Metadata-Version: 2.4
Name: trace50
Version: 5.0.0
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
License-File: LICENSE
Summary: TRACE-5.0: Dynamic Molecular Surveillance of Viral Transmission Networks
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

# TRACE-5.0 — Molecular Transmission Surveillance (Python package)

Python-fronted distribution of the TRACE-5.0 engine. The compiled extension
(`trace50._native`, built by maturin from `native/`) carries the clap parser
that used to live in the standalone `trace50` cargo bin, so the command-line
surface is unchanged:

```console
$ pip install trace50
$ trace50 --fasta alignment.fasta --meta dates.csv --out-dir trace50_results
```

`python -m trace50` is equivalent to `trace50`.

## Development install

```console
$ cd trace50 && maturin develop
```

requires a Rust toolchain (`rustup`). The engine crate itself lives at
`rust/trace-5.0/crates/trace50` and stays a pure library (no clap; the only
bin is the `conformance` dev driver) so `trace50-wasm` builds clean.

