swcgeom 0.18.3__tar.gz → 0.19.1__tar.gz

{swcgeom-0.18.3/swcgeom.egg-info → swcgeom-0.19.1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: swcgeom
-Version: 0.18.3
+Version: 0.19.1
 Summary: Neuron geometry library for swc format
 Author-email: yzx9 <pypi@yzx9.xyz>
 License: Apache-2.0
@@ -15,12 +15,12 @@ Requires-Dist: numpy>=1.22.3
 Requires-Dist: pandas>=1.4.2
 Requires-Dist: pynrrd>=1.1.0
 Requires-Dist: scipy>=1.9.1
-Requires-Dist: sdflit>=0.2.1
+Requires-Dist: sdflit>=0.2.6
 Requires-Dist: seaborn>=0.12.0
 Requires-Dist: tifffile>=2022.8.12
-Requires-Dist: typing_extensions>=4.4.0
+Requires-Dist: typing-extensions>=4.4.0
 Requires-Dist: tqdm>=4.46.1
-Requires-Dist: v3d-py-helper>=0.4.1
+Requires-Dist: v3d-py-helper>=0.4.1; python_version < "3.13"
 Provides-Extra: all
 Requires-Dist: beautifulsoup4>=4.11.1; extra == "all"
 Requires-Dist: certifi>=2023.5.7; extra == "all"
@@ -28,6 +28,7 @@ Requires-Dist: chardet>=5.2.0; extra == "all"
 Requires-Dist: lmdb>=1.4.1; extra == "all"
 Requires-Dist: requests>=2.0.0; extra == "all"
 Requires-Dist: urllib3>=1.26.0; extra == "all"
+Dynamic: license-file
 
 # SWCGEOM
 

{swcgeom-0.18.3 → swcgeom-0.19.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "swcgeom"
-version = "0.18.3"
+version = "0.19.1"
 description = "Neuron geometry library for swc format"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -14,12 +14,12 @@ dependencies = [
     "pandas>=1.4.2",
     "pynrrd>=1.1.0",
     "scipy>=1.9.1",
-    "sdflit>=0.2.1",
+    "sdflit>=0.2.6",
     "seaborn>=0.12.0",
     "tifffile>=2022.8.12",
-    "typing_extensions>=4.4.0",
+    "typing-extensions>=4.4.0",
     "tqdm>=4.46.1",
-    "v3d-py-helper>=0.4.1",
+    "v3d-py-helper>=0.4.1; python_version < '3.13'",
 ]
 
 [project.optional-dependencies]
@@ -34,3 +34,14 @@ all = [
 
 [project.urls]
 repository = "https://github.com/yzx9/swcgeom"
+
+[dependency-groups]
+dev = [
+    "pytest>=8.3.4",
+]
+
+[tool.ruff]
+target-version = "py310"
+src = [ "tests", "swcgeom" ]
+format.docstring-code-format = true
+lint.pydocstyle.convention = "google"

{swcgeom-0.18.3 → swcgeom-0.19.1}/swcgeom/analysis/feature_extractor.py

@@ -15,10 +15,8 @@
 
 """Easy way to compute and visualize common features for feature.
 
-Notes
------
-For development, see method `Features.get_evaluator` to confirm the
-naming specification.
+NOTE: For development, see method `Features.get_evaluator` to confirm the naming
+specification.
 """
 
 from abc import ABC, abstractmethod
@@ -83,23 +81,31 @@ class Features:
 
     tree: Tree
 
-    # fmt:off
     # Modules
     @cached_property
-    def node_features(self) -> NodeFeatures: return NodeFeatures(self.tree)
+    def node_features(self) -> NodeFeatures:
+        return NodeFeatures(self.tree)
+
     @cached_property
-    def furcation_features(self) -> FurcationFeatures: return FurcationFeatures(self.node_features)
+    def furcation_features(self) -> FurcationFeatures:
+        return FurcationFeatures(self.node_features)
+
     @cached_property
-    def tip_features(self) -> TipFeatures: return TipFeatures(self.node_features)
+    def tip_features(self) -> TipFeatures:
+        return TipFeatures(self.node_features)
+
     @cached_property
-    def branch_features(self) -> BranchFeatures: return BranchFeatures(self.tree)
+    def branch_features(self) -> BranchFeatures:
+        return BranchFeatures(self.tree)
+
     @cached_property
-    def path_features(self) -> PathFeatures: return PathFeatures(self.tree)
+    def path_features(self) -> PathFeatures:
+        return PathFeatures(self.tree)
 
     # Caches
     @cached_property
-    def sholl(self) -> Sholl: return Sholl(self.tree)
-    # fmt:on
+    def sholl(self) -> Sholl:
+        return Sholl(self.tree)
 
     def __init__(self, tree: Tree) -> None:
         self.tree = tree
@@ -136,22 +142,17 @@ class Features:
 class FeatureExtractor(ABC):
     """Extract features from tree."""
 
-    # fmt:off
     @overload
     def get(self, feature: Feature, **kwargs) -> NDArrayf32: ...
     @overload
     def get(self, feature: list[FeatAndKwargs]) -> list[NDArrayf32]: ...
     @overload
     def get(self, feature: dict[Feature, dict[str, Any]]) -> dict[str, NDArrayf32]: ...
-    # fmt:on
     def get(self, feature, **kwargs):
         """Get feature.
 
