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[PRE REVIEW]: qMRLab: Quantitative MRI Analysis, under one umbrella #2188

Closed whedon closed 4 years ago

whedon commented 4 years ago

Submitting author: @agahkarakuzu (Agah Karakuzu) Repository: https://github.com/qMRLab/qMRLab Version: v2.4.0 Editor: @Kevin-Mattheus-Moerman Reviewers: @grlee77, @mfroeling, @62442katieb Managing EiC: Arfon Smith

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Author instructions

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

@agahkarakuzu if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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
whedon commented 4 years ago

PDF failed to compile for issue #2188 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/2188 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:incollect!' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon/processor.rb:61:infind_paper_paths' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' 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:indispatch' 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-45a043c4bfc2/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

'

whedon commented 4 years ago 
Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.21105/joss.00656 may be missing for title: QUIT: QUantitative imaging tools
- https://doi.org/10.1016/b978-012372560-8/50002-4 may be missing for title: Statistical parametric mapping
- https://doi.org/10.1101/343079 may be missing for title: Let’s talk about cardiac T1 mapping
- https://doi.org/10.1016/j.softx.2019.100369 may be missing for title: Total Mapping Toolbox (TOMATO): An open source library for cardiac magnetic resonance parametric mapping
- https://doi.org/10.4135/9781412950657.n33 may be missing for title: The cathedral and the bazaar

INVALID DOIs

- None
arfon commented 4 years ago

Whedon is struggling with compiling the paper here as the repository is very large (~500Mb) - it might be a good idea to look at reducing this @agahkarakuzu. For now, I have compiled the paper locally: 10.21105.joss.02188.pdf

👋 @cMadan - would you be able to take this paper? Ariel would be the ideal editor but he's unable to edit for JOSS right now.

agahkarakuzu commented 4 years ago

Hi @arfon, thank you for the quick response and the feedback!

The repo had some large files in the past, hence the large size with deep clone depth. Right now the documentation files are stored in this repo, moving them elsewhere would free some considerable space, but the same issue would still persist with clone. Do you have a suggestion how we might approach this?

We discussed with the team about removing the large files from the history, but it looked like a tricky operation, so we did not act on it.

mathieuboudreau commented 4 years ago

@arfon (Hi, one of @agahkarakuzu 's coauthors here) Does Whedon clone the entire repo's git history, or just the master branch and/or a single commit of it?

arfon commented 4 years ago

@whedon generate pdf

arfon commented 4 years ago

@arfon (Hi, one of @agahkarakuzu 's coauthors here) Does Whedon clone the entire repo's git history, or just the master branch and/or a single commit of it?

It does a full clone. I could investigate how to do a shallow clone.

arfon commented 4 years ago

I've done a little digging here and it turns out we need the full history for calculating things like the repository statistics.

We discussed with the team about removing the large files from the history, but it looked like a tricky operation, so we did not act on it.

This is the only thing that will truly fix this issue but it's not essential for the JOSS review as I can compile the paper locally and update the thread with the PDF as we go.

That said, I would encourage you to address this issue as all of your future users will have to clone a very large repository which isn't a great user experience.

Kevin-Mattheus-Moerman commented 4 years ago

@arfon I can take this one if @cMadan can't

arfon commented 4 years ago

Thanks @Kevin-Mattheus-Moerman. Feel free to grab this now if you feel able to handle it.

Kevin-Mattheus-Moerman commented 4 years ago

@whedon assign @Kevin-Mattheus-Moerman as editor

whedon commented 4 years ago

OK, the editor is @Kevin-Mattheus-Moerman

Kevin-Mattheus-Moerman commented 4 years ago

@mfroeling, @oliverchampion, @grlee77, @JoshKarpel, @rljacobson, @angielaird, @Lestropie would you be interested in reviewing: qMRLab: Quantitative MRI Analysis, under one umbrella, for JOSS (the Journal of Open Source Software). The review takes place on GitHub and focuses on the software and this short paper: https://github.com/openjournals/joss-reviews/files/4662829/10.21105.joss.02188.pdf

If you agree to review this work you can let me know here and I'll add you as a reviewer. Once I have sufficient reviewers I'll open a dedicated review issues.

Thanks!

grlee77 commented 4 years ago

Yes, I can review this

Kevin-Mattheus-Moerman commented 4 years ago

@whedon add @grlee77 as reviewer

whedon commented 4 years ago

OK, @grlee77 is now a reviewer

Kevin-Mattheus-Moerman commented 4 years ago

@mfroeling, @oliverchampion, @JoshKarpel, @rljacobson, @Lestropie, @mriedel56 @62442katieb would you be interested in reviewing: qMRLab: Quantitative MRI Analysis, under one umbrella, for JOSS (the Journal of Open Source Software). The review takes place on GitHub and focuses on the software and this short paper: https://github.com/openjournals/joss-reviews/files/4662829/10.21105.joss.02188.pdf

If you agree to review this work you can let me know here and I'll add you as a reviewer. Once I have sufficient reviewers I'll open a dedicated review issues.

Thanks!

JoshKarpel commented 4 years ago

I am not familiar with either QMRI or MATLAB, so I think I should pass. Thanks for the offer!

rljacobson commented 4 years ago

@Kevin-Mattheus-Moerman Unfortunately, I am unavailable.

mriedel56 commented 4 years ago

Hi @Kevin-Mattheus-Moerman, I dont think I’m knowledgeable enough about qMRI to provide a sufficient review; but happy to be considered for other submissions.

Lestropie commented 4 years ago

While I would like to do so and familiarise myself with JOSS prior to hopefully submitting my own work there in the future, I unfortunately cannot commit to a thorough review right now due to other obligations. But thank you for the offer.

Kevin-Mattheus-Moerman commented 4 years ago

@mfroeling agreed to review in an email, thanks Martijn

Kevin-Mattheus-Moerman commented 4 years ago

@whedon add @mfroeling as reviewer

whedon commented 4 years ago

OK, @mfroeling is now a reviewer

Kevin-Mattheus-Moerman commented 4 years ago

@Lestropie @mriedel56 @rljacobson understood, and thanks for your reply

Kevin-Mattheus-Moerman commented 4 years ago

@62442katieb @exmakhina @cMadan @WIAS-BERLIN @JPolzehl would you be interested in reviewing: qMRLab: Quantitative MRI Analysis, under one umbrella, for JOSS (the Journal of Open Source Software).

The review takes place on GitHub and focuses on the software and this short paper: https://github.com/openjournals/joss-reviews/files/4662829/10.21105.joss.02188.pdf

If you agree to review this work you can let me know here and I'll add you as a reviewer. Once I have sufficient reviewers I'll open a dedicated review issue.

Thanks!

62442katieb commented 4 years ago

Hi @Kevin-Mattheus-Moerman, I'd be happy to review.

Kevin-Mattheus-Moerman commented 4 years ago

@whedon add @62442katieb as reviewer

whedon commented 4 years ago

OK, @62442katieb is now a reviewer

Kevin-Mattheus-Moerman commented 4 years ago

@whedon start review

whedon commented 4 years ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2343.