cgeniepy
cgeniepy: A Python package for analysing cGENIE Earth System Model output - Published in JOSS (2024)
Science Score: 100.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 11 DOI reference(s) in README and JOSS metadata -
✓Academic publication links
Links to: joss.theoj.org, zenodo.org -
✓Committers with academic emails
1 of 4 committers (25.0%) from academic institutions -
○Institutional organization owner
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✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords
Repository
A Python package for analysing the cGENIE model output
Basic Info
- Host: GitHub
- Owner: ruiying-ocean
- License: gpl-3.0
- Language: Roff
- Default Branch: master
- Homepage: https://cgeniepy.readthedocs.io/en/latest
- Size: 31 MB
Statistics
- Stars: 7
- Watchers: 1
- Forks: 2
- Open Issues: 3
- Releases: 3
Topics
Metadata Files
README.md
cgeniepy is a Python package to analyse the output of cGENIE Earth System Model. It aims to provide a set of convenient tools for the post-simulation work, including analysing the model output, plotting publication-quality figures, and conducting model-data comparison.
Installation
- Install from PyPI by running commands below in your terminal.
bash
python3 -m pip install cgeniepy
- Install from GitHub:
bash
python3 -m pip install git+https://github.com/ruiying-ocean/cgeniepy.git@master
3. Install from conda
bash
conda install --channel "ruiying" cgeniepy
Install extra dependency
bash python3 -m pip install "cgeniepy[extra]"Update package
bash pip install --upgrade cgeniepy
Quickstart
I have uploaded a sample model run, which is a preindustrial spinup configuration with marine ecosystem and biogeochemistry enabled (C, P, Fe, Si, O).
```python import cgeniepy from cgeniepy.model import GenieModel
model = cgeniepy.sample_model()
for your own model experiment
model = GenieModel("directorytoyourmodeloutput")
select variable -> select coordinate -> operation like mean or plot
model.getvar('ocnsur_temp').isel(time=-1).plot(colorbar=True) ```
- If you want to try other cGENIE model runs, you may go to this zenodo record (https://zenodo.org/records/10575295).
- If you want to try non-cGENIE model, I have also uploaded two example files to here (https://zenodo.org/records/13786014).
Documentation
An online documentation is hosted in readthedoc.
Citation
Ying, R. (2024). cgeniepy: A Python package for analysing cGENIE Earth System Model output. Journal of Open Source Software, 9(101), 6762. https://doi.org/10.21105/joss.06762
Logo
Logo is designed by me using free righteous font.
Alternative
- Prof. Andy Ridgwell's muffinplot
- Dr. Alex Phol's genie_basicdiags
Raise a bug
Please use GitHub's Issues to raise a bug. This makes the issues traceable so that future users having the same problem can find the answer in the public domain.
Contributing
Owner
- Login: ruiying-ocean
- Kind: user
- Location: Bristol, UK
- Company: University of Bristol
- Website: www.ruiying.online
- Twitter: YingRui17
- Repositories: 4
- Profile: https://github.com/ruiying-ocean
PhD student studying marine system and biogeochemical cycle. Emacs lover.
JOSS Publication
cgeniepy: A Python package for analysing cGENIE Earth System Model output
Authors
School of Earth Sciences, University of Bristol, UK
Editor
Rachel Wegener
Tags
cGENIE Earth System Model Ocean ClimateCitation (CITATION.cff)
cff-version: "1.2.0"
authors:
- email: rui.ying@bristol.ac.uk
family-names: Ying
given-names: Rui
orcid: "https://orcid.org/0000-0001-5811-2388"
contact:
- email: rui.ying@bristol.ac.uk
family-names: Ying
given-names: Rui
orcid: "https://orcid.org/0000-0001-5811-2388"
doi: 10.5281/zenodo.13835532
message: If you use this software, please cite our article in the
Journal of Open Source Software.
preferred-citation:
authors:
- email: rui.ying@bristol.ac.uk
family-names: Ying
given-names: Rui
orcid: "https://orcid.org/0000-0001-5811-2388"
date-published: 2024-09-30
doi: 10.21105/joss.06762
issn: 2475-9066
issue: 101
journal: Journal of Open Source Software
publisher:
name: Open Journals
start: 6762
title: "cgeniepy: A Python package for analysing cGENIE Earth System
Model output"
type: article
url: "https://joss.theoj.org/papers/10.21105/joss.06762"
volume: 9
title: "cgeniepy: A Python package for analysing cGENIE Earth System
Model output"
GitHub Events
Total
- Issues event: 18
- Watch event: 1
- Delete event: 1
- Issue comment event: 6
- Push event: 64
- Pull request event: 1
- Create event: 9
Last Year
- Issues event: 18
- Watch event: 1
- Delete event: 1
- Issue comment event: 6
- Push event: 64
- Pull request event: 1
- Create event: 9
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Rui Ying (Mac) | 3****n | 487 |
| Rachel Wegener | 3****2 | 2 |
| Kristen Thyng | k****g@g****m | 1 |
| Rui Ying (UEA MAC) | r****g@u****k | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 21
- Total pull requests: 3
- Average time to close issues: 29 days
- Average time to close pull requests: about 4 hours
- Total issue authors: 2
- Total pull request authors: 3
- Average comments per issue: 0.81
- Average comments per pull request: 0.33
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 21
- Pull requests: 3
- Average time to close issues: 29 days
- Average time to close pull requests: about 4 hours
- Issue authors: 2
- Pull request authors: 3
- Average comments per issue: 0.81
- Average comments per pull request: 0.33
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- ruiying-ocean (20)
- koldunovn (3)
Pull Request Authors
- kthyng (2)
- ruiying-ocean (2)
- rwegener2 (2)