JOSS paper (#100)

* Saved new PDF of paper * don't run CI on joss-paper branch * Saved new PDF of paper * don't run CI on joss-paper branch * Saved new PDF of paper * aekiss is clex * Saved new PDF of paper * minor changes * Saved new PDF of paper * add gebco * missing comma * Saved new PDF of paper * typos and citations for era5 and glorys' * Saved new PDF of paper * new title; bit of rephrasing * capitalize ECMWF * Saved new PDF of paper * add 2 refs for regional MOM6 modeling * Saved new PDF of paper * a lot of changes * Saved new PDF of paper * mention cookbook seemed a bit out of place * Saved new PDF of paper * update figure * Saved new PDF of paper * fig caption * Saved new PDF of paper * cite arakawa * Saved new PDF of paper * alignment * is it the dash? * Saved new PDF of paper * simplify caption * Saved new PDF of paper * testfig * Saved new PDF of paper * testfig * Saved new PDF of paper * testfig * Saved new PDF of paper * testfig * Saved new PDF of paper * cite tasman-tides * Saved new PDF of paper * more details * Saved new PDF of paper * more details * more details * Saved new PDF of paper * add ref for mom5 * missed a comma * Saved new PDF of paper * AK edits to paper (#141) * AK suggestions * Saved new PDF of paper * tweak acknowledgements Co-authored-by: Navid C. Constantinou <[email protected]> * Saved new PDF of paper * Update paper/paper.md Co-authored-by: Navid C. Constantinou <[email protected]> * Saved new PDF of paper * Update paper/paper.md * Saved new PDF of paper * consult -> dig into a compromise from "decipher" --------- Co-authored-by: aekiss <[email protected]> Co-authored-by: Navid C. Constantinou <[email protected]> * Saved new PDF of paper * JOSS paper edits/comments by Chris (#144) * CC modifications to paper document * Saved new PDF of paper * add griffies2020ALE * Saved new PDF of paper * Update paper/paper.md Co-authored-by: Navid C. Constantinou <[email protected]> * Update paper/paper.md Co-authored-by: Navid C. Constantinou <[email protected]> * Update paper/paper.md Co-authored-by: Navid C. Constantinou <[email protected]> * Saved new PDF of paper --------- Co-authored-by: Chris Chapman <[email protected]> Co-authored-by: ChrisC28 <[email protected]> Co-authored-by: Navid C. Constantinou <[email protected]> Co-authored-by: ashjbarnes <[email protected]> * Saved new PDF of paper * fix refs * Saved new PDF of paper * bring back some commented details * Saved new PDF of paper * clarification * Saved new PDF of paper * minor changes * add note for citation * Saved new PDF of paper * rephrase the use in classroom * Saved new PDF of paper * don't define acronyms we never use * Saved new PDF of paper * ESMG -> Earth System Modeling Group * Saved new PDF of paper * change author order in gridtools ref * Saved new PDF of paper * capitalize ESMG * Saved new PDF of paper * package is regional-mom6; mention install via conda * Saved new PDF of paper * Saved new PDF of paper * a bit on why regional ocean modeling is needed * Saved new PDF of paper * fix refs * Saved new PDF of paper * slight rephrase * slight rephrase * Saved new PDF of paper * slight rephrase * Saved new PDF of paper * slight rephrase * Saved new PDF of paper * Fix CLEx affiliation * Saved new PDF of paper * Update paper/paper.md * Saved new PDF of paper * minor rephrase * Saved new PDF of paper * mention+cite OBC * Saved new PDF of paper * fix typo * Saved new PDF of paper * josue suggested rephasing for clarity * Saved new PDF of paper * red so we don't forget * Saved new PDF of paper * Small corrections * Saved new PDF of paper * cite Richardson 1922 book * fix ref * Saved new PDF of paper * bit of rephrase * Saved new PDF of paper * bit of rephrase * Saved new PDF of paper * apply Andrew's suggestions Co-authored-by: Andrew Kiss <[email protected]> * Saved new PDF of paper * Saved new PDF of paper * better seam discussion Co-authored-by: Andrew Kiss <[email protected]> * Saved new PDF of paper * add intro + cite Bleck 2002 * address andrew's and chris's remarks * Saved new PDF of paper * nuke commented text * Saved new PDF of paper * add 21CW * Saved new PDF of paper * rephrase * Saved new PDF of paper * who develops MOM6 is not relevant * Saved new PDF of paper * add back reference to fig * Saved new PDF of paper * better caption * Saved new PDF of paper * remove winstress fig * Saved new PDF of paper * fix citation to Bleck 2002 * Saved new PDF of paper * repetitive ocean model * Saved new PDF of paper * cite Polton et al 2023 * Saved new PDF of paper * add remark about downscaling * Saved new PDF of paper * slight rephrase * Saved new PDF of paper * Saved new PDF of paper * incorporate Callum's remarks * Saved new PDF of paper * it's double ell * Saved new PDF of paper * add UniMelb * Saved new PDF of paper * Apply suggestions from code review Co-authored-by: Andrew Kiss <[email protected]> * Saved new PDF of paper * Saved new PDF of paper * no need to cite Griffies 2020 twice * Saved new PDF of paper * add cheeky remark about cosima * Saved new PDF of paper * add citation * Saved new PDF of paper * in-text cite * Saved new PDF of paper * equal contrib * Saved new PDF of paper * try subheadings to see how it looks * Saved new PDF of paper * cite CEFIregional-mom6 * Saved new PDF of paper * minor rephrasing * Saved new PDF of paper * rephrase * Saved new PDF of paper * rephrase * Saved new PDF of paper * rephrase * Saved new PDF of paper * change title * Saved new PDF of paper * Automatic -> automatic * Saved new PDF of paper * add missing dois * add missing commas * Saved new PDF of paper * Saved new PDF of paper * add doi * Saved new PDF of paper * code alignment * Saved new PDF of paper * add orcid * Saved new PDF of paper * use nested figure * Saved new PDF of paper * add colorbar in fig * Saved new PDF of paper * Added caption details for nested figure * Saved new PDF of paper * add Luwei + update caption * Saved new PDF of paper * shorten caption * Saved new PDF of paper * move fig? * Saved new PDF of paper * move fig? * Saved new PDF of paper * resize fig? * Saved new PDF of paper * add CLEx affiliation + CoE grants * Saved new PDF of paper * slight rephrase * Saved new PDF of paper * differentiate inner-outer regions * Saved new PDF of paper * update refs * Saved new PDF of paper * Update paper.bib remove duplicate reference * Saved new PDF of paper * Saved new PDF of paper * Delete paper/tasman_speed.png * Saved new PDF of paper * thanks to reviewers and editor * Saved new PDF of paper * add published version + citation info * fix title * joss badge on its own line --------- Co-authored-by: ashjbarnes <[email protected]> Co-authored-by: ashjbarnes <[email protected]> Co-authored-by: Andrew Kiss <[email protected]> Co-authored-by: aekiss <[email protected]> Co-authored-by: Ashley Barnes <[email protected]> Co-authored-by: Chris Chapman <[email protected]> Co-authored-by: ChrisC28 <[email protected]> Co-authored-by: Dhruv Bhagtani <[email protected]> Co-authored-by: dhruvbhagtani <[email protected]> Co-authored-by: John Reilly <[email protected]> Co-authored-by: reillyja <[email protected]>
COSIMA · Aug 9, 2024 · 4a863ad · 4a863ad
1 parent 4781919
commit 4a863ad
Show file tree

