Joss-reviews: [PRE REVIEW]: idpflex: Analysis of Intrinsically Disordered Proteins by Comparing Simulations to Small Angle Scattering Experiments

Created on 15 Aug 2018  Â·  39Comments  Â·  Source: openjournals/joss-reviews

Submitting author: @jmborr (Jose M. Borreguero)
Repository: https://github.com/jmborr/idpflex.git
Version: v0.1.5
Editor: @brainstorm
Reviewers: @gjeuken

Author instructions

Thanks for submitting your paper to JOSS @jmborr. The JOSS editor (shown at the top of this issue) will work with you on this issue to find a reviewer for your submission before creating the main review issue.

@jmborr 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
Jupyter Notebook Makefile Python pre-review
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picture whedon

All 39 comments

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
whedon picture whedon on 15 Aug 2018 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 15 Aug 2018

PDF failed to compile for issue #895 with the following error:

/app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in parse': (tmp/895/paper/paper.md): could not find expected ':' while scanning a simple key at line 12 column 7 (Psych::SyntaxError) from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:inparse_stream'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:327:in parse' from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:254:inload'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:475:in block in load_file' from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:474:inopen'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:474:in load_file' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon.rb:68:ininitialize'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/processor.rb:32:inset_paper'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:37:in prepare' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:99:in from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in load' from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in

'

whedon picture whedon on 15 Aug 2018

@jmborr - it looks like the orcid fields in your paper.md file aren't formed correctly. Instead of 

ORCID 0000-0002-0866-8158

they should be 

orcid: 0000-0002-0866-8158

In addition, your paper doesn't look to be complete?

arfon picture arfon on 15 Aug 2018

@arfon First, let me thank you for taking the time to review the submission. Second, let me apologize for a silly mistake. I prepared the submission to JOSS in a dedicated branch and I became engrossed to the point that I forgot to merge it into master :blush:
I've just merged the branch, I believe the paper is now complete.

jmborr picture jmborr on 16 Aug 2018

@whedon generate pdf

arfon picture arfon on 16 Aug 2018 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 16 Aug 2018

PDF failed to compile for issue #895 with the following error:

/app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in parse': (tmp/895/paper/paper.md): could not find expected ':' while scanning a simple key at line 12 column 7 (Psych::SyntaxError) from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:inparse_stream'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:327:in parse' from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:254:inload'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:475:in block in load_file' from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:474:inopen'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:474:in load_file' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon.rb:68:ininitialize'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/processor.rb:32:inset_paper'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:37:in prepare' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:99:in from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in load' from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in

'

whedon picture whedon on 16 Aug 2018

Hi @jmborr, please note the orcid fields need colons separating the key/value pairs.

i.e. change this orcid 0000-0002-0866-8158 to this orcid: 0000-0002-0866-8158 for each author.

arfon picture arfon on 16 Aug 2018

@arfon I just corrected them, thank you.

jmborr picture jmborr on 16 Aug 2018

@whedon generate pdf

arfon picture arfon on 16 Aug 2018 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 16 Aug 2018

--> Check article proof :page_facing_up: <--

whedon picture whedon on 16 Aug 2018

@whedon generate pdf

jmborr picture jmborr on 16 Aug 2018 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 16 Aug 2018

--> Check article proof :page_facing_up: <--

whedon picture whedon on 16 Aug 2018

@arfon I have proof-read the paper and I have two issues I don't know how to resolve.

  1. Affiliations (there are two) show up together in the same line. Is this the intended behavior?
  2. Hyperlinks in the PDF are not functional but I assume this is the intended behavior.
jmborr picture jmborr on 16 Aug 2018

Affiliations (there are two) show up together in the same line. Is this the intended behavior?

Yes, this is expected.

Hyperlinks in the PDF are not functional but I assume this is the intended behavior.

Are they not functional when rendering on GitHub, or not functional when downloading the PDF? If the former, this is simply GitHub's security policy.

arfon picture arfon on 20 Aug 2018

@arfon I was viewing the PDF in Github. I downloaded it and the links work and the links are fine 😄

jmborr picture jmborr on 20 Aug 2018
👍1

@arfon Everything seems in order. Do I have to take any other step or simply wait until I'm assigned a reviewer?

jmborr picture jmborr on 24 Aug 2018

@arfon Everything seems in order. Do I have to take any other step or simply wait until I'm assigned a reviewer?

