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[PRE REVIEW]: SubZero: a Discrete element sea ice model that simulates floes as evolving concave polygons #4984

Closed editorialbot closed 1 year ago

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@bpm5026<!--end-author-handle-- (Brandon Montemuro) Repository: https://github.com/SeaIce-Math/SubZero Branch with paper.md (empty if default branch): JOSS Version: v1.0.2 Editor: !--editor-->@hugoledoux<!--end-editor-- Reviewers: @ZijieZhaoMMHW, @zhaohuiwang-imas Managing EiC: Kristen Thyng

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HTML: <a href="https://joss.theoj.org/papers/264a3399e133b5418de0f3c1993b076c"><img src="https://joss.theoj.org/papers/264a3399e133b5418de0f3c1993b076c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/264a3399e133b5418de0f3c1993b076c/status.svg)](https://joss.theoj.org/papers/264a3399e133b5418de0f3c1993b076c)

Author instructions

Thanks for submitting your paper to JOSS @bpm5026. Currently, there isn't a JOSS editor assigned to your paper.

@bpm5026 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands
editorialbot commented 1 year ago

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
editorialbot commented 1 year ago

Couldn't check the bibtex because branch name is incorrect: https://github.com/bpm5026/JOSS-Subzero-paper

editorialbot commented 1 year ago

Couldn't check the bibtex because branch name is incorrect: https://github.com/bpm5026/JOSS-Subzero-paper

editorialbot commented 1 year ago

:warning: An error happened when generating the pdf.

kthyng commented 1 year ago

Hi @bpm5026 and thanks for your submission. Did you perhaps give the wrong address for the JOSS paper? The system is having trouble finding it.

bpm5026 commented 1 year ago

I Kristen,

Sorry, I had forgotten to make the repo public. I have switched that setting now, so let me know if that fixes the problem.

Thanks, Brandon

On Wed, Nov 30, 2022 at 2:47 PM Kristen Thyng @.***> wrote:

Hi @bpm5026 https://github.com/bpm5026 and thanks for your submission. Did you perhaps give the wrong address for the JOSS paper? The system is having trouble finding it.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4984#issuecomment-1332833604, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIBLVKZFQIXIVWCUSVVXPA3WK7KRFANCNFSM6AAAAAASQECLLM . You are receiving this because you were mentioned.Message ID: @.***>

kthyng commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:warning: An error happened when generating the pdf.

kthyng commented 1 year ago

Thanks @bpm5026, though we require the paper to be in the same repository as the software:

Your paper (paper.md and BibTeX files, plus any figures) must be hosted in a Git-based repository together with your software (although they may be in a short-lived branch which is never merged with the default).

Could you move the paper to the software repo?

bpm5026 commented 1 year ago

Hi Kristen,

Sorry about the mixup. I have included the new branch I created off the software with everything in it below. I just tested it, and the paper looks to have been compiled. Let me know if sending you the branch here is okay or if I need to resubmit with the new link.

https://github.com/SeaIce-Math/SubZero/tree/JOSS

Thanks, Brandon

On Wed, Nov 30, 2022 at 3:08 PM Kristen Thyng @.***> wrote:

Thanks @bpm5026 https://github.com/bpm5026, though we require https://joss.readthedocs.io/en/latest/submitting.html#submission-requirements the paper to be in the same repository as the software:

Your paper (paper.md and BibTeX files, plus any figures) must be hosted in a Git-based repository together with your software (although they may be in a short-lived branch which is never merged with the default).

