icepyx

icepyx: querying, obtaining, analyzing, and manipulating ICESat-2 datasets - Published in JOSS (2023)

https://github.com/icesat2py/icepyx

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Python tools for obtaining and working with ICESat-2 data

README.rst

icepyx
======

**Python tools for obtaining and working with ICESat-2 data**

|Contributors| |GitHub license| |Conda install| |Pypi install|

|JOSS| |Zenodo-all|

Latest release (main branch): |Docs Status main| |Unit Tests Status (main)| |Integration Tests Status (main)| |Code Coverage main|

Current development version (development branch): |Docs Status dev| |Unit Tests Status (dev)| |Integration Tests Status (main)| |Code Coverage dev| |Pre-commit dev|

.. |GitHub license| image:: https://img.shields.io/badge/License-BSD%203--Clause-blue.svg
   :target: https://opensource.org/licenses/BSD-3-Clause

.. |Conda install| image:: https://anaconda.org/conda-forge/icepyx/badges/version.svg
    :target: https://anaconda.org/conda-forge/icepyx

.. |Pypi install| image:: https://badge.fury.io/py/icepyx.svg
    :target: https://pypi.org/project/icepyx

.. |Contributors| image:: https://img.shields.io/github/all-contributors/icesat2py/icepyx?color=ee8449&style=flat-square(#contributors)
    :alt: All Contributors
    :target: https://github.com/icesat2py/icepyx/blob/main/CONTRIBUTORS.rst

.. |JOSS| image:: https://joss.theoj.org/papers/10.21105/joss.04912/status.svg
    :alt: JOSS publication link and DOI
    :target: https://doi.org/10.21105/joss.04912

.. |Zenodo-all| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.7729175.svg
    :alt: Zenodo all-versions DOI for icepyx
    :target: https://doi.org/10.5281/zenodo.7729175

.. |Docs Status main| image:: https://readthedocs.org/projects/icepyx/badge/?version=latest
   :target: http://icepyx.readthedocs.io/?badge=latest

.. |Docs Status dev| image:: https://readthedocs.org/projects/icepyx/badge/?version=development
   :target: https://icepyx.readthedocs.io/en/development

.. |Unit Tests Status (main)| image:: https://github.com/icesat2py/icepyx/actions/workflows/unit_test.yml/badge.svg?branch=main
    :target: https://github.com/icesat2py/icepyx/actions/workflows/unit_test.yml

.. |Integration Tests Status (main)| image:: https://github.com/icesat2py/icepyx/actions/workflows/integration_test.yml/badge.svg?branch=main
    :target: https://github.com/icesat2py/icepyx/actions/workflows/integration_test.yml

.. |Unit Tests Status (dev)| image:: https://github.com/icesat2py/icepyx/actions/workflows/unit_test.yml/badge.svg?branch=development
    :target: https://github.com/icesat2py/icepyx/actions/workflows/unit_test.yml

.. |Integration Tests Status (dev)| image:: https://github.com/icesat2py/icepyx/actions/workflows/integration_test.yml/badge.svg?branch=development
    :target: https://github.com/icesat2py/icepyx/actions/workflows/integration_test.yml

.. |Code Coverage main| image:: https://codecov.io/gh/icesat2py/icepyx/branch/main/graph/badge.svg
    :target: https://codecov.io/gh/icesat2py/icepyx

.. |Code Coverage dev| image:: https://codecov.io/gh/icesat2py/icepyx/branch/development/graph/badge.svg
    :target: https://codecov.io/gh/icesat2py/icepyx

.. |Pre-commit dev| image:: https://results.pre-commit.ci/badge/github/icesat2py/icepyx/development.svg
   :target: https://results.pre-commit.ci/latest/github/icesat2py/icepyx/development
   :alt: pre-commit.ci status


Origin and Purpose
------------------
icepyx is both a software library and a community composed of ICESat-2 data users, developers, and the scientific community. We are working together to develop a shared library of resources - including existing resources, new code, tutorials, and use-cases/examples - that simplify the process of querying, obtaining, analyzing, and manipulating ICESat-2 and (via the QUEST module) relevant ancillary datasets to enable scientific discovery.

icepyx aims to provide a clearinghouse for code, functionality to improve interoperability, documentation, examples, and educational resources that tackle disciplinary research questions while minimizing the amount of repeated effort across groups utilizing similar datasets. icepyx also hopes to foster collaboration, open-science, and reproducible workflows by integrating and sharing resources.

Many of the underlying tools from which icepyx was developed began as Jupyter Notebooks developed for and during the cryosphere-themed ICESat-2 Hackweek at the University of Washington in June 2019 or as scripts written and used by the ICESat-2 Science Team members.
Originally called icesat2py, the project combined and generalized these scripts into a unified framework, adding examples, documentation, and testing where necessary and making them accessible for everyone. Similar scripts were conceived at the 2021 Hackweek, which in turn led to the development of QUEST.
icepyx is now a domain-agnostic, standalone software package and community (under the broader `icesat2py GitHub organization `_) that continues to build functionality for obtaining and working with ICESat-2 data products locally and in the cloud.
It also improves interoperability for ICESat-2 datasets with other open-source tools.

