Installation

Installing with pip

The easiest way to install goss is using pip

python -m pip install pygoss

Install with conda

TODO: We should make it possible to install goss with conda. Preferable, we should add it to conda-forge.

Install from source

If you want the latest version or you want to develop goss you can install the code on the main branch

python -m pip install git+https://github.com/ComputationalPhysiology/goss.git@main

or clone the repository and install it from there

git clone git@github.com:ComputationalPhysiology/goss.git
cd goss
python -m pip install .

Docker

goss is also available through Docker. This is a good choice if you want to use goss in an isolated environment.

We provide both a pre-built docker image which you can get by pulling from docker hub

docker pull ghcr.io/computationalphysiology/goss:latest

Building your own docker image

An alternative to pulling the image from docker hub, is to build it yourselves. We provide a Dockerfile in the root of the repo that contain all the instructions for building the docker image. You can do this by executing the following command in the root folder of the project

docker build -t goss .

This will create a docker image with the name goss.

Development installation

Developers should use editable install and install the development requirements using the following command

python -m pip install -e ".[dev]"

It is also recommended to install the pre-commit hook that comes with the package

pre-commit install

Note that linters and formatters will run in the CI system.

OpenMP support

By default goss is linked to OpenMP. If you want to turn off this behavior then you want set the environment variable OPENMP=0, e.g

OPENMP=0 python -m pip install pygoss --no-binary=pygoss