Metadata-Version: 2.4
Name: hyphaeon-core
Version: 0.1.0
Summary: Aeon-Core: Shared bioinformatics infrastructure for Aeon-family packages
Author-email: "Sergei L. Kosakovsky Pond" <spond@temple.edu>
License: MIT
Project-URL: Homepage, https://github.com/veg/HyphAeon
Project-URL: Bug Tracker, https://github.com/veg/HyphAeon/issues
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: torch>=2.0.0
Requires-Dist: biopython>=1.80
Requires-Dist: numpy>=1.22.0
Requires-Dist: scipy>=1.9.0
Requires-Dist: pandas>=1.5.0
Requires-Dist: huggingface-hub>=0.20.0
Requires-Dist: safetensors>=0.4.0
Provides-Extra: tn93
Requires-Dist: tn93>=1.2.0; extra == "tn93"
Provides-Extra: dev
Requires-Dist: pytest>=7.0; extra == "dev"
Dynamic: license-file

# aeon-core

Shared infrastructure for the HyphAeon family of packages (HyphAeon, ChronAeon).

Contains the `PhyloAxialTransformer` foundation model, pretrained weight resolution (HuggingFace Hub), and core utilities for alignment processing, inference, spectral splits, temporal parsing, I/O, and statistics.

## Installation

```bash
pip install hyphaeon-core
```

## Components

- **`model`** — `PhyloAxialTransformer`, `BustedMultiTaskHead`, `decode_soft_ordinal_lrt`
- **`weights`** — Weight resolution from HuggingFace Hub (`datamonkey/hyphaeon`), safetensors loading
- **`inference`** — Device management, adaptive batch sizing, model loading, alignment preparation
- **`dataset`** — Alignment parsing, TN93 distance matrices, tree handling, MDS coordinates
- **`splits`** — Cross-taxa attention extraction, fused affinity matrices
- **`temporal`** — Date parsing utilities (`parse_date_to_decimal`, `extract_date_from_string`)
- **`io`** — JSON/CSV writers, directory helpers
- **`stats`** — LRT p-value computation, Benjamini-Hochberg, Cauchy combination
- **`_progress`** — `ChunkProgress` progress bar utility
