faster-fishers 0.1.1

Rust version of Scipy's Fisher exact test.

faster_fishers

Fast implementation of Fisher's exact test in Rust for Python.
Benchmarks show that this version is about 20x faster than scipy's version when running on a large range of inputs and about 10x faster when running on 1 input:

--------------------------------------------------------------------------------------------- benchmark: 2 tests ---------------------------------------------------------------------------------------------
Name (time in ms)                        Min                   Max                  Mean             StdDev                Median                IQR            Outliers     OPS            Rounds  Iterations
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
test_benchmark_faster_fischer       114.5763 (1.0)        119.2121 (1.0)        116.1288 (1.0)       1.6386 (1.0)        115.5922 (1.0)       1.6018 (1.0)           2;1  8.6111 (1.0)           9           1
test_benchmark_scipy              2,403.8024 (20.98)    2,458.8598 (20.63)    2,423.2871 (20.87)    21.4687 (13.10)    2,415.6504 (20.90)    24.6082 (15.36)         1;0  0.4127 (0.05)          5           1
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Usage:

>>> import numpy as np
>>> import faster_fishers
>>> lefts, right, two_tails = faster_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])

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}

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: maturin develop --release *python: pytest --benchmark-warmup -m benchmark