Computer setup
Most projects developed in the lab will require you to have a computer with git, a terminal, and Python properly setup. Below are some instructions on how to get started.
Git and a terminal
Git is what we use to collaborate on projects, track a history of changes, and backup to the cloud (GitHub).
A terminal with a decent shell (like bash) is the primary interface for using git and other command line utilities (LaTeX compilers, make, etc).
Windows
You can get both git and a bash-enabled terminal with “Git Bash”. Follow the Software Carpentry setup instructions to get going.
Linux
You should already have a terminal with bash (look for the “terminal” app). Git is often already installed as well or you can install it with your distributions package manager.
On Ubuntu or Linux Mint:
sudo apt-get install git
Python
DO NOT download Python from python.org! We need a bunch of libraries that don’t come pre-installed and can be hard to install using the official distribution of Python.
The best way to get setup with Python for your project is by getting a Python
distribution that has the conda package manager.
Anaconda is very popular and is good for
some cases but for your project work it will likely cause more harm than
good because it comes with too many libraries that we won’t need (and is thus
a huge pain to update).
The recommended distribution to install for Windows, Linux, and Mac
is Miniforge.
This is a minimalist version of Anaconda made by the
conda-forge team.
It comes only with Python and conda (which we use to install other
libraries).
Follow the instructions below to download and setup Miniforge.
Windows
Download the latest Miniforge.
Run the installer and the default should save the installation in a sub folder
AppData/Local/ within your home folder. For example,
C:/Users/YOUR_USERNAME/AppData/Local/miniforge3.
This should create a miniforge3 folder in your home directory.
Working with Git Bash as well?
If so, we need to make Git Bash aware of Miniforge so that
you have access to the conda package manager.
Add the following initialization code to a file called .bashrc in your home
folder (use any text editor you want to do that):
# Miniforge initialization code
source ~/AppData/Local/miniforge3/etc/profile.d/conda.sh
conda activate
If you had Git Bash open, close it and open it again.
Testing your install
To test that your setup worked, open Git Bash or the “Miniforge Prompt” program
(on Windows) or your terminal (on Linux).
Run python and check if the output looks something like the following (look
for the packaged by conda-forge part in particular):
Python 3.9.0 | packaged by conda-forge | (default, Nov 26 2020, 07:57:39)
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>>
Installing other Python packages
Now that you have Python installed and properly configured, open Git Bash or
the “Miniforge Prompt” program (on Windows) or your terminal (on Linux).
Then, use conda to install the standard Python libraries that we will most
likely be using:
conda install numpy scipy pandas matplotlib jupyterlab
You may also want to install some additional libraries for geophysics:
conda install xarray netcdf4 pygmt verde harmonica boule bordado
You should be good to go from here.
To start JupyterLab, run (it’s a good idea to return to your home folder before
doing this by running cd):
jupyter lab
Credit and terms of reuse: This manual is based on the excellent Lab Carpentry blueprints, with material adapted from the Data Intensive Biology Lab and the Data Exploration Lab. The manual contents are available under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.