treeswift

library1.1.45pypypi✓ verified 86d ago

TreeSwift is a fast tree manipulation library for Python 2 and 3, providing a simple interface for reading, writing, and analyzing phylogenetic trees. The current version is 1.1.45, with regular updates and bug fixes.

data ai-ml

pip install treeswift

github ↗package ↗

INSTALL

IMPORT

SIG · TREESWIFT

treeswift

datapythonv1.1.45

Install

1.6s avg

Import

10ms

Disk

16MB

Pass rate

10/ 10

Env Coverage10 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v1.1.45 · 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

py 3.10–3.95 runs

installs and imports cleanly · install 0.0s · import 0.010s · 18MB

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 1.6s · import 0.008s · 18MB

16MB installed

● package 16MB

Code

Verified usage

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

Tree

✓ from treeswift import Tree

✗ from treeswift import read_tree

read_tree is a function; Tree is the class.

Node

✓ from treeswift import Node

✗ from treeswift.tree import Node

Node is exported from treeswift directly.

Initialize a tree, read a Newick string, print the tree, and compute the distance between two leaves.

from treeswift import Tree tree = Tree() tree.read('((A:0.1,B:0.2):0.3,C:0.4);') print(tree) # Newick string dist = tree.distance_between('A', 'C') print(dist) # 0.8

Debug

Known issues

gotcha`extract_tree_with` and `extract_tree_without` convert string input to a set of individual characters. If you pass a single string like 'ABC', it will be treated as {'A','B','C'} rather than preserving the string as a single label. Pass a set or list instead.

fix

Use `extract_tree_with(set(['ABC']))` or `extract_tree_with(['ABC'])` to keep the label intact.

affects: <=1.1.41

deprecated`Tree.read` can read gzip files directly, but file extension handling may be simplified in future versions.

fix

Pass an open file handle or a path; gzip is detected internally.

affects: all

gotcha`distance_between` may return incorrect values when one node is an ancestor of the other in versions prior to 1.1.39. Ensure you have the latest version.

fix

Upgrade to >=1.1.39: `pip install --upgrade treeswift`.

affects: <1.1.39

Errors

Common errors & fixes

ModuleNotFoundError: No module named 'treeswift'

Library not installed or installed in a different environment.

fix

Run `pip install treeswift` in the correct Python environment.

TypeError: extract_tree_with() argument after * must be an iterable, not str

Passing a string directly to `extract_tree_with` where an iterable of labels is expected.

fix

Wrap the string in a list: `tree.extract_tree_with(['label'])` instead of `tree.extract_tree_with('label')`.

Upgrade

Version history

1.1.45latest on PyPI · released Nov 19, 2024

Audit

Dependencies

No dependency data recorded yet.

Agent activity

26 hits · last 30 days

node

OpenAI (training)

Resources

githubhttps://github.com/niemasd/TreeSwift ↗

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