDCKHESva68DMCZpg,16008
+anndata/_core/xarray.py,sha256=pvAMSxrHmuz2d-xbalYmuNi56GrLPw_2Ehko8nss9Xg,16157
 anndata/_io/__init__.py,sha256=GTNeUZ8d8aA3sK4P33tyljIc60KapLbkqBC6J1y3l9U,346
-anndata/_io/h5ad.py,sha256=tGLXm9N6BqD2XQuaKbi9e1rcvXCQT9tK5ano_9ncqHc,13617
-anndata/_io/read.py,sha256=stAFfVBbc5Z_rYbDqm6bWeD5nh3dtJ724TtMyaK1c5U,15565
+anndata/_io/h5ad.py,sha256=ekfuxldN6LuhR3b1aXJKvjfivOBlRP_A4rhEqvej-8Q,13633
+anndata/_io/read.py,sha256=oc8Af3r9ieh0-SFN3GKRIFxenijrbng55-Ds-WUhbdE,15691
 anndata/_io/utils.py,sha256=dB2RRaWm9V-CMGI46KhqpmzBGA6LLBnsJc83Q85OcgM,9613
 anndata/_io/write.py,sha256=r55w6yPIIuUSLW9wyYL8GnkzHHQdAxy6xiCEw9cAC38,4811
-anndata/_io/zarr.py,sha256=Q5QAxdpT2doNuIYAyFarI8QHlG9RaT_e4ts__YxnWGU,5730
+anndata/_io/zarr.py,sha256=6ejnp9VNsxSihSd3HXAv2uVkrv7dRnuox4Jt1Y0yyGY,5261
 anndata/_io/specs/__init__.py,sha256=Z6l8xqa7B480U3pqrNIg4-fhUvpBW85w4xA3i3maAUM,427
-anndata/_io/specs/lazy_methods.py,sha256=4G7GyF3lZ5WKEAjQyIaZrqriamr1w1iJlSXHINniysk,11891
-anndata/_io/specs/methods.py,sha256=Dd5CWGXR2Of_AZwnWFwkamtIPn2Oi7N3Z2QHGT1QGeg,46354
-anndata/_io/specs/registry.py,sha256=VohbazEZFJfLv9M0n02GnMLaAqxWbgejeIYS3mkQMGE,16937
-anndata/compat/__init__.py,sha256=9jp9fXHewQ4jj0YXQDUXB7cZlSVlfRubeXdmeYbdNT0,12227
+anndata/_io/specs/lazy_methods.py,sha256=64rr1C83aaiN-iO7m1R03dqd6TbiJQbhzOQI5lXHD0o,12270
+anndata/_io/specs/methods.py,sha256=qRRZfz4pqjaxRrkhiYiZe9_mXuWjAj4OLhbL-CO_VSM,46485
+anndata/_io/specs/registry.py,sha256=hno-mvefhcDHmACrBjcKmlf5T87FPoe-N1Gd3i9otYo,17459
+anndata/compat/__init__.py,sha256=FZZbV36BG0L0v-N5IXQbrCa5jNgBRsFY44vmdG-2y_4,12227
 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/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=IQb9w7SpFlpVP26dFGouwe66VNoihTiS7jM4-1Jkvbc,6355
+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/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=LQ3K7PwFm8-CYGJqkJF7li0lfxda4UMEgsok93nPKzI,35546
+anndata/tests/helpers.py,sha256=yVFdqB2PDDw8jNOkKAo-6VR7vk8yUlbafZbtDyibB8c,35111
 testing/anndata/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 testing/anndata/_doctest.py,sha256=Qew0N0zLLNiPKN1CLunqY5cTinFLaEhY5GagiYfm6KI,344
-testing/anndata/_pytest.py,sha256=TrQoIxsTuSAfNbFnVUjFAJfhUw7GJDFgkBcyh5QQHoM,4065
+testing/anndata/_pytest.py,sha256=a1Qn5KR5mjCcQI05negkMEv0e2aJX2P_teyl0UMfoeQ,4160
 testing/anndata/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-anndata-0.12.0rc4.dist-info/METADATA,sha256=5u8E-KwCrX8Brhu3Pu2t1WCIv7cJ9wHvyo5bkUhWrMw,9750
-anndata-0.12.0rc4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-anndata-0.12.0rc4.dist-info/licenses/LICENSE,sha256=VcrXoEVMhtNuvMvKYGP-I5lMT8qZ_6dFf22fsL180qA,1575
-anndata-0.12.0rc4.dist-info/RECORD,,
+anndata-0.12.1.dist-info/METADATA,sha256=ah9uvJCDn4h1tspyYlcwiSC7mGBhwWHVs6irKQ8LzXY,9643
+anndata-0.12.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+anndata-0.12.1.dist-info/licenses/LICENSE,sha256=VcrXoEVMhtNuvMvKYGP-I5lMT8qZ_6dFf22fsL180qA,1575
+anndata-0.12.1.dist-info/RECORD,,

testing/anndata/_pytest.py

@@ -93,6 +93,10 @@ def pytest_addoption(parser: pytest.Parser) -> None:
 def pytest_collection_modifyitems(
     session: pytest.Session, config: pytest.Config, items: Iterable[pytest.Item]
 ):
+    for item in items:
+        if "zarr" in item.name:
+            item.add_marker("zarr_io")
+
     if not config.getoption("--strict-warnings"):
         return