Deep dive into vector data cubes

The material for the LPS '25 tutorial

Setting up to follow the workshop

Step 1: Download the workshop material

If you are a git user, you can get the workshop materials by cloning this repo:

git clone https://github.com/martinfleis/lps25.git
cd lps25

Otherwise, to download the repository to your local machine as a zip-file, click the download ZIP on the repository page https://github.com/martinfleis/lps25 (green button "Code"). After the download, unzip on the location you prefer within your user account (e.g. My Documents, not C:\).

Step 2: Install the required Python packages

You can set the environment to run the notebook in a few ways - Pixi (recommended) uv (also recommended[^1]), Conda/Mamba, pip.

[^1]: I prefer Pixi as it installs packages from conda-forge which are using same binaries of compiled dependencies. uv installs from PyPI, so each package will bring its own version.

Pixi

If you'd like to run the notebook, you can create an environment using Pixi. See the Pixi installation instructions.

With Pixi installed, open a command line and start Jupyter Lab from the included Pixi environment. Pixi will automatically install all required dependencies and start the Jupyter Lab IDE with the notebook.

pixi run jupyter lab workshop.ipynb

uv

If you'd like to run the notebook, you can create an environment using uv. See the uv installation instructions.

With uv installed, open a command line, and start Jupyter Lab from the included uv environment. uv will automatically install all required dependencies and start the Jupyter Lab IDE with the notebook.

uv run jupyter lab workshop.ipynb

Conda/Mamba

If you prefer to use conda-based solutions (conda, mamba, anaconda, micromamba), you can create a conda environment using attached environment.yml file.

Using conda, we recommend to create a new environment with all packages using the following commands (after cloning or downloading this GitHub repo and navigating to the directory, see above):

# setting the configuation so all packages come from the conda-forge channel
conda config --add channels conda-forge
conda config --set channel_priority strict
# mamba provides a faster implementation of conda
conda install mamba
# creating the environment
mamba env create --file environment.yml
# activating the environment
conda activate lps25

Then you can start the notebook.

jupyter lab workshop.ipynb

pip / Google Colab

You can also install the necessary dependencies from PyPI using pip. The instructions can be used both locally and within Google Colab.

pip install xvec cf-xarray exactextract geopandas matplotlib netcdf4 zarr fsspec pooch rioxarray joblib cfgrib contextily -U

If you are working locally (not using Google Colab), you may want to install Jupyter Lab as well.

pip install jupyterlab

Then you can start the notebook.

jupyter lab workshop.ipynb

Data

• ERA5 data from Copernicus Climate Data Store
• GHS UCBD data from GHSL
• FUA data from GHSL