swcgeom 0.17.0__py3-none-any.whl → 0.17.2__py3-none-any.whl

swcgeom/transforms/images.py

@@ -1,10 +1,8 @@
 """Image stack related transform."""
 
-import warnings
-from typing import Tuple
-
 import numpy as np
 import numpy.typing as npt
+from typing_extensions import deprecated
 
 from swcgeom.transforms.base import Identity, Transform
 
@@ -28,7 +26,7 @@ NDArrayf32 = npt.NDArray[np.float32]
 class ImagesCenterCrop(Transform[NDArrayf32, NDArrayf32]):
     """Get image stack center."""
 
-    def __init__(self, shape_out: int | Tuple[int, int, int]):
+    def __init__(self, shape_out: int | tuple[int, int, int]):
         super().__init__()
         self.shape_out = (
             shape_out
@@ -46,6 +44,7 @@ class ImagesCenterCrop(Transform[NDArrayf32, NDArrayf32]):
         return f"shape_out=({','.join(str(a) for a in self.shape_out)})"
 
 
+@deprecated("use `ImagesCenterCrop` instead", stacklevel=2)
 class Center(ImagesCenterCrop):
     """Get image stack center.
 
@@ -53,14 +52,6 @@ class Center(ImagesCenterCrop):
         Use :class:`ImagesCenterCrop` instead.
     """
 
-    def __init__(self, shape_out: int | Tuple[int, int, int]):
-        warnings.warn(
-            "`Center` is deprecated, use `ImagesCenterCrop` instead",
-            DeprecationWarning,
-            stacklevel=2,
-        )
-        super().__init__(shape_out)
-
 
 class ImagesScale(Transform[NDArrayf32, NDArrayf32]):
     def __init__(self, scaler: float) -> None:

swcgeom/transforms/neurolucida_asc.py

@@ -4,9 +4,7 @@ import os
 import re
 from enum import Enum, auto
 from io import TextIOBase
-from typing import Any, List, NamedTuple, Optional, cast
-
-import numpy as np
+from typing import Any, NamedTuple, Optional, cast
 
 from swcgeom.core import Tree
 from swcgeom.core.swc_utils import SWCNames, SWCTypes, get_names, get_types
@@ -116,8 +114,8 @@ class ASTNode:
         self,
         type: ASTType,
         value: Any = None,
-        tokens: Optional[List["Token"]] = None,
-        children: Optional[List["ASTNode"]] = None,
+        tokens: Optional[list["Token"]] = None,
+        children: Optional[list["ASTNode"]] = None,
     ):
         self.type = type
         self.value = value
@@ -149,7 +147,7 @@ class ASTNode:
 
 
 class AST(ASTNode):
-    def __init__(self, children: Optional[List[ASTNode]] = None, source: str = ""):
+    def __init__(self, children: Optional[list[ASTNode]] = None, source: str = ""):
         super().__init__(ASTType.ROOT, children=children)
         self.source = source
 

swcgeom/transforms/population.py

@@ -1,7 +1,5 @@
 """Transformation in population."""
 
-from typing import List
-
 from swcgeom.core import Population, Tree
 from swcgeom.transforms.base import Transform
 
@@ -16,7 +14,7 @@ class PopulationTransform(Transform[Population, Population]):
         self.transform = transform
 
     def __call__(self, population: Population) -> Population:
-        trees: List[Tree] = []
+        trees: list[Tree] = []
         for t in population:
             new_t = self.transform(t)
             if new_t.source == "":

swcgeom/transforms/tree.py

@@ -1,9 +1,10 @@
 """Transformation in tree."""
 
