xcube-gedidb

The xcube-gedidb Python package provides an xcube data store that enables access to datasets hosted by the Global Ecosystem Dynamics Investigation (GEDI). The data store is called "gedidb" and implemented as an xcube plugin.

It uses the gedidb package as a dependency, which is licensed under the European Union Public License v1.2.

Setup

Installing the xcube-gedidb plugin from the repository

To install xcube-gedidb directly from the git repository, clone the repository, cd into xcube-gedidb as follows and follow the steps below:

git clone https://github.com/xcube-dev/xcube-gedidb.git
cd xcube-gedidb
conda env create -f environment.yml
conda activate xcube-gedidb
pip install .

This sets up a new conda environment, installs all the dependencies required for xcube-gedidb, and then installs xcube-gedidb directly from the repository into the environment.

Installing the xcube-gedidb plugin from the PyPi

This method assumes that you have an existing environment created from the environment.yml, and you want to install xcube-gedidb into it. With the existing environment activated, execute this command:

pip install xcube-gedi

If xcube and any other necessary dependencies are not already installed, they will be installed automatically.

Testing

To run the unit test suite:

pytest

Some notes on the strategy of unit-testing for some tests

The unit test suite uses pytest-recording to mock https requests via the Python library requests for some of the unit tests. During development an actual HTTP request is performed and the responses are saved in cassettes/*.yaml files. During testing, only the cassettes/*.yaml files are used without an actual HTTP request. During development, to save the responses to cassettes/*.yaml, run:

pytest -v -s --record-mode new_episodes

Note that --record-mode new_episodes overwrites all cassettes. If one only wants to write cassettes which are not saved already, --record-mode once can be used. pytest-recording supports all records modes given by [VCR.py](https://vcrpy.readthedocs.io/en/latest/usage.html#record-modes. After recording the cassettes, testing can be then performed as usual.

Citation:

This project uses the gediDB API (Besnard et al., 2025) as a dependency.

Besnard, S., Dombrowski, F., & Holcomb, A. (2025). gediDB (2025.2.0). Zenodo. https://doi.org/10.5281/zenodo.13885229