2 - Onboarding and Installation

The first goal of the workshop is to get everyone into a consistent working environment. CUDEM workflows depend on several geospatial and scientific Python libraries, so we want all participants using the same cudem conda environment before we begin running DEM examples.

By the end of this section, participants should be able to:

• Join the Zulip chat space for technical support

• Install and open a conda terminal

• Activate the workshop cudem conda environment

• Confirm that the core CUDEM tools are installed

• Run basic help and version checks

Before we build any DEMs, we need to make sure everyone is working from the same software environment. The first part of the workshop will focus on activating the cudem environment and confirming that the main tools are available.

If you have a machine-specific installation issue during the workshop, use the Zulip chat space to message the workshop support team. The goal is to get everyone to a stable enough environment to run the Fiji test DEM. If someone has a deeper issue with their computer, we will use shared example outputs so they can still follow along with the workflow discussion.

1. Join the Zulip Chat Space¶

We will use the Zulip chat space for technical support during the workshop. This gives participants a place to ask questions, report installation issues, share screenshots, and get help from the workshop team.

Please join the chat space before continuing with the installation steps:

CUDEM Zulip chat space

Use the workshop stream:

#CUDEM Workshop - GEBCO/NIPPON Scholars > GEBCO/Nippon Scholars

2. Install and Open a Miniforge Terminal¶

Install Miniforge for your operating system:

https://conda-forge.org/download/

After installation, open a Miniforge terminal.

On Windows, open:

Miniforge Prompt

On macOS or Linux, open a terminal.

All workshop commands should be run from the Miniforge Prompt or terminal unless otherwise noted.

3. Create the CUDEM Environment¶

Run the following commands to create and activate the workshop environment:

conda create -n cudem -c conda-forge python=3.12
conda activate cudem
conda install -c conda-forge libgdal-netcdf copernicusmarine pygmt globato ivert

This creates a separate cudem environment instead of installing workshop tools into the base environment.

The install command provides the core tools used during the workshop:

fetchez
transformez
globato
ivert

Activate the environment:

conda activate cudem

Your prompt should now begin with:

(cudem)

4. Install HTDP¶

transformez uses NOAA/NGS HTDP for horizontal time-dependent positioning and frame transformations. HTDP must be installed separately before running some CUDEM transformation workflows.

Download HTDP here:

https://github.com/noaa-ngs/HTDP/archive/refs/tags/v3.5.0.zip

Follow the HTDP installation instructions for your operating system.

5. Copernicus Marine Credentials¶

Some CUDEM recipes use the Copernicus Marine data module. If a recipe accesses Copernicus Marine data, the module needs valid Copernicus Marine credentials.

Create a free Copernicus Marine account:

https://data.marine.copernicus.eu/register

After registering, create a .netrc file so the data module can log in on the backend.

Windows¶

On Windows, open the .netrc file in your user home directory:

notepad %USERPROFILE%\.netrc

Add the following entry, replacing YOUR_USERNAME and YOUR_PASSWORD with your Copernicus Marine credentials:

machine data.marine.copernicus.eu
login YOUR_USERNAME
password YOUR_PASSWORD

Save and close the file.

Confirm the file exists:

dir %USERPROFILE%\.netrc*

If the file was accidentally saved as .netrc.txt, rename it to remove the extension:

ren %USERPROFILE%\.netrc.txt .netrc

macOS / Linux¶

On macOS or Linux, create or edit the .netrc file in your home directory:

nano ~/.netrc

Add the following entry, replacing YOUR_USERNAME and YOUR_PASSWORD with your Copernicus Marine credentials:

machine data.marine.copernicus.eu
login YOUR_USERNAME
password YOUR_PASSWORD

Save the file, then update the file permissions:

chmod 600 ~/.netrc

6. (Optional) NASA EarthData Credentials¶

The ivert tool uses NASA’s EarthData tools to fetch and subset ICESat-2 data. We will provide some pre-computed data for use during the workshop, so this step is optional. However, if you would like to perform your own validations later, you will need to register for a free NASA EarthData account and put your credentials into your .netrc file.

Create a free NASA EarthData account:

https://urs.earthdata.nasa.gov/users/new

When you register, remember the username and password you choose — you will need them in the next step.

After registering, run the ivert setup command:

ivert setup

At the username: and password: prompts, enter your NASA EarthData credentials. These credentials will be saved in your .netrc file, the same as your Copernicus Marine credentials were.

Alternately, you can follow the same instructions as in the previous section and append your NASA EarthData credentials into your .netrc file manually, using this entry:

machine urs.earthdata.nasa.gov
login YOUR_USERNAME
password YOUR_PASSWORD

This can go immediately after your Copernicus Marine entry from above.

7. Run Setup Checks¶

After installation, confirm the environment and tools are working.

Make sure the cudem environment is active:

conda activate cudem

Check Python:

python --version

Expected:

Python 3.12.x

Check the CUDEM tools:

fetchez --help
transformez --help
globato --help
ivert --help

If these commands print help text, the environment is ready for the Fiji test DEM.

8. Next Step¶

Once everyone has a working cudem environment, we will move to the Fiji test DEM exercise.

The next module will use globato to run a test DEM workflow and generate a shared output that we can inspect together.