Computer setup

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:

sudo apt-get install git

Python

The best way to get setup with Python for your project is by getting a Python distribution that has the conda or mamba package managers. Anaconda itself (which you likely have from one of Leo’s classes) 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 Mambaforge. This is a minimalist version of Anaconda made by the conda-forge team. It comes only with Python and mamba (which we use to install other libraries).

Follow the instructions below to download and setup Mambaforge.

Windows

Download the latest Mambaforge.

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/mambaforge.

This should create a mambaforge folder in your home directory (open Git Bash and run cd to get to your home).

Now we need to make Git Bash aware of Mambaforge so that you have access to the mamba package manager.

Run the commands below on Git Bash.

Add the following initialization code to a file called .bashrc in your home folder:

# Mambaforge initialization code
source ~/AppData/Local/mambaforge/etc/profile.d/conda.sh
conda activate

After that, close Git Bash and open it again. To test that your setup worked, run python and check if the output looks something like the following:

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.
>>>

Also try running mamba and check that the output is something like:

usage: mamba [-h] [-V] command ...

conda is a tool for managing and deploying applications, environments and packages.

Options:

positional arguments:
  command
    clean        Remove unused packages and caches.
    compare      Compare packages between conda environments.
    config       Modify configuration values in .condarc. This is modeled after the git config command. Writes to the user .condarc file (/home/leo/.condarc) by default.
    create       Create a new conda environment from a list of specified packages.
    help         Displays a list of available conda commands and their help strings.
    info         Display information about current conda install.
    init         Initialize conda for shell interaction. [Experimental]
    install      Installs a list of packages into a specified conda environment.
    list         List linked packages in a conda environment.
    package      Low-level conda package utility. (EXPERIMENTAL)
    remove       Remove a list of packages from a specified conda environment.
    uninstall    Alias for conda remove.
    run          Run an executable in a conda environment. [Experimental]
    search       Search for packages and display associated information. The input is a MatchSpec, a query language for conda packages. See examples below.
    update       Updates conda packages to the latest compatible version.
    upgrade      Alias for conda update.
    repoquery    Query repositories using mamba.

optional arguments:
  -h, --help     Show this help message and exit.
  -V, --version  Show the conda version number and exit.

conda commands available from other packages:
  env

Now that you have Python installed and properly configured, use mamba to install the standard Python libraries that we will most likely be using:

mamba install numpy scipy pandas matplotlib xarray netcdf4 make \
    jupyter jupyterlab pyproj verde harmonica boule pooch

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

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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.