Script 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 Script 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).

Note

This documentation uses pixi environments. You can either prefix commands with pixi run <command>, which runs the command in the pixi environment without requiring you to activate it first, or you can run pixi shell once to start an interactive environment and then run the commands without the pixi run prefix (e.g. pixi run python script.py is equivalent to pixi shell then python script.py).

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

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

pixi run build

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. Use pixi run rebuild to clean and rebuild in one step.

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

Test it by running:

pixi run python -c "import avaframe"

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

pixi run --environment prod python -c "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.