-        Notes
-        -----
-        Shape of returned array is not uniform, `TreeFeatureExtractor`
-        returns array of shape (L, ), `PopulationFeatureExtracor`
-        returns array of shape (N, L).
+        NOTE: Shape of returned array is not uniform, `TreeFeatureExtractor` returns
+        array of shape (L, ), `PopulationFeatureExtracor` returns array of shape (N, L).
         """
         if isinstance(feature, dict):
             return {k: self._get(k, **v) for k, v in feature.items()}
@@ -164,11 +165,8 @@ class FeatureExtractor(ABC):
     def plot(self, feature: FeatAndKwargs, title: str | bool = True, **kwargs) -> Axes:
         """Plot feature with appropriate way.
 
-        Notes
-        -----
-        The drawing method is different in different classes, different
-        in different features, and may different between versions,
-        there are NO guarantees.
+        NOTE: The drawing method is different in different classes, different in
+        different features, and may different between versions, there are NO guarantees.
         """
         feat, feat_kwargs = _get_feat_and_kwargs(feature)
         if callable(custom_plot := getattr(self, f"plot_{feat}", None)):

{swcgeom-0.18.3 → swcgeom-0.19.1}/swcgeom/analysis/features.py

@@ -13,7 +13,7 @@
 # limitations under the License.
 
 
-"""Feature anlysis of tree."""
+"""Feature analysis of tree."""
 
 from abc import ABC, abstractmethod
 from functools import cached_property
@@ -53,22 +53,17 @@ class NodeFeatures:
     def get_count(self) -> npt.NDArray[np.float32]:
         """Get number of nodes.
 
-        Returns
-        -------
-        count : array of shape (1,)
+        Args:
+            count: array of shape (1,)
         """
-
         return np.array([self.tree.number_of_nodes()], dtype=np.float32)
 
     def get_radial_distance(self) -> npt.NDArray[np.float32]:
         """Get the end-to-end straight-line distance to soma.
 
-        Returns
-        -------
-        radial_distance : npt.NDArray[np.float32]
-            Array of shape (N,).
+        Returns:
+            radial_distance: Array of shape (N,).
         """
-
         xyz = self.tree.xyz() - self.tree.soma().xyz()
         radial_distance = np.linalg.norm(xyz, axis=1)
         return radial_distance
@@ -81,12 +76,9 @@ class NodeFeatures:
 
         Criticle node means that soma, bifucation nodes, tips.
 
-        Returns
-        -------
-        order : npt.NDArray[np.int32]
-            Array of shape (N,), which k is the number of branchs.
+        Returns:
+            order: Array of shape (N,), which k is the number of branches.
         """
-
         order = np.zeros_like(self._branch_tree.id(), dtype=np.int32)
 
         def assign_depth(n: Tree.Node, pre_depth: int | None) -> int:
@@ -112,23 +104,17 @@ class _SubsetNodesFeatures(ABC):
     def get_count(self) -> npt.NDArray[np.float32]:
         """Get number of nodes.
 
-        Returns
-        -------
-        count : npt.NDArray[np.float32]
-            Array of shape (1,).
+        Returns:
+            count: Array of shape (1,).
         """
-
         return np.array([np.count_nonzero(self.nodes)], dtype=np.float32)
 
     def get_radial_distance(self) -> npt.NDArray[np.float32]:
         """Get the end-to-end straight-line distance to soma.
 
-        Returns
-        -------
-        radial_distance : npt.NDArray[np.float32]
-            Array of shape (N,).
+        Returns:
+            radial_distance: Array of shape (N,).
         """
-
         return self._features.get_radial_distance()[self.nodes]
 
     @classmethod
@@ -148,11 +134,9 @@ class FurcationFeatures(_SubsetNodesFeatures):
 class BifurcationFeatures(FurcationFeatures):
     """Evaluate bifurcation node feature of tree.
 
-    Notes
-    -----
-    Deprecated due to the wrong spelling of furcation. For now, it
-    is just an alias of `FurcationFeatures` and raise a warning. It
-    will be change to raise an error in the future.
+    NOTE: Deprecated due to the wrong spelling of furcation. For now, it is just an
+    alias of `FurcationFeatures` and raise a warning. It will be change to raise an
+    error in the future.
     """
 
 
@@ -219,24 +203,18 @@ class BranchFeatures:
     def get_angle(self, eps: float = 1e-7) -> npt.NDArray[np.float32]:
         """Get agnle between branches.
 
-        Returns
-        -------
-        angle : npt.NDArray[np.float32]
-            An array of shape (N, N), which N is length of branches.
+        Returns:
+            angle: An array of shape (N, N), which N is length of branches.
         """
-
         return self.calc_angle(self._branches, eps=eps)
 
     @staticmethod
     def calc_angle(branches: list[T], eps: float = 1e-7) -> npt.NDArray[np.float32]:
         """Calc agnle between branches.
 
-        Returns
-        -------
-        angle : npt.NDArray[np.float32]
-            An array of shape (N, N), which N is length of branches.
+        Returns:
+            angle: An array of shape (N, N), which N is length of branches.
         """
-
         vector = np.array([br[-1].xyz() - br[0].xyz() for br in branches])
         vector_dot = np.matmul(vector, vector.T)
         vector_norm = np.linalg.norm(vector, ord=2, axis=1, keepdims=True)