Joss-reviews: [PRE REVIEW]: wolfexplorer: a tool for visualization and exploration of complex multi-year multi-specimen datasets

Created on 10 Oct 2018  Β·  42Comments  Β·  Source: openjournals/joss-reviews

Submitting author: @zkuralt (Ε½an Kuralt)
Repository: https://github.com/romunov/wolfexplorer
Version: v0.9
Editor: @trallard
Reviewers: @amoeba

Author instructions

Thanks for submitting your paper to JOSS @zkuralt. 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.

@zkuralt 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
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picture whedon

All 42 comments

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @trallard it looks like you're currently assigned as the editor for this paper :tada:

For a list of things I can do to help you, just type:

@whedon commands
whedon picture whedon on 10 Oct 2018 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 10 Oct 2018

PDF failed to compile for issue #1009 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon.rb:83:in check_fields': Paper YAML header is missing expected fields: tags, authors, affiliations, date, bibliography (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon.rb:69:ininitialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon/processor.rb:32:inset_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/bin/whedon:37:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/bin/whedon:99: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

'

whedon picture whedon on 10 Oct 2018

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

arfon picture arfon on 10 Oct 2018
👍1

Sure @arfon
@whedon assign @trallard as editor

trallard picture trallard on 10 Oct 2018
👍1

@whedon assign @trallard as editor

@whedon needs commands to be issues in separate comments currently sorry.

arfon picture arfon on 10 Oct 2018
😄1

@zkuralt - please take at look at the example paper in our submission requirements and format the YAML header of your paper the same way. Also, please note that YAML is white-space sensitive when making these changes.

Once you've made your changes you can ask @whedon to recompile your paper with the command @whedon generate pdf

arfon picture arfon on 10 Oct 2018

πŸ‘‹πŸΌ Hi @zkuralt I am happy to serve as the editor for this submission. As Arfon pointed out it seems that the title header is not properly indented.

Also, do you have any reviewers in mind? You can see the list of reviewers using the command @whedon list reviewers

trallard picture trallard on 10 Oct 2018

I hope that the YAML header is now okay - there was a whitespace that i missed initially

zkuralt picture zkuralt on 10 Oct 2018

@whedon generate pdf

zkuralt picture zkuralt on 10 Oct 2018 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 10 Oct 2018

PDF failed to compile for issue #1009 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1009/joss/paper.md): did not find expected '-' indicator while parsing a block collection at line 8 column 3 (Psych::SyntaxError) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:inparse_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:inload'
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:inopen'
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-dbdd2bfb2d31/lib/whedon.rb:68:ininitialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon/processor.rb:32:inset_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/bin/whedon:37:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/bin/whedon:99: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

'

whedon picture whedon on 10 Oct 2018

@whedon generate pdf

zkuralt picture zkuralt on 10 Oct 2018 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 10 Oct 2018

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

whedon picture whedon on 10 Oct 2018

@whedon list reviewers

zkuralt picture zkuralt on 11 Oct 2018

Here's the current list of reviewers: https://bit.ly/joss-reviewers

whedon picture whedon on 11 Oct 2018

@trallard I checked the list of reviewers and the ones listed below fit the area of wolfexplorer.

amoeba
jsta
pboesu
jhollist
ethanwhite

zkuralt picture zkuralt on 11 Oct 2018

Hello :wave: @amoeba @jsta @pboesu @jhollist @ethanwhite would any of you be interested in reviewing this submission?
We'd ideally like to have two editors looking at this

trallard picture trallard on 11 Oct 2018

Hi @trallard I could probably commit to getting a review on by November 15th if that works for you. Please let me know and I can plan on it.

amoeba picture amoeba on 15 Oct 2018

Hi @amoeba, thanks for offering πŸŽ‰. This would work perfectly, that would give us time to find a second reviewer

trallard picture trallard on 15 Oct 2018
👍1

I can't right now. Sorry

ethanwhite picture ethanwhite on 15 Oct 2018

@whedon assign @amoeba as reviewer

trallard picture trallard on 23 Oct 2018

No worries @ethanwhite

@jsta @pboesu @jhollist would any of you have a chance to help with this review?

trallard picture trallard on 23 Oct 2018

Sorry for not responding sooner.

Unfortunately I am going to have to pass as well.

On Tue, Oct 23, 2018, 3:12 AM Tania Allard notifications@github.com wrote:

No worries @ethanwhite https://github.com/ethanwhite

@jsta https://github.com/jsta @pboesu https://github.com/pboesu
@jhollist https://github.com/jhollist would any of you have a chance to
help with this review?

β€”
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/openjournals/joss-reviews/issues/1009#issuecomment-432122964,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AFL8S1h74Ak7WAyMeLkczd-1Ahp3iyRYks5unsFogaJpZM4XVEc6
.

jhollist picture jhollist on 23 Oct 2018

Likewise, my review queue is full. Best of luck!

jsta picture jsta on 23 Oct 2018

@whedon assign @amoeba as reviewer

trallard picture trallard on 30 Oct 2018
👍1

OK, the reviewer is @amoeba

whedon picture whedon on 30 Oct 2018
🎉1

I am going to open the review issue for this submission for now since we have @amoeba confirmed for mid-November

I will try and find a second reviewer in the meantime 🀞

trallard picture trallard on 4 Nov 2018

@whedon start review

trallard picture trallard on 4 Nov 2018

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1064. Feel free to close this issue now!

whedon picture whedon on 4 Nov 2018

@whedon generate pdf

zkuralt picture zkuralt on 16 Nov 2018 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 16 Nov 2018

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

whedon picture whedon on 16 Nov 2018

I suspect that whedon generates PDF from master branch. We will generate it again after merging joss_review branch to master.

zkuralt picture zkuralt on 16 Nov 2018

Yes by default it uses master

I can see the paper correctly unless you have been working on an alternate branch for corrections and stuff @zkuralt

trallard picture trallard on 16 Nov 2018

@whedon commands

trallard picture trallard on 16 Nov 2018

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Open the review issue
@whedon start review

# Compile the paper
@whedon generate pdf

🚧 🚧 🚧 Experimental Whedon features 🚧 🚧 🚧

# Compile the paper from a custom git branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to accept the paper and deposit with Crossref
@whedon accept
whedon picture whedon on 16 Nov 2018

@whedon generate pdf from branch joss_review

trallard picture trallard on 16 Nov 2018 
Attempting PDF compilation from custom branch joss_review. Reticulating splines etc...
whedon picture whedon on 16 Nov 2018

PDF failed to compile for issue #1009 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 15 0 15 0 0 304 0 --:--:-- --:--:-- --:--:-- 306
Error reading bibliography ./paper.bib (line 121, column 5):
unexpected "y"
expecting space, ",", white space or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

whedon picture whedon on 16 Nov 2018

@whedon generate pdf from branch joss_review

This functionality _rarely_ works for some reason. Use it with caution :grin: ...

arfon picture arfon on 16 Nov 2018
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