Joss-reviews: [PRE REVIEW]: Miet: an R package for region of interest analysis from magnetic reasonance images

[whedon]

Submitting author: @benoit-combes (Benoit Combès)
Repository: https://gitlab.inria.fr/miet/miet
Version: 0.1.0
Editor: @arokem
Reviewers: @janfreyberg, @neuroimaginador

Author instructions

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

@benoit-combes if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

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]

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

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

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1842 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/1842 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:incollect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-74bc29a6a731/lib/whedon/processor.rb:61:infind_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-74bc29a6a731/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun'
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:indispatch'
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-74bc29a6a731/bin/whedon:116:in 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

'

[danielskatz]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1842 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/1842 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:incollect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-74bc29a6a731/lib/whedon/processor.rb:61:infind_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-74bc29a6a731/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun'
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:indispatch'
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-74bc29a6a731/bin/whedon:116:in 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

'

[danielskatz]

👋 @arfon - I'm a bit confused about what the error is here - is this related to the figure? Perhaps you can help? (and maybe open a whedon issue related to better error message?)

[arfon]

@danielskatz - I think this is because the URL at the top can't be cloned by Git. It needs changing to https://gitlab.inria.fr/miet/miet

[danielskatz]

👋 @benoit-combes - Please change the paper.md as @arfon suggests, then enter a new comment here with @whedon generate pdf to try recompiling

[arfon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[arfon]

@danielskatz - just to clarify, the URL for the repo needed editing at the top of the issue (I've done this).

[whedon]

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

[danielskatz]

ah, sorry, I thought you meant in the paper.md - How did this wrong URL get in? User error in the submission form?

[arfon]

ah, sorry, I thought you meant in the paper.md - How did this wrong URL get in? User error in the submission form?

Yeah, it was an error in the submission form. I've opened an issue to track this (https://github.com/openjournals/whedon/issues/60)

[benoit-combes]

May I suggest @neuroimaginador that appears to gather expertise in R, data analysis and neuroimaging (that are relevant for the paper) for reviewing ?

[benoit-combes]

@whedon commands

[whedon]

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

[benoit-combes]

@whedon list editors

[whedon]

Current editors:

@Kevin-Mattheus-Moerman
@VivianePons
@alexhanna
@arfon
@arokem
@brainstorm
@cMadan
@csoneson
@danielskatz
@dfm
@drvinceknight
@gkthiruvathukal
@jedbrown
@karthik
@katyhuff
@kbarnhart
@kthyng
@kyleniemeyer
@labarba
@leouieda
@lheagy
@lpantano
@majensen
@mbobra
@meg-simula
@melissawm
@mgymrek
@mjsottile
@oliviaguest
@poulson
@terrytangyuan
@trallard
@usethedata
@will-rowe
@xuanxu

[benoit-combes]

May I suggest @arokem as editor ?
In addition to @neuroimaginador that appears to gather expertise in R, data analysis and neuroimaging (that are relevant for the paper) for reviewer ?

[arokem]

Yes. I can edit this.

[arokem]

@whedon assign arokem as editor

[whedon]

OK, the editor is arokem

[arokem]

👋 @neuroimaginador : would you be willing to review this paper for JOSS?

[arfon]

@arokem @brechmos (who's here at STScI) might be a good additional reviewer.

[arokem]

@brechmos : would you be willing to review this paper for JOSS?

On Thu, Oct 31, 2019 at 7:47 AM Arfon Smith [e-mail]
wrote:

@arokem https://github.com/arokem @brechmos
https://github.com/brechmos (who's here at STScI) might be a good
additional reviewer.

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[arokem]

👋 @janfreyberg : would you be willing to review this paper for JOSS? You are one of the only people among our reviewer pool who are neuro-savvy and also R-literate, so it would be a great help.

[janfreyberg]

@arokem yes, of course!

[arokem]

Wonderful. Thank you! I will assign you first, and then stand by until I find another reviewer and kick off the review for this.

[arokem]

@whedon assign @janfreyberg as reviewer

[whedon]

OK, the reviewer is @janfreyberg

[neuroimaginador]

Hello, I'd like to review this work!!

El jue., 31 oct. 2019 15:17, Ariel Rokem [e-mail]
escribió:

👋 @neuroimaginador https://github.com/neuroimaginador : would you be
willing to review this paper for JOSS?

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[arokem]

Thanks @neuroimaginador ! You are on!

[arokem]

@whedon add @neuroimaginador as reviewer

[whedon]

OK, @neuroimaginador is now a reviewer

[arokem]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1862. Feel free to close this issue now!

[arokem]

Alright, @janfreyberg and @neuroimaginador, please head over to #1862 for your reviewer check-lists. Feel free to tag me into issues, if you have any questions, as you work through this. I'll close this now. Thanks again!