Skip to content

/joss-reviews

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[REVIEW]: VIVO: a system for research discovery #1182

Open
whedon opened this issue Jan 16, 2019 · 17 comments

Comments

Assignees

@jasonclark jasonclark

@sonal-raj sonal-raj

Labels
review
Projects
None yet
Milestone
No milestone
7 participants
@whedon @jasonclark @labarba @sonal-raj @mconlon17 @arfon @danielskatz
@whedon
Copy link
Collaborator

commented Jan 16, 2019 •
edited by sonal-raj

Submitting author: @mconlon17 (Michael Conlon)
Repository: https://github.com/vivo-project/VIVO
Version: v1.10.0
Editor: @jasonclark
Reviewer: @sonal-raj
Archive: Pending

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/d08957ac44d38d23c10f073872c8c5b4"><img src="http://joss.theoj.org/papers/d08957ac44d38d23c10f073872c8c5b4/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/d08957ac44d38d23c10f073872c8c5b4/status.svg)](http://joss.theoj.org/papers/d08957ac44d38d23c10f073872c8c5b4)

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) 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

@sonal-raj, 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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @jasonclark know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @sonal-raj

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 (v1.10.0)?
  • Authorship: Has the submitting author (@mconlon17) 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 jasonclark Jan 16, 2019

@whedon whedon added the review label Jan 16, 2019

@whedon whedon referenced this issue Jan 16, 2019

Closed

[PRE REVIEW]: VIVO: a system for research discovery #943

@whedon

This comment has been minimized.

Sign in to view
Copy link
Collaborator Author

commented Jan 16, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @sonal-raj it looks like you're currently assigned as the reviewer for 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
@whedon

This comment has been minimized.

Sign in to view
Copy link
Collaborator Author

commented Jan 16, 2019 

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Sign in to view
Copy link
Collaborator Author

commented Jan 16, 2019

👉 Check article proof 📄 👈

@jasonclark

This comment has been minimized.

Sign in to view
Copy link

commented Jan 17, 2019

@sonal-raj Thanks for making time for this review later this month. I/We appreciate it. Checklist and instructions are above. Let me know if schedules change. Hope the conference goes well. cc @mconlon17
@labarba

This comment has been minimized.

Sign in to view
Copy link
Member

commented Mar 13, 2019

👋 @sonal-raj — I see from a comment in the Pre-review issue that you agreed to get to this review by the end of January. We have a few items ticked off on your review checklist, so it looks like you did get started! Do you have an idea when you might get finished, though?
@sonal-raj

This comment has been minimized.

Sign in to view
Copy link
Collaborator

commented Mar 13, 2019

@labarba - I am done with most of the review. I will update it by this weekend. Apologies for the delay, been drowning in work of late!
@sonal-raj

This comment has been minimized.

Sign in to view
Copy link
Collaborator

commented Mar 14, 2019

The VIVO software has been reviewed against all the recommended criteria in the checklist. The installation, functionality and documentation are sound and the current version is operational without issues. I recommend the acceptance of this submission.
@labarba

This comment has been minimized.

Sign in to view
Copy link
Member

commented Mar 16, 2019

@jasonclark — this one is ready for your final checks.
@jasonclark

This comment has been minimized.

Sign in to view
Copy link

commented Apr 5, 2019

@whedon generate pdf
@whedon

This comment has been minimized.

Sign in to view
Copy link
Collaborator Author

commented Apr 5, 2019 

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Sign in to view
Copy link
Collaborator Author

commented Apr 5, 2019

👉 Check article proof 📄 👈

@jasonclark

This comment has been minimized.

Sign in to view
Copy link

commented Apr 5, 2019

Hi, @mconlon17. We are close to finishing this paper. There is a final step where you make an archive of the software in Zenodo and report the DOI. Can you do that and let me know the DOI here?
@mconlon17

This comment has been minimized.

Sign in to view
Copy link

commented Apr 5, 2019

Very good to hear. Will do.
@mconlon17

This comment has been minimized.

Sign in to view
Copy link

commented Apr 14, 2019

Here is the DOI: https://doi.org/10.5281/zenodo.2639713
@arfon

This comment has been minimized.

Sign in to view
Copy link
Member

commented Apr 15, 2019 •
edited

@mconlon17 - there are a couple of issues with your paper. One of the grant numbers looks to be a placeholder (xxxxxxx) - could you please address that.

Also, none of the references are included in the body text which means they won't be compiled into the paper pdf. You can read how to do that here.

@whedon whedon assigned sonal-raj May 6, 2019

@danielskatz

This comment has been minimized.

Sign in to view
Copy link

commented May 20, 2019

👋 @mconlon17 - Please note we are waiting for your changes to the paper, as requested by @arfon about 5 weeks ago.
@arfon

This comment has been minimized.

Sign in to view
Copy link
Member

commented May 20, 2019

I should have updated here to say I emailed the author last night about this and he replied immediately. I would expect an update shortly.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
You can’t perform that action at this time.