refactor: replace aliases to types in collections

examples/pytorch/branch.py

@@ -1,6 +1,7 @@
 """Transformations in branch requires pytorch."""
 
-from typing import Callable, Literal
+from collections.abc import Callable
+from typing import Literal
 
 import numpy as np
 import numpy.typing as npt

examples/pytorch/branch_dataset.py

@@ -2,7 +2,8 @@
 
 import os
 import warnings
-from typing import Generic, Iterable, TypeVar, cast
+from collections.abc import Iterable
+from typing import Generic, TypeVar, cast
 
 import torch
 import torch.utils.data

swcgeom/analysis/feature_extractor.py

@@ -7,10 +7,11 @@
 """
 
 from abc import ABC, abstractmethod
+from collections.abc import Callable
 from functools import cached_property
 from itertools import chain
 from os.path import basename
-from typing import Any, Callable, Literal, overload
+from typing import Any, Literal, overload
 
 import numpy as np
 import numpy.typing as npt

swcgeom/analysis/trunk.py

@@ -2,8 +2,9 @@
 
 # pylint: disable=invalid-name
 
+from collections.abc import Iterable
 from itertools import chain
-from typing import Any, Iterable, Literal, Optional, cast
+from typing import Any, Literal, Optional, cast
 
 import numpy as np
 import numpy.typing as npt

swcgeom/core/branch.py

@@ -1,6 +1,7 @@
 """Branch is a set of node points."""
 
-from typing import Generic, Iterable
+from collections.abc import Iterable
+from typing import Generic
 
 import numpy as np
 import numpy.typing as npt

swcgeom/core/compartment.py

@@ -1,6 +1,7 @@
 """The segment is a branch with two nodes."""
 
-from typing import Generic, Iterable, TypeVar
+from collections.abc import Iterable
+from typing import Generic, TypeVar
 
 import numpy as np
 import numpy.typing as npt

swcgeom/core/node.py

@@ -1,7 +1,7 @@
 """Nueron node."""
 
-import warnings
-from typing import Any, Generic, Iterable
+from collections.abc import Iterable
+from typing import Any, Generic
 
 import numpy as np
 import numpy.typing as npt

swcgeom/core/path.py

@@ -1,7 +1,8 @@
 """Nueron path."""
 
 import warnings
-from typing import Generic, Iterable, Iterator, overload
+from collections.abc import Iterable, Iterator
+from typing import Generic, overload
 
 import numpy as np
 import numpy.typing as npt

swcgeom/core/population.py

@@ -2,19 +2,10 @@
 
 import os
 import warnings
+from collections.abc import Callable, Iterable, Iterator
 from concurrent.futures import ProcessPoolExecutor
 from functools import reduce
-from typing import (
-    Any,
-    Callable,
-    Iterable,
-    Iterator,
-    Optional,
-    Protocol,
-    TypeVar,
-    cast,
-    overload,
-)
+from typing import Any, Optional, Protocol, TypeVar, cast, overload
 
 import numpy as np
 import numpy.typing as npt

swcgeom/core/swc.py

@@ -2,8 +2,9 @@
 
 import warnings
 from abc import ABC, abstractmethod
+from collections.abc import Iterable
 from copy import deepcopy
-from typing import Any, Iterable, Optional, TypeVar, overload
+from typing import Any, Optional, TypeVar, overload
 
 import numpy as np
 import numpy.typing as npt

swcgeom/core/swc_utils/base.py

@@ -1,6 +1,7 @@
 """Base SWC format utils."""
 
-from typing import Callable, Literal, NamedTuple, Optional, TypeVar, overload
+from collections.abc import Callable
+from typing import Literal, NamedTuple, Optional, TypeVar, overload
 
 import numpy as np
 import numpy.typing as npt

swcgeom/core/swc_utils/io.py

@@ -2,7 +2,8 @@
 
 import re
 import warnings
-from typing import Callable, Iterable, Literal, Optional
+from collections.abc import Callable, Iterable
+from typing import Literal, Optional
 
 import numpy as np
 import numpy.typing as npt

swcgeom/core/swc_utils/normalizer.py

@@ -3,7 +3,8 @@
 Methods ending with a underline imply an in-place transformation.
 """
 
-from typing import Callable, Literal, Optional
+from collections.abc import Callable
+from typing import Literal, Optional
 
 import numpy as np
 import numpy.typing as npt

swcgeom/core/tree.py

@@ -2,16 +2,8 @@
 
 import itertools
 import os
-from typing import (
-    Callable,
-    Iterable,
-    Iterator,
-    Literal,
-    Optional,
-    TypeVar,
-    Union,
-    overload,
-)
+from collections.abc import Callable, Iterable, Iterator
+from typing import Literal, Optional, TypeVar, Union, overload
 
 import numpy as np
 import numpy.typing as npt

swcgeom/core/tree_utils.py

@@ -1,7 +1,8 @@
 """SWC util wrapper for tree."""
 
 import warnings
-from typing import Callable, Iterable, Optional, TypeVar, overload
+from collections.abc import Callable, Iterable
+from typing import Optional, TypeVar, overload
 
 import numpy as np
 

swcgeom/images/folder.py

@@ -4,8 +4,9 @@
 import os
 import re
 import warnings
+from collections.abc import Callable, Iterable
 from dataclasses import dataclass
-from typing import Callable, Generic, Iterable, Literal, Optional, TypeVar, overload
+from typing import Generic, Literal, Optional, TypeVar, overload
 
 import numpy as np
 import numpy.typing as npt

swcgeom/images/io.py

@@ -4,18 +4,9 @@
 import re
 import warnings
 from abc import ABC, abstractmethod
+from collections.abc import Callable, Iterable
 from functools import cache, lru_cache
-from typing import (
-    Any,
-    Callable,
-    Generic,
-    Iterable,
-    Literal,
-    Optional,
-    TypeVar,
-    cast,
-    overload,
-)
+from typing import Any, Generic, Literal, Optional, TypeVar, cast, overload
 
 import nrrd
 import numpy as np

swcgeom/transforms/image_stack.py

@@ -12,7 +12,8 @@
 import os
 import re
 import time
-from typing import Iterable, Optional
+from collections.abc import Iterable
+from typing import Optional
 
 import numpy as np
 import numpy.typing as npt

swcgeom/transforms/tree.py

@@ -1,7 +1,8 @@
 """Transformation in tree."""
 
 import warnings
-from typing import Callable, Optional
+from collections.abc import Callable
+from typing import Optional
 
 import numpy as np
 

swcgeom/transforms/tree_assembler.py

@@ -1,7 +1,8 @@
 """Assemble a tree."""
 
+from collections.abc import Iterable
 from copy import copy
-from typing import Iterable, Optional
+from typing import Optional
 
 import numpy as np
 import pandas as pd

swcgeom/utils/neuromorpho.py

@@ -81,7 +81,8 @@
 import math
 import os
 import urllib.parse
-from typing import Any, Callable, Iterable, Literal, Optional
+from collections.abc import Callable, Iterable
+from typing import Any, Literal, Optional
 
 from tqdm import tqdm
 

swcgeom/utils/sdf.py

@@ -10,7 +10,7 @@
 
 import warnings
 from abc import ABC, abstractmethod
-from typing import Iterable
+from collections.abc import Iterable
 
 import numpy as np
 import numpy.typing as npt