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[PRE REVIEW]: REMORA: Regional Modeling of Oceans Refined Adptively (built on AMReX) #7737

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editorialbot opened this issue Jan 29, 2025 · 14 comments

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Submitting author: @hklion (Hannah Klion)
Repository: https://github.com/seahorce-scidac/REMORA
Branch with paper.md (empty if default branch):
Version: v1.0
Editor: Pending
Reviewers: Pending
Managing EiC: Kristen Thyng

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Markdown: [![status](https://joss.theoj.org/papers/367c07ee49433c26a00573f69a002683/status.svg)](https://joss.theoj.org/papers/367c07ee49433c26a00573f69a002683)

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Thanks for submitting your paper to JOSS @hklion. Currently, there isn't a JOSS editor assigned to your paper.

@hklion if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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@editorialbot editorialbot added pre-review Track: 6 (ESE) Earth Sciences and Ecology labels Jan 29, 2025
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Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.21105/joss.01370 is OK
- 10.1177/10943420211022811 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: A tidal model of the northwest European continenta...
- No DOI given, and none found for title: Ocean forecasting in terrain-following coordinates...

❌ MISSING DOIs

- 10.1175/1520-0485(1985)015<1060:ntocso>2.0.co;2 may be a valid DOI for title: Numerical treatment of cross-shelf open boundaries...
- 10.1016/s1463-5003(00)00013-5 may be a valid DOI for title: Open boundary conditions for long-term integration...
- 10.1016/0021-9991(76)90023-1 may be a valid DOI for title: A simple boundary condition for unbounded hyperbol...
- 10.1357/002224003322005087 may be a valid DOI for title: A generic length-scale equation for geophysical tu...
- 10.1029/2004jc002691 may be a valid DOI for title: Numerical modeling of an estuary: A comprehensive ...
- 10.1016/j.ocemod.2004.08.002 may be a valid DOI for title: The regional oceanic modeling system (ROMS): a spl...
- 10.1175/1520-0426(1995)012<0381:maohpt>2.0.co;2 may be a valid DOI for title: Minimal adjustment of hydrographic profiles to ach...

❌ INVALID DOIs

- None

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Software report:

github.com/AlDanial/cloc v 1.98  T=0.11 s (1881.6 files/s, 301040.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             67           2660           2024          13898
reStructuredText                33           1111            738           2949
C/C++ Header                    21            658            536           2642
YAML                            17            125             98            693
SWIG                            12            196              0            597
CMake                           20            108             79            583
Markdown                         3             85              0            421
make                            11            100             56            416
DOS Batch                        1             36              2            243
Bourne Shell                    11             50             55            201
diff                             1             25            109            184
TeX                              1             10              0            103
Python                           1             74            239             35
Text                             2              0              0             20
-------------------------------------------------------------------------------
SUM:                           201           5238           3936          22985
-------------------------------------------------------------------------------

Commit count by author:

   449	Hannah Klion
   343	Jean M. Sexton
   170	Ann Almgren
    20	melbarkerlbl
    19	Iulian Grindeanu
    12	Weiqun Zhang
     5	Rob Hetland
     4	Andrew Myers
     1	Hannah
     1	JessCG
     1	asalmgren
     1	kyle-hinson

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Paper file info:

📄 Wordcount for paper.md is 768

✅ The paper includes a Statement of need section

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License info:

🟡 License found: Other (Check here for OSI approval)

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@kthyng
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kthyng commented Jan 29, 2025

Hi @hklion and thanks for your submission! I am looking for some specific items to make sure your submission fits our requirements at a high level (not at the more detailed review level) before moving on to finding an editor or putting this on our waitlist if no relevant editors are available. I'll comment over time as I have a chance to go through them:

In the meantime, please take a look at the comments above ⬆️ from the editorialbot to address any DOI, license, or paper issues if you're able (there may not be any), or suggest reviewers. For reviewers, please suggest 5 reviewers from the database listed above or your own (non-conflicted) extended network. Their github handles are most useful to receive but please don't use "@" to reference them since it will prematurely ping them.

@hklion
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hklion commented Jan 29, 2025

@editorialbot check references

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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.21105/joss.01370 is OK
- 10.1177/10943420211022811 is OK
- 10.1175/1520-0485(1985)015<1060:NTOCSO>2.0.CO;2 is OK
- 10.1016/s1463-5003(00)00013-5 is OK
- 10.1016/0021-9991(76)90023-1 is OK
- 10.1357/002224003322005087 is OK
- 10.1029/2004jc002691 is OK
- 10.1016/j.ocemod.2004.08.002 is OK
- 10.1016/j.jcp.2007.06.016 is OK
- 10.1175/1520-0426(1995)012<0381:maohpt>2.0.co;2 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: A tidal model of the northwest European continenta...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

@hklion
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hklion commented Jan 30, 2025

Thanks @kthyng! A few suggestions for reviewers:

  • parkermac
  • jcwarner-usgs
  • glwagner
  • adcroft
  • markusReinert
  • JessCG (COI note: In summer/fall 2023, we had a few meetings to discuss how Jessica and others at Oregon State might be able to use REMORA (then ROMS-X) when it was more mature. When building REMORA, Jessica corrected a directory name in our documentation (PR), so she appears on the commit author list. We have not had any contact since fall 2023. I don't believe there's a conflict here, but still wanted to flag it.)

@kthyng
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kthyng commented Jan 30, 2025

@hklion Thanks! A few notes on your paper:

  • Please check the capitalization in your references. You can preserve capitalization by placing {} around characters/words in your .bib file. For example, "european" is not capitalized in one reference, but please check thoroughly for others.
  • Please check that your inline vs. parenthetical references are correct. You can compare with the example paper here: https://joss.readthedocs.io/en/latest/example_paper.html

@hklion
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hklion commented Jan 30, 2025

@kthyng Thanks for the examples. I've updated the citations so the formatting and capitalization are more consistent.

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kthyng commented Jan 30, 2025

@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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