[REVIEW]: A Julia package for bilevel optimization problems

whedon commented 5 years ago

Submitting author: @matbesancon (Mathieu Besançon) Repository: https://github.com/matbesancon/BilevelOptimization.jl Version: v0.2.1 Editor: @poulson Reviewer: @HaoZeke, @vissarion Archive: 10.5281/zenodo.3249188

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/78ebab36f82fc977eb78b989aeb2f972"><img src="http://joss.theoj.org/papers/78ebab36f82fc977eb78b989aeb2f972/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/78ebab36f82fc977eb78b989aeb2f972/status.svg)](http://joss.theoj.org/papers/78ebab36f82fc977eb78b989aeb2f972)

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

@HaoZeke & @vissarion, 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 @poulson know.

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

Review checklist for @HaoZeke

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: v0.2.1
[x] Authorship: Has the submitting author (@matbesancon) 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 @vissarion

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: v0.2.1
[x] Authorship: Has the submitting author (@matbesancon) 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?
[ ] 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 commented 5 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @HaoZeke, 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 commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

HaoZeke commented 5 years ago

Hi, @matbesancon I've initiated the review process and hope to finish in the next couple of days. I will be opening pull requests and issues on the repository tracker, but I might also ask for clarifications here (typically with matters pertaining to the paper itself). In addition, for the paper.md, I request that a copy to make changes on hackmd.io is made available to me and @vissarion since it is not appropriate to make changes to it via pull requests.

HaoZeke commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

whedon commented 5 years ago


OK DOIs

- http://doi.org/10.1007/s00446-006-0020-y is OK
- http://doi.org/10.1109/TPWRS.2019.2892607 is OK

MISSING DOIs

- https://doi.org/10.1007/978-1-4613-0307-7_12 may be missing for title: Bilevel optimization: theory, algorithms and applications
- https://doi.org/10.1137/15m1020575 may be missing for title: JuMP: A modeling language for mathematical optimization
- https://doi.org/10.1287/trsc.35.4.345.10433 may be missing for title: A bilevel model for toll optimization on a multicommodity transportation network
- https://doi.org/10.1016/j.ejor.2019.01.059 may be missing for title: Toll Caps in Privatized Road Networks

INVALID DOIs

- None

HaoZeke commented 5 years ago

@matbesancon, please update the paper.md file to fix the missing DOIs.

matbesancon commented 5 years ago

The hackmd can be found there: https://hackmd.io/s/B1e2UUNIE#

matbesancon commented 5 years ago

@HaoZeke the first DOI seems invalid (the preprint does not correspond to the article suggested), I'm fixing the others in https://github.com/matbesancon/BilevelOptimization.jl/pull/9

matbesancon commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

whedon commented 5 years ago


OK DOIs

- http://doi.org/10.1137/15m1020575 is OK
- http://doi.org/10.1287/trsc.35.4.345.10433 is OK
- http://doi.org/10.1007/s00446-006-0020-y is OK
- http://doi.org/10.1016/j.ejor.2019.01.059 is OK
- http://doi.org/10.1109/TPWRS.2019.2892607 is OK

MISSING DOIs

- https://doi.org/10.1007/978-1-4613-0307-7_12 may be missing for title: Bilevel optimization: theory, algorithms and applications

INVALID DOIs

- None

matbesancon commented 5 years ago

missing DOI still invalid

HaoZeke commented 5 years ago

Yeah, we'll just have to let that one go. It does not seem to correspond to any DOI. Even the ISSN number does not seem valid. @matbesancon

matbesancon commented 5 years ago

yup I just saw it is considered as a book and not article on google scholar now, I'll update the bib

matbesancon commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

matbesancon commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

whedon commented 5 years ago


OK DOIs

- http://doi.org/10.1137/15m1020575 is OK
- http://doi.org/10.1287/trsc.35.4.345.10433 is OK
- http://doi.org/10.1007/s00446-006-0020-y is OK
- http://doi.org/10.1016/j.ejor.2019.01.059 is OK
- http://doi.org/10.1109/TPWRS.2019.2892607 is OK

MISSING DOIs

- None

INVALID DOIs

- None

poulson commented 5 years ago

:wave: @HaoZeke, just checking in as it's been about a week since any comments were provided. I know that reviewing requires a significant amount of your (volunteered!) time and appreciate your commitment on this.