-import warnings
-from typing import Callable, List, Optional, Tuple
+from collections.abc import Callable
+from typing import Optional
 
 import numpy as np
+from typing_extensions import deprecated
 
 from swcgeom.core import BranchTree, DictSWC, Path, Tree, cut_tree, to_subtree
 from swcgeom.core.swc_utils import SWCTypes, get_types
@@ -19,7 +20,7 @@ __all__ = [
     "CutByType",
     "CutAxonTree",
     "CutDendriteTree",
-    "CutByBifurcationOrder",
+    "CutByFurcationOrder",
     "CutShortTipBranch",
 ]
 
@@ -68,6 +69,7 @@ class TreeSmoother(Transform[Tree, Tree]):  # pylint: disable=missing-class-docs
         return f"n_nodes={self.n_nodes}"
 
 
+@deprecated("Use `Normalizer` instead")
 class TreeNormalizer(Normalizer[Tree]):
     """Noramlize coordinates and radius to 0-1.
 
@@ -75,15 +77,6 @@ class TreeNormalizer(Normalizer[Tree]):
         Use :cls:`Normalizer` instead.
     """
 
-    def __init__(self, *args, **kwargs) -> None:
-        warnings.warn(
-            "`TreeNormalizer` has been replaced by `Normalizer` since "
-            "v0.6.0 beacuse it applies more widely, and this will be "
-            "removed in next version",
-            DeprecationWarning,
-        )
-        super().__init__(*args, **kwargs)
-
 
 class CutByType(Transform[Tree, Tree]):
     """Cut tree by type.
@@ -102,7 +95,7 @@ class CutByType(Transform[Tree, Tree]):
     def __call__(self, x: Tree) -> Tree:
         removals = set(x.id()[x.type() != self.type])
 
-        def leave(n: Tree.Node, keep_children: List[bool]) -> bool:
+        def leave(n: Tree.Node, keep_children: list[bool]) -> bool:
             if n.id in removals and any(keep_children):
                 removals.remove(n.id)
             return n.id not in removals
@@ -131,28 +124,48 @@ class CutDendriteTree(CutByType):
         super().__init__(type=types.basal_dendrite)  # TODO: apical dendrite
 
 
-class CutByBifurcationOrder(Transform[Tree, Tree]):
-    """Cut tree by bifurcation order."""
+class CutByFurcationOrder(Transform[Tree, Tree]):
+    """Cut tree by furcation order."""
 
-    max_bifurcation_order: int
+    max_furcation_order: int
 
     def __init__(self, max_bifurcation_order: int) -> None:
-        self.max_bifurcation_order = max_bifurcation_order
+        self.max_furcation_order = max_bifurcation_order
 
     def __call__(self, x: Tree) -> Tree:
         return cut_tree(x, enter=self._enter)
 
     def __repr__(self) -> str:
-        return f"CutByBifurcationOrder-{self.max_bifurcation_order}"
+        return f"CutByBifurcationOrder-{self.max_furcation_order}"
 
-    def _enter(self, n: Tree.Node, parent_level: int | None) -> Tuple[int, bool]:
+    def _enter(self, n: Tree.Node, parent_level: int | None) -> tuple[int, bool]:
         if parent_level is None:
             level = 0
-        elif n.is_bifurcation():
+        elif n.is_furcation():
             level = parent_level + 1
         else:
             level = parent_level
-        return (level, level >= self.max_bifurcation_order)
+        return (level, level >= self.max_furcation_order)
+
+
+@deprecated("Use CutByFurcationOrder instead")
+class CutByBifurcationOrder(CutByFurcationOrder):
+    """Cut tree by bifurcation order.
+
+    Notes
+    -----
+    Deprecated due to the wrong spelling of furcation. For now, it
+    is just an alias of `CutByFurcationOrder` and raise a warning. It
+    will be change to raise an error in the future.
+    """
+
+    max_furcation_order: int
+
+    def __init__(self, max_bifurcation_order: int) -> None:
+        super().__init__(max_bifurcation_order)
+
+    def __repr__(self) -> str:
+        return f"CutByBifurcationOrder-{self.max_furcation_order}"
 
