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The scripts in this repository coded in Python, but use several dependencies which can be installed by the following instructions.

All the required packages should work on any platform and on linux based systems. The code has been tested in Python v.3.8

Install dependencies with conda (all platforms)

This is the recommended way to install all the dependencies.

Prerequisites

You should have a recent version of the conda package manager. You can get conda by installing miniconda, if you want a light version of the package manager.

Conda environment

Once conda is installed on your system you can easily create a fixed python environment to use in every run by:

conda create --name sst_env python=3.8

Then activate it:

conda activate sst_env

To install the code dependencies you must have activated your environment. You will know is activated once you see the name of the environment (e.g sst_env) in () at the beginning of your bash alias:

(sst_env) [brecinos@jasmin-sci2 ~]$

Make sure conda-forge channel is your default channel to install dependencies:

conda config --add channels conda-forge

To install dependencies simply do:

conda install -c conda-forge numpy pyreadr pandas xarray scipy cartopy pyproj configobj seaborn

We then need to install netCDF4 and the library salem, to use such libraries we need to install some dependencies with pip:

pip install shapely rasterio Pillow geopandas netcdf4 scikit-image joblib motionless dask descartes

Now we can install netCDF4 and joblib:

conda install -c conda-forge netCDF4 joblib

Finally, we can install salem:

pip install git+https://github.com/fmaussion/salem.git

If you want to run the jupyter-notebooks in the repository make sure you also install those tools in your environment:

conda install -c conda-forge ipykernel

You can add to your jupyter notebook installation a kernel to select this environment every time you activate the notebook.

python -m ipykernel install --user --name sst_env --display-name "sst_env"

Install the repository itself

For this to work you'll need to have the git software installed on your system. Then, clone the latest repository version:

git clone git@git.noc.ac.uk:brecinosrivas/orchestra-sst.git

If you are inside JASMIN, you might have to configure your Gitlab ssh keys (under Gitlab Profile >> Settings > Ssh keys). And add a JASMIN pub key to your profile (generated from within a JASMIN's sci-server). This in order to enable access from JASMIN sci servers to your NOC gitlab platform and to clone the repository within one of JASMIN's sci servers.

For more information on gitlab ssh keys click here.