Installation Guide

BactoVision is designed to work within Jupyter notebooks and can be installed via pip. The package is compatible with Python 3.7+ and includes all necessary dependencies.

Prerequisites

Before installing BactoVision, ensure you have Python 3.7 or higher.

Installation Methods

Standard Installation

The easiest way to install BactoVision is using pip:

pip install bactovision

This will install BactoVision along with all its dependencies.

Installation from Source

For the latest development version or to contribute to the project, you can install from source:

git clone https://github.com/mlcolab/bactovision.git
cd bactovision
pip install .

Verifying Installation

To verify that BactoVision is installed correctly, open a Jupyter notebook and run:

from bactovision.widget import BactoWidget

If the installation was successful, this should import the widget class without any errors.

Troubleshooting

Common Issues

Missing Dependencies

If you encounter errors about missing dependencies, try reinstalling with:

pip install bactovision --force-reinstall

JupyterLab Extension Issues

For JupyterLab users, if the widget doesn't display properly, ensure that the widget extension is installed:

jupyter labextension list

The output should include anywidget or similar entries. If not, you may need to run

jupyter labextension install @jupyter-widgets/jupyterlab-manager

and restart the jupyter server.

Getting Help

If you experience any issues with installation, please open an issue on our GitHub repository with details about the problem and your environment.