 
 class CutShortTipBranch(Transform[Tree, Tree]):
@@ -164,7 +177,7 @@ class CutShortTipBranch(Transform[Tree, Tree]):
     """
 
     thre: float
-    callbacks: List[Callable[[Tree.Branch], None]]
+    callbacks: list[Callable[[Tree.Branch], None]]
 
     def __init__(
         self, thre: float = 5, callback: Optional[Callable[[Tree.Branch], None]] = None
@@ -176,7 +189,7 @@ class CutShortTipBranch(Transform[Tree, Tree]):
             self.callbacks.append(callback)
 
     def __call__(self, x: Tree) -> Tree:
-        removals: List[int] = []
+        removals: list[int] = []
         self.callbacks.append(lambda br: removals.append(br[1].id))
         x.traverse(leave=self._leave)
         self.callbacks.pop()
@@ -186,8 +199,8 @@ class CutShortTipBranch(Transform[Tree, Tree]):
         return f"threshold={self.thre}"
 
     def _leave(
-        self, n: Tree.Node, children: List[Tuple[float, Tree.Node] | None]
-    ) -> Tuple[float, Tree.Node] | None:
+        self, n: Tree.Node, children: list[tuple[float, Tree.Node] | None]
+    ) -> tuple[float, Tree.Node] | None:
         if len(children) == 0:  # tip
             return 0, n
 

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, List, Optional, Tuple
+from typing import Optional
 
 import numpy as np
 import pandas as pd
@@ -18,7 +19,7 @@ from swcgeom.transforms.base import Transform
 EPS = 1e-5
 
 
-class LinesToTree(Transform[List[pd.DataFrame], Tree]):
+class LinesToTree(Transform[list[pd.DataFrame], Tree]):
     """Assemble lines to swc."""
 
     def __init__(self, *, thre: float = 0.2, undirected: bool = True):
@@ -97,7 +98,7 @@ class LinesToTree(Transform[List[pd.DataFrame], Tree]):
         undirected: bool = True,
         sort_nodes: bool = True,
         names: Optional[SWCNames] = None,
-    ) -> Tuple[pd.DataFrame, List[pd.DataFrame]]:
+    ) -> tuple[pd.DataFrame, list[pd.DataFrame]]:
         """Trying assemble lines to a tree.
 
         Treat the first line as a tree, find a line whose shortest distance

swcgeom/utils/download.py

@@ -13,6 +13,7 @@ import itertools
 import logging
 import multiprocessing
 import os
+from functools import partial
 from urllib.parse import urljoin
 
 __all__ = ["download", "fetch_page", "clone_index_page"]
@@ -26,7 +27,7 @@ def download(dst: str, url: str) -> None:
     r = conn.request("GET", url)
 
     dirname = os.path.dirname(dst)
-    if not os.path.exists(dirname):
+    if dirname != "" and not os.path.exists(dirname):
         os.makedirs(dirname)
 
     with open(dst, "wb") as file:
@@ -41,7 +42,7 @@ def fetch_page(url: str):
     conn = connection_from_url(url)
     r = conn.request("GET", url)
     data = r.data.decode("utf-8")
-    return BeautifulSoup(data)
+    return BeautifulSoup(data, features="html.parser")
 
 
 def clone_index_page(
@@ -62,31 +63,35 @@ def clone_index_page(
     multiprocess : int, default `4`
         How many process are available for download.
     """
-    from urllib3.exceptions import HTTPError
-
     files = get_urls_in_index_page(index_url)
     logging.info("downloader: search `%s`, found %s files.", index_url, len(files))
 
-    def task(url: str) -> None:
-        filepath = url.removeprefix(index_url)
-        dist = os.path.join(dist_dir, filepath)
-        if os.path.exists(filepath):
-            if not override:
-                logging.info("downloader: file `%s` exits, skiped.", dist)
-                return
+    task = partial(
+        _clone_index_page, index_url=index_url, dist_dir=dist_dir, override=override
+    )
+    with multiprocessing.Pool(multiprocess) as p:
+        p.map(task, files)
 
