swcgeom 0.16.0__py3-none-any.whl → 0.18.3__py3-none-any.whl

swcgeom/core/path.py

@@ -1,10 +1,26 @@
+# Copyright 2022-2025 Zexin Yuan
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 """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
+from typing_extensions import deprecated
 
 from swcgeom.core.node import Node
 from swcgeom.core.swc import DictSWC, SWCLike, SWCTypeVar
@@ -15,7 +31,7 @@ __all__ = ["Path"]
 class Path(SWCLike, Generic[SWCTypeVar]):
     """Neuron path.
 
-    A path is a linear set of points without bifurcations.
+    A path is a linear set of points without furcations.
     """
 
     attach: SWCTypeVar
@@ -44,7 +60,7 @@ 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
@@ -74,6 +90,7 @@ class Path(SWCLike, Generic[SWCTypeVar]):
     def get_ndata(self, key: str) -> npt.NDArray:
         return self.attach.get_ndata(key)[self.idx]
 
+    @deprecated("Use `path.node` instead.")
     def get_node(self, idx: int | np.integer) -> Node:
         """Get the count of intersection.
 
@@ -81,11 +98,6 @@ class Path(SWCLike, Generic[SWCTypeVar]):
             Use :meth:`path.node` instead.
         """
 
-        warnings.warn(
-            "`Path.get_node` has been deprecated since v0.16.0 and "
-            "will be removed in future version",
-            DeprecationWarning,
-        )
         return self.node(idx)
 
     def node(self, idx: int | np.integer) -> Node:

swcgeom/core/population.py

@@ -1,22 +1,26 @@
+# Copyright 2022-2025 Zexin Yuan
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 """Neuron population is a set of tree."""
 
 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 +48,16 @@ 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 +85,7 @@ class LazyLoadingTrees:
 class ChainTrees:
     """Chain trees."""
 
-    trees: List[Trees]
+    trees: list[Trees]
     cumsum: npt.NDArray[np.int64]
 
     def __init__(self, trees: Iterable[Trees]) -> None:
@@ -108,6 +112,19 @@ class ChainTrees:
         return (self[i] for i in range(self.__len__()))
 
 
+class NestTrees:
+    def __init__(self, trees: Trees, idx: Iterable[int], /) -> None:
+        super().__init__()
+        self.trees = trees
+        self.idx = list(idx)
+
+    def __getitem__(self, key: int, /) -> Tree:
+        return self.trees[self.idx[key]]
+
+    def __len__(self) -> int:
+        return len(self.idx)
+
+
 class Population:
     """Neuron population."""
 
@@ -146,13 +163,14 @@ class Population:
 
     # fmt:off
     @overload
-    def __getitem__(self, key: slice) -> List[Tree]: ...
+    def __getitem__(self, key: slice) -> Trees: ...
     @overload
     def __getitem__(self, key: int) -> Tree: ...
     # fmt:on
-    def __getitem__(self, key):
+    def __getitem__(self, key: int | slice):
         if isinstance(key, slice):
-            return [cast(Tree, self.trees[i]) for i in range(*key.indices(len(self)))]
+            trees = NestTrees(self.trees, range(*key.indices(len(self))))
+            return cast(Trees, trees)
 
         if isinstance(key, (int, np.integer)):
             return cast(Tree, self.trees[int(key)])
@@ -216,9 +234,9 @@ 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 +249,8 @@ 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 +266,9 @@ 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 +277,7 @@ 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 +306,7 @@ 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`
@@ -339,3 +357,14 @@ def _get_idx(key: int, length: int) -> int:
         key += length
 
     return key
+
+
+# experimental
+def filter_population(
+    pop: Population, predicate: Callable[[Tree], bool]
+) -> "Population":
+    """Filter trees in the population."""
+
+    # TODO: how to avoid load trees
+    idx = [i for i, t in enumerate(pop) if predicate(t)]
+    return Population(NestTrees(pop.trees, idx), root=pop.root)

swcgeom/core/swc.py

@@ -1,9 +1,25 @@
+# Copyright 2022-2025 Zexin Yuan
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 """SWC format."""
 
 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 +48,7 @@ __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 +58,7 @@ 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 +71,7 @@ class SWCLike(ABC):
     """ABC of SWC."""
 
     source: str = ""
-    comments: List[str] = []
+    comments: list[str] = []
     names: SWCNames
     types: SWCTypes
 
@@ -131,15 +147,15 @@ 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 +193,7 @@ 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 +215,7 @@ 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 +237,7 @@ 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/__init__.py

@@ -1,3 +1,18 @@
+# Copyright 2022-2025 Zexin Yuan
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 """SWC format utils.
 
