pykdtree

library1.4.3pypypi✓ verified 87d ago

A fast kd-tree implementation in Cython with OpenMP-enabled parallel queries. Current version 1.4.3, supports Python >=3.9 and NumPy >=1.25. Release cadence is irregular, with several maintenance releases addressing bugs and build compatibility.

data ai-ml

pip install pykdtree

github ↗package ↗

INSTALL

IMPORT

SIG · PYKDTREE

pykdtree

datapythonv1.4.3

Install

—

Import

—

Disk

—

Pass rate

0/ 10

Env Coverage0 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v1.4.3 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

glibc

py 3.10

1/2 runs

py 3.11

1/2 runs

py 3.12

1/2 runs

py 3.13

1/2 runs

py 3.9

1/2 runs

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

KDTree

✓ from pykdtree.kdtree import KDTree

Direct import from kdtree submodule.

Create a KDTree from 100 random 3D points and query nearest 4 neighbors for 5 new points.

import numpy as np from pykdtree.kdtree import KDTree data = np.random.randn(100, 3) tree = KDTree(data) query = np.random.randn(5, 3) dists, idx = tree.query(query, k=4) print(dists, idx)

Debug

Known issues

gotchaInput data must be a 2D NumPy array with dtype float64 or float32. If using float32, queries disable OpenMP parallelization.

fix

Ensure data is np.float64 or np.float32, and for large data prefer float64 to benefit from OpenMP.

affects: all

breakingVersion 1.4.0 changed internal integer sizes to handle large arrays. Trees built with older versions cannot be pickled and loaded in 1.4.0+.

fix

Rebuild trees after upgrading pykdtree.

affects: 1.4.0 and later

deprecatedImporting KDTree directly from pykdtree (e.g., from pykdtree import KDTree) is no longer supported as of 1.4.0.

fix

Use from pykdtree.kdtree import KDTree instead.

affects: >=1.4.0

Errors

Common errors & fixes

ModuleNotFoundError: No module named 'pykdtree.kdtree'

Import path changed; users try from pykdtree import KDTree.

fix

Use: from pykdtree.kdtree import KDTree

pykdtree.kdtree.KDTree not returning correct results for large arrays

Integer overflow in tree indexing before version 1.4.0.

fix

Upgrade to pykdtree >= 1.4.0.

Segmentation fault (core dumped) when querying empty array

Bug in versions < 1.3.13 when input data has zero rows.

fix

Upgrade to pykdtree >= 1.3.13.

Upgrade

Version history

1.4.3latest on PyPI · released Aug 6, 2025

Audit

Dependencies

numpyrequiredCore dependency for array handling and API compatibility.

Agent activity

16 hits · last 30 days

node

Amazon

OpenAI (training)

Resources

githubhttps://github.com/storpipfugl/pykdtree ↗

packagehttps://pypi.org/project/pykdtree/ ↗