search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
721 stars 38 forks source link

[REVIEW]: A Julia package for bilevel optimization problems #1278

Closed whedon closed 5 years ago

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

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:

  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 @poulson know.

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

Review checklist for @HaoZeke

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @vissarion

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

kyleniemeyer commented 5 years ago

Hi @poulson, checking on on this review—it looks like both reviewers have given their ok.

poulson 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:

poulson commented 5 years ago

@matbesancon Would you mind fixing the following typo/grammatical/citation/clarification issues?

"at the two level" -> "at the two levels"

"with possibly a disjoint feasible set" -> "with a possibly disjoint feasible set"

"solving method" -> "solver"

"for such case" -> "for such cases"

"the two principal being" -> "with the two primary approaches being" [Citations needed for what the two approaches roughly are.]

Clarification: "into a regular one"? [Citation of Special Ordered Sets of type 1]

"forcing at least one of them to 0" -> "forcing at least one of them to zero"

"m the JuMP model" -> "m: the JuMP model,", etc., adding an "and" in the second-to-last item.

"Where CM is the complementarity" -> "where CM is the..."

"Each arc has an initial cost, the lower-level" -> "Each arc has an initial cost, and the lower-level"

"This problem can entirely be modeled using the framework presented above, a" -> "This problem can be entirely modeled using the framework presented above, using a composite datatype defined in the package for holding all required data,"

Add commas and an "and" in the final list, such as: "The initial matrix of arc costs init_cost,"

"Even though BilevelOptimization.jl is thought for" -> "Even though BilevelOptimization.jl is typically for"

After doing so, could you register a DOI on zenodo and post it here?

danielskatz commented 5 years ago

👋 @matbesancon - this review is waiting on you to make changes and then to archive the repo.

matbesancon commented 5 years ago

apologies to all for the delays! I'll edit the paper with @poulson's comments

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

I'm registering a new version to trigger the DOI creation from Zenodo

matbesancon commented 5 years ago

The version of the software is v0.2.1, the corresponding DOI is 10.5281/zenodo.3249188

poulson commented 5 years ago

@whedon commands

whedon commented 5 years ago

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to accept the paper and deposit with Crossref
@whedon accept

# Ask Whedon to check the references for missing DOIs
@whedon check references
poulson commented 5 years ago

@whedon set v0.2.1 as version

whedon commented 5 years ago

OK. v0.2.1 is the version.

poulson commented 5 years ago

@whedon set 10.5281/zenodo.3249188 as archive

whedon commented 5 years ago

OK. 10.5281/zenodo.3249188 is the archive.

poulson commented 5 years ago

Congratulations, @matbesancon, I have recommended the paper for publication! (@openjournals/joss-eics)

kyleniemeyer commented 5 years ago

Hi @matbesancon, a few little things to fix before we publish:

matbesancon commented 5 years ago

hi @kyleniemeyer thanks, I've updated the Zenodo description field, I responded on the repo for the edit, I'm not sure about the square bracket thing

kyleniemeyer 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:

kyleniemeyer commented 5 years ago

@whedon accept

whedon commented 5 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 5 years ago 

OK DOIs

- 10.1137/15m1020575 is OK
- 10.1287/trsc.35.4.345.10433 is OK
- 10.1007/s00446-006-0020-y is OK
- 10.1016/j.ejor.2019.01.059 is OK
- 10.1109/TPWRS.2019.2892607 is OK
- 10.1007/978-3-319-33461-5_9 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 5 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/808

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/808, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
kyleniemeyer commented 5 years ago

@whedon accept deposit=true

whedon commented 5 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 5 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 5 years ago

🚨🚨🚨 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/809
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01278
  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...

kyleniemeyer commented 5 years ago

Congrats @matbesancon on your submission's publication in JOSS! Thanks to @HaoZeke and @vissarion for reviewing, and @poulson for editing.

whedon commented 5 years ago

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01278/status.svg)](https://doi.org/10.21105/joss.01278)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01278">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01278/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01278/status.svg
   :target: https://doi.org/10.21105/joss.01278

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

matbesancon commented 5 years ago

Thanks all for the reviews!

On Mon, Jul 1, 2019, 17:39 whedon notifications@github.com wrote:

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:

DOI

HTML:

DOI badge

reStructuredText:

.. image:: http://joss.theoj.org/papers/10.21105/joss.01278/status.svg

:target: https://doi.org/10.21105/joss.01278

This is how it will look in your documentation:

[image: DOI] https://doi.org/10.21105/joss.01278

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/1278?email_source=notifications&email_token=AB2FDMUCOGBQMWD2R6KHI4DP5IQLXA5CNFSM4G2FIVO2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODY6Q2DI#issuecomment-507317517, or mute the thread https://github.com/notifications/unsubscribe-auth/AB2FDMTVLEBLDFZOW2BZEWLP5IQLXANCNFSM4G2FIVOQ .