Hide file tree

Showing 9 changed files with 2,005 additions and 1 deletion.
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - '**'
+      - '!joss-paper'
 
 jobs:
   formatting:

diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,35 @@
+cff-version: 1.2.0
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Barnes"
+    given-names: "Ashley J."
+    orcid: "https://orcid.org/0000-0003-3165-8676"
+  - family-names: "Constantinou"
+    given-names: "Navid C."
+    orcid: "https://orcid.org/0000-0002-8149-4094"
+  - family-names: "Gibson"
+    given-names: "Angus H."
+    orcid: "https://orcid.org/0000-0001-7577-3604"
+  - family-names: "Kiss"
+    given-names: "Andrew E."
+    orcid: "https://orcid.org/0000-0001-8960-9557"
+  - family-names: "Chapman"
+    given-names: "Chris"
+    orcid: "https://orcid.org/0000-0002-6030-1951"
+  - family-names: "Reily"
+    given-names: "John"
+    orcid: "https://orcid.org/0000-0003-4001-0230"
+  - family-names: "Bhagtani"
+    given-names: "Dhruv"
+    orcid: "https://orcid.org/0000-0002-1222-375X"
+  - family-names: "Yang"
+    given-names: "Luwei"
+    orcid: "https://orcid.org/0000-0001-8570-7424"
+  title: "regional-mom6: A Python package for automatic generation of regional configurations for the Modular Ocean Model 6"
+  journal: "Journal of Open Source Software"
+  doi: "10.21105/joss.06857"
+  volume: 9
+  issue: 100
+  start: 6857
+  year: 2024
diff --git a/README.md b/README.md
@@ -5,13 +5,14 @@
 [![Repo status](https://www.repostatus.org/badges/latest/active.svg?style=flat-square)](https://www.repostatus.org/#active)
 [![conda forge](https://img.shields.io/conda/vn/conda-forge/regional-mom6.svg)](https://anaconda.org/conda-forge/regional-mom6)
 [![pypi](https://badge.fury.io/py/regional-mom6.svg)](https://badge.fury.io/py/regional-mom6)
-[![status](https://joss.theoj.org/papers/d396435c09aae4c2f4b62cdbc1493c1e/status.svg)](https://joss.theoj.org/papers/d396435c09aae4c2f4b62cdbc1493c1e)
 [![Documentation Status](https://readthedocs.org/projects/regional-mom6/badge/?version=latest)](https://regional-mom6.readthedocs.io/en/latest/?badge=latest)
 
