swcgeom 0.16.0__py3-none-any.whl → 0.17.1__py3-none-any.whl

swcgeom/core/branch_tree.py

@@ -1,7 +1,6 @@
 """Branch tree is a simplified neuron tree."""
 
 import itertools
-from typing import Dict, List
 
 import numpy as np
 import pandas as pd
@@ -19,13 +18,13 @@ class BranchTree(Tree):
     A branch tree that contains only soma, branch, and tip nodes.
     """
 
-    branches: Dict[int, List[Branch]]
+    branches: dict[int, list[Branch]]
 
-    def get_origin_branches(self) -> List[Branch]:
+    def get_origin_branches(self) -> list[Branch]:
         """Get branches of original tree."""
         return list(itertools.chain(*self.branches.values()))
 
-    def get_origin_node_branches(self, idx: int) -> List[Branch]:
+    def get_origin_node_branches(self, idx: int) -> list[Branch]:
         """Get branches of node of original tree."""
         return self.branches[idx]
 

swcgeom/core/compartment.py

@@ -1,6 +1,7 @@
 """The segment is a branch with two nodes."""
 
-from typing import Generic, Iterable, List, TypeVar
+from collections.abc import Iterable
+from typing import Generic, TypeVar
 
 import numpy as np
 import numpy.typing as npt
@@ -43,7 +44,7 @@ class Compartment(Path, Generic[SWCTypeVar]):
 T = TypeVar("T", bound=Compartment)
 
 
-class Compartments(List[T]):
+class Compartments(list[T]):
     r"""Comparments contains a set of comparment."""
 
     names: SWCNames

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, List, overload
+from collections.abc import Iterable, Iterator
+from typing import Generic, overload
 
 import numpy as np
 import numpy.typing as npt
@@ -44,7 +45,7 @@ class Path(SWCLike, Generic[SWCTypeVar]):
     @overload
     def __getitem__(self, key: int) -> Node: ...
     @overload
-    def __getitem__(self, key: slice) -> List[Node]: ...
+    def __getitem__(self, key: slice) -> list[Node]: ...
     @overload
     def __getitem__(self, key: str) -> npt.NDArray: ...
     # fmt:on

swcgeom/core/population.py

@@ -2,21 +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,
-    Dict,
-    Iterable,
-    Iterator,
-    List,
-    Optional,
-    Protocol,
-    TypeVar,
-    cast,
-    overload,
-)
+from typing import Any, Optional, Protocol, TypeVar, cast, overload
 
 import numpy as np
 import numpy.typing as npt
@@ -44,16 +33,16 @@ class Trees(Protocol):
 class LazyLoadingTrees:
     """Lazy loading trees."""
 
-    swcs: List[str]
-    trees: List[Tree | None]
-    kwargs: Dict[str, Any]
+    swcs: list[str]
+    trees: list[Tree | None]
+    kwargs: dict[str, Any]
 
     def __init__(self, swcs: Iterable[str], **kwargs) -> None:
         """
         Paramters
         ---------
         swcs : List of str
-        kwargs : Dict[str, Any]
+        kwargs : dict[str, Any]
             Forwarding to `Tree.from_swc`
         """
 
@@ -81,7 +70,7 @@ class LazyLoadingTrees:
 class ChainTrees:
     """Chain trees."""
 
-    trees: List[Trees]
+    trees: list[Trees]
     cumsum: npt.NDArray[np.int64]
 
     def __init__(self, trees: Iterable[Trees]) -> None:
@@ -146,7 +135,7 @@ class Population:
 
     # fmt:off
     @overload
-    def __getitem__(self, key: slice) -> List[Tree]: ...
+    def __getitem__(self, key: slice) -> list[Tree]: ...
     @overload
     def __getitem__(self, key: int) -> Tree: ...
     # fmt:on
@@ -216,9 +205,9 @@ class Population:
         return cls.from_swc(root, ext, extra_cols=extra_cols, **kwargs)
 