-            logging.info("downloader: file `%s` exits, deleted.", dist)
-            os.remove(filepath)
 
-        try:
-            logging.info("downloader: downloading `%s` to `%s`", url, dist)
-            download(filepath, url)
-            logging.info("downloader: download `%s` to `%s`", url, dist)
-        except HTTPError as ex:
-            logging.info("downloader: fails to download `%s`, except `%s`", url, ex)
+def _clone_index_page(url: str, index_url: str, dist_dir: str, override: bool) -> None:
+    from urllib3.exceptions import HTTPError
 
-    with multiprocessing.Pool(multiprocess) as p:
-        p.map(task, files)
+    filepath = url.removeprefix(index_url)
+    dist = os.path.join(dist_dir, filepath)
+    if os.path.exists(dist):
+        if not override:
+            logging.info("downloader: file `%s` exits, skiped.", dist)
+            return
+
+        logging.info("downloader: file `%s` exits, deleted.", dist)
+        os.remove(dist)
+
+    try:
+        logging.info("downloader: downloading `%s` to `%s`", url, dist)
+        download(dist, url)
+        logging.info("downloader: download `%s` to `%s`", url, dist)
+    except HTTPError as ex:
+        logging.info("downloader: fails to download `%s`, except `%s`", url, ex)
 
 
 def get_urls_in_index_page(url: str) -> list[str]:
@@ -97,3 +102,21 @@ def get_urls_in_index_page(url: str) -> list[str]:
     dirs = [urljoin(url, a) for a in links if a != "../" and a.endswith("/")]
     files.extend(itertools.chain(*[get_urls_in_index_page(dir) for dir in dirs]))
     return files
+
+
+if __name__ == "__main__":
+    import argparse
+
+    parser = argparse.ArgumentParser(description="Download files from index page.")
+    parser.add_argument("url", type=str, help="URL of index page.")
+    parser.add_argument("dist", type=str, help="Directory of dist.")
+    parser.add_argument(
+        "--override", type=bool, default=False, help="Override existing file."
+    )
+    parser.add_argument(
+        "--multiprocess", type=int, default=4, help="How many process are available."
+    )
+    args = parser.parse_args()
+
+    logging.basicConfig(level=logging.INFO)
+    clone_index_page(args.url, args.dist, args.override, args.multiprocess)

swcgeom/utils/ellipse.py

@@ -3,7 +3,6 @@
 # pylint: disable=invalid-name
 
 from functools import cached_property
-from typing import Tuple
 
 import numpy as np
 import numpy.linalg as la
@@ -22,7 +21,7 @@ class Ellipse:
         self.centroid = centroid
 
     @property
-    def radii(self) -> Tuple[float, float]:
+    def radii(self) -> tuple[float, float]:
         # x, y radii.
         _U, D, _V = self.svd
         rx, ry = 1.0 / np.sqrt(D)
@@ -39,7 +38,7 @@ class Ellipse:
         return b
 
     @property
-    def axes(self) -> Tuple[float, float]:
+    def axes(self) -> tuple[float, float]:
         # Major and minor semi-axis of the ellipse.
         rx, ry = self.radii
         dx, dy = 2 * rx, 2 * ry
@@ -77,7 +76,7 @@ def mvee(points: npt.NDArray[np.floating], tol: float = 1e-3) -> Ellipse:
 
 def _mvee(
     points: npt.NDArray[np.floating], tol: float = 1e-3
-) -> Tuple[npt.NDArray[np.float64], npt.NDArray[np.float64]]:
+) -> tuple[npt.NDArray[np.float64], npt.NDArray[np.float64]]:
     """Finds the Minimum Volume Enclosing Ellipsoid.
 
     Returns

swcgeom/utils/neuromorpho.py

@@ -81,7 +81,8 @@ import logging
 import math
 import os
 import urllib.parse
-from typing import Any, Callable, Dict, Iterable, List, Literal, Optional, Tuple
+from collections.abc import Callable, Iterable
+from typing import Any, Literal, Optional
 
 from tqdm import tqdm
 
@@ -116,7 +117,7 @@ SIZE_METADATA = 2 * GB
 SIZE_DATA = 20 * GB
 
 RESOURCES = Literal["morpho_cng", "morpho_source", "log_cng", "log_source"]
-DOWNLOAD_CONFIGS: Dict[RESOURCES, Tuple[str, int]] = {
+DOWNLOAD_CONFIGS: dict[RESOURCES, tuple[str, int]] = {
     # name/path: (url, size)
     "morpho_cng": (URL_MORPHO_CNG, 20 * GB),
     "morpho_source": (URL_LOG_CNG, 512 * GB),
@@ -145,7 +146,7 @@ invalid_ids = [
 # fmt: on
 
 
-def neuromorpho_is_valid(metadata: Dict[str, Any]) -> bool:
+def neuromorpho_is_valid(metadata: dict[str, Any]) -> bool:
     return metadata["neuron_id"] not in invalid_ids
 
 
@@ -209,7 +210,7 @@ class NeuroMorpho:
             self._info("skip download metadata")
 
         # file
-        def dumps(keys: List[bytes]) -> str:
+        def dumps(keys: list[bytes]) -> str:
             return json.dumps([i.decode("utf-8") for i in keys])
 
         for name in resources:
@@ -238,8 +239,8 @@ class NeuroMorpho:
         self,
         dest: Optional[str] = None,
         *,
-        group_by: Optional[str | Callable[[Dict[str, Any]], str | None]] = None,
-        where: Optional[Callable[[Dict[str, Any]], bool]] = None,
+        group_by: Optional[str | Callable[[dict[str, Any]], str | None]] = None,
+        where: Optional[Callable[[dict[str, Any]], bool]] = None,
         encoding: str | None = "utf-8",
     ) -> None:
         r"""Convert lmdb format to SWCs.
@@ -249,11 +250,11 @@ class NeuroMorpho:
         path : str
         dest : str, optional
             If None, use `path/swc`.
-        group_by : str | (metadata: Dict[str, Any]) -> str | None, optional
+        group_by : str | (metadata: dict[str, Any]) -> str | None, optional
             Group neurons by metadata. If a None is returned then no
             grouping. If a string is entered, use it as a metadata
             attribute name for grouping, e.g.: `archive`, `species`.
-        where : (metadata: Dict[str, Any]) -> bool, optional
+        where : (metadata: dict[str, Any]) -> bool, optional
             Filter neurons by metadata.
         encoding : str | None, default to `utf-8`
             Change swc encoding, part of the original data is not utf-8
@@ -346,14 +347,14 @@ class NeuroMorpho:
         pages: Optional[Iterable[int]] = None,
         page_size: int = API_PAGE_SIZE_MAX,
         **kwargs,
-    ) -> List[int]:
+    ) -> list[int]:
         r"""Download all neuron metadata.
 
         Parameters
         ----------
         path : str
             Path to save data.
-        pages : list of int, optional
+        pages : List of int, optional
             If is None, download all pages.
         verbose : bool, default False
             Show verbose log.
@@ -362,7 +363,7 @@ class NeuroMorpho:
 
         Returns
         -------
-        err_pages : list of int
+        err_pages : List of int
             Failed pages.
         """
 
@@ -402,7 +403,7 @@ class NeuroMorpho:
         override: bool = False,
         map_size: int = 512 * GB,
         **kwargs,
-    ) -> List[bytes]:
+    ) -> list[bytes]:
         """Download files.
 
         Parameters
@@ -412,7 +413,7 @@ class NeuroMorpho:
             Path to save data.
         path_metadata : str
             Path to lmdb of metadata.
-        keys : list of bytes, optional
+        keys : List of bytes, optional
             If exist, ignore `override` option. If None, download all key.
         override : bool, default False
             Override even exists.
@@ -422,7 +423,7 @@ class NeuroMorpho:
 
         Returns
         -------
-        err_keys : list of str
+        err_keys : List of str
             Failed keys.
         """
 
@@ -459,7 +460,7 @@ class NeuroMorpho:
 
     def _get_metadata(
         self, page: int, page_size: int = API_PAGE_SIZE_MAX, **kwargs
-    ) -> Dict[str, Any]:
+    ) -> dict[str, Any]:
         params = {
             "page": page,
             "size": page_size,
@@ -470,7 +471,7 @@ class NeuroMorpho:
         resp = self._get(url, **kwargs)
         return json.loads(resp)
 
-    def _get_file(self, url: str, metadata: Dict[str, Any], **kwargs) -> bytes:
+    def _get_file(self, url: str, metadata: dict[str, Any], **kwargs) -> bytes:
         """Get file.
 
         Returns

swcgeom/utils/plotter_2d.py

@@ -1,6 +1,6 @@
-"""Rendering related utils."""
+"""2D Plotting utils."""
 
-from typing import Optional, Tuple
+from typing import Optional
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -19,7 +19,12 @@ __all__ = ["draw_lines", "draw_direction_indicator", "draw_circles", "get_fig_ax
 
 
 def draw_lines(
-    ax: Axes, lines: npt.NDArray[np.floating], camera: Camera, **kwargs
+    ax: Axes,
+    lines: npt.NDArray[np.floating],
+    camera: Camera,
+    joinstyle="round",
+    capstyle="round",
+    **kwargs,
 ) -> LineCollection:
     """Draw lines.
 
@@ -43,11 +48,12 @@ def draw_lines(
     starts, ends = np.dot(T, starts.T).T[:, 0:2], np.dot(T, ends.T).T[:, 0:2]
 
     edges = np.stack([starts, ends], axis=1)
-    return ax.add_collection(LineCollection(edges, **kwargs))  # type: ignore
+    collection = LineCollection(edges, joinstyle=joinstyle, capstyle=capstyle, **kwargs)  # type: ignore
+    return ax.add_collection(collection)  # type: ignore
 
 
 def draw_direction_indicator(
-    ax: Axes, camera: Camera, loc: Tuple[float, float]
+    ax: Axes, camera: Camera, loc: tuple[float, float]
 ) -> None:
     x, y = loc
     direction = camera.MV.dot(
@@ -120,7 +126,7 @@ def draw_circles(
 
 def get_fig_ax(
     fig: Optional[Figure] = None, ax: Optional[Axes] = None
-) -> Tuple[Figure, Axes]:
+) -> tuple[Figure, Axes]:
     if fig is None and ax is not None:
         fig = ax.get_figure()
         assert fig is not None, "expecting a figure from the axes"

swcgeom/utils/plotter_3d.py

@@ -0,0 +1,31 @@
+"""3D Plotting utils."""
+
+import numpy as np
+import numpy.typing as npt
+from mpl_toolkits.mplot3d import Axes3D
+from mpl_toolkits.mplot3d.art3d import Line3DCollection
+
+__all__ = ["draw_lines_3d"]
+
+
+def draw_lines_3d(
+    ax: Axes3D,
+    lines: npt.NDArray[np.floating],
+    joinstyle="round",
+    capstyle="round",
+    **kwargs,
+):
+    """Draw lines.
+
+    Parameters
+    ----------
+    ax : ~matplotlib.axes.Axes
+    lines : A collection of coords of lines
+        Excepting a ndarray of shape (N, 2, 3), the axis-2 holds two points,
+        and the axis-3 holds the coordinates (x, y, z).
+    **kwargs : dict[str, Unknown]
+        Forwarded to `~mpl_toolkits.mplot3d.art3d.Line3DCollection`.
+    """
+
+    line_collection = Line3DCollection(lines, joinstyle=joinstyle, capstyle=capstyle, **kwargs)  # type: ignore
+    return ax.add_collection3d(line_collection)

swcgeom/utils/renderer.py

@@ -1,7 +1,7 @@
 """Rendering related utils."""
 
