Joss-reviews: [REVIEW]: GIBBON: The Geometry and Image-Based Bioengineering add-ON

Created on 14 Dec 2017 · 45Comments · Source: openjournals/joss-reviews

Submitting author: @Kevin-Mattheus-Moerman (Kevin Moerman)
Repository: https://github.com/gibbonCode/GIBBON
Version: v3.0.0
Editor: @cMadan
Reviewer: @siboles
Archive: 10.5281/zenodo.1175348

Status

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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

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

Make sure you're logged in to your GitHub account
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 @cMadan know.

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

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

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Version: Does the release version given match the GitHub release (v2.5.0)?
[x] Authorship: Has the submitting author (@Kevin-Mattheus-Moerman) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

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

accepted published recommend-accept review

Source

whedon

Most helpful comment

I am very happy, indeed!

wspr on 14 Feb 2018

🎉2

All 45 comments

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @siboles it looks like you're currently assigned as the reviewer for this paper :tada:.

:star: Important :star:

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:

watching

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 on 14 Dec 2017

Attempting PDF compilation. Reticulating splines etc...

whedon on 14 Dec 2017

https://github.com/openjournals/joss-papers/blob/joss.00506/joss.00506/10.21105.joss.00506.pdf

whedon on 14 Dec 2017

@cMadan will you add an additional checklist for @wspr? I did this here by simply manually editing the tick box comment and coping in an additional tick box list. You also need to invite the second reviewer (ping @arfon for that) so they can be assigned to the issue and tick boxes.

Kevin-Mattheus-Moerman on 14 Dec 2017

Thanks for also agreeing to review, @wspr! Below is the reviewer checklist for you to fill out.

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

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

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Version: Does the release version given match the GitHub release (v2.5.0)?
[x] Authorship: Has the submitting author (@Kevin-Mattheus-Moerman) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

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

cMadan on 16 Dec 2017

@wspr let me know if I can help with anything. See testGibbon to run all tests.

Kevin-Mattheus-Moerman on 22 Dec 2017

@siboles, is it safe to assume that you are now satisfied with the submission and endorse it's acceptance in the current form?

@Kevin-Mattheus-Moerman, I'll still wait for @wspr, but thought I'd get that confirmation from @siboles, rather than checking later on.

cMadan on 22 Dec 2017

Hi all — the end of the year hit me rather suddenly so I haven’t had a chance to fully investigate. If you could wait a little longer (say, before the end of the year) I’d be very happy to put in my 2c as well, but if you’d rather knock it on the head immediately I am happy to give it a miss. Sorry for the hold up.

wspr on 23 Dec 2017

@wspr, I have no problem waiting a bit longer. Also feel free to take some time into January too (I'd hate to have reviewing take away from holiday plans).

That said, can you check if that second checklist works for you? If not, I'll have to see about permissions...

cMadan on 23 Dec 2017

@cMadan Checklist doesn’t work I’m afraid — if it’s a hassle I can just paste in my own :-)

wspr on 23 Dec 2017

@wspr - if you accept the invite link here: https://github.com/openjournals/joss-reviews/invitations you should be able to edit the checklist.

arfon on 24 Dec 2017

👍1

@cMadan @Kevin-Mattheus-Moerman Very sorry folks for the slow reply. Yes I am satisfied with GIBBON and
vote to accept it for publication.

On Dec 23, 2017 19:10, "Arfon Smith" notifications@github.com wrote:

@wspr https://github.com/wspr - if you accept the invite link here:
https://github.com/openjournals/joss-reviews/invitations you should be
able to edit the checklist.

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/openjournals/joss-reviews/issues/506#issuecomment-353760940,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AGOj72WqzsBHbsQo8YfK4WOjWltAtEqnks5tDbKJgaJpZM4RBVG9
.

siboles on 26 Dec 2017

👍1

No worries, @siboles! Thanks again for the review and enjoy the holidays :)

cMadan on 27 Dec 2017

@Kevin-Mattheus-Moerman - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

arfon on 10 Jan 2018

@Kevin-Mattheus-Moerman - ignore that. We're waiting for a second review here right?

arfon on 10 Jan 2018

@arfon Yes indeed. @wspr let me know if you need any help, looking forward to your comments.

Kevin-Mattheus-Moerman on 10 Jan 2018

@wspr, do you still have time/interest in doing a review of this submission? Please let me know either way.

cMadan on 21 Jan 2018

I've been working on @wspr 's comments. He had opened some issues on my repo which I believe I've addressed. There may be more to come but I'll let him comment on that.

Kevin-Mattheus-Moerman on 21 Jan 2018

@cMadan — sorry this dragged on a little; I think I'm basically there.

@Kevin-Mattheus-Moerman — did you see my last message for testing out the git update-index --chmod=+x lib_ext/tetGen/mac64/tetgen thing? I believe if you run that on your end then commit, I'll be able to check and confirm. The one thing I'm not sure about is how many more of these are needed; I guess it can't hurt to also run on the lin64 script as well.

wspr on 22 Jan 2018

👍1

Minor comments in the linked review for the text of the paper, and now good to proceed. Thanks for your patience with my review — and let me know if there's more I can do to help out.

wspr on 22 Jan 2018

Thank you for the review, @wspr! I think you're all done.

@Kevin-Mattheus-Moerman, let me know when you've made these minor changes to the paper. After that's done, please let me know the DOI for the archive.

cMadan on 22 Jan 2018

@Kevin-Mattheus-Moerman, just thought I'd check in--are you still working on @wspr's suggestions? No rush, just wanted to make sure you weren't waiting on something from me :)

cMadan on 12 Feb 2018

@whedon generate pdf