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[PRE REVIEW]: AutoClassWrapper: a Python wrapper for AutoClass C classification #1309

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whedon opened this issue Mar 10, 2019 · 35 comments
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[PRE REVIEW]: AutoClassWrapper: a Python wrapper for AutoClass C classification #1309

whedon opened this issue Mar 10, 2019 · 35 comments
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@trallard
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@whedon
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whedon commented Mar 10, 2019 •
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Submitting author: @pierrepo (Pierre Poulain)
Repository: https://github.com/pierrepo/autoclasswrapper
Version: v1.4.1
Editor: @trallard
Reviewers: @rpetit3, @lowandrew

Author instructions

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

@pierrepo 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
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whedon commented Mar 10, 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.

@whedon
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whedon commented Mar 10, 2019 

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Mar 10, 2019

PDF failed to compile for issue #1309 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1309/paper/paper.md): did not find expected key while parsing a block mapping at line 17 column 3 (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-01ece1d1d135/lib/whedon.rb:68:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon/processor.rb:32:in set_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/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-01ece1d1d135/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

'

@arfon
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arfon commented Mar 10, 2019

@pierrepo - this pull request should fix your paper: pierrepo/autoclasswrapper#11

@pierrepo
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@whedon commands

@whedon
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whedon commented Mar 10, 2019

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

@pierrepo
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@whedon generate pdf

@whedon
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whedon commented Mar 10, 2019 

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Mar 10, 2019

👉 Check article proof 📄 👈

@pierrepo
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@whedon generate pdf

@whedon
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whedon commented Mar 10, 2019 

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Mar 10, 2019

👉 Check article proof 📄 👈

@pierrepo
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The proof is OK for me.

@pierrepo
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Following @whedon recommendations, here is a list of potential reviewers (taken from this list):

@kyleniemeyer
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Hi @pierrepo, we need to assign an editor to handle your submission before reviewers—hang tight!

@kyleniemeyer
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@trallard could you edit this submission?

@trallard
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Sure @kyleniemeyer

@kyleniemeyer
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@whedon assign @trallard as editor

@whedon
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whedon commented Mar 12, 2019

OK, the editor is @trallard

@kyleniemeyer
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Thanks @trallard!

@trallard
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/ooo March 20 until April 7

@ooo
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ooo bot commented Mar 20, 2019

👍 Marked @trallard as OOO from Wednesday, March 20th 2019 to Sunday, April 7th 2019. 📆

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@labarba
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labarba commented Apr 15, 2019 •
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👋 @trallard — it looks like this submission is waiting for you to assign reviewers, now that you're back from ooo, yes?

@trallard
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trallard commented Apr 16, 2019 •
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Hi Pierre @pierrepo apologies for the long wait, let's get things moving now for you 😄

Dear potential reviewers (@rpetit3 @jdeligt @a-slide @lowandrew @afrendeiro)

You all seem to have valuable expertise that could be used in this review, I am wondering if you have the time and bandwidth to help us review this submission?

Title: AutoClassWrapper: a Python wrapper for AutoClass C classification
Repo: https://github.com/pierrepo/autoclasswrapper

Summary: AutoClass is an unsupervised Bayesian classification system.
AutoClass C is an implementation of the AutoClass algorithm made by the NASA.
AutoClassWrapper is a Python wrapper to ease the use of Autoclass C.

Submitting author: @pierrepo Pierren Poulain
Version: 1.4.1

@rpetit3
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rpetit3 commented Apr 16, 2019

Hi @trallard!

I would be glad to help reviewing @pierrepo's manuscript/software.

Full disclosure, this will be my first time formally reviewing a manuscript/software. To help get started I have read through the Review Checklist, but I still might stumble over some things (I'll do my best not to!). So, any advice, feedback, and/or instructions would be very much welcomed.

Depending on reviewer turn out, I will definitely understand if you'd like to choose a more experienced reviewer.

Thank you!
Robert

@lowandrew
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Hi @trallard!

I'm in very much the same boat as @rpetit3 with respect to software/review experience, but I'd be happy to review.

Thanks,
Andrew

@trallard
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Hi @rpetit3 and @lowandrew this is great! Do not worry at all, the review process for JOSS is very comprehensive and I will monitor the review regularly to make sure you need as much guidance/support as needed 😄

I am going to assign you as reviewers and see if any of the other folks are interested in reviewing before starting the process

@trallard
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@whedon add @rpetit3 as reviewer

@whedon whedon assigned trallard and unassigned trallard Apr 16, 2019
@whedon
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whedon commented Apr 16, 2019

OK, @rpetit3 is now a reviewer

@trallard
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@whedon add @lowandrew as reviewer

@whedon whedon assigned trallard and unassigned trallard Apr 16, 2019
@whedon
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whedon commented Apr 16, 2019

OK, @lowandrew is now a reviewer

@jdeligt
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jdeligt commented Apr 17, 2019 via email

@trallard
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No worries @jdeligt

Ok let's us move to the formal review process

@trallard
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@whedon start review

@whedon
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whedon commented Apr 17, 2019

OK, I've started the review over in #1390. Feel free to close this issue now!

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@arfon @kyleniemeyer @pierrepo @labarba @rpetit3 @jdeligt @whedon @trallard @lowandrew