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Reviews for the Journal of Open Source Software
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[PRE REVIEW]: AIBECS.jl: The ideal tool for exploring global marine biogeochemical cycles. #3758

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @briochemc (Benoit Pasquier) Repository: https://github.com/JuliaOcean/AIBECS.jl Version: v0.10.10 Editor: @kthyng Reviewers: @dankelley Managing EiC: Kristen Thyng

: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.

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/df0ebed76e349224389195ebd8b7c4a4"><img src="https://joss.theoj.org/papers/df0ebed76e349224389195ebd8b7c4a4/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/df0ebed76e349224389195ebd8b7c4a4/status.svg)](https://joss.theoj.org/papers/df0ebed76e349224389195ebd8b7c4a4)

Author instructions

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

@briochemc 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 1.88  T=0.08 s (769.8 files/s, 77469.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           45           1080            856           3503
Markdown                         7            105              0            291
YAML                             9             12              0            288
TeX                              1             35              0            254
TOML                             2              5              0             77
JSON                             1              0              0             35
-------------------------------------------------------------------------------
SUM:                            65           1237            856           4448
-------------------------------------------------------------------------------

Statistical information for the repository '0f031c0a10763faabdbf5e8d' was
gathered on 2021/09/23.
No commited files with the specified extensions were found.
whedon commented 3 years ago

PDF failed to compile for issue #3758 with the following error: 

 Can't find any papers to compile :-(
kthyng 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:

kthyng commented 3 years ago

@whedon assign me as editor

whedon commented 3 years ago

OK, the editor is @kthyng

kthyng commented 3 years ago

Hi @briochemc! Please check out the reviewer list and think through your own network of people you know (who aren't conflicted) to let me know some suggestions for reviewers. List their github handles here without the "@" prefix so they aren't preemptively pinged.

briochemc commented 3 years ago

Hi @kthyng! Here are some suggestions for reviewers :

briochemc commented 3 years ago

@whedon commands

whedon commented 3 years ago

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository
kthyng commented 3 years ago

Hi @briochemc! Sorry I missed your message but see it now.

kthyng commented 3 years ago

Hi @gregbritten! Are you interested in reviewing this submission for the Journal of Open Source Software? The reviews are done openly in github via issues in the software and a summary in a review issue. You can read more about the process here. We are asking for reviews to be finished in 4-6 weeks, but suggest you start sooner than that since the review process tends to be iterative between the reviewer and author. Thanks for your consideration.

kthyng commented 3 years ago

@dankelley I see that Julia is a secondary language for you. Are you interested in reviewing this submission that is in Julia for JOSS?

dankelley commented 3 years ago

@kthyng yes, I can look at it. (I didn't see a whedon instruction to say that, so sorry for making an extra step for you.) Dan.

kthyng commented 3 years ago

@dankelley this isn't an extra step! Do you mean you can review it?

dankelley commented 3 years ago

Yes, I can review it. (I've already started and will likely finish this afternoon. It's a holiday here, and I have a break from term but only for a day.)

kthyng commented 3 years ago

Wow ok! Do you want me to get the review started so you can fill that out? I can add in the second reviewer info by hand in that case.

dankelley commented 3 years ago

Yes, I'd like you to start the review, thanks.

kthyng commented 3 years ago

Ok I think I can make this happen.

kthyng commented 3 years ago

@whedon start review

whedon commented 3 years ago

It looks like you don't have an editor and reviewer assigned yet so I can't start the review. Try one or more of these commands:

# Change editorial assignment
@whedon assign @username as editor

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer
kthyng commented 3 years ago

@whedon assign @dankelley as reviewer

whedon commented 3 years ago

OK, @dankelley 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/3814.

kthyng commented 3 years ago

Just to be clear, I am still looking for a second reviewer and @gregbritten if you are interested or not please let me know! I have started the review so @dankelley can get to working on their review.

kthyng commented 3 years ago

Oops I think I got sidetracked by starting the review. I will continue to search for another reviewer now.

kthyng commented 3 years ago

Hi @zhenwu0728! Are you interested in reviewing this submission for the Journal of Open Source Software? The reviews are done openly in github via issues in the software and a summary in a review issue. You can read more about the process here. We are asking for reviews to be finished in 4-6 weeks, but suggest you start sooner than that since the review process tends to be iterative between the reviewer and author. Thanks for your consideration.

zhenwu0728 commented 3 years ago

Hi @kthyng! I would love to, but Benoit Pasquier and I held a workshop together a few months ago. If that's not a conflict of interest, I can do the review.

kthyng commented 3 years ago

Hmm, thanks @zhenwu0728 but I forgot a number of the suggestions are from MIT as is the author. I will try to avoid the same institution if possible, Thanks.

kthyng commented 3 years ago

@patrickcgray would you be able to review this JOSS submission? The reviews are done openly in github via issues in the software and a summary in a review issue. You can read more about the process here. We are asking for reviews to be finished in 4-6 weeks, but suggest you start sooner than that since the review process tends to be iterative between the reviewer and author. Thanks for your consideration.

briochemc commented 3 years ago

Hmm, thanks @zhenwu0728 but I forgot a number of the suggestions are from MIT as is the author. I will try to avoid the same institution if possible, Thanks.

Hi @kthyng! Just wanted to point out that I am not from or at MIT! (The reviewers I suggested from MIT are experts in at least one of Julia, modelling, biogeochemistry, or oceanography.) I didn't know the workshop we presented (with Zhen Wu but also with Gael Forget) was a conflict of interest — we each presented our own software packages — sorry about that!

kthyng commented 3 years ago

@briochemc oops, duh. Sorry I must have gotten my wires crossed on this. Ok let's see if we hear back from my recent ping and if not, it sounds like you don't consider the workshop to personally cause a conflict in your ability to be unbiased? (obviously the reviewer is the critical one here but if you feel that way it might be universally true!) I had thought you were at the same institution here which I figured superseded the workshop issue but now I realize that isn't the case.

patrickcgray commented 3 years ago

@patrickcgray would you be able to review this JOSS submission? The reviews are done openly in github via issues in the software and a summary in a review issue. You can read more about the process here. We are asking for reviews to be finished in 4-6 weeks, but suggest you start sooner than that since the review process tends to be iterative between the reviewer and author. Thanks for your consideration.

Hi @kthyng this package looks amazing! and I'd love to dig into it, but I'm not familiar enough with Julia and don't have the time over the coming month to do it justice. I look forward to seeing it in JOSS though!

kthyng commented 3 years ago

Thanks for your response @patrickcgray!

@zhenwu0728 I wanted to come back to you. Regarding the workshop you ran with @briochemc — do you feel like you could be an unbiased reviewer of the software package? If so, I think we could proceed given that we are airing the conflict of interest in the open.

zhenwu0728 commented 3 years ago

Hi @kthyng I think I can be an unbiased reviewer for this package. I can do the review later this week and the following week.

kthyng commented 3 years ago

@zhenwu0728 Excellent! I need to do a bit of manual reworking now since I previously started the review so @dankelley could do his right away. I'll ping you from the review issue itself when it's all set up.