Yes, sorry for the delay. We're a little backed up with submissions currently and are still waiting for an editor to pick up this submission. In the meantime, if you have any suggestions for potential reviewers from this list feel free to mention them here.

arfon picture arfon on 24 Aug 2018

I would think of reviewers with python as their primary language, a background in soft-matter and/or computational biology, and a hint of physics expertise. Some suggestions:

  • tacaswell
  • krother
  • khinsen
  • andim
  • afrubin
  • a-slide
  • conradstack
  • semacu
jmborr picture jmborr on 24 Aug 2018

:wave: @mgymrek - would you be willing to edit this submission for JOSS?

arfon picture arfon on 29 Aug 2018

:wave: @pjotrp @george-githinji @brainstorm - would one of you be willing to edit this submission for JOSS?

arfon picture arfon on 17 Sep 2018

Yep @arfon , I can take this one ;)

brainstorm picture brainstorm on 18 Sep 2018
🎉1

@whedon assign @brainstorm as editor

arfon picture arfon on 18 Sep 2018

OK, the editor is @brainstorm

whedon picture whedon on 18 Sep 2018

@luminita, would you like to review this JOSS paper for me? :)

brainstorm picture brainstorm on 21 Sep 2018

@arfon It's proving tricky to get reviewers for this one, unfortunately.

brainstorm picture brainstorm on 8 Oct 2018

@percolator (or one of your students), would you mind helping out reviewing this proteomics/MD software?

brainstorm picture brainstorm on 8 Oct 2018

What would such a review comprise? Would we run the software, make a
code.review or should we review a paper?

On Mon, Oct 8, 2018 at 2:31 AM Roman Valls Guimera notifications@github.com
wrote:

@percolator https://github.com/percolator (or one of your students),
would you mind helping out reviewing this proteomics/MD software?

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/openjournals/joss-reviews/issues/895#issuecomment-427700006,
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percolator picture percolator on 8 Oct 2018

@percolator Actually both, but it usually doesn't take more than 30 minutes to wrap it all up, see:

https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

The code review is mostly due diligence with unit testing, nothing like a deep full code audit.

Here you have an example checklist on what you should expect from the review:

https://github.com/openjournals/joss-reviews/issues/967

Hope that helps, feel free to inquire more :)

brainstorm picture brainstorm on 9 Oct 2018

Hi Roman,

Gustavo (cc:ed) @gjeuken could take the review. I am interested to see what
comes out of this. I like open science, and I like review processes.

Thanks
--Lukas

On Tue, Oct 9, 2018 at 2:31 AM Roman Valls Guimera notifications@github.com
wrote:

@percolator https://github.com/percolator Actually both, but it usually
doesn't take more than 30 minutes to wrap it all up, see:

https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

The code review is mostly due diligence with unit testing, nothing like a
deep full code audit.

Here you have an example checklist on what you should expect from the
review:

967 https://github.com/openjournals/joss-reviews/issues/967

Hope that helps, feel free to inquire more :)

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/openjournals/joss-reviews/issues/895#issuecomment-428021072,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AAF1ALJxRyEAeLSjfwwBIIdjn8Eh4bX3ks5ui-5egaJpZM4V-pKu
.

percolator picture percolator on 9 Oct 2018

Alright, fantastic, thanks Lukas (and Gustavo).

brainstorm picture brainstorm on 9 Oct 2018

@whedon assign @gjeuken as reviewer

brainstorm picture brainstorm on 9 Oct 2018

OK, the reviewer is @gjeuken

whedon picture whedon on 9 Oct 2018

@whedon start review magic-word=bananas

brainstorm picture brainstorm on 9 Oct 2018

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1007. Feel free to close this issue now!

whedon picture whedon on 9 Oct 2018

@whedon Thanks a lot for reviewing the package! 😄

jmborr picture jmborr on 9 Oct 2018
😄1
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