https://github.com/mmore500/hstrat-surface-concept

Algorithm development for lightweight fixed-length recency-proportional hereditary stratigraphy data structure
https://github.com/mmore500/hstrat-surface-concept

Last synced: 3 months ago
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Algorithm development for lightweight fixed-length recency-proportional hereditary stratigraphy data structure

• Host: GitHub
• URL: https://github.com/mmore500/hstrat-surface-concept
• Owner: mmore500
• License: mit
• Created: 2023-06-11T01:01:19.000Z (almost 2 years ago)
• Default Branch: master
• Last Pushed: 2025-02-23T04:29:43.000Z (3 months ago)
• Last Synced: 2025-02-23T05:25:18.203Z (3 months ago)
• Language: Python
• Size: 3.17 GB
• Stars: 0
• Watchers: 3
• Forks: 1
• Open Issues: 9
• Metadata Files:
  • Readme: README.md
  • Contributing: docs/contributing.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md
  • Citation: CITATION.cff

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README

        
# Hereditary Stratigraphic Surface (hsurf) Concept

[![CI](https://github.com/mmore500/hstrat-surface-concept/actions/workflows/ci.yaml/badge.svg)](https://github.com/mmore500/hstrat-surface-concept/actions/workflows/ci.yaml)

[![GitHub stars](https://img.shields.io/github/stars/mmore500/hstrat-surface-concept.svg?style=flat-square&logo=github&label=Stars&logoColor=white)](https://github.com/mmore500/hstrat-surface-concept)

[![DOI](https://zenodo.org/badge/652063401.svg)](https://zenodo.org/doi/10.5281/zenodo.10779240)

hsurf provides efficient, constant-space downsampling of data streams via DStream algorithms, with applications including heredity stratigraphic phylogenetic inference over distributed digital evolution populations.

-   Free software: MIT license

## Installation

`python3 -m pip install "git+https://github.com/mmore500/[email protected]#egg=hsurf"`

## Documentation

Slide deck & graphics for this project are at .

Some notes are in the template manuscript skeleton in `tex/`, which is built via GitHub actions and can be downloaded as an artifact.

See `binder` for usage examples.

## Roadmap

This repository hosts prototype code for algorithm development of a lightweight fixed-length hereditary stratigraphy data structure.

Code here is designed for use in conjunction with the mainline [`hstrat`](https://github.com/mmore500/hstrat) and [`downstream`](https://github.com/mmore500/downstream) packages.

Long-term, code in this repository will migrate to the `hstrat` and `downstream` packages and this will remain only to ensure records (and reproducibility) of prototype work.

## Citing

If pecking contributes to a scientific publication, please cite it as

> Matthew Andres Moreno. (2024). mmore500/hstrat-surface-concept. Zenodo. https://zenodo.org/doi/10.5281/zenodo.10779240

```bibtex

@software{moreno2024hsurf,

  author = {Matthew Andres Moreno},

  title = {mmore500/hstrat-surface-concept},

  month = mar,

  year = 2024,

  publisher = {Zenodo},

  doi = {10.5281/zenodo.10779240},

  url = {https://zenodo.org/doi/10.5281/zenodo.10779240}

}

```

Consider also citing [hstrat](https://hstrat.readthedocs.io/en/stable/citing.html).

And don't forget to leave a [star on GitHub](https://github.com/mmore500/hstrat-surface-concept/stargazers)!

## Credits

This package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter) and the [mmore500/cookiecutter-dishtiny-project](https://github.com/mmore500/cookiecutter-dishtiny-project) project template.