edmkit 0.0.7__tar.gz → 0.0.8__tar.gz

{edmkit-0.0.7 → edmkit-0.0.8}/PKG-INFO

@@ -1,13 +1,13 @@
 Metadata-Version: 2.3
 Name: edmkit
-Version: 0.0.7
+Version: 0.0.8
 Summary: Simple EDM (Empirical Dynamic Modeling) library
 Author: FUJISHIGE TEMMA
 Author-email: FUJISHIGE TEMMA <tenma.x0@gmail.com>
+Requires-Dist: kdtree-rs>=0.1.0
 Requires-Dist: numpy>=2.4.3
 Requires-Dist: scipy>=1.17.1
 Requires-Dist: tinygrad>=0.11.0
-Requires-Dist: usearch>=2.23.0
 Requires-Python: >=3.13
 Description-Content-Type: text/markdown
 

{edmkit-0.0.7 → edmkit-0.0.8}/pyproject.toml

@@ -1,15 +1,15 @@
 [project]
 name = "edmkit"
-version = "0.0.7"
+version = "0.0.8"
 description = "Simple EDM (Empirical Dynamic Modeling) library"
 authors = [{ name = "FUJISHIGE TEMMA", email = "tenma.x0@gmail.com" }]
 readme = "README.md"
 requires-python = ">= 3.13"
 dependencies = [
+    "kdtree-rs>=0.1.0",
     "numpy>=2.4.3",
     "scipy>=1.17.1",
     "tinygrad>=0.11.0",
-    "usearch>=2.23.0",
 ]
 
 [dependency-groups]

edmkit-0.0.8/src/edmkit/simplex_projection/knn.py

@@ -0,0 +1,31 @@
+import numpy as np
+from kdtree import KDTree
+
+
+def knn(X: np.ndarray, Q: np.ndarray, k: int) -> tuple[np.ndarray, np.ndarray]:
+    """Find the k-nearest neighbors of `Q` in `X` using `kdtree.KDTree`.
+
+    Parameters
+    ----------
+    X : np.ndarray
+        The input data (N, E)
+    Q : np.ndarray
+        The query points (M, E)
+    k : int
+        The number of nearest neighbors to find (typically E+1 for simplex projection).
+
+    Returns
+    -------
+    distances : np.ndarray
+        The distances from each query point in `Q` to its k nearest neighbors in `X` (M, k)
+    indices : np.ndarray
+        The indices of the k nearest neighbors in `X` for each query point in `Q` (M, k)
+    """
+
+    N = X.shape[0]
+
+    if N < k:
+        raise ValueError(f"Not enough points in X to find {k} neighbors, got N={N}")
+
+    tree = KDTree(X)
+    return tree.query(Q, k=k)

edmkit-0.0.7/src/edmkit/simplex_projection/knn.py

@@ -1,40 +0,0 @@
-import numpy as np
-from scipy.spatial import KDTree
-from usearch.index import Index
-
-
-def knn(X: np.ndarray, Q: np.ndarray, k: int) -> tuple[np.ndarray, np.ndarray]:
-    """Find the k-nearest neighbors of `Q` in `X` using either `usearch` or `scipy.spatial.KDTree` depending on the size and dimensionality of the data.
-
-    Parameters
-    ----------
-    X : np.ndarray
-        The input data (N, E)
-    Q : np.ndarray
-        The query points (M, E)
-    k : int
-        The number of nearest neighbors to find (typically E+1 for simplex projection).
-
-    Returns
-    -------
-    distances : np.ndarray
-        The distances from each query point in `Q` to its k nearest neighbors in `X` (M, k)
-    indices : np.ndarray
-        The indices of the k nearest neighbors in `X` for each query point in `Q` (M, k)
-    """
-
-    N, E = X.shape
-
-    if N < k:
-        raise ValueError(f"Not enough points in X to find {k} neighbors, got N={N}")
-
-    if E >= 15 and N >= 10_000:
-        index = Index(ndim=E, metric="l2sq")
-        index.add(np.arange(len(X)), np.ascontiguousarray(X, dtype=np.float32))
-        matches = index.search(np.ascontiguousarray(Q, dtype=np.float32), k)
-        distances = np.atleast_2d(np.sqrt(np.asarray(matches.distances)))
-        indices = np.atleast_2d(np.asarray(matches.keys).astype(np.intp))
-        return distances, indices
-    else:
-        tree = KDTree(X)
-        return tree.query(Q, k=k)