Add Python bindings - Githubissues

sriramlab / GENIE

Gene Environment Interaction Estimator

MIT License

2 stars 0 forks source link

Add Python bindings #2

Closed fcooper8472 closed 3 months ago

fcooper8472 commented 4 months ago

Work in progress addressing #1

fcooper8472 commented 3 months ago

Summary of changes

GitHub Actions workflows

Added workflows to test GENIE compiles and the toy examples run on Linux and macOS
Added workflow to build Python wheels for Python 3.8-3.12 (amd64) and 3.9-3.12 (arm64)

Reduced platform specific code

Removed <bits/stdc++.h> include
Conditionally include <emmintrin.h> only if detected architecture is appropriate
Removed unused rdtsc using inline amd64 assembly

Tidy dependencies

Removed GSL (unused)
Removed Boost by replacing generation of Normally distributed random numbers with calls to the standard library

CMake

Modernised script slightly
Use build types (rather than hard-coded O3)
Attempt to handle SSE support by detecting architecture
Add switch for installing GENIE executables into rhe python module

Python

Add PyPI-specific README
Add pyproject.toml to specify project
Add python module that handles args and subprocess to call GENIE executables
Add a Python test file to verify intended usage works as expected