[REVIEW]: DisjunctiveProgramming.jl: Generalized Disjunctive Programming Models and Algorithms for JuMP #117

whedon · 2022-12-11T13:13:40Z

Submitting author: @hdavid16 (Hector Perez)
Repository: https://github.com/hdavid16/DisjunctiveProgramming.jl
Branch with paper.md (empty if default branch):
Version: v0.4.1
Editor:
Reviewers: @sbolusani, @joaquimg, @joaquimg
Archive:

Status

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Markdown: [![status](https://proceedings.juliacon.org/papers/569beb65dae7d35e1ccf220df54e8a1c/status.svg)](https://proceedings.juliacon.org/papers/569beb65dae7d35e1ccf220df54e8a1c)

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Review checklist for @sbolusani

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General checks

Repository: Is the source code for this software available at the repository url?
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Authorship: Has the submitting author (@hdavid16) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

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Documentation

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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

Paper format

Authors: Does the paper.tex file include a list of authors with their affiliations?
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Content

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Review checklist for @joaquimg

Conflict of interest

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

Code of Conduct

I confirm that I read and will adhere to the JuliaCon 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?
Authorship: Has the submitting author (@hdavid16) 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

Paper format

Authors: Does the paper.tex 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)?
Page limit: Is the page limit for full papers respected by the submitted document?

Content

Context: is the scientific context motivating the work correctly presented?
Methodology: is the approach taken in the work justified, presented with enough details and reference to reproduce it?
Results: are the results presented and compared to approaches with similar goals?

The text was updated successfully, but these errors were encountered:

whedon · 2022-12-11T13:13:43Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @sbolusani, @joaquimg it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

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If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/JuliaCon/proceedings-review) 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 😿

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whedon · 2022-12-11T13:13:56Z

Failed to discover a Statement of need section in paper

whedon · 2022-12-11T13:13:57Z

Wordcount for paper.tex is 3421

whedon · 2022-12-11T13:13:58Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.09 s (406.4 files/s, 220866.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSS                              2            653             33          14577
TeX                              8            282            178           2855
Julia                           13            149            115           1009
JavaScript                       4             38             64            450
Markdown                         2             20              0             71
YAML                             4              2              0             71
Ruby                             1              8              4             45
TOML                             2              4              0             19
HTML                             2              0              0              4
-------------------------------------------------------------------------------
SUM:                            38           1156            394          19101
-------------------------------------------------------------------------------


Statistical information for the repository '4bdf66050d86061e21566b57' was
gathered on 2022/12/11.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
hdavid16                         2           609              0          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Hector Perez                609          100.0          0.0               11.17

whedon · 2022-12-11T13:13:58Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

matbesancon · 2022-12-11T13:14:56Z

@sbolusani @joaquimg the reviewer's guide is here: https://juliacon.github.io/proceedings-guide/reviewer/

whedon · 2022-12-11T13:15:30Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1287/ijoc.2015.0669 is OK
- 10.1007/978-0-387-74759-0_348 is OK
- 10.1007/978-1-4613-0215-5_8 is OK
- 10.1002/9780470400531.eorms0537 is OK
- 10.1007/11527695_15 is OK
- 10.1137/15m1020575 is OK
- 10.1137/15M1020575 is OK
- 10.3390/pr7110839 is OK
- 10.1023/a:1025154322278 is OK
- 10.1007/s10589-020-00176-0 is OK
- 10.1145/3511528.3511535 is OK

MISSING DOIs

- 10.1007/978-3-642-11503-5_12 may be a valid DOI for title: Automating mathematical program transformations
- 10.1007/s12532-017-0130-5 may be a valid DOI for title: Parallelizing the dual revised simplex method
- 10.1016/s0098-1354(98)00293-2 may be a valid DOI for title: LOGMIP: a disjunctive 0–1 non-linear optimizer for process system models
- 10.1007/s12532-011-0026-8 may be a valid DOI for title: Pyomo: modeling and solving mathematical programs in Python

