[PRE REVIEW]: UncertainData.jl: a Julia package for working with measurements and datasets with uncertainties #1652

whedon · Aug 16, 2019

Submitting author: @kahaaga (Kristian Agasøster Haaga)
Repository: https://github.com/kahaaga/UncertainData.jl
Version: v0.2.1
Editor: @oliviaguest
Reviewer: Pending

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:

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whedon · Aug 16, 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

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 😸

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 · Aug 16, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Aug 16, 2019

Failed to discover a valid open source license.

whedon · Aug 16, 2019

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

Can't find any papers to compile :-(

danielskatz · Aug 16, 2019

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

kahaaga · Aug 16, 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

danielskatz · Aug 16, 2019

@whedon generate pdf

whedon · Aug 16, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Aug 16, 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: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-80a4e9edb5a6/lib/whedon.rb:115:in load_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:in new'
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: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-80a4e9edb5a6/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 `

'

danielskatz · Aug 16, 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

kahaaga · Aug 17, 2019

@whedon generate pdf

whedon · Aug 17, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Aug 17, 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: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-80a4e9edb5a6/lib/whedon.rb:115:in load_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:in new'
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: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-80a4e9edb5a6/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 `

'

kahaaga · Aug 17, 2019

@whedon generate pdf

whedon · Aug 17, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Aug 17, 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: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-80a4e9edb5a6/lib/whedon.rb:115:in load_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:in new'
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: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-80a4e9edb5a6/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 `

'

kahaaga · Aug 17, 2019

@whedon generate pdf from branch joss_paper

whedon · Aug 17, 2019

Attempting PDF compilation from custom branch joss_paper. Reticulating splines etc...

whedon · Aug 17, 2019

👉 Check article proof 📄 👈

kahaaga · Aug 17, 2019

@whedon generate pdf from branch joss_paper

whedon · Aug 17, 2019

Attempting PDF compilation from custom branch joss_paper. Reticulating splines etc...

whedon · Aug 17, 2019

👉 Check article proof 📄 👈

kahaaga · Aug 17, 2019

@whedon generate pdf from branch joss_paper

whedon · Aug 17, 2019

Attempting PDF compilation from custom branch joss_paper. Reticulating splines etc...

whedon · Aug 17, 2019

👉 Check article proof 📄 👈

kahaaga · Aug 17, 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.

danielskatz · Aug 17, 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 kahaaga/UncertainData.jl#58 to fix some small punctuation issues?

danielskatz · Aug 17, 2019

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

danielskatz · Aug 17, 2019

@whedon generate pdf

whedon · Aug 17, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Aug 17, 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: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-80a4e9edb5a6/lib/whedon.rb:115:in load_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:in new'
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: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-80a4e9edb5a6/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 `

'

kahaaga · Aug 17, 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.

danielskatz · Aug 17, 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

kahaaga · Aug 17, 2019

@whedon generate pdf

whedon · Aug 17, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Aug 17, 2019

👉 Check article proof 📄 👈

kahaaga · Aug 17, 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 · Aug 17, 2019

@whedon generate pdf

whedon · Aug 17, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Aug 17, 2019

👉 Check article proof 📄 👈

kahaaga · Aug 17, 2019

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

danielskatz · Aug 17, 2019

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

oliviaguest · Aug 18, 2019

Yes. Happy to do it.

danielskatz · Aug 18, 2019

@whedon assign @oliviaguest as editor

whedon · Aug 18, 2019

OK, the editor is @oliviaguest

oliviaguest · Aug 19, 2019

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

lindemann09 · Aug 19, 2019

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

oliviaguest · Aug 19, 2019

@lindemann09 thanks for the speedy reply and no worries!

oliviaguest · Aug 19, 2019

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

whedon added the pre-review label Aug 16, 2019

whedon added Julia TeX labels Aug 16, 2019

whedon assigned oliviaguest Aug 18, 2019

openjournals/joss-reviews

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[PRE REVIEW]: UncertainData.jl: a Julia package for working with measurements and datasets with uncertainties #1652

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whedon commented Aug 16, 2019 • edited

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whedon commented Aug 16, 2019 •

edited