Joss-reviews: [PRE REVIEW]: UncertainData.jl: a Julia package for working with measurements and datasets with uncertainties

Created on 16 Aug 2019  Â·  58Comments  Â·  Source: openjournals/joss-reviews

Submitting author: @kahaaga (Kristian Agasøster Haaga)
Repository: https://github.com/kahaaga/UncertainData.jl
Version: v0.2.1
Editor: @oliviaguest
Reviewers: @dmbates, @ahwillia

Author instructions

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

@kahaaga 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
Julia TeX pre-review
Source
picture whedon

All 58 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

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

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 :smile_cat:

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 picture whedon on 16 Aug 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 16 Aug 2019

Failed to discover a valid open source license.

whedon picture whedon on 16 Aug 2019

PDF failed to compile for issue #1652 with the following error:

Can't find any papers to compile :-(

whedon picture whedon on 16 Aug 2019

👋 @kahaaga - we can't proceed until you add an OSI-compliant license to the repo. Also, please change manuscript.md to paper.md

danielskatz picture danielskatz on 16 Aug 2019

Done, @danielskatz! An MIT-license has been added, and the manuscript file has been renamed to paper.md.

I also had a look at the list of potential reviewers and found some Julia programmers with some relevant backgrounds (not sure if I should tag them here, so here are their github handles):

  • Datseris
  • dmbates
  • matbesancon
  • juliohm
kahaaga picture kahaaga on 16 Aug 2019

@whedon generate pdf

danielskatz picture danielskatz on 16 Aug 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 16 Aug 2019

PDF failed to compile for issue #1652 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1652/paper/paper.md): did not find expected key while parsing a block mapping at line 2 column 1 (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-80a4e9edb5a6/lib/whedon.rb:115:inload_yaml'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-80a4e9edb5a6/lib/whedon.rb:85:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-80a4e9edb5a6/lib/whedon/processor.rb:36:innew'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-80a4e9edb5a6/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-80a4e9edb5a6/bin/whedon:55:inprepare'
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:ininvoke_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:instart'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-80a4e9edb5a6/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:inload'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

whedon picture whedon on 16 Aug 2019

You’ll need to fix the affiliations. See the same paper please. Then add a new comment to this issue that is @whedon generate pdf to try again

danielskatz picture danielskatz on 16 Aug 2019

@whedon generate pdf

kahaaga picture kahaaga on 17 Aug 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 17 Aug 2019

PDF failed to compile for issue #1652 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1652/paper/paper.md): did not find expected key while parsing a block mapping at line 8 column 5 (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-80a4e9edb5a6/lib/whedon.rb:115:inload_yaml'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-80a4e9edb5a6/lib/whedon.rb:85:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-80a4e9edb5a6/lib/whedon/processor.rb:36:innew'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-80a4e9edb5a6/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-80a4e9edb5a6/bin/whedon:55:inprepare'
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:ininvoke_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:instart'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-80a4e9edb5a6/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:inload'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

whedon picture whedon on 17 Aug 2019

@whedon generate pdf

kahaaga picture kahaaga on 17 Aug 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 17 Aug 2019

PDF failed to compile for issue #1652 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1652/paper/paper.md): did not find expected key while parsing a block mapping at line 8 column 5 (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-80a4e9edb5a6/lib/whedon.rb:115:inload_yaml'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-80a4e9edb5a6/lib/whedon.rb:85:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-80a4e9edb5a6/lib/whedon/processor.rb:36:innew'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-80a4e9edb5a6/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-80a4e9edb5a6/bin/whedon:55:inprepare'
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:ininvoke_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:instart'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-80a4e9edb5a6/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:inload'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

whedon picture whedon on 17 Aug 2019

@whedon generate pdf from branch joss_paper

kahaaga picture kahaaga on 17 Aug 2019 
Attempting PDF compilation from custom branch joss_paper. Reticulating splines etc...
whedon picture whedon on 17 Aug 2019

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

whedon picture whedon on 17 Aug 2019

@whedon generate pdf from branch joss_paper

kahaaga picture kahaaga on 17 Aug 2019 
Attempting PDF compilation from custom branch joss_paper. Reticulating splines etc...
whedon picture whedon on 17 Aug 2019

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

whedon picture whedon on 17 Aug 2019

@whedon generate pdf from branch joss_paper

kahaaga picture kahaaga on 17 Aug 2019 
Attempting PDF compilation from custom branch joss_paper. Reticulating splines etc...
whedon picture whedon on 17 Aug 2019

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

whedon picture whedon on 17 Aug 2019

Affiliations are fixed!

