The easiest way to install tunacell is from wheels:

pip install tunacell

However some introductory tutorial and scripts are missing in the library. To get them you can visit the GitHub repository:

where you can copy/paste these scripts (look into the scripts folder).

To get everything, a good solution is to fork the repository to your local account and/or to clone the repository on your computer. Change directory in your local repo and do a local install:

pip install -e .

(the -e option stands for editable). With such a clone install, the scripts are in the same place, and you can use the Makefile to run tutorials/demos.

Local install

If Python is installed system-wide, you may have to sudo the command above. When it’s not possible you may give the option to install it on the user directory:

pip install -e –user .

Virtual environment

A better solution when Python is to create a virtual environment where you plan to work with tunacell. It requires pip and virtualenv to be installed on your machine. Then the Makefile does the job, run the command:

make virtualenv

that will set up the virtual environment and install pytest and flake8 locally. Activate the virtual environment with:

source venv/bin/activate

Then you can run the pip install -e., or make pipinstall command, without worrying about permissions since everything will be installed locally, and accesses only when your virtual environment is active. When you finish working with tunacell, type:


and that’s it.


tunacell depends on few libraries that are automatically installed if you are using pip.

Numpy, Scipy, matplotlib are classic libraries, as well as pandas that is used to provide the user with DataFrame objects for some statistical analyses.

The tree-like structure arising from dividing cells has been implemented using the treelib library.

We use pyYAML to parse yaml files such as metadata or other library-created files, tqdm package for progress bars, and tabulate for fancy tabular printing.

New to Python

Python is a computer programming language and to use it, you need a Python interpreter. To check whether you have the Python interpreter installed on your system, run the following command in a terminal:

python -V

If the answer shows something like Python 2.7.x, or Python 3.6.y, you’re good to go. Otherwise you should install it, either directly downloading Python, or using a friendlier package that will guide you, such as anaconda.

After that you should be ready, and pip should be automatically installed. Again try:

pip -V

If it is not installed, you may check [this to install pip][install-pip].

Then get back to install instructions above.