Could you move the paper to the software repo?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4984#issuecomment-1332854799, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIBLVKZMUOA7XVZBBUOMNUDWK7M7NANCNFSM6AAAAAASQECLLM . You are receiving this because you were mentioned.Message ID: @.***>

kthyng commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:warning: An error happened when generating the pdf.

kthyng commented 1 year ago

@editorialbot set JOSS as branch

editorialbot commented 1 year ago

Done! branch is now JOSS

kthyng commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

kthyng commented 1 year ago

@editorialbot check repository

editorialbot commented 1 year ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.33 s (516.1 files/s, 127221.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Pascal                           7            585            705           6235
C++                              7            698            619           5598
C#                              11            558            701           5461
MATLAB                          43            860           1169           4059
CSS                             18             63            273           3752
JavaScript                      35            553           1099           2405
Python                           2            261            129           2136
XML                              8             22             96            753
C/C++ Header                     3             85             97            578
Sass                            18            103             32            472
SVG                              3              1              1            459
MSBuild script                   3              0             21            271
TeX                              1             22              0            218
Markdown                         3             53              0             94
HTML                             2              3              0             31
YAML                             1              1              4             18
CMake                            1              5              1             15
Ruby                             1              1              2             11
make                             1              7              3             10
-------------------------------------------------------------------------------
SUM:                           168           3881           4952          32576
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 1 year ago

Wordcount for paper.md is 845

kthyng commented 1 year ago

@bpm5026 Since you are simultaneously publishing with JAMES, could you explain in a bit of detail the distinction between what is in the other paper vs. this submission? We have to be sure to have distinct scholarly units.

bpm5026 commented 1 year ago

Hi Kristen,

The JAMES paper is a 30+ page paper going into the detailed model physics. For example, in the JAMES paper, we discuss the specifics of the methods for the contact laws, fracture rules, and things of that nature. Whereas the intention of this JOSS paper is a short, high-level paper that we wish to be reachable to a broader audience in the software community.

Thanks, Brandon

On Thu, Dec 1, 2022 at 8:28 AM Kristen Thyng @.***> wrote:

@bpm5026 https://github.com/bpm5026 Since you are simultaneously publishing with JAMES, could you explain in a bit of detail the distinction between what is in the other paper vs. this submission? We have to be sure to have distinct scholarly units.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4984#issuecomment-1334030673, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIBLVK6LDJAOPKIV72W3MK3WLDG2RANCNFSM6AAAAAASQECLLM . You are receiving this because you were mentioned.Message ID: @.***>

kthyng commented 1 year ago

Thanks for that info, @bpm5026. Is the software being reviewed in the JAMES paper? And you mentioned at submission that there is a pdf on arxiv I think — could you post it here?

bpm5026 commented 1 year ago

Here is the link to the arxiv: https://eartharxiv.org/repository/view/3503/

The JAMES paper is not really being reviewed for the software, what they are reviewing is model physics and how it can reproduce the statistical behavior of the observed sea ice, such as the power-law appearance of the floe size distribution and the long-tailed ice thickness distribution.

On Thu, Dec 1, 2022 at 12:11 PM Kristen Thyng @.***> wrote:

Thanks for that info, @bpm5026 https://github.com/bpm5026. Is the software being reviewed in the JAMES paper? And you mentioned at submission that there is a pdf on arxiv I think — could you post it here?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4984#issuecomment-1334367091, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIBLVK2ODM6XCVOA372DTILWLEA6BANCNFSM6AAAAAASQECLLM . You are receiving this because you were mentioned.Message ID: @.***>

kthyng commented 1 year ago

@bpm5026 Ok thank you for the extra information!

kthyng commented 1 year ago

@hugoledoux or @crvernon Would either of you be able to handle this submission? I know it's not a perfect fit but not sure how far it is from your normal areas of expertise.

kthyng commented 1 year ago

I made a mistake on my previous comment — @crvernon is fully occupied with other submissions at the moment.

hugoledoux commented 1 year ago

I could do it, but I might be a bit more slow than usual because very busy coming 2w at work.

But happy to do it if @crvernon cannot.

crvernon commented 1 year ago

Hi @hugoledoux, feel free to have at it if you can. Thanks so much!

kthyng commented 1 year ago

@hugoledoux It would be great if you could take this on.