     @staticmethod
-    def find_swcs(root: str, ext: str = ".swc", relpath: bool = False) -> List[str]:
+    def find_swcs(root: str, ext: str = ".swc", relpath: bool = False) -> list[str]:
         """Find all swc files."""
-        swcs: List[str] = []
+        swcs: list[str] = []
         for r, _, files in os.walk(root):
             rr = os.path.relpath(r, root) if relpath else r
             fs = filter(lambda f: os.path.splitext(f)[-1] == ext, files)
@@ -231,8 +220,8 @@ class Populations:
     """A set of population."""
 
     len: int
-    populations: List[Population]
-    labels: List[str]
+    populations: list[Population]
+    labels: list[str]
 
     def __init__(
         self, populations: Iterable[Population], labels: Optional[Iterable[str]] = None
@@ -248,9 +237,9 @@ class Populations:
 
     # fmt:off
     @overload
-    def __getitem__(self, key: slice) -> List[List[Tree]]: ...
+    def __getitem__(self, key: slice) -> list[list[Tree]]: ...
     @overload
-    def __getitem__(self, key: int) -> List[Tree]: ...
+    def __getitem__(self, key: int) -> list[Tree]: ...
     # fmt:on
     def __getitem__(self, key):
         return [p[key] for p in self.populations]
@@ -259,7 +248,7 @@ class Populations:
         """Miniumn length of populations."""
         return self.len
 
-    def __iter__(self) -> Iterator[List[Tree]]:
+    def __iter__(self) -> Iterator[list[Tree]]:
         return (self[i] for i in range(self.len))
 
     def __repr__(self) -> str:
@@ -288,7 +277,7 @@ class Populations:
 
         Parameters
         ----------
-        roots : list of str
+        roots : List of str
         intersect : bool, default `True`
             Take the intersection of these populations.
         check_same : bool, default `False`

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, Dict, Iterable, List, Optional, Tuple, TypeVar, overload
+from typing import Any, Optional, TypeVar, overload
 
 import numpy as np
 import numpy.typing as npt
@@ -32,7 +33,7 @@ __all__ = [
 
 
 swc_names_default = get_names()
-swc_cols: List[Tuple[str, npt.DTypeLike]] = [
+swc_cols: list[tuple[str, npt.DTypeLike]] = [
     (swc_names_default.id, np.int32),
     (swc_names_default.type, np.int32),
     (swc_names_default.x, np.float32),
@@ -42,7 +43,7 @@ swc_cols: List[Tuple[str, npt.DTypeLike]] = [
     (swc_names_default.pid, np.int32),
 ]
 
-eswc_cols: List[Tuple[str, npt.DTypeLike]] = [
+eswc_cols: list[tuple[str, npt.DTypeLike]] = [
     ("level", np.int32),
     ("mode", np.int32),
     ("timestamp", np.int32),
@@ -55,7 +56,7 @@ class SWCLike(ABC):
     """ABC of SWC."""
 
     source: str = ""
-    comments: List[str] = []
+    comments: list[str] = []
     names: SWCNames
     types: SWCTypes
 
@@ -131,15 +132,15 @@ class SWCLike(ABC):
 
     # fmt: off
     @overload
-    def to_swc(self, fname: str, *, extra_cols: List[str] | None = ..., source: bool | str = ..., id_offset: int = ...) -> None: ...
+    def to_swc(self, fname: str, *, extra_cols: list[str] | None = ..., source: bool | str = ..., id_offset: int = ...) -> None: ...
     @overload
-    def to_swc(self, *, extra_cols: List[str] | None = ..., source: bool | str = ..., id_offset: int = ...) -> str: ...
+    def to_swc(self, *, extra_cols: list[str] | None = ..., source: bool | str = ..., id_offset: int = ...) -> str: ...
     # fmt: on
     def to_swc(
         self,
         fname: Optional[str] = None,
         *,
-        extra_cols: Optional[List[str]] = None,
+        extra_cols: Optional[list[str]] = None,
         source: bool | str = True,
         comments: bool = True,
         id_offset: int = 1,
@@ -177,7 +178,7 @@ class SWCLike(ABC):
         self,
         fname: Optional[str] = None,
         swc_path: Optional[str] = None,
-        extra_cols: Optional[List[str]] = None,
+        extra_cols: Optional[list[str]] = None,
         **kwargs,
     ) -> str | None:
         if swc_path is None:
@@ -199,7 +200,7 @@ SWCTypeVar = TypeVar("SWCTypeVar", bound=SWCLike)
 class DictSWC(SWCLike):
     """SWC implementation on dict."""
 