.. _`zipped file`: https://github.com/icesat2py/icepyx/archive/main.zip
.. _`Fiona`: https://pypi.org/project/Fiona/

Installation
------------

The simplest way to install icepyx is by using the
`conda `__
package manager. |Conda install|

    conda install icepyx

Alternatively, you can also install icepyx using `pip `__. |Pypi install|

    pip install icepyx

More detailed instructions for installing `icepyx` can be found at
https://icepyx.readthedocs.io/en/latest/getting_started/install.html

Quick Start
-----------

.. code-block:: python

   import icepyx as ipx
   query = ipx.Query(
       # Collection short name
       "ATL06",
       # Bounding box
       [-55, 68, -48, 71],
       # Time bounds
       ['2019-02-20','2019-02-28'],
   )
   query.download_granules('/tmp/icepyx')

.. code-block:: bash

   $ ls -1 /tmp/icepyx/
   processed_ATL06_20190221121851_08410203_006_02.h5
   processed_ATL06_20190222010344_08490205_006_02.h5
   processed_ATL06_20190225121032_09020203_006_02.h5
   processed_ATL06_20190226005526_09100205_006_02.h5

See the examples below for more things `icepyx` can do!


Examples (Jupyter Notebooks)
----------------------------

Listed below are example Jupyter notebooks for working with ICESat-2 (IS2).

`IS2_data_access `_

`IS2_data_access2_subsetting `_

`IS2_data_variables `_

`IS2_data_visualization `_

`IS2_data_read-in `_

`IS2_cloud_data_access `_

`QUEST_Finding_Argo_IS2_data `_


Citing icepyx
-------------
.. _`CITATION.rst`: ./CITATION.rst

This community and software is developed with the goal of supporting science applications. Thus, our contributors (including those who have developed the packages used within icepyx) and maintainers justify their efforts and demonstrate the impact of their work through citations. Please see  `CITATION.rst`_ for additional citation information.

Contact
-------
Working with ICESat-2 data and have ideas you want to share?
Have a great suggestion or recommendation of something you'd like to see
implemented and want to find out if others would like that tool too?
Come join the conversation at: https://discourse.pangeo.io/.
Search for "icesat-2" under the "science" topic to find us.

.. _`icepyx`: https://github.com/icesat2py/icepyx
.. _`contribution guidelines`: ./doc/source/contributing/contribution_guidelines.rst

Contribute
----------
We welcome and invite contributions to icepyx_ from anyone at any career stage and with any amount of coding experience!
Check out our `contribution guidelines`_ to see how you can contribute.

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms. |Contributor Covenant|

.. |Contributor Covenant| image:: https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg
   :target: code_of_conduct.md

Research notice
~~~~~~~~~~~~~~~

Please note that this repository is participating in a study into
sustainability of open source projects. Data will be gathered about this
repository for approximately the next 12 months, starting from June
2021.

Data collected will include number of contributors, number of PRs, time
taken to close/merge these PRs, and issues closed.

For more information, please visit `the informational
page `__ or
download the `participant information
sheet `__.

Owner

JOSS Publication

icepyx: querying, obtaining, analyzing, and manipulating ICESat-2 datasets

Published

April 12, 2023

DOI

10.21105/joss.04912

Volume 8, Issue 84, Page 4912

Authors

Jessica Scheick
University of New Hampshire, USA

Wei Ji Leong
Development Seed, USA

Kelsey Bisson
Oregon State University, USA

Anthony Arendt
University of Washington, USA

Shashank Bhushan
University of Washington, USA

Zachary Fair
NASA Goddard Space Flight Center, USA

Norland Raphael Hagen
CarbonPlan, USA

Scott Henderson
University of Washington, USA

Friedrich Knuth
University of Washington, USA

Tian Li
University of Bristol, UK

Zheng Liu
University of Washington, USA

Romina Piunno
University of Toronto, Canada

Nitin Ravinder
University of Leeds, UK

Landung "Don" Setiawan
University of Washington, USA

Tyler Sutterley
University of Washington, USA

Jp Swinski
NASA Goddard Space Flight Center, USA

Anubhav
University of Maryland, College Park, USA

Editor

Kristen Thyng

Tags

ICESat-2 LiDAR elevation community cloud

View PDF Review Thread Software Archive

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: icepyx
message: >-
  If you use this software, please cite the software version
  you used by its version-specific DOI.
  The DOI for each version is available on Zenodo (link below).
type: software
authors:
  - name: The icepyx Developers
repository-code: 'https://github.com/icesat2py/icepyx'
url: 'https://icepyx.readthedocs.io/en/latest/'
repository: 'https://zenodo.org/record/7729175'
repository-artifact: 'https://anaconda.org/conda-forge/icepyx'
abstract: >-
  icepyx is both a software library and a community composed
  of ICESat-2 data users, developers, and the scientific
  community. We are working together to develop a shared
  library of resources - including existing resources, new
  code, tutorials, and use-cases/examples - that simplify
  the process of querying, obtaining, analyzing, and
  manipulating ICESat-2 datasets to enable scientific
  discovery.
keywords:
  - ICESat-2
  - Python
  - open science
  - NASA
license: BSD-3-Clause
identifiers:
  - description: "All archived versions of icepyx."
    type: doi
    value: 10.5281/zenodo.7729175

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