Installation

General

The following commands will create a conda environment and install qsonic.

conda create -n qsonic python=VERSION
conda activate qsonic
pip install qsonic

  • Change VERSION to the desired python version. The only restriction is VERSION>=3.7 and there is no upper version restriction. However, I recommend using a python version that is one or two minor points behind the latest version to be safe.

  • Due to occasional compatibility problems between numpy, healpy and astropy, major dependencies are version limited to the following (see requirements.txt):

numpy~=1.26.0
numba~=0.58.1
scipy~=1.12.0
astropy~=6.0.0
healpy~=1.16.0
fitsio~=1.1.9
iminuit~=2.18.0
mpi4py

Note: MPI is necessary to run qsonic scripts.

NERSC

If you are a NERSC user, I recommend using the pre-installed environment. This is installed on /global/common/software and has better performance at start up.

source /global/cfs/projectdirs/desi/science/lya/scripts/activate_qsonic.sh

To have a Jupyter kernel, run the following command after activation:

python -m ipykernel install --user --name qsonic --display-name qsonic

Explicit NERSC installation instructions with pip:

module load cpu
module load python

conda create -n qsonic python
conda activate qsonic
MPICC="cc -shared" pip install --force-reinstall --no-cache-dir --no-binary=mpi4py mpi4py
pip install qsonic

Note: These instructions recompile mpi4py with NERSC specific MPI libraries. cc command here is a NERSC compiler wrapper that provides optimal compiler options and paths to MPI libraries. Other platforms may use mpicc instead.

If you want Jupyter kernel, you need to additionally install ipykernel into your environment and run the same command. See this NERSC guide on Jupyter.

Latest from the source

If you want to get the latest (possibly unstable) version:

pip install git+ssh://git@github.com/p-slash/qsonic.git

For developers:

git clone https://github.com/p-slash/qsonic.git
cd qsonic
pip install -e '.[dev]'