Installation

Quick Install

Install citk directly from GitHub:

pip install git+https://github.com/averinpa/citk.git

Development Setup (uv)

uv sync --all-extras

This installs core, docs, dev, and optional R integration dependencies declared in pyproject.toml.

Optional LightGBM Extra

LightGBM is not required for core citk functionality. Install only if you want to pass LightGBM models explicitly:

uv sync --extra ml

Optional Tigramite Extra

For tigramite wrappers (cmiknn, cmiknn_mixed, regci):

uv sync --extra tigramite

Local External Wrappers

Two optional wrappers currently expect local repositories:

1. mcmiknn -> /Users/pavelaverin/Projects/mCMIkNN/src

2. dct -> /Users/pavelaverin/Projects/DCT

If those paths are not available, these wrappers raise a clear ImportError when called.

Optional R-Based Setup

R-backed tests are optional. They require:

1. Python package rpy2 (already in the r extra)

2. R package RCIT from GitHub repository ericstrobl/RCIT

3. R package bnlearn from CRAN (for hartemink_chisq)

Example:

uv sync --extra r