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Installation

# 1. Create a new Conda environment (Choose favorite Python version)
conda create -n smoothie_env python=3.10 -y

# 2. Activate the environment
conda activate smoothie_env

# 3. Install the package directly from PyPI
pip install smoothie-st

# 4. (Optional) Make the environment available in Jupyter Lab
conda install ipykernel -y
python -m ipykernel install --user --name=smoothie_env --display-name="Python (smoothie_env)"
To use Smoothie after installation, create a new copy of one of the blank scripts from examples and follow the steps in the pipeline. Refer to the graphical overview and the supporting files from guides to correctly and confidently use Smoothie.

Quick Install

pip install smoothie-st

Github Clone Install

git clone --depth 1 https://github.com/caholdener01/Smoothie.git
cd Smoothie

Reproducibility Note

Smoothie uses the Infomap random-walk community detection algorithm to identify gene modules. Because Infomap is non-deterministic, clustering results can vary slightly across runs.

To improve reproducibility, Smoothie sets a random seed (default=0). However, exact reproducibility also depends on your Python version and installed package versions.

To reproduce the exact clustering results from the tutorials on this website, do the following installation steps: 

# 1. Clone the repository
git clone https://github.com/caholdener01/Smoothie.git
cd Smoothie

# 2. Create a new Conda environment
conda create -n smoothie_tutorials_env python=3.10 -y

# 3. Activate the environment
conda activate smoothie_tutorials_env

# 4. Install pinned and flexible dependencies
pip install -r tutorials_reproducibility.txt
pip install .

# 5. (Optional) Register the environment in Jupyter Lab
conda install ipykernel -y
python -m ipykernel install --user --name=smoothie_tutorials_env --display-name="Python (smoothie_tutorials_env)"

Previous Version Install

To install the previous Smoothie version, you can clone an old tagged version: 

git clone -b v0.2.4 --single-branch https://github.com/caholdener01/Smoothie.git
Please note that Smoothie v0.2.3 had a bug in the second-order correlation gene stability analysis. Smoothie v0.2.4 fixes this bug, leaving the rest of the code unchanged.