INVALID DOIs

- https://doi.org/10.1016/j.compchemeng.2014.03.014 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/B978-0-323-95879-0.50141-7 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.compchemeng.2021.107616 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.compchemeng.2022.107856 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cherd.2022.08.027 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/aic.14088 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.compchemeng.2015.02.013 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/S0098-1354(00)00581-0 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.compchemeng.2005.04.004 is INVALID because of 'https://doi.org/' prefix

matbesancon · 2022-12-21T10:20:13Z

@hdavid16 can you check the DOIs listed above, that's minor but can be done in parallel

hdavid16 · 2022-12-24T11:18:47Z

@hdavid16 can you check the DOIs listed above, that's minor but can be done in parallel

DOIs have been updated in the repo now.

whedon · 2022-12-25T13:13:54Z

👋 @sbolusani, please update us on how your review is going (this is an automated reminder).

whedon · 2022-12-25T13:13:54Z

👋 @joaquimg, please update us on how your review is going (this is an automated reminder).

matbesancon · 2023-01-23T17:18:19Z

ping @sbolusani @joaquimg

hdavid16 · 2023-02-20T21:50:50Z

@sbolusani @joaquimg, this is a friendly reminder to please review. Thank you.

joaquimg · 2023-04-08T23:10:31Z

Sorry for the delay, I am working on it.

hdavid16 · 2023-07-13T18:45:10Z

Hi @sbolusani and @joaquimg, I'm sure you are all super busy. But just want to remind you to review this conference paper. It's been almost a year since the last JuliaCon where this work was presented...

matbesancon · 2023-08-02T07:34:08Z

I just reminded the two reviewers

matbesancon · 2023-08-09T07:02:36Z

@whedon add @joaquimg as a reviewer

whedon · 2023-08-09T07:02:40Z

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

matbesancon · 2023-08-09T07:02:49Z

@whedon add @joaquimg as reviewer

whedon · 2023-08-09T07:02:56Z

OK, @joaquimg is now a reviewer

matbesancon · 2023-11-17T09:12:31Z

@whedon commands

whedon · 2023-11-17T09:12:36Z

Here are some things you can ask me to do:

# List all of Whedon's capabilities
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# Assign a GitHub user as the sole reviewer of this submission
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EDITORIAL TASKS

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@whedon check references

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@whedon check repository

EiC TASKS

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matbesancon · 2023-11-17T09:13:09Z

@whedon set 10.5281/zenodo.10144853 as archive

whedon · 2023-11-17T09:13:15Z

OK. 10.5281/zenodo.10144853 is the archive.

matbesancon · 2023-11-17T09:13:39Z

@whedon set v0.4.1 as version

whedon · 2023-11-17T09:13:44Z

OK. v0.4.1 is the version.

matbesancon · 2023-11-17T09:15:49Z

@hdavid16 for stylistic reasons, can we replace the successive equations by an align block? This will look much nicer

matbesancon · 2023-11-17T09:29:00Z

same for all optimization problems, prefer a template like:

\begin{align*}
\min_{x}\,\, & f(x) \\
\text{s.t. }\, & g(x) \leq 0 \\
& x_i \in X && \forall i \in .. \\
& x \in \mathcal{X}
\end{align*}

joaquimg · 2023-12-06T04:37:48Z

I do re-iterate @matbesancon comment.

Other than that, good to go on my side.

Great work and congratulations for the nice package!

hdavid16 · 2023-12-11T23:49:31Z

@joaquimg and @matbesancon the paper has been updated on master as you requested (replacing all equations/expressions with align* blocks).

matbesancon · 2023-12-12T07:44:10Z

@whedon generate pdf

whedon · 2023-12-12T07:44:26Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

matbesancon · 2023-12-12T07:45:17Z

@whedon recommend-accept

whedon · 2023-12-12T07:45:21Z

Attempting dry run of processing paper acceptance...