 from functools import cached_property
-from typing import Dict, Literal, Tuple, cast
+from typing import Literal, cast
 
 import numpy as np
 import numpy.typing as npt
@@ -15,9 +15,9 @@ from swcgeom.utils.transforms import (
 
 __all__ = ["CameraOptions", "Camera", "SimpleCamera", "palette"]
 
-CameraOption = Vec3f | Tuple[Vec3f, Vec3f] | Tuple[Vec3f, Vec3f, Vec3f]
+CameraOption = Vec3f | tuple[Vec3f, Vec3f] | tuple[Vec3f, Vec3f, Vec3f]
 CameraPreset = Literal["xy", "yz", "zx", "yx", "zy", "xz"]
-CameraPresets: Dict[CameraPreset, Tuple[Vec3f, Vec3f, Vec3f]] = {
+CameraPresets: dict[CameraPreset, tuple[Vec3f, Vec3f, Vec3f]] = {
     "xy": ((0.0, 0.0, 0.0), (+0.0, +0.0, -1.0), (+0.0, +1.0, +0.0)),
     "yz": ((0.0, 0.0, 0.0), (-1.0, +0.0, +0.0), (+0.0, +0.0, +1.0)),
     "zx": ((0.0, 0.0, 0.0), (+0.0, -1.0, +0.0), (+1.0, +0.0, +0.0)),
@@ -77,7 +77,7 @@ class SimpleCamera(Camera):
         if isinstance(camera[0], tuple):
             return cls((0, 0, 0), cast(Vec3f, camera), (0, 1, 0))
 
-        return cls(*cast(Tuple[Vec3f, Vec3f, Vec3f], camera))
+        return cls(*cast(tuple[Vec3f, Vec3f, Vec3f], camera))
 
 
 class Palette:
@@ -85,8 +85,8 @@ class Palette:
 
     # pylint: disable=too-few-public-methods
 
-    default: Dict[int, str]
-    vaa3d: Dict[int, str]
+    default: dict[int, str]
+    vaa3d: dict[int, str]
 
     def __init__(self):
         default = [

swcgeom/utils/sdf.py

@@ -10,10 +10,11 @@ the future, use `sdflit` instead.
 
 import warnings
 from abc import ABC, abstractmethod
-from typing import Iterable, Tuple
+from collections.abc import Iterable
 
 import numpy as np
 import numpy.typing as npt
+from typing_extensions import deprecated
 
 from swcgeom.utils.solid_geometry import project_vector_on_plane
 
@@ -29,7 +30,7 @@ __all__ = [
 ]
 
 # Axis-aligned bounding box, tuple of array of shape (3,)
-AABB = Tuple[npt.NDArray[np.float32], npt.NDArray[np.float32]]
+AABB = tuple[npt.NDArray[np.float32], npt.NDArray[np.float32]]
 
 
 class SDF(ABC):
@@ -173,6 +174,7 @@ class SDFDifference(SDF):
         return flags
 
 
+@deprecated("Use `SDFUnion` instead")
 class SDFCompose(SDFUnion):
     """Compose multiple SDFs.
 
@@ -181,11 +183,6 @@ class SDFCompose(SDFUnion):
     """
 
     def __init__(self, sdfs: Iterable[SDF]) -> None:
-        warnings.warn(
-            "`SDFCompose` has been replace by `SDFUnion` since v0.14.0, "
-            "and will be removed in next version",
-            DeprecationWarning,
-        )
         sdfs = list(sdfs)
         if len(sdfs) == 1:
             warnings.warn("compose only one SDF, use SDFCompose.compose instead")