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OceanSpy

OceanSpy: A Python package to facilitate ocean model data analysis and visualization - Published in JOSS (2019)

https://github.com/hainegroup/oceanspy

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 8 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: joss.theoj.org, zenodo.org
  • ✓
    Committers with academic emails
    6 of 13 committers (46.2%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.5%) to scientific vocabulary

Keywords

ocean oceanography physical-oceanography

Keywords from Contributors

energy-system graph-generation exoplanet mesh hydrology cryptocurrencies sourmash taxonomic-classification taxonomic-profiling simulations

Scientific Fields

Engineering Computer Science - 100% confidence
Mathematics Computer Science - 63% confidence
Artificial Intelligence and Machine Learning Computer Science - 62% confidence
Last synced: 4 months ago · JSON representation

Repository

A Python package to facilitate ocean model data analysis and visualization.

Basic Info
Statistics
  • Stars: 112
  • Watchers: 10
  • Forks: 34
  • Open Issues: 17
  • Releases: 9
Topics
ocean oceanography physical-oceanography
Created over 7 years ago · Last pushed 4 months ago
Metadata Files
Readme Changelog Contributing License Codeowners

README.rst 

.. _readme:

======================================================================================
OceanSpy - A Python package to facilitate ocean model data analysis and visualization.
======================================================================================

|OceanSpy|

|version| |conda forge| |docs| |CI| |pre-commit| |codecov| |black| |license| |doi| |JOSS| |binder|

.. admonition:: Interactive Demo

   Check out the interactive demonstration of OceanSpy at `www.bndr.it/gfvgd `_

For publications, please cite the following paper:

Almansi, M., R. Gelderloos, T. W. N. Haine, A. Saberi, and A. H. Siddiqui (2019). OceanSpy: A Python package to facilitate ocean model data analysis and visualization. *Journal of Open Source Software*, 4(39), 1506, doi: https://doi.org/10.21105/joss.01506 .

This material is based upon work supported by the National Science Foundation under Grant Numbers 1835640, 124330, 118123, and 1756863. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.

What is OceanSpy?
-----------------
**OceanSpy** is an open-source and user-friendly Python package that enables scientists and interested amateurs to analyze and visualize ocean model datasets.
OceanSpy builds on software packages developed by the Pangeo_ community, in particular xarray_, dask_, and xgcm_.
The integration of dask facilitates scalability, which is important for the petabyte-scale simulations that are becoming available.

Why OceanSpy?
-------------
Simulations of ocean currents using numerical circulation models are becoming increasingly realistic.
At the same time, these models generate increasingly large volumes of model output data, making the analysis of model data harder.
Using OceanSpy, model data can be easily analyzed in the way observational oceanographers analyze field measurements.

How to use OceanSpy?
--------------------
OceanSpy can be used as a standalone package for analysis of local circulation model output, or it can be run on a remote data-analysis cluster, such as the Johns Hopkins University SciServer_ system, which hosts several simulations and is publicly available (see `SciServer Access`_, and `Datasets`_).

.. note::

   OceanSpy has been developed and tested using MITgcm output. However, it is designed to work with any (structured grid) ocean general circulation model. OceanSpy's architecture allows to easily implement model-specific features, such as different grids, numerical schemes for vector calculus, budget closures, and equations of state. We actively seek input and contributions from users of other ocean models (`feedback submission`_).




.. _Pangeo: http://pangeo-data.github.io
.. _xarray: http://xarray.pydata.org
.. _dask: https://dask.org
.. _xgcm: https://xgcm.readthedocs.io
.. _SciServer: http://www.sciserver.org
.. _`SciServer Access`: https://oceanspy.readthedocs.io/en/latest/sciserver.html
.. _Datasets: https://oceanspy.readthedocs.io/en/latest/datasets.html
.. _`feedback submission`: https://github.com/hainegroup/oceanspy/issues

.. |OceanSpy| image:: https://github.com/hainegroup/oceanspy/raw/main/docs/_static/oceanspy_logo_blue.png
   :alt: OceanSpy image
   :target: https://oceanspy.readthedocs.io

.. |version| image:: https://img.shields.io/pypi/v/oceanspy.svg?style=flat
    :alt: PyPI
    :target: https://pypi.python.org/pypi/oceanspy

