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alifedata-phyloinformatics-convert

library0.19.3pypypiunverified

A library for converting standardized ALife (artificial life) phylogenetic data formats (e.g., from hstrat, phylotrackpy) into formats compatible with traditional phyloinformatics software (e.g., Newick, Nexus, FASTA). Current version 0.19.3, requires Python >=3.8. Active development with monthly releases.

data serialization

pip install alifedata-phyloinformatics-convert

github ↗package ↗

INSTALL

IMPORT

SIG · ALIFEDATA-PHYLOINF

alifedata-phyloinformatics-convert

datapythonv0.19.3

Install

15.1s avg

Import

—

Disk

223MB

Pass rate

5/ 10

Env Coverage5 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v0.19.3 · 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

py 3.10–3.95 runs

build_error

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 15.1s · import 0.000s · 212MB

223MB installed

● package 223MB

Code

Verified usage

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

AlifeDataConvert

✓ from alifedata_phyloinformatics_convert import AlifeDataConvert

✗ from alifedata_phyloinformatics_convert import SomethingElse

AlifeDataConvert is the main class for conversion. Wrong imports (e.g., AlifeDataConvert spelled differently) cause ImportError.

AlifeDataConvert

✓ import alifedata_phyloinformatics_convert as adpc

✗ import alifedata_phyloinformatics_convert

Common mistake: forgetting to use the alias adpc or misspelling the module name (underscores vs hyphens).

Initialize the converter and convert between formats. The source and target formats can be 'newick', 'nexus', 'fasta', etc.

from alifedata_phyloinformatics_convert import AlifeDataConvert # Example: convert a simple Newick string to Nexus newick_str = "(A:0.1,B:0.2):0.3;" converter = AlifeDataConvert() nexus = converter.convert(newick_str, source_format='newick', target_format='nexus') print(nexus)

Debug

Known issues

gotchaThe package name uses hyphens, but Python import requires underscores. Use pip install with hyphens, but import with underscores.

fix

Install: pip install alifedata-phyloinformatics-convert
Import: import alifedata_phyloinformatics_convert

affects: all

breakingVersion 0.19.0 changed the signature of AlifeDataConvert.convert() – the 'source_format' and 'target_format' parameters are now required (previously optional). Code that relied on defaults will break.

fix

Always provide both source_format and target_format explicitly in the call to convert().

affects: >=0.19.0

gotchaThe library only supports specific format pairs (e.g., newick->nexus, newick->fasta). Check the documentation for the exact list of supported conversions before use.

fix

Consult the official GitHub README for supported conversion matrix. Currently supports: newick, nexus, fasta, phylip (some combinations).

affects: all

Upgrade

Version history

0.19.3latest on PyPI · released Feb 14, 2025

Audit

Dependencies

No dependency data recorded yet.

Agent activity

57 hits · last 30 days

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OpenAI (training)

Resources

githubhttps://github.com/mmore500/alifedata-phyloinformatics-convert ↗

packagehttps://pypi.org/project/alifedata-phyloinformatics-convert/ ↗