lophat 0.9.2
Lockfree Persistent Homology Algorithm Toolbox
License: MIT
Requires Python: >=3.7

<div align="center">

<h1>LoPHAT</h1>

<b>Lo</b>ckfree <b>P</b>ersistent <b>H</b>omology <b>A</b>lgorithm <b>T</b>oolbox

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[![PyPi](https://img.shields.io/pypi/v/lophat)](https://pypi.org/project/lophat/)
[![docs.rs](https://img.shields.io/docsrs/lophat?label=Docs.rs)](https://docs.rs/lophat/latest/lophat/)
[![Read the Docs](https://img.shields.io/readthedocs/lophat?label=Read%20The%20Docs)](https://lophat.readthedocs.io/en/latest/)

Try in: [Your Browser](https://lophat.tomchaplin.xyz/) • [Google Colab](https://colab.research.google.com/drive/1y0_wZfvuUZfRreYPO50mo4rBlflkMcfj?usp=sharing)

</div>

## Overview

LoPHAT is a Rust library implementing the lockfree algorithm for computing persistent homology (PH), introduced in [[1]](#1).
Python bindings are provided via PyO3, with an interface familiar to those who have used PHAT [[2]](#2).

The primary goal of this library is to make the algorithm accessible to those wishing to compute PH of ___arbitrary filtered chain complexes___.
In particular, LoPHAT is **not** specialised to compute PH of common filtrations or even filtered simplicial complexes.
As such, you should expect LoPHAT to under-perform as compared to [giotto-ph [3]](#3) or [oineus  [4]](#4), both of which use the algorithm of [[1]](#1).

The only changes from the algorithm described in [[1]](#1) are:
* We use the `pinboard` library for epoch-based memory management of the matrices.
* We store the $j^{th}$ column of $R$ and $V$ alongside each other in memory, allowing a full $R=DV$ decomposition (rather than just computing pairings).
* We additionally employ the clearing optimisation [[5]](#5) and provide methods for anti-transpotion (so as to compute persistent cohomology).
* We distribute chunks via work-stealing, using the `rayon` library.

> **Warning**
> LoPHAT is currently in beta.
> The implementation is not optimised, the API is not fixed and tests are limited.

## Usage in Rust

Install with
```shell
cargo add lophat
```
For usage, please consult [the Rust docs](https://docs.rs/lophat/latest/lophat/).

## Usage in Python

The Python bindings can be installed via
```shell
pip install lophat
```
If this fails, it is probably `pip` trying to install from source without a `cargo` toolchain present.
To force installing from binary run
```shell
pip install --only-binary lophat lophat
```
This provides you with one function, `compute_pairings`, which returns the diagram as a set of paired columns and a set of unpaired columns.
By default, this uses all available threads and the lockfree algorithm of [[1]](#1).
To use serial algorithm or limit number of threads, additionally provide a `LoPhatOptions` object.

For more details, please consult [the Python docs](https://lophat.readthedocs.io/en/latest/).
For example usage, see the file `example.py` or [this Google colab notebook](https://colab.research.google.com/drive/1y0_wZfvuUZfRreYPO50mo4rBlflkMcfj?usp=sharing).

## TODO

- [ ] Change options struct for each algorithm
- [ ] Decide on new Python bindings
- [ ] Increase property testing
- [ ] Write unit tests
- [ ] Write integration tests (testing V) 
- [ ] Benchmark
- [ ] Abstract out matrix trait?
- [ ] Reduce memory usage when V not maintained
- [ ] Add contributing guide
- [ ] Fix locking in pivots vector
- [ ] Github actions

## References

<a id="1">[1]</a> Morozov, Dmitriy, and Arnur Nigmetov.
"Towards lockfree persistent homology."
Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures. 2020.

<a id="2">[2]</a> Bauer, Ulrich, et al.
"Phat–persistent homology algorithms toolbox." Journal of symbolic computation 78 (2017): 76-90.
[Bitbucket](https://bitbucket.org/phat-code/phat/src/master/)

<a id="3">[3]</a> Pérez, Julián Burella, et al.
"giotto-ph: A python library for high-performance computation of persistent homology of Vietoris-Rips filtrations."
arXiv preprint [arXiv:2107.05412](https://arxiv.org/abs/2107.05412) (2021).
[GitHub](https://github.com/giotto-ai/giotto-ph)

<a id="4">[4]</a> Nigmetov, Arnur, Morozov, Dmitriy, and USDOE.
Oineus v1.0. Computer software.
[https://www.osti.gov//servlets/purl/1774764](https://www.osti.gov//servlets/purl/1774764). USDOE. 1 Apr. 2021.
Web. [doi:10.11578/dc.20210407.1](https://doi.org/10.11578/dc.20210407.1). [GitHub](https://github.com/anigmetov/oineus)

<a id="5">[5]</a> Bauer, Ulrich, Michael Kerber, and Jan Reininghaus.
"Clear and compress: Computing persistent homology in chunks."
Topological Methods in Data Analysis and Visualization III: Theory, Algorithms, and Applications.
Springer International Publishing, 2014.