alifedata-phyloinformatics-convert

0.19.3 verified Fri May 01 auth: no python

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.

pip install alifedata-phyloinformatics-convert

Common errors

error ModuleNotFoundError: No module named 'alifedata_phyloinformatics_convert' ↓

cause The package was installed with hyphens in the name but Python import expects underscores.

fix

pip install alifedata-phyloinformatics-convert Then in Python: import alifedata_phyloinformatics_convert

error TypeError: convert() missing 2 required positional arguments: 'source_format' and 'target_format' ↓

cause Code written for older version where these arguments were optional; now required as of 0.19.0.

fix

Update call to include both arguments, e.g., converter.convert(newick_str, source_format='newick', target_format='nexus')

Warnings

gotcha The 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

breaking Version 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().

gotcha The 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).

Imports

AlifeDataConvert
wrong
```
from alifedata_phyloinformatics_convert import SomethingElse
```
correct
```
from alifedata_phyloinformatics_convert import AlifeDataConvert
```
AlifeDataConvert is the main class for conversion. Wrong imports (e.g., AlifeDataConvert spelled differently) cause ImportError.
AlifeDataConvert
wrong
```
import alifedata_phyloinformatics_convert
```
correct
```
import alifedata_phyloinformatics_convert as adpc
```
Common mistake: forgetting to use the alias adpc or misspelling the module name (underscores vs hyphens).

Quickstart

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)