 [![License](https://img.shields.io/badge/License-MIT-blue.svg?style=flat-square)](https://mit-license.org)
 [![codecov](https://codecov.io/gh/COSIMA/regional-mom6/branch/main/graph/badge.svg?token=7OEZ1UZRY4)](https://codecov.io/gh/COSIMA/regional-mom6)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
+[![status](https://joss.theoj.org/papers/d396435c09aae4c2f4b62cdbc1493c1e/status.svg)](https://joss.theoj.org/papers/d396435c09aae4c2f4b62cdbc1493c1e)
+
 Users just need to provide some information about where, when, and how big their domain is and also where raw input forcing files are. The package sorts out all the boring details and creates a set of MOM6-friendly input files along with setup directories ready to go! 
 
 The idea behind this package is that it should let the user sidestep some of the tricky issues with getting the model to run in the first place. This removes some of the steep learning curve for people new to working with MOM6. Note that the resultant model configuration might still need some tweaking (e.g., fiddling with timestep to avoid CFL-related numerical stability issues or fiddling with bathymetry to deal with very narrow fjords or channels that may exist).
@@ -129,3 +130,27 @@ the package using two different sets of input datasets.
 Please ensure that you can get at least one of these working on your setup with your MOM6 executable before trying to modify the example to suit your domain with your bathymetry, forcing, and boundary conditions.
 
 You can download the notebooks [from Github](https://github.com/COSIMA/regional-mom6/tree/main/demos) or by clicking on the download <img width="22" alt="download" src="https://github.com/COSIMA/regional-mom6/assets/7112768/2c1ae149-c6a8-4395-ab09-2f77588008d9"> button, e.g., at the top-right of the [regional Tasmania forced by ERA5 example](https://regional-mom6.readthedocs.io/en/latest/demo_notebooks/reanalysis-forced.html).
+
+## Citing
+
+If you use regional-mom6 in research, teaching, or other activities, we would be grateful 
+if you could mention regional-mom6 and cite our paper in JOSS:
+
+> Barnes et al., (2024). regional-mom6: A Python package for automatic generation of regional configurations for the Modular Ocean Model 6. _Journal of Open Source Software_, **9(100)**, 6857, doi:[10.21105/joss.06857](https://doi.org/10.21105/joss.06857).
+
+The bibtex entry for the paper is:
+
+```bibtex
+@article{regional-mom6-JOSS,
+  doi = {10.21105/joss.06857},
+  url = {https://doi.org/10.21105/joss.06857},
+  year = {2024},
+  publisher = {The Open Journal},
+  volume = {9},
+  number = {100},
+  pages = {6857},
+  author = {Ashley J. Barnes and Navid C. Constantinou and Angus H. Gibson and Andrew E. Kiss and Chris Chapman and John Reily and Dhruv Bhagtani and Luwei Yang},
+  title = {{regional-mom6: A Python package for automatic generation of regional configurations for the Modular Ocean Model 6}},
+  journal = {Journal of Open Source Software}
+}
+```
diff --git a/docs/index.rst b/docs/index.rst
@@ -53,6 +53,15 @@ What you need to get started
 
 Browse through the `demos <demos.html>`_.
 
+Citing
+------
+
+If you use regional-mom6 in research, teaching, or other activities, we would be grateful 
+if you could mention regional-mom6 and cite our paper in JOSS:
+
+Barnes et al., (2024). regional-mom6: A Python package for automatic generation of regional configurations for the Modular Ocean Model 6. *Journal of Open Source Software*, **9(100)**, 6857, doi:`10.21105/joss.06857 <https://doi.org/10.21105/joss.06857>`_.
+
+
 .. _regional-mom6: https://github.com/COSIMA/regional-mom6
 .. _Modular Ocean Model version 6: https://github.com/mom-ocean/MOM6
 .. _open a pull request: https://github.com/COSIMA/regional-mom6/pulls