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[PRE REVIEW]: GPU-Accelerated LArge-scale MOlecular Simulation Toolkit #1553

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whedon opened this issue Jul 8, 2019 · 19 comments

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commented Jul 8, 2019

Submitting author: @zhuyouliang (You-Liang Zhu)
Repository: https://bitbucket.org/galamostdevelopergroup/source-code
Version: v4.0.1
Editor: @kyleniemeyer
Reviewer: Pending

Author instructions

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

@ 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 whedon added the pre-review label Jul 8, 2019

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commented Jul 8, 2019

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

What happens now?

This submission is currently in a pre-review state which means we are waiting for an editor to be assigned and for them to find some reviewers for your submission. This may take anything between a few hours to a couple of weeks. Thanks for your patience 😸

You can help the editor by looking at this list of potential reviewers to identify individuals who might be able to review your submission (please start at the bottom of the list). Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here.

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commented Jul 8, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jul 8, 2019

PDF failed to compile for issue #1553 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1553/galamost-4.0.1/paper/paper.md): found a tab character that violate intendation while scanning a plain scalar at line 5 column 18 (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-85c572552d68/lib/whedon.rb:95:in load_yaml'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon.rb:78:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon/processor.rb:36:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/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-85c572552d68/bin/whedon:116: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 `

'

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commented Jul 8, 2019

Failed to discover a valid open source license.

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commented Jul 8, 2019

We don't have the submitting author's GitHub username yet (I've sent them an email to ask for it) but when they do get here there are a few issues.

The paper YAML header is malformed

Please update the paper to match the example paper and note that YAML is whitespace sensitive.

title: 'GALAMOST: GPU-accelerated large-scale molecular simulation toolkit'
authors:
  - name: You-Liang Zhu
    affiliation: 1
	orcid: 0000-0002-9561-0770
tags:
  - GPUs
  - Molecular dynamics 
  - Soft matters	
affiliations:
 - name: State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
   index: 1
date: 8 July 2019
output: pdf_document
bibliography: paper.bib

The paper format

The paper as it currently stands has a lot of bullet points and not much else. Please review the submission guidelines for what your paper should contain and reformat as necessary.

Open source license

Even though a license is mentioned in the README, there needs to be a separate plain text LICENSE file with an OSI approved license within.

Given the problems with this submission and my challenges contacting the submitting author I'm marking this as paused until we hear back from them.

@arfon arfon added the paused label Jul 8, 2019

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commented Jul 9, 2019

Many thanks. I have updated files again including the paper and license file.

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commented Jul 9, 2019

@whedon generate pdf

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commented Jul 9, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jul 9, 2019

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commented Jul 9, 2019

Hi @zhuyouliang - this paper could still do with some work. It currently reads mostly as a list of functionalities. Please review our guidelines on what your paper should contain

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commented Jul 9, 2019

@kyleniemeyer - would you be willing to edit this submission for JOSS?

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commented Jul 9, 2019

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commented Jul 9, 2019

@arfon ok, will take this.

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commented Jul 9, 2019

@whedon assign @kyleniemeyer as editor

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commented Jul 9, 2019

OK, the editor is @kyleniemeyer

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commented Jul 10, 2019

Hello @zhuyouliang, before trying to find some reviewers, there are some major issues that I see:

  • as @arfon pointed out, the paper is still missing some of what is expected, as described in https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain
  • There is very little documentation; all I can see is a README, which does not really explain how to build or use the software. Examples are also very helpful.
  • Research software needs tests of some kind; I do not see any sort of test suite.
  • There are no community guidelines

Please review our checklist of review items; reviewers will go through this list and try to find evidence of your software satisfying them. Before we try to find reviewers, I would like to see that you have addressed the majority of these in some way. This will allow reviewers to give more useful feedback to improve your software, rather than just saying that the basic things are missing.

I'm going to pause this submission until we see that these things have been addressed.

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commented Jul 11, 2019

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commented Jul 11, 2019

@zhuyouliang thank you for making those changes.

However, I noticed that you already published a full paper about your software in the Journal of Computational Chemistry. Would this submission (if accepted) amount to a duplicate publication of the same work?

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commented Jul 12, 2019

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