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[PRE REVIEW]: GaitPy: An Open-Source Python Package for Gait Analysis Using an Accelerometer on the Lower Back #1713

Closed whedon closed 5 years ago

whedon commented 5 years ago

Submitting author: @matt002 (Matthew Czech) Repository: https://github.com/matt002/GaitPy Version: v1.0 Editor: @arfon Reviewers: @finsberg, @abhishektha

Author instructions

Thanks for submitting your paper to JOSS @mdc007. Currently, there isn't an JOSS editor assigned to your paper.

@mdc007 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 commented 5 years ago

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 commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

PDF failed to compile for issue #1713 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1713/paper/paper.md): found character that cannot start any token while scanning for the next token at line 4 column 4 (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-61fc68877343/lib/whedon.rb:115:inload_yaml' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-61fc68877343/lib/whedon.rb:85:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-61fc68877343/lib/whedon/processor.rb:36:innew' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-61fc68877343/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-61fc68877343/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-61fc68877343/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 `

'

arfon commented 5 years ago

:wave: @matt002, many thanks for your submission to JOSS. Firstly, this pull request should fix your paper compilation: https://github.com/matt002/GaitPy/pull/1

Second, it's not immediately clear to me that your submission is currently up to standard for JOSS yet I'm afraid. In particular the fact that this is a written for Python 2.7 suggests to me that this package is close to deprecated and not 'designed for maintainable extension'.

Also, there don't currently appear to be any automated/unit tests which will be a problem during review.

Matt-pfz commented 5 years ago

Thank you for your edits and feedback. I will work to address these problems with the submission and update you when completed.

Matt-pfz commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

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

Matt-pfz commented 5 years ago

@arfon, I have worked to address the issues you brought up. The package is compatible with Python 3.6 and offers a demo in order to test the functionality. Any feedback is appreciated. I look forward to going through the process of submission.

Matt-pfz commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

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

kthyng commented 5 years ago

Hi @trallard! I see you work in biomechanics. Could you edit this submission?

danielskatz commented 5 years ago

👋 @meg-simula - would you be willing to edit this submission?

danielskatz commented 5 years ago

👋 @meg-simula - would you be willing to edit this submission? (just checking again...)

meg-simula commented 5 years ago

Thanks for checking @danielskatz - I have some open reviews and I would like to get those sorted before taking on more though.

arfon commented 5 years ago

@danielskatz - I can take this one.

arfon commented 5 years ago

@whedon assign @arfon as editor

whedon commented 5 years ago

OK, the editor is @arfon

arfon commented 5 years ago

@Matt-pfz - could you take a look at this list of people and suggest some people who might be able to review your submission?

arfon commented 5 years ago

Also, could you confirm what your GitHub handle is? It's not clear which GitHub identity should be associated with this submission.

matt002 commented 5 years ago

@arfon - Sure: moorepants, nirum, melund, ixjlyons, could be good fits to review my submission. Apologies for the confusion, I would like the matt002 identity to be associated with this submission.

arfon commented 5 years ago

@arfon - Sure: moorepants, nirum, melund, ixjlyons, could be good fits to review my submission. Apologies for the confusion, I would like the matt002 identity to be associated with this submission.

OK thanks. Many of those reviewers have been doing a lot for us recently so I'm going to look a little more broadly.

arfon commented 5 years ago

@finsberg @abhishektha - would you both be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

finsberg commented 5 years ago

@arfon, I can review this submission.

arfon commented 5 years ago

@arfon, I can review this submission.

Wonderful, thanks so much @finsberg. I'll add you as a reviewer now but will hold off starting the actual review thread until I've found a second reviewer.

arfon commented 5 years ago

@whedon add @finsberg as reviewer

whedon commented 5 years ago

OK, @finsberg is now a reviewer

abhishektha commented 5 years ago

@arfon, Sure! Would be glad to review!

arfon commented 5 years ago

@whedon add @abhishektha as reviewer

whedon commented 5 years ago

OK, @abhishektha is now a reviewer

arfon commented 5 years ago

@whedon start review

whedon commented 5 years ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1778. Feel free to close this issue now!

arfon commented 5 years ago

@finsberg, @abhishektha - many thanks for agreeing to review this submission. See you over in #1778 where the actual review will take place.