Installation

The magenpy software is written in Cython/Python3. The software is designed to be used in a variety of computing environments, including local workstations, shared computing environments, and cloud-based computing environments. Because of the dependencies on Cython, you need to ensure that a C/C++ Compiler (with appropriate flags) is present on your system.

Requirements¶

Building the magenpy package requires the following dependencies:

Python (>=3.8)
C/C++ Compiler
Cython (>=0.29.21)
NumPy (>=1.19.5)

Setting up the environment with `conda`¶

If you can use Anaconda or miniconda to manage your Python environment, we recommend using them to create a new environment with the required dependencies as follows:

python_version=3.11  # Change python version here if needed
conda create --name "magenpy_env" -c anaconda -c conda-forge python=$python_version compilers openblas -y
conda activate magenpy_env

Using conda to set up and manage your environment is especially recommended if you have trouble compiling the C/C++ extensions on your system.

Installation¶

Using `pip`¶

The package is available for easy installation via the Python Package Index (pypi) can be installed using pip:

python -m pip install magenpy>=0.1

Building from source¶

You may also build the package from source, by cloning the repository and running the make install command:

git clone https://github.com/shz9/magenpy.git
cd magenpy
make install

Using a virtual environment¶

If you wish to use magenpy on a shared computing environment or cluster, it is recommended that you install the package in a virtual environment. Here's a quick example of how to install magenpy on a SLURM-based cluster:

module load python/3.8
python -m venv magenpy_env
source magenpy_env/bin/activate
python -m pip install --upgrade pip
python -m pip install magenpy>=0.1

Using `Docker` containers¶

If you are using Docker containers, you can build a container with the viprs package and all its dependencies by downloading the relevant Dockerfile from the repository and building it as follows:

# Build the docker image:
docker build -f cli.Dockerfile -t magenpy-cli .
# Run the container in interactive mode:
docker run -it magenpy-cli /bin/bash
# Test that the package installed successfully:
magenpy_ld -h

We plan to publish pre-built Docker images on DockerHub in the future.