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

whedon · 2020-09-10T23:44:44Z

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

⚠️ JOSS reduced service mode ⚠️

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Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/7643779111039dbc7776ff49d2a6b1b0/status.svg)](https://joss.theoj.org/papers/7643779111039dbc7776ff49d2a6b1b0)

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:

Make sure you're logged in to your GitHub account
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

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@Nico-Curti) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @justusschock

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@Nico-Curti) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

The text was updated successfully, but these errors were encountered:

whedon · 2020-09-10T23:44:47Z

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 🎉.

⚠️ JOSS reduced service mode ⚠️

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.

⭐ Important ⭐

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:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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 · 2020-09-10T23:45:20Z

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 · 2020-09-10T23:45:28Z

👉 Check article proof 📄 👈

arokem · 2020-09-19T16:01:03Z

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 · 2020-09-19T16:02:39Z

👋 @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 · 2020-09-19T16:02:51Z

@whedon commands

whedon · 2020-09-19T16:02:54Z

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 · 2020-09-19T16:03:18Z

@whedon remove @bblais as reviewer

whedon · 2020-09-19T16:03:23Z

OK, @bblais is no longer a reviewer

DanielLenz · 2020-09-21T08:13:17Z

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

arokem · 2020-09-21T12:52:20Z

@whedon add @DanielLenz as reviewer

whedon · 2020-09-21T12:52:26Z

OK, @DanielLenz is now a reviewer

arokem · 2020-09-21T12:54:42Z

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 · 2020-09-21T13:56:01Z

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

arokem · 2020-09-21T15:24:56Z

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

whedon · 2020-10-19T05:32:57Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

arokem · 2020-10-19T05:44:40Z

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

Make a tagged release of your software, and list the version tag of the archived version here.
Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

Nico-Curti · 2020-10-19T09:57:59Z

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

arokem · 2020-10-19T16:20:13Z

@whedon set 10.5281/zenodo.4106174 as archive

whedon · 2020-10-19T16:20:17Z

OK. 10.5281/zenodo.4106174 is the archive.

arokem · 2020-10-19T16:20:27Z

@whedon set v1.0.3 as version

whedon · 2020-10-19T16:20:31Z

OK. v1.0.3 is the version.

arokem · 2020-10-19T16:21:08Z

@whedon accept

whedon · 2020-10-19T16:21:12Z

Attempting dry run of processing paper acceptance...

whedon · 2020-10-19T16:21:47Z

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 · 2020-10-19T16:22:00Z

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

Check final proof 👉 openjournals/joss-papers#1828

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#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 · 2020-10-20T16:27:06Z

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?

The paper is missing a Statement of Need section, which is a required element (as per our docs); not sure how this didn't come up before, since whedon looks for this at submission, but it might have been because of the original compilation problems.
In the third paragraph, please put a comma after "i.e"
On the second page, this is a bit confusing: "...despite it is a quite efficient implementation the Julia programming language stays on difficult and far from many users." Can you rewrite this bit?
In the same paragraph, I see "... C++ library called Scorer for further details)", which seems to be missing the starting parenthesis.

Nico-Curti · 2020-10-20T17:00:43Z

Hi @kyleniemeyer,
We have just uploaded a reviewed version of the paper following your suggestions.
Please let me know if there are other issues.

kyleniemeyer · 2020-10-20T17:31:38Z

@whedon generate pdf

whedon · 2020-10-20T17:32:47Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

kyleniemeyer · 2020-10-20T17:34:38Z

@Nico-Curti Looks good, thanks!

kyleniemeyer · 2020-10-20T17:34:44Z

@whedon accept

whedon · 2020-10-20T17:34:47Z

Attempting dry run of processing paper acceptance...

whedon · 2020-10-20T17:35:12Z

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 · 2020-10-20T17:35:59Z

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

Check final proof 👉 openjournals/joss-papers#1832

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1832, 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 · 2020-10-20T17:39:24Z

@whedon accept deposit=true

whedon · 2020-10-20T17:39:27Z

Doing it live! Attempting automated processing of paper acceptance...

whedon · 2020-10-20T17:41:17Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2020-10-20T17:41:18Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02663 joss-papers#1833
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02663
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer · 2020-10-20T17:45:07Z

Congrats @Nico-Curti on your article's publication in JOSS!

Many thanks to @justusschock and @DanielLenz for reviewing this, and @arokem for editing it.

whedon · 2020-10-20T17:45:11Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.02663/status.svg)](https://doi.org/10.21105/joss.02663)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02663">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02663/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02663/status.svg
   :target: https://doi.org/10.21105/joss.02663

This is how it will look in your documentation:

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whedon added the review label Sep 10, 2020

whedon assigned arokem Sep 10, 2020

whedon mentioned this issue Sep 10, 2020

[PRE REVIEW]: rFBP: Replicated Focusing Belief Propagation algorithm #2589

Closed

whedon assigned justusschock and bblais Sep 11, 2020

whedon assigned arokem and justusschock and unassigned arokem, bblais and justusschock Sep 19, 2020

whedon assigned arokem, DanielLenz and justusschock and unassigned arokem and justusschock Sep 21, 2020

whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Oct 19, 2020

whedon added accepted published Papers published in JOSS labels Oct 20, 2020

kyleniemeyer closed this as completed Oct 20, 2020

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

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

Comments

whedon commented Sep 10, 2020 • edited Loading

Status

Reviewer instructions & questions

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 Sep 10, 2020

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DanielLenz commented Sep 21, 2020

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