refactor: mark deprecated with PEP702

swcgeom/analysis/sholl.py

@@ -8,6 +8,7 @@
 import seaborn as sns
 from matplotlib.axes import Axes
 from matplotlib.figure import Figure
+from typing_extensions import deprecated
 
 from swcgeom.analysis.visualization import draw
 from swcgeom.core import Tree
@@ -160,61 +161,42 @@ def _get_rs(self, steps: int | npt.ArrayLike) -> npt.NDArray[np.float32]:
 
         return self.get_rs(self.rmax, steps)
 
+    @deprecated("Use `Sholl.get(x)` instead")
     def get_count(self) -> npt.NDArray[np.int32]:
         """Get the count of intersection.
 
         .. deprecated:: 0.5.0
-            Use :meth:`Sholl.get` instead.
+            Use :meth:`Sholl(x).get()` instead.
         """
 
-        warnings.warn(
-            "`Sholl.get_count` has been renamed to `get` since v0.5.0, "
-            "and will be removed in next version",
-            DeprecationWarning,
-        )
         return self.get().astype(np.int32)
 
+    @deprecated("Use `Shool(x).get().mean()` instead")
     def avg(self) -> float:
         """Get the average of the count of intersection.
 
         .. deprecated:: 0.6.0
             Use :meth:`Shool(x).get().mean()` instead.
         """
 
-        warnings.warn(
-            "`Sholl.avg` has been deprecated since v0.6.0 and will be "
-            "removed in next version, use `Shool(x).get().mean()` "
-            "instead",
-            DeprecationWarning,
-        )
         return self.get().mean()
 
+    @deprecated("Use `Shool(x).get().std()` instead")
     def std(self) -> float:
         """Get the std of the count of intersection.
 
         .. deprecated:: 0.6.0
             Use :meth:`Shool(x).get().std()` instead.
         """
 
-        warnings.warn(
-            "`Sholl.std` has been deprecate since v0.6.0 and will be "
-            "removed in next version, use `Shool(x).get().std()` "
-            "instead",
-            DeprecationWarning,
-        )
         return self.get().std()
 
+    @deprecated("Use `Shool(x).get().sum()` instead")
     def sum(self) -> int:
         """Get the sum of the count of intersection.
 
         .. deprecated:: 0.6.0
             Use :meth:`Shool(x).get().sum()` instead.
         """
 
-        warnings.warn(
-            "`Sholl.sum` has been deprecate since v0.6.0 and will be "
-            "removed in next version, use `Shool(x).get().sum()` "
-            "instead",
-            DeprecationWarning,
-        )
         return self.get().sum()

swcgeom/core/path.py

@@ -1,11 +1,11 @@
 """Nueron path."""
 
-import warnings
 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
@@ -75,18 +75,14 @@ def keys(self) -> Iterable[str]:
     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.
 
         .. deprecated:: 0.16.0
             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/swc_utils/checker.py

@@ -1,11 +1,11 @@
 """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
@@ -81,21 +81,18 @@ 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.
 
     .. deprecated:: 0.5.0
         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 +102,6 @@ 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/tree_utils.py

@@ -5,6 +5,7 @@
 from typing import Optional, TypeVar, overload
 
 import numpy as np
+from typing_extensions import deprecated
 
 from swcgeom.core.swc import SWCLike
 from swcgeom.core.swc_utils import (
@@ -95,6 +96,7 @@ def _leave(n: Tree.Node, children: list[K]) -> K:
     return to_subtree(tree, removals)
 
 
+@deprecated("Use `to_subtree` instead")
 def to_sub_tree(swc_like: SWCLike, sub: Topology) -> tuple[Tree, dict[int, int]]:
     """Create subtree from origin tree.
 