.. |conda forge| image:: https://anaconda.org/conda-forge/oceanspy/badges/version.svg
   :alt: conda-forge
   :target: https://anaconda.org/conda-forge/oceanspy

.. |docs| image:: http://readthedocs.org/projects/oceanspy/badge/?version=latest
    :alt: Documentation
    :target: http://oceanspy.readthedocs.io/en/latest/?badge=latest

.. |CI| image:: https://img.shields.io/github/workflow/status/hainegroup/oceanspy/CI?logo=github
    :alt: CI
    :target: https://github.com/hainegroup/oceanspy/actions

.. |codecov| image:: https://codecov.io/github/hainegroup/oceanspy/coverage.svg?branch=main
    :alt: Coverage
    :target: https://codecov.io/github/hainegroup/oceanspy?branch=main

.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
    :alt: black
    :target: https://github.com/psf/black

.. |license| image:: https://img.shields.io/github/license/mashape/apistatus.svg
   :alt: License
   :target: https://github.com/hainegroup/oceanspy

.. |doi| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3270646.svg
   :alt: doi
   :target: https://doi.org/10.5281/zenodo.3270646

.. |JOSS| image:: http://joss.theoj.org/papers/10.21105/joss.01506/status.svg
   :alt: JOSS
   :target: https://doi.org/10.21105/joss.01506

.. |binder| image:: https://mybinder.org/badge_logo.svg
   :alt: binder
   :target: https://mybinder.org/v2/gh/hainegroup/oceanspy.git/main?filepath=binder

.. |pre-commit| image:: https://results.pre-commit.ci/badge/github/hainegroup/oceanspy/main.svg
   :target: https://results.pre-commit.ci/latest/github/hainegroup/oceanspy/main
   :alt: pre-commit.ci status

Owner

  • Name: Thomas Haine Research Group
  • Login: hainegroup
  • Kind: organization

Ocean circulation and dynamics

GitHub Events

Total
  • Issues event: 6
  • Watch event: 9
  • Delete event: 12
  • Issue comment event: 23
  • Push event: 21
  • Pull request event: 34
  • Pull request review comment event: 1
  • Pull request review event: 12
  • Fork event: 2
  • Create event: 16
Last Year
  • Issues event: 6
  • Watch event: 9
  • Delete event: 12
  • Issue comment event: 23
  • Push event: 21
  • Pull request event: 34
  • Pull request review comment event: 1
  • Pull request review event: 12
  • Fork event: 2
  • Create event: 16

Committers

Last synced: 5 months ago

All Time
  • Total Commits: 1,097
  • Total Committers: 13
  • Avg Commits per committer: 84.385
  • Development Distribution Score (DDS): 0.552
Past Year
  • Commits: 19
  • Committers: 3
  • Avg Commits per committer: 6.333
  • Development Distribution Score (DDS): 0.579
Top Committers
Name Email Commits
Miguel Jimenez-Urias m****7@j****u 491
malmans2 m****i@j****u 458
pre-commit-ci[bot] 6****] 67
dependabot[bot] 4****] 36
asiddi24 a****4@j****u 17
renskegelderloos r****2@j****u 8
ThomasHaine T****e@j****u 8
MaceKuailv 5****v 7
Filipe o****f@g****m 1
Sourav Barua s****6@g****m 1
dependabot-preview[bot] 2****] 1
Atousa Saberi a****i@j****u 1
malmans2 m****i@g****m 1
Committer Domains (Top 20 + Academic)
jhu.edu: 5 jh.edu: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 151
  • Total pull requests: 323
  • Average time to close issues: 3 months
  • Average time to close pull requests: 7 days
  • Total issue authors: 20
  • Total pull request authors: 12
  • Average comments per issue: 3.58
  • Average comments per pull request: 1.92
  • Merged pull requests: 292
  • Bot issues: 0
  • Bot pull requests: 117
Past Year
  • Issues: 7
  • Pull requests: 31
  • Average time to close issues: 8 days
  • Average time to close pull requests: 15 days
  • Issue authors: 5
  • Pull request authors: 3
  • Average comments per issue: 1.29
  • Average comments per pull request: 0.81
  • Merged pull requests: 25
  • Bot issues: 0
  • Bot pull requests: 27
View more stats
Top Authors
Issue Authors
  • Mikejmnez (49)
  • malmans2 (28)
  • ThomasHaine (23)
  • MaceKuailv (11)
  • renskegelderloos (11)
  • asiddi24 (8)
  • hooteoos-waltz (6)
  • rabernat (2)
  • ammedd (1)
  • junweihua (1)
  • shiprock-1583 (1)
  • platipodium (1)
  • ocefpaf (1)
  • jdldeauna (1)
  • daanreijnders (1)
Pull Request Authors
  • malmans2 (100)
  • pre-commit-ci[bot] (81)
  • Mikejmnez (70)
  • dependabot[bot] (61)
  • asiddi24 (14)
  • MaceKuailv (9)
  • ThomasHaine (8)
  • renskegelderloos (7)
  • hooteoos-waltz (5)
  • ocefpaf (1)
  • BaruaSourav (1)
  • dependabot-preview[bot] (1)
Top Labels
Issue Labels
enhancement (26) bug (14) Documentation (9) dependencies (7) good first issue (4) question (4) help wanted (2) invalid (1)
Pull Request Labels
dependencies (62) github_actions (53)