whedon · 2023-12-12T07:45:25Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/978-3-642-11503-5_12 is OK
- 10.1007/s12532-017-0130-5 is OK
- 10.1007/978-3-030-00148-3 is OK
- 10.1016/s0098-1354(98)00293-2 is OK
- 10.1287/ijoc.2015.0669 is OK
- 10.1007/978-0-387-74759-0_348 is OK
- 10.1016/j.compchemeng.2014.03.014 is OK
- 10.1007/978-1-4613-0215-5_8 is OK
- 10.1007/978-3-030-68928-5 is OK
- 10.1007/s12532-011-0026-8 is OK
- 10.1016/B978-0-323-95879-0.50141-7 is OK
- 10.1016/j.compchemeng.2021.107616 is OK
- 10.1016/j.compchemeng.2022.107856 is OK
- 10.1016/j.cherd.2022.08.027 is OK
- 10.1002/9780470400531.eorms0537 is OK
- 10.1007/11527695_15 is OK
- 10.1137/15M1020575 is OK
- 10.1137/15M1020575 is OK
- 10.3390/pr7110839 is OK
- 10.1002/aic.14088 is OK
- 10.1007/978-3-030-00148-3 is OK
- 10.1016/j.compchemeng.2015.02.013 is OK
- 10.1016/S0098-1354(00)00581-0 is OK
- 10.1002/9781118627372 is OK
- 10.1023/a:1025154322278 is OK
- 10.1007/s10589-020-00176-0 is OK
- 10.1145/3511528.3511535 is OK
- 10.1016/j.compchemeng.2005.04.004 is OK
- 10.48550/arXiv.2202.05198 is OK
- 10.48550/arXiv.1510.01791 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2023-12-12T07:45:31Z

👋 @JuliaCon/jcon-eics, this paper is ready to be accepted and published.

Check final proof 👉 JuliaCon/proceedings-papers#74

If the paper PDF and Crossref deposit XML look good in JuliaCon/proceedings-papers#74, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

matbesancon · 2023-12-12T07:46:42Z

@whedon commands

whedon · 2023-12-12T07:46:46Z

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

# Re-invite a reviewer (if they can't update checklists)
@whedon re-invite @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

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@whedon list reviewers

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# Open the review issue
@whedon start review

EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom 
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# 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 do a dry run of accepting the paper and depositing with Crossref
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# Ask Whedon to check the references for missing DOIs
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# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

EiC TASKS

# Invite an editor to edit a submission (sending them an email)
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# Ask Whedon to actually accept the paper and deposit with Crossref
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matbesancon · 2023-12-12T07:48:04Z

@whedon accept deposit=true

whedon · 2023-12-12T07:48:09Z

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

whedon · 2023-12-12T07:48:28Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JCON! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.jcon.00117 proceedings-papers#75
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/jcon.00117
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

matbesancon · 2023-12-12T07:48:29Z

congratulations @hdavid16 !

whedon · 2023-12-15T22:09:17Z

🎉🎉🎉 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](https://proceedings.juliacon.org/papers/10.21105/jcon.00117/status.svg)](https://doi.org/10.21105/jcon.00117)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/jcon.00117">
  <img src="https://proceedings.juliacon.org/papers/10.21105/jcon.00117/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://proceedings.juliacon.org/papers/10.21105/jcon.00117/status.svg
   :target: https://doi.org/10.21105/jcon.00117

This is how it will look in your documentation:

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whedon added Julia review Ruby TeX labels Dec 11, 2022

whedon assigned matbesancon Dec 11, 2022

whedon mentioned this issue Dec 11, 2022

[PRE REVIEW]: DisjunctiveProgramming.jl: Generalized Disjunctive Programming Models and Algorithms for JuMP #107

Closed

whedon assigned joaquimg, matbesancon and sbolusani and unassigned matbesancon Aug 9, 2023

whedon added the recommend-accept label Dec 12, 2023

whedon unassigned matbesancon, sbolusani and joaquimg Dec 12, 2023

whedon added accepted published labels Dec 12, 2023

matbesancon closed this as completed Dec 15, 2023

[REVIEW]: DisjunctiveProgramming.jl: Generalized Disjunctive Programming Models and Algorithms for JuMP #117

[REVIEW]: DisjunctiveProgramming.jl: Generalized Disjunctive Programming Models and Algorithms for JuMP #117

Comments

whedon commented Dec 11, 2022 • edited by editorialbot Loading

Status

Reviewer instructions & questions

Review checklist for @sbolusani

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Paper format

Content

Review checklist for @joaquimg

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Paper format

Content

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