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 59.3260 (1.0) 65.8875 (1.0) 60.6495 (1.0) 1.4096 (1.0) 60.3958 (1.0) 0.4898 (1.0) 1;2 16.4882 (1.0) 17 1

testbenchmarkscipy 1,814.7296 (30.59) 1,864.8661 (28.30) 1,833.9733 (30.24) 21.2606 (15.08) 1,821.9229 (30.17) 32.0363 (65.41) 1;0 0.5453 (0.03) 5 1

```

Usage:

```python

import numpy as np import fasterfishers lefts, right, twotails = fasterfishers.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

todo

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