-    ndata: Dict[str, npt.NDArray]
+    ndata: dict[str, npt.NDArray]
 
     def __init__(
         self,
@@ -221,7 +222,7 @@ class DictSWC(SWCLike):
     def values(self) -> Iterable[npt.NDArray[Any]]:
         return self.ndata.values()
 
-    def items(self) -> Iterable[Tuple[str, npt.NDArray[Any]]]:
+    def items(self) -> Iterable[tuple[str, npt.NDArray[Any]]]:
         return self.ndata.items()
 
     def get_ndata(self, key: str) -> npt.NDArray[Any]:

swcgeom/core/swc_utils/base.py

@@ -1,16 +1,7 @@
 """Base SWC format utils."""
 
-from dataclasses import dataclass
-from typing import (
-    Callable,
-    List,
-    Literal,
-    NamedTuple,
-    Optional,
-    Tuple,
-    TypeVar,
-    overload,
-)
+from collections.abc import Callable
+from typing import Literal, NamedTuple, Optional, TypeVar, overload
 
 import numpy as np
 import numpy.typing as npt
@@ -29,7 +20,7 @@ __all__ = [
 ]
 
 T, K = TypeVar("T"), TypeVar("K")
-Topology = Tuple[npt.NDArray[np.int32], npt.NDArray[np.int32]]  # (id, pid)
+Topology = tuple[npt.NDArray[np.int32], npt.NDArray[np.int32]]  # (id, pid)
 
 
 class SWCNames(NamedTuple):
@@ -43,7 +34,7 @@ class SWCNames(NamedTuple):
     r: str = "r"
     pid: str = "pid"
 
-    def cols(self) -> List[str]:
+    def cols(self) -> list[str]:
         return [self.id, self.type, self.x, self.y, self.z, self.r, self.pid]
 
 
@@ -114,10 +105,10 @@ def get_dsu(
 @overload
 def traverse(topology: Topology, *, enter: Callable[[int, T | None], T], root: int | np.integer = ..., mode: Literal["dfs"] = ...) -> None: ...
 @overload
-def traverse(topology: Topology, *, leave: Callable[[int, List[K]], K], root: int | np.integer = ..., mode: Literal["dfs"] = ...) -> K: ...
+def traverse(topology: Topology, *, leave: Callable[[int, list[K]], K], root: int | np.integer = ..., mode: Literal["dfs"] = ...) -> K: ...
 @overload
 def traverse(
-    topology: Topology, *, enter: Callable[[int, T | None], T], leave: Callable[[int, List[K]], K],
+    topology: Topology, *, enter: Callable[[int, T | None], T], leave: Callable[[int, list[K]], K],
     root: int | np.integer = ..., mode: Literal["dfs"] = ...,
 ) -> K: ...
 # fmt: on
@@ -130,7 +121,7 @@ def traverse(topology: Topology, *, mode="dfs", **kwargs):
         The callback when entering node, which accepts two parameters,
         the current node id and the return value of it parent node. In
         particular, the root node receives an `None`.
-    leave : (id: int, children: List[T]) => T, optional
+    leave : (id: int, children: list[T]) => T, optional
         The callback when leaving node. When leaving a node, subtree
         has already been traversed. Callback accepts two parameters,
         the current node id and list of the return value of children,
@@ -155,7 +146,7 @@ def _traverse_dfs(topology: Topology, *, enter=None, leave=None, root=0):
         children_map[pid].append(idx)
 
     # manual dfs to avoid stack overflow in long branch
-    stack: List[Tuple[int, bool]] = [(root, True)]  # (idx, is_enter)
+    stack: list[tuple[int, bool]] = [(root, True)]  # (idx, is_enter)
     params = {root: None}
     vals = {}
 

swcgeom/core/swc_utils/io.py

@@ -2,7 +2,8 @@
 
 import re
 import warnings
-from typing import Callable, Iterable, List, Literal, Optional, Tuple
+from collections.abc import Callable, Iterable
+from typing import Literal, Optional
 
 import numpy as np
 import numpy.typing as npt
@@ -30,7 +31,7 @@ def read_swc(
     *,
     encoding: Literal["detect"] | str = "utf-8",
     names: Optional[SWCNames] = None,
-) -> Tuple[pd.DataFrame, List[str]]:
+) -> tuple[pd.DataFrame, list[str]]:
     """Read swc file.
 
