Advanced Installation (Linux)

This is a quick guide on how to install AvaFrame and the required dependencies on your machine. AvaFrame is developed on Linux machines (Ubuntu/Manjaro/Arch) with recent Python versions > 3.8. These instructions assume you are familiar with working in a terminal. This guide is described for Linux. For Windows, see Advanced Installation (Windows).

Requirements

Install git and pixi. Some operating systems might require the python headers (e.g python-dev on ubuntu) or other supporting libraries/packages (e.g. Visual Studio on Windows needs the c++ compiler components).

Setup AvaFrame

Clone the AvaFrame repository (in a directory of your choice: [YOURDIR]) and change into it:

cd [YOURDIR]
git clone https://github.com/OpenNHM/AvaFrame.git
cd AvaFrame

Run pixi:

pixi shell

Compile the cython com1DFA part. You might also have to install a c-compiler (gcc or similar) through your systems package manager:

python setup.py build_ext --inplace

Warning

You will have to do this compilation every time something changes in the cython code. We also suggest to do this everytime updates from the repositories are pulled.

All this installs avaframe in editable mode, so every time you import avaframe the current (local) version will be used.

If you want to have the lastet stable release instead, run:

pixi shell --environment prod

Test it by starting python and do an import avaframe. If no error comes up, you are good to go.

To see the current version, you can use:

pixi list avaframe

Head over to First run for the next steps.