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[REVIEW]: rFBP: Replicated Focusing Belief Propagation algorithm #2663

Closed whedon closed 4 years ago

whedon commented 4 years ago

Submitting author: @Nico-Curti (Nico Curti) Repository: https://github.com/Nico-Curti/rFBP Version: v1.0.3 Editor: @arokem Reviewers: @justusschock, @DanielLenz Archive: 10.5281/zenodo.4106174

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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

@DanielLenz & @justusschock, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @arokem know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @DanielLenz

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @justusschock

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @bblais, @justusschock it looks like you're currently assigned to review this paper :tada:.

: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.

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If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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whedon commented 4 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1073/pnas.1608103113 is OK
- 10.1073/pnas.0700324104 is OK
- 10.1103/physrevlett.96.030201 is OK
- 10.1103/physreve.93.052313 is OK
- 10.1016/S0893-6080(05)80010-3 is OK
- 10.1103/physreve.90.052813 is OK
- 10.1088/1742-5468/2016/02/023301 is OK
- 10.1142/S0217984995001868 is OK
- 10.1103/physrevlett.75.2432 is OK
- 10.1088/1742-5468/2015/08/p08008 is OK

MISSING DOIs

- 10.1051/jphys:0198900500200305700 may be a valid DOI for title: Storage capacity of memory networks with binary couplings

INVALID DOIs

- None
whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

arokem commented 4 years ago

After a private exchange with @bblais we've ascertained that he has an apparent conflict-of-interest, due to a recent joint publication with one of the authors of this paper. That means that we will have to find another reviewer to replace him here. For now, I will edit the checklist at the top to indicate that @bblais is no longer a reviewer and unassign him. Thanks @bblais! I hope we find another opportunity to call on you to review for JOSS.

arokem commented 4 years ago

👋 @DanielLenz, @zbeekman : one of the reviewers for this paper is unable to do the review. Would either of you be willing to step in as a reviewer for this article? I think that you would either be a very good match given your expertise.

arokem commented 4 years ago

@whedon commands

whedon commented 4 years ago

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# 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

# Re-invite a reviewer (if they can't update checklists)
@whedon re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

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

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom 
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# Compile the paper
@whedon generate pdf

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

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to do a dry run of accepting the paper and depositing with Crossref
@whedon accept

# 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

EiC TASKS

# Invite an editor to edit a submission (sending them an email)
@whedon invite @editor as editor

# Reject a paper
@whedon reject

# Withdraw a paper
@whedon withdraw

# Ask Whedon to actually accept the paper and deposit with Crossref
@whedon accept deposit=true
arokem commented 4 years ago

@whedon remove @bblais as reviewer

whedon commented 4 years ago

OK, @bblais is no longer a reviewer

DanielLenz commented 4 years ago

@arokem Sure, I'd be happy to review this submission.

arokem commented 4 years ago

@whedon add @DanielLenz as reviewer

whedon commented 4 years ago

OK, @DanielLenz is now a reviewer

arokem commented 4 years ago

Thank you for stepping up! I have edited the comment at the top of this issue so that you now have a checklist that you can use to check off review criteria. Please let me know if you have any questions.

DanielLenz commented 4 years ago

Will do! This week is a bit busy - I'll do my best, but it might take me a couple of days.

arokem commented 4 years ago

No problem. We generally hope to complete all items in the review within approximately six weeks.

justusschock commented 4 years ago

@arokem I finished my review. Overall I really like the submission. Regarding the checklist above:

If the above mentioned points are finished, I don't see any blockers from my side.

arokem commented 4 years ago

@justusschock : thanks for these comments.

@Nico-Curti : you can start addressing these issues in the meanwhile.

@DanielLenz : have you had a chance to take a look?

Nico-Curti commented 4 years ago

Hi @justusschock, thanks for your comments. We are working on your issues and we will provide an updated version of the project documentation as soon as possible.

DanielLenz commented 4 years ago

@arokem Will finish my review this weekend!

arokem commented 4 years ago

Super. Thanks for the update!

DanielLenz commented 4 years ago

Hey @arokem , I've finished my review and agree with @justusschock in that I really like the submission and think the software is well-written and follows many best practices, big thanks to @Nico-Curti .

There are a couple of points that we raised on the projects github issue tracker which should be taken care of first. All of these are fairly minor and shouldn't take long.

One point that I ran into, but didn't raise an issue about is the loading of the C++ library on Mac OS with clang to run the tests. You mention this in your travis config and I can confirm the issue, but I'm unsure how to address it.

Regarding the paper itself, there are a couple of minor points that I'll list here. All of these refer to the latest draft compiled by wheadon

Thanks for working on this project over the years and for submitting to JOSS, I'm really looking forward to seeing it published!

Could you ping us here once these minor issues are addressed? Thank you!

arokem commented 4 years ago

Thanks @DanielLenz for these comments.