HaoZeke commented 5 years ago

Sorry I was hospitalized in a road accident. I'll be discharged today but have some appointments with an orthodontist... I might take a few days before I get home and am able to finish.

From: Jack Poulson notifications@github.com Sent: Thursday, March 7, 2019 8:00 AM To: openjournals/joss-reviews Cc: Rohit Goswami; Mention Subject: Re: [openjournals/joss-reviews] [REVIEW]: A Julia package for bilevel optimization problems (#1278)

👋 @HaoZeke, just checking in as it's been about a week since any comments were provided. I know that reviewing requires a significant amount of your (volunteered!) time and appreciate your commitment on this.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

matbesancon commented 5 years ago

sorry to read that, great recover! :/

poulson commented 5 years ago

@HaoZeke I am so sorry to hear about the accident but am glad to hear you are okay. Please excuse the distraction of my message; your recovery is obviously much more important.

HaoZeke commented 5 years ago

Thank you @matbesancon and @poulson for your kind wishes and for waiting so long. I have finally recovered enough to complete this review. I believe everything is in order.. Sorry the final signing off was delayed so much.

matbesancon commented 5 years ago

Absolutely no trouble, glad to hear you're doing good

poulson commented 5 years ago

:wave: @vissarion -- it's been a little while and the other reviewer has provided their feedback. Would you be able to provide your input some time in the near future?

vissarion commented 5 years ago

@poulson sorry for being inactive here, I can do it by the end of next week if this is not an issue.

vissarion commented 5 years ago

Hello, and again sorry for the late review. It is now complete. I raised an issue here: https://github.com/matbesancon/BilevelOptimization.jl/issues/14 regarding documentation.

matbesancon commented 5 years ago

thanks, on it today

vissarion commented 5 years ago

@matbesancon thanks for addressing the issue on documentation. I closed https://github.com/matbesancon/BilevelOptimization.jl/issues/14 and finished my review check-list.

matbesancon commented 5 years ago

@vissarion thanks for the discussion, I will adapt the paper to also include the signatures of build_blp_model

matbesancon commented 5 years ago

@whedon generate pdf from branch doc-joss

whedon commented 5 years ago

Attempting PDF compilation from custom branch doc-joss. Reticulating splines etc...

whedon commented 5 years ago

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

matbesancon commented 5 years ago

@whedon generate pdf from branch doc-joss

whedon commented 5 years ago

Attempting PDF compilation from custom branch doc-joss. Reticulating splines etc...

whedon commented 5 years ago

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

matbesancon commented 5 years ago

@whedon generate pdf from branch doc-joss

whedon commented 5 years ago

Attempting PDF compilation from custom branch doc-joss. Reticulating splines etc...

whedon commented 5 years ago

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

matbesancon commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

labarba commented 5 years ago

👋 @HaoZeke, @vissarion — it looks like this submission is ready for you to take a second look now, and possibly make a recommendation?

HaoZeke commented 5 years ago

@labarba, having taken a second look, I believe all previous concerns raised were addressed and I would recommend that this be accepted.

poulson commented 5 years ago

Thank you, @HaoZeke!

@vissarion: you still haven't checked the 'Performance' box. It would be great to get a response from you on this and whether or not you feel this submission is ready for acceptance.

vissarion commented 5 years ago

@poulson I recommend acceptance. However, I am not clicking the box because, as far as I understand, there are no performance claims by the submitted software to confirm.

openjournals / joss-reviews