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

whedon · 2020-08-20T20:42:50Z

Submitting author: @Nico-Curti (Nico Curti)
Repository: https://github.com/Nico-Curti/rFBP
Version: v1.0.0
Editor: @arokem
Reviewers: @bblais, @justusschock
Managing EiC: Kevin M. Moerman

⚠️ JOSS reduced service mode ⚠️

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

The author's suggestion for the handling editor is @arokem.

@Nico-Curti 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).

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

whedon · 2020-08-20T20:42:53Z

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

⚠️ 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.

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 · 2020-08-20T20:43:05Z

PDF failed to compile for issue #2589 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/2589/paper/paper.md): did not find expected alphabetic or numeric character while scanning an alias at line 16 column 19 (Psych::SyntaxError) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse_stream'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:325:in parse' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:252:in load'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:473:in block in load_file' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in open'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in load_file' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e09ec0a48e3/lib/whedon.rb:125:in load_yaml'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e09ec0a48e3/lib/whedon.rb:85:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e09ec0a48e3/lib/whedon/processor.rb:36:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e09ec0a48e3/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e09ec0a48e3/bin/whedon:55:in prepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e09ec0a48e3/bin/whedon:119:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

Kevin-Mattheus-Moerman · 2020-08-20T20:54:16Z

@openjournals/dev can you help trouble shoot this error ☝️

arfon · 2020-08-21T10:21:42Z

The metadata header is non-standard (see contributions block added):

---
title: 'rFBP: Replicated Focusing Belief Propagation algorithm'
tags:
  - belief-propagation
  - deep-neural-networks
  - sping-glass
  - statistical-mechanics
  - learning-algorithm
  - machine-learning-algorithms
  - python3
  - cpp17
authors:
 - name: Nico Curti
   orcid: 0000-0001-5802-1195
   affiliation: 1
   contributions: *
 - name: Daniele Dall'Olio
   orcid: 0000-0003-0196-6870
   affiliation: 2
   contributions: *
 - name: Daniel Remondini
   orcid: 0000-0003-3185-7456
   affiliation: 2
 - name: Gastone Castellani
   orcid: 0000-0003-4892-925X
   affiliation: 1
- name: Enrico Giampieri
   orcid: 0000-0003-2269-2338
   affiliation: 1
affiliations:
 - name: Department of Experimental, Diagnostic and Specialty Medicine of Bologna University
   index: 1
 - name: Department of Physics and Astronomy of Bologna University
   index: 2
contributions:
 - name: Both authors contributed equally to this work
   index: *

date: 18 August 2020
bibliography: paper.bib
---

@Nico-Curti - please format your metadata exactly as specified in the example paper. If you want to denote equal authorship you will need to use footnotes.

Nico-Curti · 2020-08-21T13:18:22Z

@arfon Thanks for the help!
I should have fixed the error in the last commit by moving the footnote to the end of the document.
I also tested the new version of the document using whedon and it seems to work now.

I'm sorry for the inconvenience.
Let me know if there are any other issues.

arokem · 2020-08-21T14:11:56Z

@whedon assign me as editor

whedon · 2020-08-21T14:12:00Z

OK, the editor is @arokem

arokem · 2020-08-21T14:12:49Z

@whedon generate pdf

whedon · 2020-08-21T14:13:07Z

PDF failed to compile for issue #2589 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/2589/paper/paper.md): did not find expected key while parsing a block mapping at line 2 column 1 (Psych::SyntaxError) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse_stream'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:325:in parse' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:252:in load'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:473:in block in load_file' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in open'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in load_file' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/lib/whedon.rb:125:in load_yaml'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/lib/whedon.rb:85:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/lib/whedon/processor.rb:36:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/bin/whedon:55:in prepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/bin/whedon:119:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

arfon · 2020-08-21T15:51:35Z

@Nico-Curti - this PR should fix your paper Nico-Curti/rFBP#1

arokem · 2020-08-22T02:00:39Z

@whedon generate pdf

whedon · 2020-08-22T02:01:52Z

👉 Check article proof 📄 👈

arokem · 2020-08-24T15:12:44Z

Hi @Nico-Curti and co-authors: thank you for this submission. I have now read the article and looked through the software. The next steps are for me to offer some comments on this initial submission and for us to find appropriate reviewers.

