Summary and Setup

Data Carpentry’s teaching is hands-on, so participants are encouraged to use their own computers to ensure the proper setup of tools for an efficient workflow. To most effectively use these materials, please make sure to download the data and install everything before working through this lesson.

The data used in this lesson includes optical satellite images from the Copernicus Sentinel-2 mission and public geographical datasets from the dedicated distribution platform of the Dutch government. These are real-world data sets that entail sufficient complexity to teach many aspects of data analysis and management. They have been selected to allow students to focus on the core ideas and skills being taught while offering the chance to encounter common challenges with geospatial data.

Data Sets

  1. Create a new directory on your Desktop called geospatial-python.
  2. Within geospatial-python, create a directory called data.
  3. Download the following files and save them to the just created data directory (do not unzip the files, we will read from them directly):

Software Setup

Installing Python Using Anaconda

Python is a popular language for scientific computing, and great for general-purpose programming as well. Installing all of its scientific packages individually can be a bit difficult, however, so we recommend the all-in-one installer Anaconda.

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.9 is fine). Also, please set up your python environment at least a day in advance of the workshop. If you encounter problems with the installation procedure, ask your workshop organizers via e-mail for assistance so you are ready to go as soon as the workshop begins.

Installing Anaconda

Video tutorial

  1. Open https://www.anaconda.com/download with your web browser.

  2. Download the Anaconda for Windows installer with Python 3.

  3. Install Python 3 by running the Anaconda Installer, using all of the defaults for installation except make sure that:

  • Register Anaconda as my default Python 3.x option is checked (it should be in the latest version of Anaconda).
  • Add Anaconda to my PATH environment variable is selected.

Video tutorial

  1. Open https://www.anaconda.com/download with your web browser.

  2. Download the Anaconda installer with Python 3 for OS X. These instructions assume that you use the “Graphical Installer” .pkg file

  3. Follow the Python 3 installation instructions. Make sure that the install location is set to Install only for me so Anaconda will install its files locally, relative to your home directory. Installing the software for all users tends to create problems in the long run and should be avoided.

Note that the following installation steps require you to work from the shell. If you run into any difficulties, please request help before the workshop begins.

  1. Open https://www.anaconda.com/download with your web browser.

  2. Download the Anaconda installer with Python 3 for Linux.

  3. Open a terminal window and navigate to the directory where the executable is downloaded (e.g., cd ~/Downloads).

  4. Type:

    BASH 

    bash Anaconda3-

    and press “Tab” to autocomplete the full file name. The name of file you just downloaded should appear.

  5. Press “Enter” (or “Return” depending on your keyboard).

  6. Follow the text-only prompts. When the license agreement appears (a colon will be present at the bottom of the screen) press “Spacebar” until you see the bottom of the text. Type yes and press “Enter” to approve the license. Press “Enter” again to approve the default location for the files. Type yes and press “Enter” to prepend Anaconda to your PATH (this makes the Anaconda distribution your user’s default Python).

  7. Close the terminal window.

Setting up the workshop environment

If Anaconda was properly installed, you should have access to the conda command in your terminal (use the Anaconda prompt on Windows).

  1. Test that conda is correctly installed by typing:

    BASH 

    conda --version

    which should print the version of conda that is currently installed, e.g. :

    OUTPUT 

    conda 22.9.0

  2. Run the following command:

    BASH 

    conda install -c conda-forge mamba

    IMPORTANT: If your terminal responds to the above command with conda: command not found see the Troubleshooting section.

  3. Create the Python environment for the workshop by running:

    BASH 

    mamba env create -n geospatial -f https://raw.githubusercontent.com/carpentries-incubator/geospatial-python/main/files/environment.yaml

    Note that this step can take several minutes.

  4. When installation has finished you should see the following message in the terminal:

    OUTPUT 

    # To activate this environment, use
#    $ conda activate geospatial
#
# To deactivate an active environment, use
#    $ conda deactivate

  5. Activate the geospatial environment:

    BASH 

    conda activate geospatial

If successful, the text (base) in your terminal prompt will now read (geospatial) indicating that you are now in the Anaconda virtual environment named geospatial. The command which python should confirm that we’re using the Python installation in the geospatial virtual environment. For example:

BASH 

which python

OUTPUT 

/Users/your-username/anaconda3/envs/geospatial/bin/python

IMPORTANT: If you close the terminal, you will need to reactivate this environment with conda activate geospatial to use the Python libraries required for the lesson and to start JupyterLab, which is also installed in the geospatial environment.

Starting JupyterLab

In order to follow the lesson, you should launch JupyterLab. After activating the geospatial conda environment, enter the following command in your terminal (use the Anaconda prompt on Windows):

BASH 

jupyter lab

Once you have launched JupyterLab, create a new Python 3 notebook, type the following code snippet in a cell and press the “Play” button:

PYTHON 

import rioxarray

If all the steps above completed successfully you are ready to follow along with the lesson!

Troubleshooting conda: command not found

  • Mac OS and Linux users:

    1. First, find out where Anaconda is installed.

      The typical install location is in your $HOME directory (i.e., /Users/your-username/) so use ls ~ to check whether an anaconda3 directory is present in your home directory:

      BASH 

      ls ~

      OUTPUT 

      Applications      Downloads       Pictures
anaconda3         Library         Public
Desktop           Movies
Documents         Music

      If, like above, you see a directory called anaconda3 in the output we’re in good shape. If not, contact the instructor for help.

    2. Activate the conda command-line program by entering the following command:

      BASH 

      source ~/anaconda3/bin/activate

      If all goes well, nothing will print to the terminal and your prompt will now have (base) floating around somewhere on the left. This is an indication that you are in the base Anaconda environment.

      Continue from the beginning of step 3 to complete the creation of the geospatial virtual environment.