Installation

Vaxflux is a Python package and can be installed using pip, conda, or any other standard package managers. It is compatible with Python 3.10, 3.11, and 3.12. However, vaxflux is currently in development and not available on PyPI or conda-forge, so it must be installed directly from GitHub.

Using pip

To install vaxflux using pip, run the following command in your terminal:

pip install git+https://github.com/ACCIDDA/vaxflux.git

Using conda

To install vaxflux using conda, you can create a new environment and install it from GitHub. Run the following commands in your terminal:

conda install pip
pip install git+https://github.com/ACCIDDA/vaxflux.git

Using uv

To add vaxflux to your uv environment, you can use the following command:

uv add git+https://github.com/ACCIDDA/vaxflux.git

Optional Dependencies

The vaxflux package also provides two optional dependency groups:

• plot: This adds additional dependencies that enable plotting functionality, without it you can still use the package to construct and fit models but will not be able to plot the results with built in functionality. It's recommended for local use that you include this optional dependency group, but it is not recommended for production usage (e.g. in an HPC environment).
• demo: This adds additional dependencies that are needed for running the jupyter notebooks in the demos/ directory. This optional dependency group is generally not needed unless you are learning the package and want to run those demos locally yourself.

To install these optional dependency groups you can change the installation urls above to git+https://github.com/ACCIDDA/vaxflux.git[plot] or git+https://github.com/ACCIDDA/vaxflux.git[demo].