Installation

We recommend creating a clean Conda environment to ensure dependencies don’t conflict with your existing Python installations. You will need to have installed or already have mini-conda and git on your system.

Step 1: Install Mini-conda

Download and install Conda for your operating system, following the instructions. We recommend the Conda distribution mini-condaIf prompted, add Conda to the PATH variable during installation.

Step 2: Download and Install u-Unwrap3D repository

Clone the u-Unwrap3D repository onto your system

git clone https://github.com/DanuserLab/u-unwrap3D.git

Step 3: Create Conda environment for u-Unwrap3D

Open a terminal or command prompt in the root folder of the u-Unwrap3D repository. Create and activate a new conda environment with Python=3.9. Later versions should also work.

conda create -n u_Unwrap3D_env python=3.9
conda activate u_Unwrap3D_env

Step 4: Install u-Unwrap3D from cloned repository

Perform pip install in the root folder of the u-Unwrap3D repository

pip install .

alternatively, if you don’t want to clone you can use pip to also install the package directly without cloning from the github repository.

pip install u-unwrap3D@git+https://github.com/DanuserLab/u-unwrap3D.git

Known Installation Issues

• scikit-fmm compilation error The scikit-fmm dependency does not have pre-compiled wheels available in pip. This can create an error for operating systems without the necessary compilation tools installed. It is a minor dependency, therefore either remove this from the file requirements.txt, if you have cloned the repository or install scikit-fmm first using conda using the conda-forge channel:

conda install -c conda-forge scikit-fmm