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Reviews for the Journal of Open Source Software
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[PRE REVIEW]: IndividualDisplacements.jl: a Julia package to simulate and study particle displacements within the climate system #2713

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @gaelforget (Gael Forget) Repository: https://github.com/JuliaClimate/IndividualDisplacements.jl Version: v0.2.0 Editor: @kthyng Reviewers: @milankl, @visr Managing EiC: Kevin M. Moerman

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Author instructions

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

@gaelforget 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 @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands
whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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

@whedon commands

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

@whedon generate pdf
whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.08 s (453.0 files/s, 45135.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           22            561            422           2085
Markdown                         6             71              0            128
TOML                             3              2              0             60
YAML                             3              6              0             53
-------------------------------------------------------------------------------
SUM:                            34            640            422           2326
-------------------------------------------------------------------------------

Statistical information for the repository '2713' was gathered on 2020/10/01.
No commited files with the specified extensions were found.
whedon commented 3 years ago

PDF failed to compile for issue #2713 with the following error:

Can't find any papers to compile :-(

Kevin-Mattheus-Moerman commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

PDF failed to compile for issue #2713 with the following error:

Can't find any papers to compile :-(

Kevin-Mattheus-Moerman commented 3 years ago

@whedon generate pdf from branch josspaper

whedon commented 3 years ago 
Attempting PDF compilation from custom branch josspaper. Reticulating splines etc...
whedon commented 3 years ago

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

Kevin-Mattheus-Moerman commented 3 years ago

@gaelforget thanks for your submission. I've flagged this submission for additional review by our board to check if it is in scope for JOSS. In particular it looks like it is close to being too minor (to me at first sight) in terms of functionality / the amount of scholarly work it contains. This internal review will take about a week. In the mean time if you could clearly and concisely outline the different types of functionality this work offers and how these differ (or are novel) in relation to other work that may help us judge the scope of this work. Thanks.

gaelforget commented 3 years ago

Hi @Kevin-Mattheus-Moerman

Thanks for taking this on and for your amazingly quick first assessment. I am especially grateful for such efficiency in light of the strain that COVID has been putting on all of us and the fact that joss is operating in reduced service mode in particular.

Will get back to you with specifics asap after I re-read the journal docs another time in light of your comment -- I feel I may have overlooked something subtle in the language of the submission guidelines as I was under the impression that this submission would rather easily clear the bar for getting to the open review stage.

In any event, I look forward to additional feedback that you or any other editor may post here, will do my best to respond as rapidly as I can, and hope that I will get a chance to address possible concerns about e.g. functionality or scholarly work over the course of the review process if needed.

By the way, is it ok for me to ask follow up questions here if that's going to help me respond to your comment in more detail?

Kevin-Mattheus-Moerman commented 3 years ago

@gaelforget yes fire away, feel free to ask questions.

gaelforget commented 3 years ago

Hi @Kevin-Mattheus-Moerman

A quick post to apologize for the delay in my response -- it's been a rather hectic week on on my end ...

If that's ok, let me start with

clearly and concisely outline the different types of functionality this work offers

and then turn to the scope and scholarly effort aspects later today and tomorrow

gaelforget commented 3 years ago

Below I outline the different types of functionality this work offers. Additionally the three_dimensional_ocean notebook and the corresponding animation provide a representative example of these functionalities put to action.

A few notes on this outline (and maybe relevant to scope and scholarly effort as well):

Does this suffice as an outline the different types of functionality this work offers? Should I consider including something like this in the joss paper itself?

kthyng commented 3 years ago

@gaelforget thanks for the extra information! We can move forward with this submission. I will be your editor since I do particle tracking too, though not with Julia. I will need particular help from you finding reviewers who can review this software in Julia. Please provide github handles or another way to reach people from either your own network (but not conflicting) or from the list of volunteers. Do not use "@" when mentioning github handles here so we don't spam people unnecessarily.

kthyng commented 3 years ago

@whedon add me as editor

whedon commented 3 years ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands
kthyng commented 3 years ago

@whedon assign me as editor

whedon commented 3 years ago

OK, the editor is @kthyng

gaelforget commented 3 years ago

@gaelforget thanks for the extra information! We can move forward with this submission. I will be your editor since I do particle tracking too, though not with Julia. I will need particular help from you finding reviewers who can review this software in Julia. Please provide github handles or another way to reach people from either your own network (but not conflicting) or from the list of volunteers. Do not use "@" when mentioning github handles here so we don't spam people unnecessarily.

This is great news! Thanks @kthyng for taking on this submission as editor.

I will work on reviewer suggestions asap and hope to get back to you later today on this. Thanks for your patience

kthyng commented 3 years ago

@gaelforget Can you add a short section to your paper also to compare your software with other particle tracking software? This will help give context.

kthyng commented 3 years ago

@gaelforget Still waiting to hear back from you about reviewer suggestions too.

gaelforget commented 3 years ago

@gaelforget Still waiting to hear back from you about reviewer suggestions too.

Based on the list of volunteers (Preferred Language + Domain Expertise, mostly) and from my own network (incl. https://github.com/JuliaClimate) I may suggest:

Would this work?

ps. Others that came to mind but I felt may be too closely connected to me (conflicting?) include: ali-ramadhan and hdrake who are in my department at MIT; the CLIMA project which involves many close collaborators although not myself.

kthyng commented 3 years ago

Hi @visr and @milankl! Are you interested in reviewing this submission to the Journal for Open Source Software? The review is done openly through github and is checklist-driven. Acknowledging the global pandemic, we're asking for reviews in 5-6 weeks. You can get more information from our docs (though looks like they are offline at the moment). Please feel free to ask questions too.

I encourage you to sign up as a JOSS reviewer if you'd like!

milankl commented 3 years ago

Thanks @kthyng for the invitiation, I'm happy to accept.

kthyng commented 3 years ago

@milankl Excellent! I'll add you now, though we will wait in this pre-review stage until we have two reviewers before beginning the actual review issue.

kthyng commented 3 years ago

@whedon assign @milankl as reviewer

whedon commented 3 years ago

OK, @milankl is now a reviewer

visr commented 3 years ago

I would also be happy to review.

kthyng commented 3 years ago

Thanks @visr! We'll proceed now.

kthyng commented 3 years ago

@whedon add @visr as reviewer

whedon commented 3 years ago

OK, @visr is now a reviewer

kthyng commented 3 years ago

@whedon start review

whedon commented 3 years ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2813.