SNAPSI conda environment

This repository contains a conda environment for use within the SNAPSI project. Using this environment will help to ensure that our results are reproducible.

Using the environment via SSH

The recommended way to implement the environment on JASMIN is to use Mamba (though the below is also possible with Conda). This can be installed by copying and pasting the following:

curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
bash Mambaforge-$(uname)-$(uname -m).sh

After this you'll need to close and then restart your shell session. Then the environment can be created as follows (the command below assumes you are within the snapsi_conda_env directory created by cloning this respository):

mamba env create -f env_frozen.yml

This may take 5-10 minutes. The environment can then be activated with

mamba activate snapsi

Now you're all set to use the environment.

Using the environment via Jupyter notebook service

To use the SNAPSI conda environment on the JASMIN notebook service, we'll first create the environment using the Terminal window option and following the instructions above (you can skip this step if you have already created the environment via SSH as above). The following command will then allow the snapsi environment to be used within a notebook:

conda run -n snapsi python -m ipykernel install --user --name snapsi

You can use this environment by selecting the snapsi kernel when creating a notebook.

Adding packages

If you would like to add some packages you can do this by adding them to the env.yml file. You can then install them to the environment with

mamba env update --name snapsi --file env.yml

and export the solved frozen dependencies with

mamba env export > env_frozen.yml