Joss-reviews: [REVIEW]: pfla: A Python Package for Dental Facial Analysis using Computer Vision and Statistical Shape Analysis

[whedon]

Submitting author: @maxrousseau (Maxime Rousseau)
Repository: https://github.com/maxrousseau/pfla
Version: v0.1.4
Editor: @arokem
Reviewer: @glemaitre, @mnarayan
Archive: 10.5281/zenodo.1761769

Status

Status badge code:

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Markdown: [![status](http://joss.theoj.org/papers/d86beb0eb37afd606630b2535e88c4a2/status.svg)](http://joss.theoj.org/papers/d86beb0eb37afd606630b2535e88c4a2)

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

@glemaitre & @mnarayan, 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 @arokem know.

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

Review checklist for @glemaitre

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 (v0.1.4)?
• [x] Authorship: Has the submitting author (@maxrousseau) 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)?

Review checklist for @mnarayan

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 (v0.1.4)?
• [x] Authorship: Has the submitting author (@maxrousseau) 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)?

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @glemaitre, 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:

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

1. 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

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[maxrousseau]

Is there an issue with my paper.md? The file still has not been compiled to a pdf.

[arfon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[maxrousseau]

Thank you @arfon!

[arokem]

@glemaitre : have you been able to resolve the installation issue mentioned in https://github.com/maxrousseau/pfla/issues/4?

@mnarayan : have you had a chance to take a look at this?

[glemaitre]

I did not have time last week. I should be able to finish up the review this week.

Sent from my phone - sorry to be brief and potential misspell.

[mnarayan]

I have looked at the repository and it still needs some work. Will finish submitting all the issues around documentation this weekend.

As of now I see problems in community guidelines https://github.com/maxrousseau/pfla/issues/5 and the software paper
https://github.com/maxrousseau/pfla/issues/6

[maxrousseau]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[arokem]

@glemaitre : have you had a chance to take a look?

@mnarayan : did the author address your issues to your satisfaction? Any more issues?

[glemaitre]

I open 2 issues which need to be addressed (for unit testing and file fetching).
I need to open another one but if those could be addressed first, it could be great.

[maxrousseau]

I am working on the installation instruction and will move to the other issues as soon as possible.

[maxrousseau]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[maxrousseau]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[maxrousseau]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[maxrousseau]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[maxrousseau]

Hello @arokem!
Any updates on the review process?
Thank you

[arokem]

@mnarayan : I see that all your issues on the software repo are closed. Does that mean that the software now meets all the criteria in your estimation?

@glemaitre : have you had a chance to take a look whether the issues you raised were properly addressed?

[arokem]

@glemaitre, @mnarayan: any word about this review?

[maxrousseau]

Hello @arokem, @glemaitre and @mnarayan!
Is it possible to confirm that this is still under active review?
Thank you

[mnarayan]

I am satisfied with all the corrections and have no more issues to raise.

[maxrousseau]

@mnarayan Perfect! I think you still need to finish checking the boxes of your review section (above) for the paper to be published.

[arokem]

@glemaitre : could you please confirm that you are still reviewing this?

Is there anything left to do from your perspective?

[glemaitre]

I will have a final look in this week. 

[maxrousseau]

@glemaitre: Any final thoughts?

[glemaitre]

Sorry for the delay regarding this review. Let me book some time in
the week to finalize it.
Since that you have the +1 of @mnarayan, I assume that it should be ok.

[maxrousseau]

@glemaitre: Have you had time to take a look?

[arokem]

@whedon render pdf

[arokem]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[arokem]

OK. Since this review has gone on for a while, one reviewer has already provided a +1, and since the author has addressed the issues raised by the remaining reviewer, I'm going to call it.

@mnarayan, @glemaitre : thanks for your reviews!

@maxrousseau : your article is ready to be accepted by JOSS.

To proceed, please create an archive of the accepted version of the software (e.g., using zenodo) and post the DOI here for archiving.

[maxrousseau]

Thank you!

[maxrousseau]

EDIT: DO NOT USE, OLD RELEASE

[glemaitre]

I just made a PR to correct the last glitch. Nothing important regarding the paper.

[arokem]

@maxrousseau : would you like to include @glemaitre's additional suggestion in the version that will go along with the paper? If so, please create another archived version.

[maxrousseau]

perfect just pushed the fixed docs and will accept the pull request as soon as it passes the CI

[maxrousseau]

@arokem: I have just merge @glemaitre 's PR, I will be creating a new archive soon.

[glemaitre]

@maxrousseau you could also make a PyPi release at the same time.

[maxrousseau]

@arokem: Here is the final version DOI for publication -->

Thank you @glemaitre and @mnarayan for your reviews.

[maxrousseau]

@glemaitre I just made PyPi release 0.2.2

[arokem]

@whedon set 10.5281/zenodo.1761769 as archive

[whedon]

OK. 10.5281/zenodo.1761769 is the archive.

[arokem]

@arfon : I believe this article is ready to go!

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/94

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/94, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[arfon]

@whedon accept deposit=true

[whedon]

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

[whedon]

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/95
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.00855
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...

[maxrousseau]

All looks good! Thank you all!

[arfon]

@glemaitre, @mnarayan - many thanks for your reviews here and to @arokem for editing this submission ✨

@maxrousseau - your paper is now accepted into JOSS :zap::rocket::boom:

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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