Packages

  • Total packages: 3
  • Total downloads:
    • pypi 87 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 1
    (may contain duplicates)
  • Total versions: 44
  • Total maintainers: 4
proxy.golang.org: github.com/hainegroup/oceanspy
  • Versions: 20
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 4 months ago
pypi.org: oceanspy

A Python package to facilitate ocean model data analysis and visualization.

  • Documentation: https://oceanspy.readthedocs.io/
  • License: MIT License Copyright (c) 2018, Mattia Almansi Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  • Latest release: 0.3.5
    published about 2 years ago
  • Versions: 20
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 87 Last month
Rankings
Dependent packages count: 10.1%
Average: 18.3%
Dependent repos count: 21.6%
Downloads: 23.2%
Maintainers (4)
malmans2 Mikejmnez ThomasHaine WJiang
Last synced: 4 months ago
conda-forge.org: oceanspy
  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Forks count: 28.5%
Stargazers count: 33.5%
Dependent repos count: 34.0%
Average: 36.8%
Dependent packages count: 51.2%
Last synced: 4 months ago

Dependencies

.github/workflows/ci.yaml actions
  • actions/checkout v3 composite
  • codecov/codecov-action v3.1.1 composite
  • mamba-org/provision-with-micromamba v15 composite
.github/workflows/pypi.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • pypa/gh-action-pypi-publish release/v1 composite
pyproject.toml pypi
  • dask *
  • xarray >= 0.14.1
  • xgcm >= 0.2.0
binder/environment.yml conda
  • bokeh
  • bottleneck
  • cartopy
  • dask
  • distributed
  • esmf
  • esmpy
  • ffmpeg
  • geopy
  • intake-xarray
  • ipython
  • matplotlib
  • netcdf4
  • numpy
  • pandas
  • pip
  • python 3.10.*
  • rise
  • tqdm
  • xarray
  • xesmf >0.6.3
  • xgcm
  • xmitgcm
  • xoak
docs/environment.yml conda
  • nbsphinx
  • numpydoc
  • pandoc
  • pip
  • python 3.9.*
  • sphinx
  • sphinx_rtd_theme
sciserver_catalogs/environment.yml conda
  • aiohttp
  • black <20.8b1
  • bottleneck
  • cartopy
  • cf_xarray
  • cfgrib
  • cftime
  • cmasher
  • cmocean
  • codecov
  • dask
  • distributed
  • eofs
  • esmf
  • esmpy
  • fastjmd95
  • ffmpeg
  • flake8
  • fsspec
  • geopy
  • gsw
  • h5netcdf
  • imageio
  • intake-xarray
  • ipykernel
  • ipython
  • matplotlib
  • nc-time-axis
  • netcdf4
  • numba
  • pandas
  • pip
  • pooch
  • pre-commit
  • pycwt
  • pydap
  • pys2index
  • pytest
  • pytest-cov
  • pytest-env
  • python 3.10.*
  • rasterio
  • scikit-learn
  • scipy
  • seaborn
  • tqdm
  • xarray
  • xesmf >0.6.3
  • xgcm
  • xhistogram
  • xmitgcm
  • xoak
  • zarr
ci/environment.yml pypi