There was some confusion about a parsing error on line 8 which I thought to be due to the Norwegian letter ø in my middle name. However, this which turned out to be due to incorrect formatting of the affiliation field, not an error in parsing the letter ø. The pdf is now rendered correctly.

kahaaga picture kahaaga on 17 Aug 2019

Thanks! Also, sorry for the perhaps confusing message I sent - it was meant to say "sample" paper but ended up saying "same" paper, as I was typing on my phone on a plane that was getting ready to leave...

Can you also merge https://github.com/kahaaga/UncertainData.jl/pull/58 to fix some small punctuation issues?

danielskatz picture danielskatz on 17 Aug 2019

👋 @oliviaguest - Would you be willing to edit this submission?

danielskatz picture danielskatz on 17 Aug 2019
👍1

@whedon generate pdf

danielskatz picture danielskatz on 17 Aug 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 17 Aug 2019

PDF failed to compile for issue #1652 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1652/paper/paper.md): did not find expected key while parsing a block mapping at line 8 column 5 (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-80a4e9edb5a6/lib/whedon.rb:115:inload_yaml'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-80a4e9edb5a6/lib/whedon.rb:85:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-80a4e9edb5a6/lib/whedon/processor.rb:36:innew'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-80a4e9edb5a6/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-80a4e9edb5a6/bin/whedon:55:inprepare'
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:ininvoke_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:instart'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-80a4e9edb5a6/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:inload'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

whedon picture whedon on 17 Aug 2019

No problem, it was obvious enough that I had made a mistake there, so no confusion about that!

I've merged your punctuation fixes. I'm also merging the joss_paper branch with the final fixes in paper.md to master. Once the CI tests pass in ten minutes or so, I'll get whedon to generate a new pdf.

kahaaga picture kahaaga on 17 Aug 2019

ah, sorry, my error in doing this in the middle of your changes - I'll leave it for you to do when you are ready

danielskatz picture danielskatz on 17 Aug 2019

@whedon generate pdf

kahaaga picture kahaaga on 17 Aug 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 17 Aug 2019

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

whedon picture whedon on 17 Aug 2019

Hehe, no problem! I wasn't expecting to get a response so swiftly - thanks for the quick follow up.

Anyways, here we go: The pdf looks good, and everything is ready from my side.

kahaaga picture kahaaga on 17 Aug 2019

@whedon generate pdf

kahaaga picture kahaaga on 17 Aug 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 17 Aug 2019

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

whedon picture whedon on 17 Aug 2019

I added an additional reference to a Julia package pending reviewer assignment.

kahaaga picture kahaaga on 17 Aug 2019

Thanks, but before that, we need to assign an editor who will take on finding reviewers and managing the review process.

danielskatz picture danielskatz on 17 Aug 2019

Yes. Happy to do it.

oliviaguest picture oliviaguest on 18 Aug 2019

@whedon assign @oliviaguest as editor

danielskatz picture danielskatz on 18 Aug 2019

OK, the editor is @oliviaguest

whedon picture whedon on 18 Aug 2019

Hi @dmbates and @lindemann09, would you be interested and able to review this JOSS submission? 😄

oliviaguest picture oliviaguest on 19 Aug 2019

I don't know much about Julia. I'm afraid I do not have the required expertise to review this submission.

lindemann09 picture lindemann09 on 19 Aug 2019
👍1

@lindemann09 thanks for the speedy reply and no worries!

oliviaguest picture oliviaguest on 19 Aug 2019

Hey 👋 @ahwillia, would you be interested and able to review this JOSS submission? 😄

oliviaguest picture oliviaguest on 19 Aug 2019

@whedon add @dmbates as reviewer

oliviaguest picture oliviaguest on 20 Aug 2019

OK, @dmbates is now a reviewer

whedon picture whedon on 20 Aug 2019

Sure I can review. It may take me a couple weeks to get around to this.

ahwillia picture ahwillia on 20 Aug 2019
👍1

@ahwillia so in about 2 weeks you think you can get started?

oliviaguest picture oliviaguest on 20 Aug 2019

Yes - I have a few deadlines and am wrapping up summer travel, so in 2
weeks I'll have some time.

On Tue, Aug 20, 2019 at 12:49 PM Olivia Guest notifications@github.com
wrote:

@ahwillia https://github.com/ahwillia so in about 2 weeks you think you
can get started?

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You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
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or mute the thread
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ahwillia picture ahwillia on 20 Aug 2019
👍1

@whedon add @ahwillia as reviewer

oliviaguest picture oliviaguest on 21 Aug 2019

OK, @ahwillia is now a reviewer

whedon picture whedon on 21 Aug 2019

@whedon start review

oliviaguest picture oliviaguest on 21 Aug 2019

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1666. Feel free to close this issue now!

whedon picture whedon on 21 Aug 2019
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