Metadata-Version: 2.1
Name: arg-needle-lib
Version: 1.0.2
Summary: Ancestral recombination graph (ARG) data structure and operations.
Home-page: https://palamaralab.github.io/software/argneedle/
Author: ARG-Needle Developers
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: click
Requires-Dist: h5py
Requires-Dist: msprime >=1.0.0
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: scipy
Requires-Dist: tskit >=0.1.5
Provides-Extra: dev
Requires-Dist: pytest ; extra == 'dev'
Requires-Dist: tszip >=0.2.1 ; extra == 'dev'
Provides-Extra: docs
Requires-Dist: sphinx ; extra == 'docs'
Requires-Dist: sphinx-rtd-theme ; extra == 'docs'

# arg-needle-lib

This repository contains arg-needle-lib, which implements an ARG data structure and ARG-based analyses such as genealogy-wide association.

## Quickstart

### Install the Python module from PyPI

Most functionality is available through a Python module which can be installed with:

```bash
pip install arg-needle-lib
```

This Python module is currently available on Linux and macOS.

### Documentation

Please see the [ARG-Needle manual](https://palamaralab.github.io/software/argneedle/) for all usage instructions and documentation.

## License

arg-needle-lib is distributed under the GNU General Public License v3.0 (GPLv3). For any questions or comments on arg-needle-lib, please contact Pier Palamara using `<lastname>@stats.ox.ac.uk`.

## Acknowledgements

arg-needle-lib is developed by (in alphabetical order) Arjun Biddanda, Fergus Cooper, Árni Freyr Gunnarsson, Pier Francesco Palamara, Sinan Shi, Brian C. Zhang, and Jiazheng Zhu.

## Reference

If you use this software, please cite:

B. C. Zhang, A. Biddanda, Á. F. Gunnarsson, F. Cooper, P. F. Palamara, Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits. [Nature Genetics, 2023](https://www.nature.com/articles/s41588-023-01379-x).

# arg-needle-lib Release Notes


## v1.0.2 (2023-09-29)

### Breaking changes

None

### Other changes

- Improve documentation.
- Build Python wheels for macOS arm64 (Apple Silicon)
- Build wheels for Python 3.12


## v1.0.1 (2023-07-14)

### Breaking changes

None

### Other changes

- Clean-up and release of the source code.
- Improved mutation class.
- Added from-to parameters to some functions.


## v1.0.0 (2023-03-07)

Initial PyPI release of arg-needle-lib.
