HARP Library

HARP comes as a Python module called harp that has a command line interface (CLI) program called harpcalc. Installing the harp module into a separate Python environment is recommended practice, because it allows you to maintain required library dependencies. You can use conda or venv to do this.

Environment 1: conda

conda is a Python environment manager. You’ll have to download and install conda or the smaller miniconda. With that installed, you need to get the HARP code, make an environment for HARP, and then install HARP. Here is an example of how to do that from a terminal window:

git clone https://github.com/bayes-shape-calc/HARP.git
cd HARP
conda env create
conda activate harp
pip install ./

Environment 2: venv + pip

If you don’t want to use conda, you can use venv to make an environment and pip to handle installing all the libraries. Here is an exmaple of how to do that from a terminal window:

python -m venv harpenv
source harpenv/bin/activate
git clone https://github.com/bayes-shape-calc/HARP.git
cd HARP
pip install ./

Dependencies

These are not the absolute minimum required versions. They should be automatically installed by the pip command above (step 4).

Library	Version	Required?	Use
python	3.7	Yes	Programming
mrcfile	1.3	Yes	For loading density maps
numba	0.55	Yes	For fast model building
numpy	1.22	Yes	Math
gemmi	0.5.5	No	(optional) For X-ray SF loading