yeoda

Earth Observation (EO) data, I must handle.

Contents

• Description
• Installation
  • Pip
  • Conda
• Docker
• Contribution
• Citation

Description

yeoda stands for your earth observation data access and provides datacube classes for reading and writing well-defined and structured earth observation data. These datacubes allow to filter, select, split, read and write data independently from the way the data is structured on disk. Internally, yeoda relies on functionalities provided by geopathfinder (filepath/filename and folder structure handling library), veranda (IO classes and higher-level data structure classes for vector and raster data) and geospade (raster and vector geometry/mosaic definitions and operations).

For more details about yeoda's functionality and many use case examples, please check out yeoda's RTD documentation!

Installation

The package can be either installed via pip or if you solely want to work with yeoda or contribute, we recommend installing it as a conda environment. If you work already with your own environment, please have look at conda_env.yml or setup.cfg for the required dependencies.

Pip

To install yeoda via pip in your own environment, use:

pip install yeoda

ATTENTION: Packages like gdal, cartopy, or geopandas need more OS support and have more dependencies than other packages and can therefore not be installed solely via pip. Thus, for a fresh setup, an existing environment with the conda dependencies listed in conda_env.yml is expected. To create such an environment, you can run:

conda create -n "yeoda" -c conda-forge python=3.8 mamba
conda activate yeoda
mamba install -c conda-forge python=3.8 gdal geopandas cartopy

Conda

The packages also comes along with a pre-defined conda environment (conda_env.yml). This is especially recommended if you want to contribute to the project. The following script will install miniconda and setup the environment on a UNIX like system. Miniconda will be installed into $HOME/miniconda.

wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
bash miniconda.sh -b -p $HOME/miniconda
export PATH="$HOME/miniconda/bin:$PATH"
mamba env create -f conda_env.yml
source activate yeoda

This script adds $HOME/miniconda/bin temporarily to the PATH to do this permanently add export PATH="$HOME/miniconda/bin:$PATH" to your .bashrc or .zshrc.

For Windows, use the following setup:

• Download the latest miniconda 3 installer for Windows
• Click on .exe file and complete the installation.
• Add the folder condabin folder to your environment variable PATH. You can find the condabin folder usually under: C:\Users\username\AppData\Local\Continuum\miniconda3\condabin
• Finally, you can set up the conda environment via:

  conda env create -f conda_env.yml
  source activate yeoda
  

After that you should be able to run

python setup.py test

to run the test suite.

Docker

We also provide a docker image with example data and some Jupyter Notebooks, which were used to generate yeoda's documentation. You can pull the image with the following command:

docker pull tuwgeomrs/yeoda:v1.0.0

Then, you can directly start the Jupyter server via

docker run -it -p 8888:8888 tuwgeomrs/yeoda:v1.0.0 notebook

Copy-paste the link including a token in a web-browser of your choice, and try out yeoda's rich set of features. For detailed explanation on further docker commands, see the official docker documentation. Also, have a look at other docker images we provide at docker hub.

Contribution

We are happy if you want to contribute. Please raise an issue explaining what is missing or if you find a bug. We will also gladly accept pull requests against our master branch for new features or bug fixes. If you want to contribute please follow these steps:

• Fork the yeoda repository to your account
• Clone the yeoda repository
• Make a new feature branch from the yeoda master branch
• Add your feature
• Please include tests for your contributions in one of the test directories. We use py.test so a simple function called test_my_feature is enough
• Submit a pull request to our master branch

Citation

If you use this software in a publication then please cite it using the Zenodo DOI. Be aware that this badge links to the latest package version.

Please select your specific version at https://doi.org/10.5281/zenodo.3540693 (link to first release) to get the DOI of that version. You should normally always use the DOI for the specific version of your record in citations. This is to ensure that other researchers can access the exact research artefact you used for reproducibility.

You can find additional information regarding DOI versioning at http://help.zenodo.org/#versioning.