Joss-reviews: [PRE REVIEW]: ytree: A Python package for analyzing merger trees

Created on 1 Nov 2019  路  42Comments  路  Source: openjournals/joss-reviews

Submitting author: @brittonsmith (Britton Smith)
Repository: https://github.com/ytree-project/ytree
Version: v2.2
Editor: @xuanxu
Reviewers: @mgckind, @aureliocarnero

Author instructions

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

@brittonsmith 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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Python TeX pre-review
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picture whedon

Most helpful comment

@danielskatz yes, I can take this

picture xuanxu on 1 Nov 2019
👍2

All 42 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 1 Nov 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 1 Nov 2019

PDF failed to compile for issue #1853 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1853/paper/paper.md): could not find expected ':' while scanning a simple key at line 27 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-74bc29a6a731/lib/whedon.rb:115:inload_yaml'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-74bc29a6a731/lib/whedon.rb:85:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-74bc29a6a731/lib/whedon/processor.rb:36:innew'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-74bc29a6a731/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-74bc29a6a731/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-74bc29a6a731/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 1 Nov 2019

@brittonsmith Your paper has compilation issues. Please study our guidelines and see if you can trouble shoot these issues.
https://joss.readthedocs.io/en/latest/submitting.html#checking-that-your-paper-compiles

You can use this link to test the compilation of your paper: https://whedon.theoj.org/

Kevin-Mattheus-Moerman picture Kevin-Mattheus-Moerman on 1 Nov 2019

@Kevin-Mattheus-Moerman, thanks for the note. I think the problem is that the paper is in a subdirectory of the repo linked above. The paper can be found here. I thought that was the url I gave in the submission form. In any case, if I use that url in the compilation tester, it tells me that paper compilation is complete, although I get a "Not Found" message when I click to download the preview. Can you tell me what action I should take now?

brittonsmith picture brittonsmith on 1 Nov 2019

@openjournals/dev do you know what is going on here?

Kevin-Mattheus-Moerman picture Kevin-Mattheus-Moerman on 1 Nov 2019

@whedon generate pdf

danielskatz picture danielskatz on 1 Nov 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 1 Nov 2019

PDF failed to compile for issue #1853 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1853/paper/paper.md): could not find expected ':' while scanning a simple key at line 27 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-74bc29a6a731/lib/whedon.rb:115:inload_yaml'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-74bc29a6a731/lib/whedon.rb:85:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-74bc29a6a731/lib/whedon/processor.rb:36:innew'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-74bc29a6a731/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-74bc29a6a731/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-74bc29a6a731/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 1 Nov 2019

馃憢 @brittonsmith - It looks the the line after the metadata containing --- is missing - please add this line to the paper.md and issue @whedon generate pdf as a new comment here to try again

danielskatz picture danielskatz on 1 Nov 2019

Oh, thanks for catching that, @danielskatz!

brittonsmith picture brittonsmith on 1 Nov 2019

@whedon generate pdf

brittonsmith picture brittonsmith on 1 Nov 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 1 Nov 2019

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

whedon picture whedon on 1 Nov 2019

Ok, I think we're back on track. Thanks everyone for their help.

brittonsmith picture brittonsmith on 1 Nov 2019

馃憢 @dfm or @xuanxu, would one of you be willing to edit this submission?

danielskatz picture danielskatz on 1 Nov 2019

@danielskatz: I'd like to finish my first two before taking on another. Let me know if you can't get it sorted.

dfm picture dfm on 1 Nov 2019
👍1

@danielskatz yes, I can take this

xuanxu picture xuanxu on 1 Nov 2019
👍2

@whedon assign @xuanxu as editor

xuanxu picture xuanxu on 1 Nov 2019

OK, the editor is @xuanxu

whedon picture whedon on 1 Nov 2019

:wave: @mgckind: Any chance you're available to review this submission?

xuanxu picture xuanxu on 5 Nov 2019

:wave: @ceb8: would you be willing to review this paper? I think your knowledge of astronomy and Python makes you a great fit for this submission.

xuanxu picture xuanxu on 5 Nov 2019

@whedon check references

xuanxu picture xuanxu on 5 Nov 2019 
Attempting to check references...
whedon picture whedon on 5 Nov 2019

```Reference check summary:

OK DOIs

  • 10.1088/0067-0049/192/1/9 is OK
  • 10.5281/zenodo.1174374 is OK
  • 10.1109/MCSE.2011.37 is OK
  • 10.21105/joss.00809 is OK
  • 10.1088/0004-637X/763/1/18 is OK
  • 10.3847/1538-4357/aabe8f is OK
  • 10.3847/1538-4357/ab378f is OK
  • 10.1093/mnras/sty2103 is OK
  • 10.1093/mnras/stz2507 is OK

MISSING DOIs

  • https://doi.org/10.1002/1097-024x(200009)30:11<1203::aid-spe338>3.3.co;2-e may be missing for title: An open graph visualization system and its applications to software engineering

INVALID DOIs

  • None
    ```
whedon picture whedon on 5 Nov 2019

@mgckind: Any chance you're available to review this submission?

Hi, I'm traveling this week but I might be able to review it next week if that's okay?

mgckind picture mgckind on 5 Nov 2019
👍1

@mgckind it is totally OK, thanks!
I'll assign you now and wait to have the second reviewer ready before starting the review issue.

xuanxu picture xuanxu on 5 Nov 2019

@whedon add @mgckind as reviewer

xuanxu picture xuanxu on 5 Nov 2019

OK, @mgckind is now a reviewer

whedon picture whedon on 5 Nov 2019

@xuanxu Unfortunately I don't have time right now, I need to finish the review I am already working on before I take on another.

ceb8 picture ceb8 on 5 Nov 2019
👍1

:wave: @cmbiwer would you be willing to review this paper? I think your knowledge of astronomy and Python makes you a great fit for this submission.

xuanxu picture xuanxu on 5 Nov 2019

@whedon check references

xuanxu picture xuanxu on 6 Nov 2019 
Attempting to check references...
whedon picture whedon on 6 Nov 2019

```Reference check summary:

OK DOIs

  • 10.1088/0067-0049/192/1/9 is OK
  • 10.5281/zenodo.1174374 is OK
  • 10.1109/MCSE.2011.37 is OK
  • 10.21105/joss.00809 is OK
  • 10.1002/1097-024X(200009)30:11<1203::AID-SPE338>3.0.CO;2-N is OK
  • 10.1088/0004-637X/763/1/18 is OK
  • 10.3847/1538-4357/aabe8f is OK
  • 10.3847/1538-4357/ab378f is OK
  • 10.1093/mnras/sty2103 is OK
  • 10.1093/mnras/stz2507 is OK

MISSING DOIs

  • None

INVALID DOIs

  • None
    ```
whedon picture whedon on 6 Nov 2019

@whedon generate pdf

brittonsmith picture brittonsmith on 6 Nov 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 6 Nov 2019

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

whedon picture whedon on 6 Nov 2019

@whedon add @aureliocarnero as reviewer

xuanxu picture xuanxu on 11 Nov 2019

OK, @aureliocarnero is now a reviewer

whedon picture whedon on 11 Nov 2019

@whedon start review

xuanxu picture xuanxu on 11 Nov 2019

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1881. Feel free to close this issue now!

whedon picture whedon on 11 Nov 2019

@aureliocarnero, @mgckind please head over to #1881 where the review will take place.

xuanxu picture xuanxu on 11 Nov 2019
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