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[REVIEW]: Virtual Scanner: MRI on a Browser #1637

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whedon opened this issue Aug 9, 2019 · 86 comments
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@whedon whedon commented Aug 9, 2019

Submitting author: @imr-framework (Sairam Geethanath)
Repository: https://github.com/imr-framework/virtual-scanner
Version: 1.0.0
Editor: @arokem
Reviewers: @nstikov, @vsoch, @mathieuboudreau
Archive: 10.5281/zenodo.3550315

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/45280f505cac55a966f8842a651ef48a"><img src="https://joss.theoj.org/papers/45280f505cac55a966f8842a651ef48a/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/45280f505cac55a966f8842a651ef48a/status.svg)](https://joss.theoj.org/papers/45280f505cac55a966f8842a651ef48a)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@nstikov, @mathieuboudreau, & @vsoch, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @arokem know.

Please try and complete your review in the next two weeks

Review checklist for @nstikov & @mathieuboudreau

Conflict of interest

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?
  • Version: Does the release version given match the GitHub release (1.0.0)?
  • Authorship: Has the submitting author (@imr-framework) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @vsoch

Conflict of interest

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?
  • Version: Does the release version given match the GitHub release (1.0.0)?
  • Authorship: Has the submitting author (@imr-framework) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
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@whedon whedon commented Aug 9, 2019

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

⭐️ 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:

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

watching

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

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
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@whedon whedon commented Aug 9, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Aug 9, 2019

@vsoch

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@vsoch vsoch commented Aug 9, 2019

Wowza this is my third this week, will get started when I can!

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@mathieuboudreau mathieuboudreau commented Aug 14, 2019

Just as a clarifying point, I am reviewing this in tandem with @nstikov (I'm a research fellow of his), and will likely be the one most active out of both of us in this discussion/review on GitHub. This was determined in the pre-review (#1590)

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@vsoch vsoch commented Aug 14, 2019

Great, thanks for the update @mathieuboudreau.

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@mathieuboudreau mathieuboudreau commented Aug 14, 2019

@vsoch is it possible to make me able to edit the checklist status?

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@vsoch vsoch commented Aug 14, 2019

You can't click in the top right and see this menu?

image

If not, I think @arokem would need to add you as a collaborator or with appropriate permissions to do that. Worst case, I can offer to update it for you (note that I'm another reviewer, not an editor).

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@mathieuboudreau mathieuboudreau commented Aug 14, 2019

Ahh sorry, I didn't realize your were another reviewer, sorry about that!

No, I don't have access to Edit, as only @nstikov was assigned as the sole reviewer instead of both of us for "his" review.

Capture d’écran 2019-08-14 à 14 49 07

@arokem can this be resolved?

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@arokem arokem commented Aug 14, 2019

@whedon add @mathieuboudreau as reviewer

@whedon whedon assigned arokem, mathieuboudreau and vsoch and unassigned arokem and vsoch Aug 14, 2019
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@whedon whedon commented Aug 14, 2019

OK, @mathieuboudreau is now a reviewer

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@arokem arokem commented Aug 14, 2019

Sorry about that. Does it work now that I added you as a reviewer?

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@mathieuboudreau mathieuboudreau commented Aug 14, 2019

I just checked, and no unfortunately not.

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@mathieuboudreau mathieuboudreau commented Aug 14, 2019

If it's too much trouble, I could just keep track of them and ask @nstikov to check them off in bulk periodically.

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@arokem arokem commented Aug 14, 2019

How about now, that I've added a section for you at the top.

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@kthyng kthyng commented Nov 21, 2019

great, @tonggehua, this looks better. Report it back here when you have your Zenodo archive.

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@tonggehua tonggehua commented Nov 21, 2019

@whedon generate pdf

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@whedon whedon commented Nov 21, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 21, 2019

@tonggehua

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@tonggehua tonggehua commented Nov 25, 2019

@kthyng Here is the DOI : 10.5281/zenodo.3550315

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@kthyng kthyng commented Nov 25, 2019

@whedon set 10.5281/zenodo.3550315 as archive

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@whedon whedon commented Nov 25, 2019

OK. 10.5281/zenodo.3550315 is the archive.

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@kthyng kthyng commented Nov 25, 2019

@whedon accept

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@whedon whedon commented Nov 25, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Nov 25, 2019


OK DOIs

- 10.1002/mrm.26235 is OK
- 10.1016/j.mri.2018.03.008 is OK
- 10.1016/j.jmr.2017.05.007 is OK
- 10.1002/mrm.24138 is OK
- 10.1002/mrm.1910150117 is OK
- 10.1126/science.1925560 is OK
- 10.1002/jmri.26638 is OK
- 10.1002/mrm.22406 is OK
- 10.1002/mrm.25528 is OK
- 10.1088/0022-3719/10/3/004 is OK
- 10.1007/s12045-015-0268-2 is OK

MISSING DOIs

- https://doi.org/10.1016/j.crad.2003.09.015 may be missing for title: MRI from Picture to Proton

INVALID DOIs

- None
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@whedon whedon commented Nov 25, 2019

Check final proof 👉 openjournals/joss-papers#1129

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1129, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@kthyng kthyng commented Nov 25, 2019

@imr-framework, @tonggehua I have added the doi stated as missing in the previous references check in PR 43 if you want to merge

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@tonggehua tonggehua commented Nov 25, 2019

@kthyng Thank you! I merged it.

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@kthyng kthyng commented Nov 25, 2019

@whedon generate pdf

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@whedon whedon commented Nov 25, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 25, 2019

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@kthyng kthyng commented Nov 25, 2019

@whedon accept

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@whedon whedon commented Nov 25, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Nov 25, 2019


OK DOIs

- 10.1002/mrm.26235 is OK
- 10.1016/j.mri.2018.03.008 is OK
- 10.1016/j.jmr.2017.05.007 is OK
- 10.1002/mrm.24138 is OK
- 10.1002/mrm.1910150117 is OK
- 10.1126/science.1925560 is OK
- 10.1002/jmri.26638 is OK
- 10.1002/mrm.22406 is OK
- 10.1002/mrm.25528 is OK
- 10.1088/0022-3719/10/3/004 is OK
- 10.1007/s12045-015-0268-2 is OK
- 10.1016/j.crad.2003.09.015 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Nov 25, 2019

Check final proof 👉 openjournals/joss-papers#1130

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1130, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@kthyng kthyng commented Nov 25, 2019

@whedon accept deposit=true

@whedon whedon added the accepted label Nov 25, 2019
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@whedon whedon commented Nov 25, 2019

Doing it live! Attempting automated processing of paper acceptance...
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@whedon whedon commented Nov 25, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Nov 25, 2019

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#1131
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01637
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

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@kthyng kthyng commented Nov 25, 2019

Congratulations to @imr-framework, @tonggehua on your new paper!!

Thanks to @arokem for editing and @nstikov, @vsoch, @mathieuboudreau for reviewing... this wouldn't be possible without your time and expertise! 🎉 🎉

@kthyng kthyng closed this Nov 25, 2019
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@whedon whedon commented Nov 25, 2019

🎉🎉🎉 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.01637/status.svg)](https://doi.org/10.21105/joss.01637)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01637">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01637/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01637/status.svg
   :target: https://doi.org/10.21105/joss.01637

This is how it will look in your documentation:

DOI

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Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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@vsoch vsoch commented Nov 25, 2019

Congrats @imr-framework, @tonggehua you guys worked hard on this!

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@mathieuboudreau mathieuboudreau commented Nov 25, 2019

Congrats - well done!

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