     Parameters
@@ -55,7 +56,7 @@ def read_swc(
     Returns
     -------
     df : ~pandas.DataFrame
-    comments : list of string
+    comments : List of string
     """
 
     names = get_names(names)
@@ -137,14 +138,14 @@ def parse_swc(
     names: SWCNames,
     extra_cols: Iterable[str] | None = None,
     encoding: Literal["detect"] | str = "utf-8",
-) -> Tuple[pd.DataFrame, List[str]]:
+) -> tuple[pd.DataFrame, list[str]]:
     """Parse swc file.
 
     Parameters
     ----------
     fname : PathOrIO
     names : SWCNames
-    extra_cols : list of str, optional
+    extra_cols : List of str, optional
     encoding : str | 'detect', default `utf-8`
         The name of the encoding used to decode the file. If is
         `detect`, we will try to detect the character encoding.
@@ -152,7 +153,7 @@ def parse_swc(
     Returns
     -------
     df : ~pandas.DataFrame
-    comments : list of string
+    comments : List of string
     """
 
     # pylint: disable=too-many-locals

swcgeom/core/swc_utils/normalizer.py

@@ -3,7 +3,8 @@
 Methods ending with a underline imply an in-place transformation.
 """
 
-from typing import Callable, List, Literal, Optional, Tuple
+from collections.abc import Callable
+from typing import Literal, Optional
 
 import numpy as np
 import numpy.typing as npt
@@ -111,7 +112,7 @@ def sort_nodes_(df: pd.DataFrame, *, names: Optional[SWCNames] = None) -> None:
     df[names.id], df[names.pid] = new_ids, new_pids
 
 
-def sort_nodes_impl(topology: Topology) -> Tuple[Topology, npt.NDArray[np.int32]]:
+def sort_nodes_impl(topology: Topology) -> tuple[Topology, npt.NDArray[np.int32]]:
     """Sort the indices of neuron tree.
 
     Returns
@@ -127,7 +128,7 @@ def sort_nodes_impl(topology: Topology) -> Tuple[Topology, npt.NDArray[np.int32]
     new_pids = np.full_like(old_ids, fill_value=-3)
     new_id = 0
     first_root = old_ids[(old_pids == -1).argmax()]
-    s: List[Tuple[npt.NDArray[np.int32], int]] = [(first_root, -1)]
+    s: list[tuple[npt.NDArray[np.int32], int]] = [(first_root, -1)]
     while len(s) != 0:
         old_id, new_pid = s.pop()
         id_map[new_id] = old_id

swcgeom/core/swc_utils/subtree.py

@@ -6,7 +6,7 @@ but in more cases, you can use the high-level methods provided in
 high-level API.
 """
 
-from typing import Tuple, cast
+from typing import cast
 
 import numpy as np
 import numpy.typing as npt
@@ -18,7 +18,7 @@ __all__ = ["REMOVAL", "to_sub_topology", "propagate_removal"]
 REMOVAL = -2  # A marker in utils, place in the ids to mark it removal
 
 
-def to_sub_topology(sub: Topology) -> Tuple[Topology, npt.NDArray[np.int32]]:
+def to_sub_topology(sub: Topology) -> tuple[Topology, npt.NDArray[np.int32]]:
     """Create sub tree from origin tree.
 
     Mark the node to be removed, then use this method to get a child

swcgeom/core/tree.py

@@ -2,20 +2,8 @@
 
 import itertools
 import os
-import warnings
-from typing import (
-    Callable,
-    Dict,
-    Iterable,
-    Iterator,
-    List,
-    Literal,
-    Optional,
-    Tuple,
-    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
@@ -44,12 +32,12 @@ class Tree(DictSWC):
         def parent(self) -> Union["Tree.Node", None]:
             return Tree.Node(self.attach, self.pid) if self.pid != -1 else None
 
-        def children(self) -> List["Tree.Node"]:
+        def children(self) -> list["Tree.Node"]:
             children = self.attach.id()[self.attach.pid() == self.id]
             return [Tree.Node(self.attach, idx) for idx in children]
 
         def branch(self) -> "Tree.Branch":
-            ns: List["Tree.Node"] = [self]
+            ns: list["Tree.Node"] = [self]
             while not ns[-1].is_bifurcation() and (p := ns[-1].parent()) is not None:
                 ns.append(p)
 
@@ -68,7 +56,7 @@ class Tree(DictSWC):
 
             Parameters
             ----------
-            out_mapping : List of int or Dict[int, int], optional
+            out_mapping : List of int or dict[int, int], optional
                 Map from new id to old id.
             """
 
@@ -160,7 +148,7 @@ class Tree(DictSWC):
 
     # fmt:off
     @overload
-    def __getitem__(self, key: slice) -> List[Node]: ...
+    def __getitem__(self, key: slice) -> list[Node]: ...
     @overload
     def __getitem__(self, key: int) -> Node: ...
     @overload
@@ -199,18 +187,18 @@ class Tree(DictSWC):
             raise ValueError(f"no soma found in: {self.source}")
         return n
 
-    def get_bifurcations(self) -> List[Node]:
+    def get_bifurcations(self) -> list[Node]:
         """Get all node of bifurcations."""
-        bifurcations: List[int] = []
+        bifurcations: list[int] = []
 
-        def collect_bifurcations(n: Tree.Node, children: List[None]) -> None:
+        def collect_bifurcations(n: Tree.Node, children: list[None]) -> None:
             if len(children) > 1:
                 bifurcations.append(n.id)
 
         self.traverse(leave=collect_bifurcations)
         return [self.node(i) for i in bifurcations]
 
-    def get_tips(self) -> List[Node]:
+    def get_tips(self) -> list[Node]:
         """Get all node of tips."""
         tip_ids = np.setdiff1d(self.id(), self.pid(), assume_unique=True)
         return [self.node(i) for i in tip_ids]
@@ -221,16 +209,16 @@ class Tree(DictSWC):
     def get_segments(self) -> Compartments[Compartment]:  # Alias
         return self.get_compartments()
 
-    def get_branches(self) -> List[Branch]:
+    def get_branches(self) -> list[Branch]:
         def collect_branches(
-            node: "Tree.Node", pre: List[Tuple[List[Tree.Branch], List[int]]]
-        ) -> Tuple[List[Tree.Branch], List[int]]:
+            node: "Tree.Node", pre: list[tuple[list[Tree.Branch], list[int]]]
+        ) -> tuple[list[Tree.Branch], list[int]]:
             if len(pre) == 1:
                 branches, child = pre[0]
                 child.append(node.id)
                 return branches, child
 
-            branches: List[Tree.Branch] = []
+            branches: list[Tree.Branch] = []
 
             for sub_branches, child in pre:
                 child.append(node.id)
@@ -244,19 +232,19 @@ class Tree(DictSWC):
         branches, _ = self.traverse(leave=collect_branches)
         return branches
 
-    def get_paths(self) -> List[Path]:
+    def get_paths(self) -> list[Path]:
         """Get all path from soma to tips."""
-        path_dic: Dict[int, List[int]] = {}
+        path_dic: dict[int, list[int]] = {}
 
-        def assign_path(n: Tree.Node, pre_path: List[int] | None) -> List[int]:
+        def assign_path(n: Tree.Node, pre_path: list[int] | None) -> list[int]:
             path = [] if pre_path is None else pre_path.copy()
             path.append(n.id)
             path_dic[n.id] = path
             return path
 
         def collect_path(
-            n: Tree.Node, children: List[List[List[int]]]
-        ) -> List[List[int]]:
+            n: Tree.Node, children: list[list[list[int]]]
+        ) -> list[list[int]]:
             if len(children) == 0:
                 return [path_dic[n.id]]
 
@@ -283,7 +271,7 @@ class Tree(DictSWC):
     @overload
     def traverse(self, *,
                  enter: Optional[Callable[[Node, T | None], T]] = ...,
-                 leave: Callable[[Node, List[K]], K],
+                 leave: Callable[[Node, list[K]], K],
                  root: int | np.integer = ..., mode: Literal["dfs"] = ...) -> K: ...
     # fmt: on
 
