Installation
There are two and a half main parts to Koopa – the core package koopa (and the prefect-pipeline koopa-flows used to actually run everything) as well as the subsequent visualization steps koopa-viz.
For people at the institute there is no installation required. Just log into the provided cloud interface and follow the usage chapter.
All others can use koopa-flows by cloning the repository. Either use the CLI entry point and run it using python src/cli.py --config PATH or by deploying the src/flows.py:workflow to a on-prem/cloud prefect instance.
It’s advised to use conda/anaconda as an environment manager and to create a conda environment using:
conda create --name NAME python=3.8
Don’t forget to activate your environment before every use:
conda activate NAME
Your environment must have napari installed since koopa-viz is only a plugin to it. You can install it using:
pip install "napari[all]"
The visualization can then be installed through python’s package index pypi.
pip install koopa-viz