[PRE REVIEW]: AnyPyTools: A Python package for reproducible research with the AnyBody Modeling System.

whedon commented 5 years ago

Submitting author: @melund (Morten Enemark Lund) Repository: https://github.com/AnyBody-Research-Group/AnyPyTools Version: 1.0.0 Editor: @trallard Reviewers: @tonygon, @marcopus, @acolum

Author instructions

Thanks for submitting your paper to JOSS @melund. 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.

@melund 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. @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

What happens now?

This submission is currently in a pre-review state which means we are waiting for the assigned editor (@trallard) 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 #1099 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1099/docs/paper/paper.md): found unexpected document indicator while scanning a quoted scalar at line 2 column 8 (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-c44264c87f39/lib/whedon.rb:68:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/processor.rb:32:inset_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/bin/whedon:52: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-c44264c87f39/bin/whedon:113: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

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arfon commented 5 years ago

👋 @trallard - the submitting author suggested you as the handling editor.

arfon commented 5 years ago

@melund - I think this OR should fix your paper: https://github.com/AnyBody-Research-Group/AnyPyTools/pull/55

melund commented 5 years ago

Thanks, @arfon. I merged AnyBody-Research-Group/AnyPyTools#55

melund 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:

melund 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:

melund commented 5 years ago

@trallard Most of the review can probably be handled by someone who knows Python/GitHub/OpenSource.

But having reviewers with knowledge on multibody musculoskeletal modeling and the AnyBody Modeling System is probably also required.

So here are a few suggestions on reviewers who have used the AnyBody Modeling System, and have some Python and GitHub/Git experience.

Antonio Gonzales Marin (@tonygon). Research Scientist at the German Aerospace Center (DLR)
Marco Antonio Marra (@marcopus) Assistant Professor at University of Twente

trallard commented 5 years ago

👋 Hi @melund thanks for the submission. Since you suggested me as an editor I will be performing the editorial duties for this submission. If you have any questions over the review process please feel free to @ me.

Let's start by pinging some suitable reviewers with Python and biomechanics expertise. We can start the review once two or more of them accept the request to review.

Dear reviewers,

@tonygon as suggested: Antonio, are you able to and interested in taking on this review? @marcopus as suggested: Marco, are you able to and interested in taking on this review? @moorepants: Jason, are you able to and interested in taking on this review? @nirum: Niru, are you able to and interested in taking on this review? @acolum: Alyssa, are you able to and interested in taking on this review?

Title: AnyPyTools: A Python package for reproducible research with the AnyBody Modeling System. Summary: AnyPyTools is a toolkit for working with the AnyBody Modeling System (AMS) from Python. It enables reproducible research with the AnyBody Modeling System and bridges the gap to the whole ecosystem of open source scientific Python. Topic: reproducible science, musculoskeletal modelling Article proof: https://github.com/openjournals/joss-papers/blob/joss.01099/joss.01099/10.21105.joss.01099.pdf Submitting author: @melund Repository: https://github.com/AnyBody-Research-Group/AnyPyTools

marcopus commented 5 years ago

Hi Tania, I am willing to review this. Thanks, Marco

Il giorno mer 28 nov 2018 alle ore 15:34 Tania Allard < notifications@github.com> ha scritto:

👋 Hi @melund https://github.com/melund thanks for the submission. Since you suggested me as an editor I will be performing the editorial duties for this submission. If you have any questions over the review process please feel free to ping me.

Let's start by pinging some suitable reviewers with Python and biomechanics expertise. We can start the review once two or more of them accept the request to review.

Dear reviewers,

@tonygon https://github.com/tonygon as suggested: Antonio, are you able to and interested in taking on this review? @marcopus https://github.com/marcopus as suggested: Marco, are you able to and interested in taking on this review? @moorepants https://github.com/moorepants: Jason, are you able to and interested in taking on this review? @nirum https://github.com/nirum: Niru, are you able to and interested in taking on this review? @acolum https://github.com/acolum: Alyssa, are you able to and interested in taking on this review?

Title: AnyPyTools: A Python package for reproducible research with the AnyBody Modeling System. Summary: AnyPyTools is a toolkit for working with the AnyBody Modeling System (AMS) from Python. It enables reproducible research with the AnyBody Modeling System and bridges the gap to the whole ecosystem of open source scientific Python. Topic: reproducible science, musculoskeletal modelling Article proof: https://github.com/openjournals/joss-papers/blob/joss.01099/joss.01099/10.21105.joss.01099.pdf Submitting author: @melund https://github.com/melund Repository: https://github.com/AnyBody-Research-Group/AnyPyTools

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/1099#issuecomment-442467696, or mute the thread https://github.com/notifications/unsubscribe-auth/AZQpts_4FlOckxG1M3XSCYMXRIxACHg3ks5uzp8IgaJpZM4Y1XqK .

tonygon commented 5 years ago

wave Hi @melund thanks for the submission. Since you suggested me as an editor I will be performing the editorial duties for this submission. If you have any questions over the review process please feel free to @ me.

Let's start by pinging some suitable reviewers with Python and biomechanics expertise. We can start the review once two or more of them accept the request to review.

Dear reviewers,

@tonygon as suggested: Antonio, are you able to and interested in taking on this review? @marcopus as suggested: Marco, are you able to and interested in taking on this review? @moorepants: Jason, are you able to and interested in taking on this review? @nirum: Niru, are you able to and interested in taking on this review? @acolum: Alyssa, are you able to and interested in taking on this review?

Title: AnyPyTools: A Python package for reproducible research with the AnyBody Modeling System. Summary: AnyPyTools is a toolkit for working with the AnyBody Modeling System (AMS) from Python. It enables reproducible research with the AnyBody Modeling System and bridges the gap to the whole ecosystem of open source scientific Python. Topic: reproducible science, musculoskeletal modelling Article proof: https://github.com/openjournals/joss-papers/blob/joss.01099/joss.01099/10.21105.joss.01099.pdf Submitting author: @melund Repository: https://github.com/AnyBody-Research-Group/AnyPyTools

@trallard I'm able and interested to take the review.

trallard commented 5 years ago

Thanks for the quick response @tonygon and @marcopus I'll wait and see if anyone else can review before jumping into the formal review

trallard commented 5 years ago

@whedon assign @tonygon as reviewer

trallard commented 5 years ago

@whedon add @marcopus as reviewer

whedon commented 5 years ago

OK, @marcopus is now a reviewer

trallard commented 5 years ago

@whedon assign @tonygon as reviewer

whedon commented 5 years ago

OK, the reviewer is @tonygon

trallard commented 5 years ago

@whedon add @marcopus as reviewer

whedon commented 5 years ago

OK, @marcopus is now a reviewer

acolum commented 5 years ago

Hi Tania, I'm also able and interested to take this review. Thanks, Alyssa

trallard commented 5 years ago

@whedon add @acolum as reviewer

whedon commented 5 years ago

OK, @acolum is now a reviewer

trallard commented 5 years ago

Awesome, thanks for agreeing to review this submission @acolum

We can now move onto the review for this submission 🎊🎊

trallard 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/1108. Feel free to close this issue now!

openjournals / joss-reviews

[PRE REVIEW]: AnyPyTools: A Python package for reproducible research with the AnyBody Modeling System. #1099

Let's start by pinging some suitable reviewers with Python and biomechanics expertise. We can start the review once two or more of them accept the request to review.