@Nico-Curti : please let us know when you've had a chance to address everything.

Nico-Curti commented 4 years ago

Hi @DanielLenz We worked on your issues, trying to address all of your points.

One point that I ran into, but didn't raise an issue about is the loading of the C++ library on Mac OS with clang to run the tests. You mention this in your travis config and I can confirm the issue, but I'm unsure how to address it.

We don't have a MacOS machine available in any sort and we aren't experts on this system. We have tried to solve the issue using the travis CI but unfortunately we haven't found any patch. If someone else have any suggestion please let us know.

The hyperlinks in the pdf didn't work for me. Is this normal or am I the only one experiencing this?

The hyperlinks don't work on the online version of the paper as displayed by github. They seems to work fine if you download the pdf.

Remove the line that contains the bibliography file name

We have removed the duplicated lines from the paper as you have pointed out. Let us know if the issue persists.

Affiliations: Please use one line per affiliation

We follow the guidelines on the JOSS website but the affiliations are still displayed on the same line. Maybe @arokem could suggest us how we can fix it.

Can we move the "Joint first author" footnote closer to the author list, perhaps right next to the affiliations?

We noticed that other already published papers in JOSS has the footnote at the end of the page. Also in this case we can fix this issue but we need some help by @arokem

About the typos that you have highlighted we have followed all your comments and fix the paper document.

Nico-Curti commented 4 years ago

Hi @arokem , With the latest commits we think we have answered all the issues raised by the reviewers. We will wait for some feedback.

DanielLenz commented 4 years ago

Thanks for addressing all the issues @Nico-Curti ! I'll give another detailed look this weekend, but we should be good to go :)

DanielLenz commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

zbeekman commented 4 years ago

Sorry to have missed the boat on this one, looks interesting! Thanks for inviting me and I'll keep my eye out for the final publication!

DanielLenz commented 4 years ago

Hi @arokem , @Nico-Curti ,

I've taken another detailed look at the paper and the repo, and I'm happy to say that I recommend the publication at this point.

There are some minor formatting issues that we discussed, perhaps @arokem can shed some light on this.

Thanks again for your submission and for including the feedback so quickly!

arokem commented 4 years ago

Thanks @DanielLenz! I will look into the formatting issues.

@justusschock : when you get a chance, could you please take a look and see whether the outstanding issues you had are addressed in the revision? In particular, I see that you have two check-boxes un-checked at this point. Are both of these points (license and documentation of functionality) addressed?

justusschock commented 4 years ago

@arokem, yes they have all been addressed. I would also recommend the publication at this point.

arokem commented 4 years ago

Hi @Nico-Curti : just a couple small comments on my end:

Let me know when you have these done and I will pass this on to the editors-in-chief for their final review.

Nico-Curti commented 4 years ago

Hi @arokem, I have solved both the issues. Let me know if everything is ok now.

arokem commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

arokem commented 4 years ago

Thank you. Could you please make sure that the Krauth and Mézard reference has the same format as the other references? It currently has the word "In" before the name of the journal (not needed) and the word "Vol" explicitly mentioned. It should look like this:

Krauth, W., & Mézard, M. (1989). Storage capacity of memory networks with binary couplings. Journal de Physique, 50, 3057–3066. doi:10.1051/jphys: 0198900500200305700

Nico-Curti commented 4 years ago

Hi @arokem, now it should work properly. Sorry for the inconvenience.

arokem commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

arokem commented 4 years ago

Thanks! Looks good. At this point, could you please:

I can then move forward with accepting the submission.

Nico-Curti commented 4 years ago

Hi @arokem. We have just uploaded the latest version of the package as v1.0.3. The corresponding Zenodo doi is DOI. Let me know if everything is ok now.

arokem commented 4 years ago

@whedon set 10.5281/zenodo.4106174 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.4106174 is the archive.

arokem commented 4 years ago

@whedon set v1.0.3 as version

whedon commented 4 years ago

OK. v1.0.3 is the version.

arokem commented 4 years ago

@whedon accept

whedon commented 4 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 4 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1073/pnas.1608103113 is OK
- 10.1073/pnas.0700324104 is OK
- 10.1103/physrevlett.96.030201 is OK
- 10.1103/physreve.93.052313 is OK
- 10.1016/S0893-6080(05)80010-3 is OK
- 10.1051/jphys:0198900500200305700 is OK
- 10.1103/physreve.90.052813 is OK
- 10.1088/1742-5468/2016/02/023301 is OK
- 10.1142/S0217984995001868 is OK
- 10.1103/physrevlett.75.2432 is OK
- 10.1088/1742-5468/2015/08/p08008 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 4 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1828

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1828, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
kyleniemeyer commented 4 years ago

Hi @Nico-Curti, I'm the EIC on duty this week, and doing some final checks before publishing your article. Can you fix a few small things?