 Notes
@@ -8,10 +23,9 @@ If you use the method here, please review the code more frequently, we
 will try to flag all breaking changes but NO promises.
 """
 
-
-from swcgeom.core.swc_utils.assembler import *
-from swcgeom.core.swc_utils.base import *
-from swcgeom.core.swc_utils.checker import *
-from swcgeom.core.swc_utils.io import *
-from swcgeom.core.swc_utils.normalizer import *
-from swcgeom.core.swc_utils.subtree import *
+from swcgeom.core.swc_utils.assembler import *  # noqa: F403
+from swcgeom.core.swc_utils.base import *  # noqa: F403
+from swcgeom.core.swc_utils.checker import *  # noqa: F403
+from swcgeom.core.swc_utils.io import *  # noqa: F403
+from swcgeom.core.swc_utils.normalizer import *  # noqa: F403
+from swcgeom.core.swc_utils.subtree import *  # noqa: F403

swcgeom/core/swc_utils/assembler.py

@@ -1,3 +1,18 @@
+# Copyright 2022-2025 Zexin Yuan
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 """Assemble lines to swc.
 
 Notes

swcgeom/core/swc_utils/base.py

@@ -1,16 +1,22 @@
+# Copyright 2022-2025 Zexin Yuan
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 """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 +35,7 @@ __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 +49,7 @@ 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 +120,10 @@ 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 +136,7 @@ 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 +161,7 @@ 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/checker.py

@@ -1,11 +1,26 @@
-"""Check common """
+# Copyright 2022-2025 Zexin Yuan
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+"""Check common"""
 
-import warnings
 from collections import defaultdict
 from typing import Optional
 
 import numpy as np
 import pandas as pd
+from typing_extensions import deprecated
 
 from swcgeom.core.swc_utils.base import SWCNames, Topology, get_dsu, get_names, traverse
 from swcgeom.utils import DisjointSetUnion
@@ -81,6 +96,7 @@ def has_cyclic(topology: Topology) -> bool:
     return False
 
 
+@deprecated("Use `is_single_root` instead")
 def check_single_root(*args, **kwargs) -> bool:
     """Check if the tree is single root.
 
@@ -88,14 +104,10 @@ def check_single_root(*args, **kwargs) -> bool:
         Use :meth:`is_single_root` instead.
     """
 
-    warnings.warn(
-        "`check_single_root` has been renamed to `is_single_root` since"
-        "v0.5.0, and will be removed in next version",
-        DeprecationWarning,
-    )
     return is_single_root(*args, **kwargs)
 
 
+@deprecated("Use `is_bifurcate` instead")
 def is_binary_tree(
     df: pd.DataFrame, exclude_root: bool = True, *, names: Optional[SWCNames] = None
 ) -> bool:
@@ -105,11 +117,6 @@ def is_binary_tree(
         Use :meth:`is_bifurcate` instead.
     """
 
-    warnings.warn(
-        "`is_binary_tree` has been replaced by to `is_bifurcate` since"
-        "v0.8.0, and will be removed in next version",
-        DeprecationWarning,
-    )
     names = get_names(names)
     topo = (df[names.id].to_numpy(), df[names.pid].to_numpy())
     return is_bifurcate(topo, exclude_root=exclude_root)

swcgeom/core/swc_utils/io.py

@@ -1,8 +1,24 @@
+# Copyright 2022-2025 Zexin Yuan
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 """Read and write swc format."""
 
 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 +46,7 @@ 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 +71,7 @@ def read_swc(
     Returns
     -------
     df : ~pandas.DataFrame
-    comments : list of string
+    comments : List of string
     """
 
     names = get_names(names)
@@ -137,14 +153,14 @@ 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 +168,7 @@ def parse_swc(
     Returns
     -------
     df : ~pandas.DataFrame
-    comments : list of string
+    comments : List of string
     """
 
     # pylint: disable=too-many-locals
@@ -171,7 +187,8 @@ def parse_swc(
         RE_FLOAT,  # r
         r"(-?[0-9]+)",  # pid
     ] + [
-        RE_FLOAT for _ in extras  # assert float
+        RE_FLOAT
+        for _ in extras  # assert float
     ]
 
     re_swc_cols_str = r"\s+".join(re_swc_cols)

swcgeom/core/swc_utils/normalizer.py

@@ -1,9 +1,25 @@
+# Copyright 2022-2025 Zexin Yuan
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 """SWC format utils.
 
 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
@@ -76,7 +92,7 @@ def link_roots_to_nearest_(
         vs = df[[names.x, names.y, names.z]] - row[[names.x, names.y, names.z]]
         dis = np.linalg.norm(vs.to_numpy(), axis=1)
         subtree = dsu == dsu[i]  # type: ignore
-        dis = np.where(subtree, np.Infinity, dis)  # avoid link to same tree
+        dis = np.where(subtree, np.inf, dis)  # avoid link to same tree
         dsu = np.where(subtree, dsu[dis.argmin()], dsu)  # merge set
         df.loc[i, names.pid] = df[names.id].iloc[dis.argmin()]  # type: ignore
 
@@ -111,7 +127,7 @@ 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 +143,7 @@ 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