Closed whedon closed 3 years ago
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @funsim, @ysimillides it looks like you're currently assigned to review this paper :tada:.
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@whedon generate pdf
PDF failed to compile for issue #2018 with the following error:
Can't find any papers to compile :-(
@whedon generate pdf from branch joss-paper
Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...
Thanks so much @funsim and @ysimillides for agreeing to review our submission!
Please let me know if you guys need access to GPUs and we can figure something out.
Reference check summary:
OK DOIs
- 10.1029/96JC02775 is OK
- 10/f9wkpj is OK
- 10.1109/TPDS.2018.2872064 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5670/oceanog.2016.66 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Overall this software package is very well set up and I recommend the submission to be accepted by JOSS after addressing the following comments:
Software paper I cannot find the software paper - could you please send me a link?
Performance
Functionality documentation
Functionality:
I would like to thank @jakobes for helping me in this review.
@funsim You can find the paper above by clicking "check article proof"
Please note, for both @funsim and @ali-ramadhan: if there will be more discussion on the points noted above, it's preferable to have that discussion in individual issues that are opened and linked to this review issue. That way this issue remains more of an overview and details can be hashed out elsewhere. Thanks!
Found the paper, thanks. Apart from the comments above, I have no further comments.
Thank you @funsim for the quick review! You bring up good points that will improve the package. Certainly the documentation needs more work as you've pointed out, and we've been meaning to add a verification experiment with some convergence results so thank you for bringing it up.
I have opened an issue for each of your comments where we will work towards addressing them:
Hi @ysimillides! When do you think you'll be able to work on your review?
@whedon re-invite @ysimillides as reviewer
Sorry, I couldn't re-invite @ysimillides.
π @arfon - can you explain this?
@danielskatz - I think this is because they have already been invited (I can see a pending invite on the repository). I don't think GitHub gives us any kind of semantic response when issuing these invites.
OK, errors should be more semantic now as of https://github.com/openjournals/whedon-api/pull/94
Apologies for the delay, will try and get it done by the end of this week!
Dear authors and reviewers
We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.
Thanks in advance for your understanding.
Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team.
@ysimillides Everyone's situation is totally different, so not sure if you have any time for work right now, but if you do, we'd appreciate hearing from you on this review at some point. Thank you.
Hi everyone! We are officially starting JOSS back up today. We know that everyone has different circumstances with work and home life right now, so we want to figure out a way forward that will work for everyone.
@ysimillides β are you still able to review this submission? If so, what timeline would work for you?
Hello, I can't access the checklist above, but by going through the items my main concern is that there is no comparison / mention of other similar software which can be found ( state of the field on the checklist). If a few lines in the paper could be added to reflect this, that would be ideal ( and likewise if their are no similar packages, this should be explicitly stated).
Otherwise everything seems fine and the package follows best practices for Julia packages ( integrated with the package manager, automated tests +documentation )
@whedon re-invite @ysimillides as reviewer
The reviewer already has a pending invite.
@ysimillides please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations
@ysimillides - it sounds like you might need to accept the invite above to the repository - this will allow you to update the checklist above.
Hi @ysimillides! Were you able to accept the invitation above to gain permissions for your checklist? Have you been able to install the software and try it out?
Hi @ysimillides β will you be able to work on this review? Everything is in disarray right now so it's totally understandable if you won't be able to finish it, but in that case please do let me know so we can get a new reviewer.
Note for reference: just reached out to @ysimillides by email to confirm.
@ali-ramadhan I'm sorry about the delay on reviewing your submission. I am going to remove the delinquent reviewer and find another to replace so we can finally move forward.
@whedon remove @ysimillides as reviewer
OK, @ysimillides is no longer a reviewer
@mancellin β would you be interested in reviewing this submission to JOSS? We already have one review completed but the other reviewer went MIA. You look like a good reviewer knowing Julia and related CFD.
Sure, I can do that. It looks like an interesting work.
@mancellin awesome! Thank you!!
@whedon add @mancellin as reviewer
OK, @mancellin is now a reviewer
@mancellin You should be good to go, but let me know if you have any permissions problems or questions. Thank you!
@kthyng No worries about the delay, thank you for keeping this review moving forward!
I've fallen off the grid in the past few months myself but I believe we've addressed most of the points from @funsim's review so I'll reply more formally to the review soon.
@mancellin Thanks so much for agreeing to review our submission! Please let me know if you hit any issues or have any questions.
@mancellin just a friendly reminder about this review. When might you be able to work on this? Thanks again.
@kthyng Thank you for the reminder. I've started working on the review. I plan to complete it after some more tests in one or two weeks.
Overall, this is a very nice package. The documentation is extensive, the package is easy to install and works as expected.
I have some issues running simulations on GPU, but I believe it to be due to my own setup and not to the package itself. I'll give it another try in the next days and open an issue if I need help.
One minor issue (already mentioned by @ysimillides): the review check-list requires the authors to compare their code to other commonly-used packages. Could you add a few lines in the paper about the state of the art, citing other simulation codes targetting the same problem (if they exist)?
Besides, have the minor issues raised by @funsim in January been addressed?
Thank you for the review and the kind words @mancellin!
I have some issues running simulations on GPU, but I believe it to be due to my own setup and not to the package itself. I'll give it another try in the next days and open an issue if I need help.
Apologies about this. We discovered a major bug concerning running GPU simulations that we fixed in Oceananigans v0.32.0 last week, so maybe try a more recent version if you were trying an older one. Otherwise we'd love to hear more about the issue so we can fix it.
One minor issue (already mentioned by @ysimillides): the review check-list requires the authors to compare their code to other commonly-used packages. Could you add a few lines in the paper about the state of the art, citing other simulation codes targetting the same problem (if they exist)?
Thank you for bringing this up. I will update the software paper with a discussion of other similar packages.
Besides, have the minor issues raised by @funsim in January been addressed?
Yes I believe so (the issues have been closed) but I think I still need to post a formal reply. Sorry about this delay on my part. I will do it today.
@whedon generate pdf from branch joss-paper
Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...
PDF failed to compile for issue #2018 with the following error:
Error reading bibliography ./paper.bib (line 64, column 3): unexpected "y" expecting space, ",", white space or "}" Error running filter pandoc-citeproc: Filter returned error status 1 Looks like we failed to compile the PDF
@whedon generate pdf from branch joss-paper
Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...
@whedon generate pdf from branch joss-paper
Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...
Submitting author: @ali-ramadhan (Ali Ramadhan) Repository: https://github.com/CliMA/Oceananigans.jl Version: v0.36.0 Editor: @kthyng Reviewers: @funsim, @mancellin Archive: 10.5281/zenodo.4019272
Status
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Reviewers and authors:
Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)
Reviewer instructions & questions
@funsim & @mancellin, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @kthyng know.
β¨ Please try and complete your review in the next two weeks β¨
Review checklist for @funsim
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
Review checklist for @mancellin
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper