faster_fishers

Python的Rust实现的Fisher精确检验，运行速度快。
基准测试表明，该版本在大量输入时比Scipy版本快约30倍，在单个输入时快约10倍

---------------------------------------------------------------------------------------------- benchmark: 2 tests ---------------------------------------------------------------------------------------------
Name (time in ms)                        Min                   Max                  Mean             StdDev                Median                IQR            Outliers      OPS            Rounds  Iterations
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
test_benchmark_faster_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
test_benchmark_scipy              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
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

用法

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

>>> import numpy as np
>>> import fishers
>>> lefts, right, two_tails = 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])
>>> two_tails
array([1.0, 0.03970749246529451])

开发中

使用cargo构建

• 在主目录中运行 cargo build 构建项目。

在PyPI上发布

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

在Cargo上发布

cargopublish

本地使用

• 安装环境: poetry install
• 将环境添加到当前shell poetry shell
• 在当前环境中安装faster_fishers: maturin develop
• 检查是否正常工作: python -"import faster_fishers; print(dir(faster_fishers))"

在不同的环境中尝试库
1. maturin build --release
2. cd folder
3. pip install {wheel_path}.whl

基准测试

• 首先使用maturin以发布模式编译： RUSTFLAGS='-C target-cpu=native' maturin develop --release *python: pytest --benchmark-warmup -m benchmark