Update to python 3.9

.azure-pipelines.yml

@@ -16,8 +16,8 @@ jobs:
         Python3.11:
           python.version: "3.11"
           RUN_COVERAGE: yes
-        Python3.8:
-          python.version: "3.8"
+        Python3.9:
+          python.version: "3.9"
         PreRelease:
           python.version: "3.11"
           PRERELEASE_DEPENDENCIES: yes

anndata/__init__.py

@@ -1,4 +1,5 @@
 """Annotated multivariate observation data."""
+from __future__ import annotations
 
 try:  # See https://github.com/maresb/hatch-vcs-footgun-example
     from setuptools_scm import get_version
@@ -34,12 +35,14 @@
     read_zarr,
 )
 from ._warnings import (
+    ExperimentalFeatureWarning,
+    ImplicitModificationWarning,
     OldFormatWarning,
     WriteWarning,
-    ImplicitModificationWarning,
-    ExperimentalFeatureWarning,
 )
-from . import experimental
+
+# Experimental needs to be imported last
+from . import experimental  # isort: skip
 
 
 def read(*args, **kwargs):

anndata/_core/access.py

@@ -1,13 +1,16 @@
+from __future__ import annotations
+
 from functools import reduce
-from typing import NamedTuple, Tuple
+from typing import TYPE_CHECKING, NamedTuple
 
-from . import anndata
+if TYPE_CHECKING:
+    from anndata import AnnData
 
 
 class ElementRef(NamedTuple):
-    parent: "anndata.AnnData"
+    parent: AnnData
     attrname: str
-    keys: Tuple[str, ...] = ()
+    keys: tuple[str, ...] = ()
 
     def __str__(self) -> str:
         return f".{self.attrname}" + "".join(map(lambda x: f"['{x}']", self.keys))

anndata/_core/aligned_mapping.py

@@ -1,26 +1,36 @@
+from __future__ import annotations
+
+import warnings
 from abc import ABC, abstractmethod
 from collections import abc as cabc
+from collections.abc import Iterator, Mapping, Sequence
 from copy import copy
-from typing import Union, Optional, Type, ClassVar, TypeVar  # Special types
-from typing import Iterator, Mapping, Sequence  # ABCs
-from typing import Tuple, List, Dict  # Generic base types
-import warnings
+from typing import (
+    TYPE_CHECKING,
+    ClassVar,
+    TypeVar,
+    Union,
+)
 
 import numpy as np
 import pandas as pd
 from scipy.sparse import spmatrix
 
-from ..utils import deprecated, ensure_df_homogeneous, dim_len
-from . import raw, anndata
-from .views import as_view, view_update
+from anndata._warnings import ExperimentalFeatureWarning, ImplicitModificationWarning
+from anndata.compat import AwkArray
+
+from ..utils import deprecated, dim_len, ensure_df_homogeneous
 from .access import ElementRef
 from .index import _subset
-from anndata.compat import AwkArray
-from anndata._warnings import ExperimentalFeatureWarning, ImplicitModificationWarning
+from .views import as_view, view_update
+
+if TYPE_CHECKING:
+    from .anndata import AnnData
+    from .raw import Raw
 
 
 OneDIdx = Union[Sequence[int], Sequence[bool], slice]
-TwoDIdx = Tuple[OneDIdx, OneDIdx]
+TwoDIdx = tuple[OneDIdx, OneDIdx]
 
 I = TypeVar("I", OneDIdx, TwoDIdx, covariant=True)
 # TODO: pd.DataFrame only allowed in AxisArrays?
@@ -36,16 +46,16 @@ class AlignedMapping(cabc.MutableMapping, ABC):
     _allow_df: ClassVar[bool]
     """If this mapping supports heterogeneous DataFrames"""
 
-    _view_class: ClassVar[Type["AlignedViewMixin"]]
+    _view_class: ClassVar[type[AlignedViewMixin]]
     """The view class for this aligned mapping."""
 
-    _actual_class: ClassVar[Type["AlignedActualMixin"]]
+    _actual_class: ClassVar[type[AlignedActualMixin]]
     """The actual class (which has it’s own data) for this aligned mapping."""
 
     def __repr__(self):
         return f"{type(self).__name__} with keys: {', '.join(self.keys())}"
 
-    def _ipython_key_completions_(self) -> List[str]:
+    def _ipython_key_completions_(self) -> list[str]:
         return list(self.keys())
 
     def _validate_value(self, val: V, key: str) -> V:
@@ -94,7 +104,7 @@ def attrname(self) -> str:
 
     @property
     @abstractmethod
-    def axes(self) -> Tuple[int, ...]:
+    def axes(self) -> tuple[int, ...]:
         """Which axes of the parent is this aligned to?"""
         pass
 
