style: Upgrade deprecated type annotations

src/cooler/_reduce.py

@@ -4,7 +4,8 @@
 import warnings
 from bisect import bisect_right
 from collections import OrderedDict, defaultdict
-from typing import Any, Iterator, Literal
+from collections.abc import Iterator
+from typing import Any, Literal
 
 import h5py
 import multiprocess as mp

src/cooler/_typing.py

@@ -1,15 +1,16 @@
 from __future__ import annotations
 
-from typing import Callable, Dict, Iterable, Optional, Tuple, TypeVar, Union
+from collections.abc import Iterable
+from typing import Callable, Optional, TypeVar, Union
 
 import numpy as np
 import pandas as pd
 
 T = TypeVar('T')
 U = TypeVar('U')
 MapFunctor = Callable[[Callable[[T], U], Iterable[T]], Iterable[U]]
-GenomicRangeSpecifier = Union[str , Tuple[str, Optional[int], Optional[int]]]
-GenomicRangeTuple = Tuple[str, int, int]
-Tabular = Union[pd.DataFrame, Dict[str, np.ndarray]]
+GenomicRangeSpecifier = Union[str , tuple[str, Optional[int], Optional[int]]]
+GenomicRangeTuple = tuple[str, int, int]
+Tabular = Union[pd.DataFrame, dict[str, np.ndarray]]
 
 __all__ = ["MapFunctor", "GenomicRangeSpecifier", "GenomicRangeTuple", "Tabular"]

src/cooler/core/_rangequery.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
-from typing import Any, Callable, Iterator
+from collections.abc import Iterator
+from typing import Any, Callable
 
 import h5py
 import numpy as np

src/cooler/core/_selectors.py

@@ -1,11 +1,11 @@
 from __future__ import annotations
 
-from typing import Any, Callable, List, Optional, Tuple, Union, overload
+from typing import Any, Callable, Optional, Union, overload
 
 import pandas as pd
 
-ColumnsArg = Optional[Union[str, List[str]]]
-GenomicRangeArg = Optional[Union[str, Tuple[str, Optional[int], Optional[int]]]]
+ColumnsArg = Optional[Union[str, list[str]]]
+GenomicRangeArg = Optional[Union[str, tuple[str, Optional[int], Optional[int]]]]
 FieldArg = Optional[str]
 
 

src/cooler/create/_create.py

@@ -5,8 +5,9 @@
 import posixpath
 import tempfile
 import warnings
+from collections.abc import Iterable
 from datetime import datetime
-from typing import Any, Iterable
+from typing import Any
 
 import h5py
 import numpy as np

src/cooler/create/_ingest.py

@@ -12,8 +12,9 @@
 import warnings
 from bisect import bisect_left
 from collections import Counter, OrderedDict
+from collections.abc import Iterator
 from functools import partial
-from typing import Any, Callable, Iterator
+from typing import Any, Callable
 
 import h5py
 import numpy as np

src/cooler/parallel.py

@@ -5,8 +5,9 @@
 """
 from __future__ import annotations
 
+from collections.abc import Iterable, Iterator, Sequence
 from functools import partial, reduce
-from typing import Any, Callable, Iterable, Iterator, Sequence
+from typing import Any, Callable
 
 from multiprocess import Lock
 

src/cooler/util.py

@@ -3,8 +3,9 @@
 import os
 import re
 from collections import OrderedDict, defaultdict
+from collections.abc import Generator, Iterable, Iterator
 from contextlib import contextmanager
-from typing import IO, Any, Generator, Iterable, Iterator
+from typing import IO, Any
 
 import h5py
 import numpy as np