Installation

PySMACKS is provided as a Python package and is freely available from https://pypi.org/project/PySMACKS/.

Using pip

The suggested installation method is to use pip within a virtual environment.

pip install PySMACKS

You can then run the PySMACKS GUI by typing PySMACKS_GUI directly inside the console:

PySMACKS_GUI

Setting a Python virtual environment

To create a virtual environment, you can type the following in your Python console:

1. Select a folder:

   cd PATH_TO_THE_FOLDER_WHERE_TO_INSTALL_VENV
   

   with PATH_TO_THE_FOLDER_WHERE_TO_INSTALL_VENV replaced by the path to the folder where you want to install your virtual environment.

2. Create your virtual environment:

   python -m venv NAME_OF_YOUR_VENV
   

   with NAME_OF_YOUR_VENV replaced by the name you want to give to your virtual environment (for instance PySMACKS_venv)

3. Activate your virtual environment:

   NAME_OF_YOUR_VENV\Scripts\activate
   

Dependencies

Libraries	Licence	Note
numpy	BSD-3-Clause
matplotlib	Python Software Foundation License
pandas	BSD 3-Clause
PyQt5	GPL v3
scipy	BSD License
scikit-image	BSD License
big-fish	BSD 3-Clause	paper
hmmlearn	BSD License
opencv-python	Apache 2.0
openfret	MIT	GitHub repo
pillow	MIT-CMU
ruptures	BSD-2-Clause	paper * not used in the current version of PySMACKS*
seaborn	BSD License
trackpy		GitHub repo
tvdcondat2013	CeCILL FREE SOFTWARE	GitHub repo
uuid7	MIT