Metadata-Version: 2.4
Name: rhizaeon
Version: 0.1.0b3
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Dist: pytest>=7.0 ; extra == 'dev'
Provides-Extra: dev
Summary: RhizAeon PA-FF v2.1: Phylo-Attention Force Field Recombination Scanner
Author-email: "Sergei L. Kosakovsky Pond" <spond@temple.edu>
License: MIT
Requires-Python: >=3.8
Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
Project-URL: Bug Tracker, https://github.com/veg/HyphAeon/issues
Project-URL: Homepage, https://github.com/veg/HyphAeon

# RhizAeon — PA-FF v2.1 Recombination Scanner (Python package)

Python-fronted distribution of the RhizAeon PA-FF engine. The compiled
extension (`rhizaeon._native`, built by maturin from `native/`) carries the
clap parser that used to live in the standalone `rhizaeon` cargo bin, so the
command-line surface is unchanged:

```console
$ pip install rhizaeon
$ rhizaeon --input alignment.fasta --output scan.json --viz viz.json --html report.html
```

`python -m rhizaeon` is equivalent to `rhizaeon`. Manuscript figure/benchmark
helpers (`export_figure1_data`, `export_figure2_data`, `grand_sweep`) live in
the unpublished `rust/rhizaeon/crates/rhizaeon-tools` crate — run them via
`cargo run -p rhizaeon-tools --release --bin <name>` from a source checkout.

## Development install

```console
$ cd rhizaeon && maturin develop
```

requires a Rust toolchain (`rustup`). The engine crate itself lives at
`rust/rhizaeon/crates/rhizaeon` and stays a pure library (no clap, no bins)
so `rhizaeon-wasm` builds clean.