First, my comments on the article:

The readership of JOSS is expected to be very broad, so you will need to provide a bit more context for the software. For example, the first sentence of the article really drops the reader off the deep end, where more general context would have been helpful.
Since an important element in a JOSS paper is the potential research applications of the software, it would be good to flesh out the examples that you provided as bullet points. How was the software used in these applications? What kinds of research questions were answered? In general, as I understand it, since this is a re-implementation of an existing algorithm, what is the need that is addressed through this implementation of the algorithm?

Second: do you have particular suggestions for people who would be appropriate reviewers for your paper? If you include their GitHub handles here, please do not use the "@" sign before their name, so that I can take a look before tagging them into this issue.

arokem · 2020-08-30T22:48:30Z

👋 @justusschock : would you be willing to review this article for JOSS? This submissions seems like a good match for your expertise.

arokem · 2020-08-30T22:49:15Z

👋 @georgiastuart : would you be willing to review this article for JOSS? It seems like a good match for your expertise.

justusschock · 2020-08-31T07:54:35Z

@arokem Sure!

arokem · 2020-08-31T13:43:32Z

@whedon assign @justusschock as reviewer

whedon · 2020-08-31T13:43:38Z

OK, @justusschock is now a reviewer

arokem · 2020-08-31T13:43:59Z

Thanks! Let's wait until I find one more person, before starting the review.

Nico-Curti · 2020-09-01T08:51:40Z

@arokem Thanks for your comments. We will provide an updated version of the paper with your suggestions in few days.
As for the second reviewer we would like to suggest professor Brian Blais since he is an expert in the field and a very competent Python programmer.

arokem · 2020-09-01T13:31:20Z

Hi @bblais -- would you be willing to review this software contribution to The Journal of Open Source Software? The reviews are conducted openly, through a GitHub issue. More instructions are available here

arokem · 2020-09-10T22:13:09Z

👋 @DanielLenz : would you be willing to review this article for JOSS?

arokem · 2020-09-10T22:13:25Z

👋 @zbeekman : would you be willing to review this article for JOSS?

bblais · 2020-09-10T22:22:38Z

Hi @bblais -- would you be willing to review this software contribution to The Journal of Open Source Software? The reviews are conducted openly, through a GitHub issue. More instructions are available here

Sure, I can review (didn't notice this invite the first time). I see the editorial guide, but is there a guide for the process of submitting a review? is it by individual issues or all at once? is there a deadline or expected timeframe for review? thanks!

arokem · 2020-09-10T23:43:58Z

@whedon assign @bblais as reviewer

whedon · 2020-09-10T23:44:03Z

OK, @bblais is now a reviewer

arokem · 2020-09-10T23:44:27Z

@whedon add @justusschock as reviewer

whedon · 2020-09-10T23:44:32Z

OK, @justusschock is now a reviewer

arokem · 2020-09-10T23:44:41Z

@whedon start review

whedon · 2020-09-10T23:44:45Z

OK, I've started the review over in #2663.

arokem · 2020-09-10T23:46:17Z

@bblais , @justusschock : please head over to #2663. There you will have a checklist with items to check off. As you go along, feel free to comment and make suggestions in that review issue, or to post issues on the software repository (might want to mention that the issue stems from the JOSS review). And please do let me know if you have any further questions.

arokem · 2020-09-10T23:47:01Z

@DanielLenz, @zbeekman : sorry for the false alarm. Looks like we will not your service as reviewers this time around

whedon added the pre-review label Aug 20, 2020

whedon assigned arokem Aug 21, 2020

whedon assigned arokem and justusschock and unassigned arokem Aug 31, 2020

arokem mentioned this issue Sep 3, 2020

[PRE REVIEW]: DeepReg: a deep learning toolkit for medical image registration #2633

Closed

whedon assigned arokem and bblais and unassigned arokem and justusschock Sep 10, 2020

whedon assigned arokem, bblais and justusschock and unassigned arokem and bblais Sep 10, 2020

whedon closed this as completed Sep 10, 2020

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

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

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

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

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