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COSIMA

Ocean and sea-ice model analysis tools and examples.
https://github.com/COSIMA/cosima-cookbook

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analysis ocean

Last synced: over 1 year ago
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Framework for indexing and querying ocean-sea ice model output.

README.md

cosima-cookbook

The COSIMA Cookbook is a framework for analysing output from ocean-sea ice models. The focus is on the ACCESS-OM2 suite of models being developed and run by members of COSIMA: Consortium for Ocean-Sea Ice Modelling in Australia. But this framework is suited to analysing any MOM5/MOM6 output, as well as output from other models.

The cookbook is structured as follows:

  • This repository includes boiler-plate code and scripts that underpin the cookbook.
  • The cosima-recipes repository includes example notebooks on which you can base your analyses.
  • The cosima-recipes template provides you with a template if you want to contribute your own scripts to the analysis.

Getting Started

The easiest way to use the COSIMA Cookbook is through NCI's HPC systems (either VDI or Gadi). The cookbook is preinstalled in the latest conda/analysis3 environment.

Once you have an account on the VDI, you should:

  1. Clone the cosima-recipes repository to your local file space.
  2. Start a jupyter notebook session using the following commands:
>> module use /g/data/hh5/public/modules/
>> module load conda/analysis3-unstable
>> jupyter notebook
  1. Navigate to one of the COSIMA recipes and run the analysis.

Alternatively, you might prefer to download vdi_jupyter or the gadi_jupyter scripts hosted in the CLEx CMS Github Repository coecms/nci_scripts. These scripts will allow you to open a Jupyter notebook in your local browser window.

Using the Cookbook

The COSIMA Cookbook relies on several components:

  1. There needs to be a database of simulations -- on the NCI system, model output that is stored in the COSIMA space on the /g/data/ik11/ directory.
  2. Once you have access to data, the best place to start is the cosima-recipes repository which includes a series of jupyter notebooks containing examples that guide you through to use the cookbook to load model output and then proceed doing simple (or elaborate) computations. The best starting point of exploring the cosima-recipes is the Documented Examples. A collection of useful examples leveraging the cosima-cookbook is also found here.

Contributing to the Cookbook

If you like the cookbook, you may like to interact more closely with us:

  • Contributions of new notebooks or analysis scripts are always welcome. Please check out the cosima-recipes repository.
  • If you find a problem, or have a suggestion for improvement, please log an issue.
  • All code submitted as part of the cosima-cookbook itself must be formatted with black

Conditions of use for ACCESS-OM2 data

We request that users of ACCESS-OM2 model code or output data:

  1. consider citing Kiss et al. (2020) (http://doi.org/10.5194/gmd-13-401-2020)

  2. include an acknowledgement such as the following:

    The authors thank the Consortium for Ocean-Sea Ice Modelling in Australia (COSIMA; http://www.cosima.org.au) for making the ACCESS-OM2 suite of models available at https://github.com/COSIMA/access-om2.

  3. let us know of any publications which use these models or data so we can add them to our list.

Documentation Status

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Last synced: over 1 year ago

Total Commits: 335
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Avg Commits per committer: 25.769
Development Distribution Score (DDS): 0.71

Commits in past year: 8
Committers in past year: 3
Avg Commits per committer in past year: 2.667
Development Distribution Score (DDS) in past year: 0.25

Name Email Commits
James Munroe j****e@m****a 97
Angus Gibson a****s@a****e 91
Aidan Heerdegen a****n@a****u 50
andy A****g@a****u 37
Andrew 3****s 26
Navid C. Constantinou n****y 12
Paul Spence i****e@g****m 6
Micael Oliveira m****a@a****u 6
Josué Martínez Moreno j****o@a****u 3
Scott Wales s****s@u****u 3
rbeucher r****r@a****u 2
Ed Doddridge e****e 1
dougiesquire d****e@g****m 1

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Last synced: over 1 year ago

Total issues: 177
Total pull requests: 147
Average time to close issues: 6 months
Average time to close pull requests: 16 days
Total issue authors: 23
Total pull request authors: 15
Average comments per issue: 3.48
Average comments per pull request: 1.89
Merged pull request: 137
Bot issues: 0
Bot pull requests: 0

Past year issues: 15
Past year pull requests: 3
Past year average time to close issues: about 7 hours
Past year average time to close pull requests: about 14 hours
Past year issue authors: 11
Past year pull request authors: 2
Past year average comments per issue: 2.4
Past year average comments per pull request: 1.33
Past year merged pull request: 3
Past year bot issues: 0
Past year bot pull requests: 0

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Package metadata

proxy.golang.org: github.com/cosima/cosima-cookbook

proxy.golang.org: github.com/COSIMA/cosima-cookbook

Dependencies

docs/requirements.txt pypi
  • sphinx ==2
setup.py pypi
  • bokeh *
  • cftime *
  • dask *
  • f90nml *
  • ipywidgets *
  • joblib *
  • lxml *
  • matplotlib *
  • netcdf4 *
  • numpy *
  • sqlalchemy <=1.4
  • tqdm *
  • xarray *
.github/workflows/tests.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • codecov/codecov-action v3 composite
  • lgeiger/black-action v1.0.1 composite
conda/environment.yml pypi
requirements.txt pypi

Score: -Infinity