Installation guide

Basic Installation

pyHarm is provided as a complete Python package. To install the package, use the pip Python package installer with the following command:

pip install pyHarm-os

We strongly recommend using the package within a virtual environment dedicated to the library. A pyharm_env.yml file is available in the directory, enabling you to easily build a conda environment with the following command:

conda env create --name YOUR_ENV_NAME -f pyharm_env.yml

where YOUR_ENV_NAME is your chosen name for the environment. Otherwise, the default name pyHarm_env will be used and can be accessed via:

conda activate YOUR_ENV_NAME

Required Libraries

The required packages to run pyHarm are described in pyproject.toml:

  • numpy

  • scipy

  • numba

  • jax

  • jaxlib

  • pandas

  • h5py

  • matplotlib

  • notebook

We strongly recommend building pyHarm projects using Jupyter notebooks.

Notes for Developers

To include new developments into pyHarm, it is advised to work in an environment where pyHarm is installed editable after cloning the repo in the folder of your choice:

git clone https://gitlab.com/drti/pyharm.git

cd pyharm

pip install -e .[dev]

The [dev] tag allows for the installation of the optional dependencies specific for pyHarm’s development :

  • pytest in order to run the unitests

  • sphinx in order to build the documentation locally

This way, any modification to the source files can be updated by reimporting the pyHarm module after restarting the Python kernel, without reinstalling the package in the environment.

Running the Unitary Tests and the Non-Regression Test Suite

The unitary tests are provided using the pytest library. They must be downloaded from the source repository at https://gitlab.com/drti/pyharm. The tests are classified into two categories:

  • unit: Unit tests for basic features.

  • nonregression: Tests to ensure code non-regression, including proper physics problems.

To run the tests, use the following command with your pyHarm environment activated, replacing NAME_TEST_CAT with one of the aforementioned categories:

pytest -m NAME_TEST_CAT