@@ -111,13 +113,6 @@ def to_sub_tree(swc_like: SWCLike, sub: Topology) -> tuple[Tree, dict[int, int]]
     id_map : dict[int, int]
     """
 
-    warnings.warn(
-        "`to_sub_tree` will be removed in v0.6.0, it is replaced by "
-        "`to_subtree` beacuse it is easy to use, and this will be "
-        "removed in next version",
-        DeprecationWarning,
-    )
-
     sub = propagate_removal(sub)
     (new_id, new_pid), id_map_arr = to_sub_topology(sub)
 

swcgeom/images/folder.py

@@ -3,15 +3,14 @@
 import math
 import os
 import re
-import warnings
 from collections.abc import Callable, Iterable
 from dataclasses import dataclass
 from typing import Generic, Literal, Optional, TypeVar, overload
 
 import numpy as np
 import numpy.typing as npt
 from tqdm import tqdm
-from typing_extensions import Self
+from typing_extensions import Self, deprecated
 
 from swcgeom.images.io import ScalarType, read_imgs
 from swcgeom.transforms import Identity, Transform
@@ -65,21 +64,14 @@ def scan(root: str, *, pattern: Optional[str] = None) -> list[str]:
         return fs
 
     @staticmethod
+    @deprecated("Use `~swcgeom.images.io.read_imgs(fname).get_full()` instead")
     def read_imgs(fname: str) -> npt.NDArray[np.float32]:
         """Read images.
 
         .. deprecated:: 0.16.0
             Use :meth:`~swcgeom.images.io.read_imgs(fname).get_full()` instead.
         """
 
-        warnings.warn(
-            "`ImageStackFolderBase.read_imgs` serves as a "
-            "straightforward wrapper for `~swcgeom.images.io.read_imgs(fname).get_full()`. "
-            "However, as it is not utilized within our internal "
-            "processes, it is scheduled for removal in the "
-            "forthcoming version.",
-            DeprecationWarning,
-        )
         return read_imgs(fname).get_full()
 
 

swcgeom/images/io.py

@@ -12,6 +12,7 @@
 import numpy as np
 import numpy.typing as npt
 import tifffile
+from typing_extensions import deprecated
 from v3dpy.loaders import PBD, Raw
 
 __all__ = ["read_imgs", "save_tiff", "read_images"]
@@ -601,16 +602,12 @@ def shape(self) -> tuple[int, int, int]:
         return self.imgs.shape[:-1]
 
 
+@deprecated("Use `read_imgs` instead")
 def read_images(*args, **kwargs) -> GrayImageStack:
     """Read images.
 
     .. deprecated:: 0.16.0
         Use :meth:`read_imgs` instead.
     """
 
-    warnings.warn(
-        "`read_images` has been replaced by `read_imgs` because it"
-        "provide rgb support, and this will be removed in next version",
-        DeprecationWarning,
-    )
     return GrayImageStack(read_imgs(*args, **kwargs))

swcgeom/transforms/images.py

@@ -1,9 +1,8 @@
 """Image stack related transform."""
 
-import warnings
-
 import numpy as np
 import numpy.typing as npt
+from typing_extensions import deprecated
 
 from swcgeom.transforms.base import Identity, Transform
 
@@ -45,21 +44,14 @@ def extra_repr(self) -> str:
         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.
 
     .. deprecated:: 0.16.0
         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/tree.py

@@ -1,10 +1,10 @@
 """Transformation in tree."""
 
-import warnings
 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
@@ -69,22 +69,14 @@ def extra_repr(self):
         return f"n_nodes={self.n_nodes}"
 
 
+@deprecated("Use `Normalizer` instead")
 class TreeNormalizer(Normalizer[Tree]):
     """Noramlize coordinates and radius to 0-1.
 
     .. deprecated:: 0.6.0
         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.

swcgeom/utils/sdf.py

@@ -14,6 +14,7 @@
 
 import numpy as np
 import numpy.typing as npt
+from typing_extensions import deprecated
 
 from swcgeom.utils.solid_geometry import project_vector_on_plane
 
@@ -173,6 +174,7 @@ def is_in(self, p: npt.NDArray[np.float32]) -> npt.NDArray[np.bool_]:
         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")