@@ -104,7 +114,7 @@ def is_view(self) -> bool:
         pass
 
     @property
-    def parent(self) -> Union["anndata.AnnData", "raw.Raw"]:
+    def parent(self) -> AnnData | Raw:
         return self._parent
 
     def copy(self):
@@ -117,7 +127,7 @@ def copy(self):
                 d[k] = v.copy()
         return d
 
-    def _view(self, parent: "anndata.AnnData", subset_idx: I):
+    def _view(self, parent: AnnData, subset_idx: I):
         """Returns a subset copy-on-write view of the object."""
         return self._view_class(self, parent, subset_idx)
 
@@ -127,7 +137,7 @@ def as_dict(self) -> dict:
 
 
 class AlignedViewMixin:
-    parent: "anndata.AnnData"
+    parent: AnnData
     """Reference to parent AnnData view"""
 
     attrname: str
@@ -177,7 +187,7 @@ def __len__(self) -> int:
 
 
 class AlignedActualMixin:
-    _data: Dict[str, V]
+    _data: dict[str, V]
     """Underlying mapping to the data"""
 
     is_view = False
@@ -216,7 +226,7 @@ def attrname(self) -> str:
         return f"{self.dim}m"
 
     @property
-    def axes(self) -> Tuple[int]:
+    def axes(self) -> tuple[int]:
         """Axes of the parent this is aligned to"""
         return (self._axis,)
 
@@ -225,7 +235,7 @@ def dim(self) -> str:
         """Name of the dimension this aligned to."""
         return self._dimnames[self._axis]
 
-    def flipped(self) -> "AxisArraysBase":
+    def flipped(self) -> AxisArraysBase:
         """Transpose."""
         new = self.copy()
         new.dimension = abs(self._axis - 1)
@@ -265,9 +275,9 @@ def dim_names(self) -> pd.Index:
 class AxisArrays(AlignedActualMixin, AxisArraysBase):
     def __init__(
         self,
-        parent: Union["anndata.AnnData", "raw.Raw"],
+        parent: AnnData | Raw,
         axis: int,
-        vals: Union[Mapping, AxisArraysBase, None] = None,
+        vals: Mapping | AxisArraysBase | None = None,
     ):
         self._parent = parent
         if axis not in (0, 1):
@@ -282,7 +292,7 @@ class AxisArraysView(AlignedViewMixin, AxisArraysBase):
     def __init__(
         self,
         parent_mapping: AxisArraysBase,
-        parent_view: "anndata.AnnData",
+        parent_view: AnnData,
         subset_idx: OneDIdx,
     ):
         self.parent_mapping = parent_mapping
@@ -306,15 +316,15 @@ class LayersBase(AlignedMapping):
     axes = (0, 1)
 
     # TODO: I thought I had a more elegant solution to overriding this...
-    def copy(self) -> "Layers":
+    def copy(self) -> Layers:
         d = self._actual_class(self.parent)
         for k, v in self.items():
             d[k] = v.copy()
         return d
 
 
 class Layers(AlignedActualMixin, LayersBase):
-    def __init__(self, parent: "anndata.AnnData", vals: Optional[Mapping] = None):
+    def __init__(self, parent: AnnData, vals: Mapping | None = None):
         self._parent = parent
         self._data = dict()
         if vals is not None:
@@ -325,7 +335,7 @@ class LayersView(AlignedViewMixin, LayersBase):
     def __init__(
         self,
         parent_mapping: LayersBase,
-        parent_view: "anndata.AnnData",
+        parent_view: AnnData,
         subset_idx: TwoDIdx,
     ):
         self.parent_mapping = parent_mapping
@@ -351,7 +361,7 @@ def attrname(self) -> str:
         return f"{self.dim}p"
 
     @property
-    def axes(self) -> Tuple[int, int]:
+    def axes(self) -> tuple[int, int]:
         """Axes of the parent this is aligned to"""
         return self._axis, self._axis
 
@@ -364,9 +374,9 @@ def dim(self) -> str:
 class PairwiseArrays(AlignedActualMixin, PairwiseArraysBase):
     def __init__(
         self,
-        parent: "anndata.AnnData",
+        parent: AnnData,
         axis: int,
-        vals: Optional[Mapping] = None,
+        vals: Mapping | None = None,
     ):
         self._parent = parent
         if axis not in (0, 1):
@@ -381,7 +391,7 @@ class PairwiseArraysView(AlignedViewMixin, PairwiseArraysBase):
     def __init__(
         self,
         parent_mapping: PairwiseArraysBase,
-        parent_view: "anndata.AnnData",
+        parent_view: AnnData,
         subset_idx: OneDIdx,
     ):
         self.parent_mapping = parent_mapping