faster_fishers

Fast implementation of Fisher's exact test in Rust for Python.
Benchmarks show that this version is about 30x faster than scipy's version when running on a large range of inputs and about 10x faster when running on 1 input:

```asm ---------------------------------------------------------------------------------------------- benchmark: 2 tests ---------------------------------------------------------------------------------------------

Name (time in ms) Min Max Mean StdDev Median IQR Outliers OPS Rounds Iterations

testbenchmarkfaster_fischer 59.8543 (1.0) 61.0522 (1.0) 60.5012 (1.0) 0.2816 (1.0) 60.5717 (1.0) 0.3114 (1.0) 3;1 16.5286 (1.0) 17 1

testbenchmarkscipy 1,859.7465 (31.07) 1,935.8237 (31.71) 1,885.3549 (31.16) 30.7295 (109.12) 1,871.9271 (30.90) 38.2479 (122.85) 1;0 0.5304 (0.03) 5 1

```

Usage:

Rust: rust use faster_fishers::{fishers_exact_with_odds_ratio, Alternative}; let table = [3, 5, 4, 50]; let alternative = Alternative::Less; let (p_value, odds_ratio) = fishers_exact_with_odds_ratio(&table, alternative).unwrap();

Python:

```python

import numpy as np import fishers lefts, right, twotails = fishers.exact(np.array([1, 3]), np.array([2, 5]), np.array([1, 4]), np.array([5, 50])) lefts array([0.9166666666666647, 0.9963034765672586]) rights array([0.5833333333333326, 0.03970749246529451]) twotails array([1.0, 0.03970749246529451]) ```

Developing

Building with cargo

• Run cargo build in the main directory to build the project.

Publishing on pypi

docker run --rm -v $(pwd):/io ghcr.io/pyo3/maturin publish -u {USER} -p {PASSWORD}

Publishing on cargo

cargo publish

Using locally

• Install environment: poetry install
• Add environment to current shell poetry shell
• Install faster_fishers in current environment: maturin develop
• Check that it works: python -c "import faster_fishers; print(dir(faster_fishers))"

To try the library in a different environment:
1. maturin build --release
2. cd folder
3. pip install {wheel_path}.whl

Benchmarks

• Make sure to compile in release mode with maturin first: RUSTFLAGS='-C target-cpu=native' maturin develop --release *python: pytest --benchmark-warmup -m benchmark