Setup Python on Linux

Preparing the Python environment on Linux

Learn how to setup Python on Linux and follow along with the eReefs tutorials.

Install Python

In Ubuntu Linux, you can install Python using the following command:

sudo apt-get install python3

Install Miniconda

Miniconda is a Package manager. It’s used to install packages and resolve transitive dependencies.

Download and install Miniconda

wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-py38_23.5.2-0-Linux-x86_64.sh -O miniconda.sh
/bin/bash miniconda.sh

Run this command if you do not want conda to automatically activate its base environment

conda config --set auto_activate_base false

Install dependencies

Create and activate a new Python virtual environment that will be used for the tutorials

conda create --name tutorial python=3.8.17
conda activate tutorial

The prompt should start with (tutorial), to indicate that you are now in the tutorial venv.

From now on, make sure you are always in the tutorial venv. If you restart your terminal, you might need to re-activate the tutorial venv before running any command.

Install Python dependencies in the tutorial venv, using Conda

conda install conda-libmamba-solver
conda config --set solver libmamba
conda install jupyter
conda install -c conda-forge netcdf4=1.5.8 pandas=1.4.2 pyjanitor=0.27.0 folium=0.16.0 cartopy=0.21.1 pip=24.0

The version of matplotlib we need to install is not available on the conda repository. We need to install it using pip.

python3 -m pip install matplotlib==3.7.5