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

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whedon opened this issue Aug 9, 2019 · 20 comments

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commented Aug 9, 2019 •
edited by arokem

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: Pending

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 & @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

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)?

Review checklist for @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)?

@whedon whedon assigned arokem Aug 9, 2019

@whedon whedon added the review label Aug 9, 2019

@whedon whedon referenced this issue Aug 9, 2019

Closed

[PRE REVIEW]: Virtual Scanner: MRI on a Browser #1590

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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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commented Aug 9, 2019 

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

👉 Check article proof 📄 👈

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commented Aug 9, 2019

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

This was referenced Aug 9, 2019

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@whedon whedon assigned vsoch Aug 10, 2019

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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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commented Aug 14, 2019

Great, thanks for the update @mathieuboudreau.
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commented Aug 14, 2019

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

This was referenced Aug 14, 2019

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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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commented Aug 14, 2019

OK, @mathieuboudreau is now a reviewer
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commented Aug 14, 2019

Sorry about that. Does it work now that I added you as a reviewer?
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commented Aug 14, 2019

I just checked, and no unfortunately not.
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commented Aug 14, 2019 •
edited

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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commented Aug 14, 2019

How about now, that I've added a section for you at the top.
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commented Aug 14, 2019

Still unable, sorry.
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commented Aug 14, 2019

@mathieuboudreau here is the markdown https://gist.github.com/vsoch/c9f65143293acb975af251608b314579

Just view the raw, make changes somewhere that I can view raw (another gist) and I'll copy paste it in for you.

@mathieuboudreau mathieuboudreau referenced this issue Aug 14, 2019

Closed

JOSS REVIEW: Running exam results in ModuleNotFoundError: No module named 'virtualscanner' #27

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commented Aug 14, 2019

@arfon needs to invite @mathieuboudreau to the org...
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commented Aug 14, 2019

@mathieuboudreau - did you accept in the invite to the organization here? https://github.com/openjournals/joss-reviews/invitations
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commented Aug 14, 2019

Ahh, I must of missed the notification of that invite - my apologies. It works now!
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