@bpm5026 Please take a look at our list of volunteers for reviewing and list 5+ github handles (without the "@" so they aren't preemptively pinged) that would be appropriate for reviewing your software. https://bit.ly/joss-reviewers You're also welcome to list people by github handle or email address that aren't on that list as long as you are not conflicted with them. This will help @hugoledoux get reviewers assigned to start the process more quickly. Thank you!

kthyng commented 1 year ago

@editorialbot assign @hugoledoux as editor

editorialbot commented 1 year ago

Assigned! @hugoledoux is now the editor

bpm5026 commented 1 year ago

Thanks Hugo! Here are 6 names from the list that say Matlab for languages, have either oceanography or discrete element methods on their domains, and are not listed as having any active reviews.

vsangelidakis

mvdh7

ZijieZhaoMMHW

wingtorres

chadagreene

chouj

Best,

Brandon

On Wed, Dec 7, 2022 at 6:51 AM Kristen Thyng @.***> wrote:

@hugoledoux https://github.com/hugoledoux It would be great if you could take this on.

@bpm5026 https://github.com/bpm5026 Please take a look at our list of volunteers for reviewing and list 5+ github handles (without the "@" so they aren't preemptively pinged) that would be appropriate for reviewing your software. https://bit.ly/joss-reviewers You're also welcome to list people by github handle or email address that aren't on that list as long as you are not conflicted with them. This will help @hugoledoux https://github.com/hugoledoux get reviewers assigned to start the process more quickly. Thank you!

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4984#issuecomment-1341079867, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIBLVKYRQROCICKBJKQMN5DWMCP6FANCNFSM6AAAAAASQECLLM . You are receiving this because you were mentioned.Message ID: @.***>

hugoledoux commented 1 year ago

Just an update: I was off and now back at work, so this is positive.

The bad news is that either reviewers don't answer or they refuse... Working on it, sorry for the delay!

hugoledoux commented 1 year ago

@ZijieZhaoMMHW would you be interested in doing that review?

(btw you're a hard person to email, I've tried 10min+ to find your email and I failed...)

ZijieZhaoMMHW commented 1 year ago

@ZijieZhaoMMHW would you be interested in doing that review?

(btw you're a hard person to email, I've tried 10min+ to find your email and I failed...)

Dear Hugo @hugoledoux ,

Thanks for the nomination of reviewing. My studies focus on meteorology and oceanography and I am not an expert in sea ice, so I should probably decline the invitation. I think @chadagreene may be a good reviewer for this as he is an expert in both MATLAB and Antarctic science.

I now add my personal email to my github profile. Sorry for the inconvenience.

Cheers, Zijie

hugoledoux commented 1 year ago

Hello @ZijieZhaoMMHW, since @chadagreene cannot do it, finding a reviewer is turning out to be impossible, everyone says they are not an expert or no MATLAB expertise...

JOSS is about the content but also and foremost about the software, so if you were willing to do this that would help us.

ZijieZhaoMMHW commented 1 year ago

Hello @ZijieZhaoMMHW, since @chadagreene cannot do it, finding a reviewer is turning out to be impossible, everyone says they are not an expert or no MATLAB expertise...

JOSS is about the content but also and foremost about the software, so if you were willing to do this that would help us.

Dear Hugo @hugoledoux

Ok I can be the reviewer for this one. Another potential reviewer I know can be @ZhaohuiWang-imas, an expert in Antarctic science and MATLAB. He is also willing to do this review. However, he has no publications with JOSS, I am not sure if it can be a problem ....

hugoledoux commented 1 year ago

This is super news @ZijieZhaoMMHW , thanks a lot.

@zhaohuiwang-imas Glad you can do this review. Since it's your first review for JOSS, don't hesitate to contact me (directly in the issue using @hugoledoux) if it's not clear. The review is open to everyone, and we expect you to have a dialogue with the authors, the review is often formed of several iterations.

The review will be in a new GitHub issue that I will open in a moment.

hugoledoux commented 1 year ago

@editorialbot add @ZijieZhaoMMHW as reviewer

editorialbot commented 1 year ago

@ZijieZhaoMMHW added to the reviewers list!

hugoledoux commented 1 year ago

@editorialbot add @zhaohuiwang-imas as reviewer

editorialbot commented 1 year ago

@zhaohuiwang-imas added to the reviewers list!

hugoledoux commented 1 year ago

@editorialbot start review

editorialbot commented 1 year ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5039.