[REVIEW]: PyQMRI: An accelerated Python based Quantitative MRI Python toolbox #2727

whedon · 2020-10-07T14:09:00Z

Submitting author: @MaierOli2010 (Oliver Maier)
Repository: https://github.com/IMTtugraz/PyQMRI
Version: v1.0.0
Editor: @Kevin-Mattheus-Moerman
Reviewer: @grlee77, @agahkarakuzu, @DARSakthi
Archive: 10.5281/zenodo.4313301

⚠️ JOSS reduced service mode ⚠️

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Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/4578e430042552e15b49d1d72789b72c/status.svg)](https://joss.theoj.org/papers/4578e430042552e15b49d1d72789b72c)

Reviewers and authors:

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Reviewer instructions & questions

@grlee77 & @agahkarakuzu & @DARSakthi, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @grlee77

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@MaierOli2010) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @agahkarakuzu

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@MaierOli2010) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @DARSakthi

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@MaierOli2010) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

The text was updated successfully, but these errors were encountered:

whedon · 2020-10-07T14:09:04Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @grlee77, @ @agahkarakuzu, @DARSakthi it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

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.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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 · 2020-10-07T14:09:16Z

PDF failed to compile for issue #2727 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 - e1e19e2b7e83c454b0cb0797 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in collect!'
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-d14a699185fb/lib/whedon/processor.rb:66:in find_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/bin/whedon:53: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-d14a699185fb/bin/whedon:131: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

'

Kevin-Mattheus-Moerman · 2020-10-07T14:10:38Z

@whedon generate pdf from branch joss-paper

whedon · 2020-10-07T14:10:41Z

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

whedon · 2020-10-07T14:10:55Z

PDF failed to compile for issue #2727 with the following error:

sh: 1: cd: can't cd to 09e65fba2022502e74700760
/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - 09e65fba2022502e74700760 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in collect!'
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-d14a699185fb/lib/whedon/processor.rb:66:in find_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/bin/whedon:53: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-d14a699185fb/bin/whedon:131: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

'

Kevin-Mattheus-Moerman · 2020-10-07T14:15:40Z

@whedon generate pdf from branch JOSS_pub

whedon · 2020-10-07T14:15:43Z

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

whedon · 2020-10-07T14:16:14Z

PDF failed to compile for issue #2727 with the following error:

pandoc-citeproc: reference agahkarakuzu not found
Error producing PDF.
! TeX capacity exceeded, sorry [input stack size=5000].
\reserved@a ->\def \reserved@a
*{\let @xs@assign @xs@expand@and@detokenize...
l.336 }

Looks like we failed to compile the PDF

Kevin-Mattheus-Moerman · 2020-10-07T14:18:48Z

@MaierOli2010 can you check ☝️ that reference?

MaierOli2010 · 2020-10-07T14:21:16Z

@Kevin-Mattheus-Moerman agahkarakuzu should be the git name of one of the reviewers. I do not have any reference that could conatin that name though (just checked the paper.bib file).

Kevin-Mattheus-Moerman · 2020-10-07T15:05:01Z

@openjournals/dev @arfon have a look at this issue ☝️, it looks like when I assigned agahkarakuzu as reviewer over at #2718 they got a double @ in their assigned name, see also at the top of this issue. Looks like that might be causing this.
How will I fix this? Will I remove @ @agahkarakuzu, and add @agahkarakuzu as reviewer again?

arfon · 2020-10-07T15:57:40Z

@whedon generate pdf from branch JOSS_pub

whedon · 2020-10-07T15:57:44Z

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

arfon · 2020-10-07T15:57:57Z

@Kevin-Mattheus-Moerman - I just edited the issue manually.

whedon · 2020-10-07T15:58:27Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

agahkarakuzu · 2020-10-16T16:12:11Z

@Kevin-Mattheus-Moerman I came back to this issue to see the latest changes, then noticed that I still don't appear on the list of reviewers.

Kevin-Mattheus-Moerman · 2020-11-02T10:30:03Z

@agahkarakuzu I think this looks good now right? Can you confirm you are able to tick boxes?

Kevin-Mattheus-Moerman · 2020-11-02T10:31:37Z

@grlee77, @agahkarakuzu, @DARSakthi thanks for your review efforts!!!

If see some of you have left some boxes unticked. If you could summarize for the authors what work is needed that would be great.

Thanks.

agahkarakuzu · 2020-11-02T13:04:26Z

@Kevin-Mattheus-Moerman I cannot check the boxes :/

arfon · 2020-11-02T13:59:36Z

@whedon re-invite @agahkarakuzu as reviewer

Kevin-Mattheus-Moerman · 2020-12-11T21:37:33Z

@whedon generate pdf

Kevin-Mattheus-Moerman · 2020-12-11T21:38:23Z

@whedon generate pdf from branch JOSS_pub

whedon · 2020-12-11T21:38:33Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

whedon · 2020-12-11T21:39:17Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

Kevin-Mattheus-Moerman · 2020-12-11T21:43:25Z

@MaierOli2010 I have two minor points about the paper:

For consistency, can you add "Austria" to the 3rd affiliation?
Should the heading "Algorithmic" be "Algorithms" instead?

MaierOli2010 · 2020-12-12T08:17:53Z

@Kevin-Mattheus-Moerman
Added "Austria" to the 3rd affiliation and renamed "Algorithmic" to "Algorithms"
Both changes are done to "master" branch as I've merged everything there.