@@ -293,7 +281,7 @@ class Tree(DictSWC):
         Parameters
         ----------
         enter : (n: Node, parent: T | None) => T, optional
-        leave : (n: Node, children: List[T]) => T, optional
+        leave : (n: Node, children: list[T]) => T, optional
 
         See Also
         --------
@@ -355,7 +343,7 @@ class Tree(DictSWC):
 
     @classmethod
     def from_eswc(
-        cls, swc_file: str, extra_cols: Optional[List[str]] = None, **kwargs
+        cls, swc_file: str, extra_cols: Optional[list[str]] = None, **kwargs
     ) -> "Tree":
         """Read neuron tree from eswc file.
 

swcgeom/core/tree_utils.py

@@ -1,7 +1,8 @@
 """SWC util wrapper for tree."""
 
 import warnings
-from typing import Callable, Dict, Iterable, List, Optional, Tuple, TypeVar, overload
+from collections.abc import Callable, Iterable
+from typing import Optional, TypeVar, overload
 
 import numpy as np
 
@@ -50,9 +51,9 @@ def sort_tree(tree: Tree) -> Tree:
 
 # fmt:off
 @overload
-def cut_tree(tree: Tree, *, enter: Callable[[Tree.Node, T | None], Tuple[T, bool]]) -> Tree: ...
+def cut_tree(tree: Tree, *, enter: Callable[[Tree.Node, T | None], tuple[T, bool]]) -> Tree: ...
 @overload
-def cut_tree(tree: Tree, *, leave: Callable[[Tree.Node, List[K]], Tuple[K, bool]]) -> Tree: ...
+def cut_tree(tree: Tree, *, leave: Callable[[Tree.Node, list[K]], tuple[K, bool]]) -> Tree: ...
 # fmt:on
 def cut_tree(tree: Tree, *, enter=None, leave=None):
     """Traverse and cut the tree.
@@ -60,11 +61,11 @@ def cut_tree(tree: Tree, *, enter=None, leave=None):
     Returning a `True` can delete the current node and its children.
     """
 
-    removals: List[int] = []
+    removals: list[int] = []
 
     if enter:
 
-        def _enter(n: Tree.Node, parent: Tuple[T, bool] | None) -> Tuple[T, bool]:
+        def _enter(n: Tree.Node, parent: tuple[T, bool] | None) -> tuple[T, bool]:
             if parent is not None and parent[1]:
                 removals.append(n.id)
                 return parent
@@ -79,7 +80,7 @@ def cut_tree(tree: Tree, *, enter=None, leave=None):
 
     elif leave:
 
-        def _leave(n: Tree.Node, children: List[K]) -> K:
+        def _leave(n: Tree.Node, children: list[K]) -> K:
             res, removal = leave(n, children)
             if removal:
                 removals.append(n.id)
@@ -94,7 +95,7 @@ def cut_tree(tree: Tree, *, enter=None, leave=None):
     return to_subtree(tree, removals)
 
 
-def to_sub_tree(swc_like: SWCLike, sub: Topology) -> Tuple[Tree, Dict[int, int]]:
+def to_sub_tree(swc_like: SWCLike, sub: Topology) -> tuple[Tree, dict[int, int]]:
     """Create subtree from origin tree.
 
     You can directly mark the node for removal, and we will remove it,
@@ -107,7 +108,7 @@ def to_sub_tree(swc_like: SWCLike, sub: Topology) -> Tuple[Tree, Dict[int, int]]
     Returns
     -------
     tree : Tree
-    id_map : Dict[int, int]
+    id_map : dict[int, int]
     """
 
     warnings.warn(
@@ -145,7 +146,7 @@ def to_subtree(
     swc_like : SWCLike
     removals : List of int
         A list of id of nodes to be removed.
-    out_mapping: List of int or Dict[int, int], optional
+    out_mapping: List of int or dict[int, int], optional
         Map new id to old id.
     """
 
@@ -170,7 +171,7 @@ def get_subtree(
     swc_like : SWCLike
     n : int
         Id of the root of the subtree.
-    out_mapping: List of int or Dict[int, int], optional
+    out_mapping: List of int or dict[int, int], optional
         Map new id to old id.
     """