Kevin-Mattheus-Moerman · 2020-12-12T08:20:34Z

@whedon generate pdf

whedon · 2020-12-12T08:21:32Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

Kevin-Mattheus-Moerman · 2020-12-12T08:27:42Z

@whedon accept

whedon · 2020-12-12T08:27:45Z

Attempting dry run of processing paper acceptance...

whedon · 2020-12-12T08:28:44Z

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1978

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1978, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

whedon · 2020-12-12T08:29:44Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1137/090769521 is OK
- 10.1002/mrm.27502 is OK
- 10.1007/s10851-010-0251-1 is OK
- 10.1016/j.parco.2011.09.001 is OK
- 10.1016/0167-2789(92)90242-F is OK
- 10.1109/TMI.2016.2564989 is OK
- 10.1002/mrm.22595 is OK
- 10.1109/TMI.2009.2023119 is OK
- 10.1109/TIT.2006.871582 is OK
- 10.1002/mrm.21391 is OK
- 10.1002/mrm.22483 is OK
- 10.1007/978-3-642-54774-4_3 is OK
- 10.24355/dbbs.084-201305311128-0 is OK
- 10.1002/ima.22196 is OK
- 10.1137/16M1092015 is OK
- 10.1007/s10589-012-9476-9 is OK
- 10.1002/mrm.20283 is OK
- 10.1016/j.neuroimage.2019.01.029 is OK
- 10.21105/joss.00656 is OK
- 10.21105/joss.02343 is OK
- 10.3389/fninf.2014.00008 is OK
- 10.1038/nm.3390 is OK
- 10.1016/B978-012372560-8/50002-4 is OK
- 10.1186/s12968-019-0570-3 is OK
- 10.1002/mrm.26726 is OK

MISSING DOIs

- None

INVALID DOIs

- None

Kevin-Mattheus-Moerman · 2020-12-12T08:35:29Z

@whedon accept deposit=true

whedon · 2020-12-12T08:35:33Z

Doing it live! Attempting automated processing of paper acceptance...

whedon · 2020-12-12T08:36:46Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2020-12-12T08:36:46Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02727 joss-papers#1979
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02727
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman · 2020-12-12T08:54:40Z

Congratulations @MaierOli2010!

Thanks for another excellent review @grlee77, @agahkarakuzu, @DARSakthi!!!

whedon · 2020-12-12T09:01:16Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.02727/status.svg)](https://doi.org/10.21105/joss.02727)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02727">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02727/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02727/status.svg
   :target: https://doi.org/10.21105/joss.02727

This is how it will look in your documentation:

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whedon added C Python review Shell labels Oct 7, 2020

whedon assigned Kevin-Mattheus-Moerman Oct 7, 2020

whedon mentioned this issue Oct 7, 2020

[PRE REVIEW]: PyQMRI: An accelerated Python based Quantitative MRI Python toolbox #2718

Closed

lorenanicole mentioned this issue Oct 7, 2020

[PRE REVIEW]: GRLC - the Git Repository Linked data api Constructor #2220

Closed

whedon assigned DARSakthi and grlee77 Oct 8, 2020

whedon assigned agahkarakuzu Oct 17, 2020

whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Dec 12, 2020

whedon added accepted published Papers published in JOSS labels Dec 12, 2020

Kevin-Mattheus-Moerman closed this as completed Dec 12, 2020

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Open

[REVIEW]: PyQMRI: An accelerated Python based Quantitative MRI Python toolbox #2727

[REVIEW]: PyQMRI: An accelerated Python based Quantitative MRI Python toolbox #2727

Comments

whedon commented Oct 7, 2020 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @grlee77

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @agahkarakuzu

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @DARSakthi

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Oct 7, 2020

whedon commented Oct 7, 2020

Kevin-Mattheus-Moerman commented Oct 7, 2020

whedon commented Oct 7, 2020

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Kevin-Mattheus-Moerman commented Oct 7, 2020

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Kevin-Mattheus-Moerman commented Oct 7, 2020

MaierOli2010 commented Oct 7, 2020 • edited Loading

Kevin-Mattheus-Moerman commented Oct 7, 2020

arfon commented Oct 7, 2020

whedon commented Oct 7, 2020

arfon commented Oct 7, 2020

whedon commented Oct 7, 2020

agahkarakuzu commented Oct 16, 2020

Kevin-Mattheus-Moerman commented Nov 2, 2020

Kevin-Mattheus-Moerman commented Nov 2, 2020

agahkarakuzu commented Nov 2, 2020

arfon commented Nov 2, 2020

Kevin-Mattheus-Moerman commented Dec 11, 2020

Kevin-Mattheus-Moerman commented Dec 11, 2020

whedon commented Dec 11, 2020

whedon commented Dec 11, 2020

Kevin-Mattheus-Moerman commented Dec 11, 2020 • edited Loading

MaierOli2010 commented Dec 12, 2020

Kevin-Mattheus-Moerman commented Dec 12, 2020

whedon commented Dec 12, 2020

Kevin-Mattheus-Moerman commented Dec 12, 2020

whedon commented Dec 12, 2020

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Kevin-Mattheus-Moerman commented Dec 12, 2020

whedon commented Dec 12, 2020

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whedon commented Dec 12, 2020

Kevin-Mattheus-Moerman commented Dec 12, 2020

whedon commented Dec 12, 2020

whedon commented Oct 7, 2020 •

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MaierOli2010 commented Oct 7, 2020 •

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Kevin-Mattheus-Moerman commented Dec 11, 2020 •

edited

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