[REVIEW]: DCISolver.jl: A Julia Solver for Nonlinear Optimization using Dynamic Control of Infeasibility

[whedon]

Submitting author: @tmigot (Tangi Migot)
Repository: https://github.com/JuliaSmoothOptimizers/DCISolver.jl
Version: v0.2.6
Editor: @jbytecode
Reviewer: @odow, @jbcaillau
Archive: 10.5281/zenodo.6040222

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Markdown: [![status](https://joss.theoj.org/papers/771e48a0ee4949b0e8b145bdbcc71ae2/status.svg)](https://joss.theoj.org/papers/771e48a0ee4949b0e8b145bdbcc71ae2)

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Reviewer instructions & questions

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

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Review checklist for @odow

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS 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?
• Contribution and authorship: Has the submitting author (@tmigot) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality of the software can be verified? #4057
• 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @jbcaillau

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS 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?
• Contribution and authorship: Has the submitting author (@tmigot) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

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

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

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:

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For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.03 s (1161.1 files/s, 109233.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           20            261            198           2071
Markdown                         6            152              0            627
YAML                             6              3              3            153
TOML                             4              5              0             76
Bourne Shell                     1              4              0             12
TeX                              1              0              0             10
-------------------------------------------------------------------------------
SUM:                            38            425            201           2949
-------------------------------------------------------------------------------


Statistical information for the repository 'f1301324261094a58bb61737' was
gathered on 2021/12/14.
No commited files with the specified extensions were found.

[whedon]

PDF failed to compile for issue #3991 with the following error:

 Can't find any papers to compile :-(

[jbytecode]

Dear @odow and @jbcaillau

This is the review issue. There are 20 tasks for each reviewer. Whenever an item is solved, you can check them.

You can interact with the other reviewers, the author(s), and me. You don't have to complete your review in one step, so while the authors improve the software and paper, you can continue your review with the other tasks.

Reviewers can also contribute to repository, open new issues in the target repo as well. Please mention this issue in your review in the target repo so we can keep our eyes on what is going on broadside.

Please do not hesitate to ask me anything, any time.

[jbytecode]

@whedon check references from branch joss-paper-branch

[whedon]

Attempting to check references... from custom branch joss-paper-branch

[whedon]

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

OK DOIs

- 10.1137/070679557 is OK
- 10.1007/s10589-014-9687-3 is OK
- 10.1007/s10107-004-0559-y is OK
- 10.21105/joss.00615 is OK
- 10.5281/zenodo.3969045 is OK
- 10.1287/ijoc.2021.1067 is OK
- 10.5281/zenodo.3948381 is OK
- 10.5281/zenodo.1188851 is OK
- 10.5281/zenodo.2558627 is OK
- 10.5281/zenodo.822073 is OK
- 10.5281/zenodo.3900668 is OK
- 10.5281/zenodo.2658672 is OK
- 10.1145/992200.992202 is OK
- 10.1109/TPDS.2018.2872064 is OK
- 10.1147/rd.471.0057 is OK
- 10.1145/962437.962438 is OK
- 10.1145/1236463.1236467 is OK
- 10.3390/pr6080106 is OK
- 10.13140/rg.2.1.2846.6803 is OK
- 10.1007/978-1-4419-6935-4_15 is OK
- 10.1007/978-1-4614-3226-5 is OK
- 10.1007/s00158-011-0666-3 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1137/141000671 is OK
- 10.1287/ijoc.2014.0623 is OK
- 10.5281/zenodo.3994983 is OK
- 10.5281/zenodo.2629034 is OK
- 10.1007/0-387-30065-1_4 is OK
- 10.1137/15M1020575 is OK
- 10.1287/mnsc.36.5.519 is OK
- 10.5281/zenodo.2655082 is OK
- 10.5281/zenodo.5056629 is OK
- 10.47749/T/UNICAMP.2013.918998 is OK
- 10.1007/s101070100263 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[jbytecode]

@whedon generate pdf from branch joss-paper-branch

[whedon]

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

[whedon]

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

[odow]

This is a very nice submission that was trivial to review. The paper and software are well written and a great fit for JOSS.

The only suggestion I had was to fix the plot (JuliaSmoothOptimizers/DCISolver.jl#70), but other than that I'm happy for this to be accepted.

[tmigot]

@whedon generate pdf from branch joss-paper-branch

[whedon]

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

[whedon]

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

[jbytecode]

@tmigot - is it possible to enhance the documentation with parameters (function arguments), their types, their descriptions, return values, and examples as shown in here?

[odow]

as shown in here?

This link might be better: https://docs.julialang.org/en/v1/manual/documentation/

[tmigot]

@jbytecode @odow Thanks for the suggestion. I opened a PR that improve the documentation of the main functions.
Would that answer your question?

[jbytecode]

looks better. thank you for adding documentation. but I think there is still some room to improve the documentation. you can add

• function definition
• arguments, their types, and a description
• a minimal example or more
• references

to each function. if you need help please have a look at the popular repos, if you still need help I can suggest some.

thanks.

[tmigot]

Ok, I updated only the external functions in the PR 74. I will also update the internal functions in the same way.

[jbytecode]

here is an example:

https://github.com/jbytecode/LinRegOutliers/blob/master/src/hs93.jl

[jbytecode]

one more thing:

Why are there some functions in test case, e.g., here

we can use nested test cases like

@testset "...." begin
   @testset "...." begin
       ....
   end
end

so you don't need to wrap more than one testcase in a function and then call this function manually in test environments. This is unusual. Please tell me if there is a specific reason to do that.

Thanks.

[whedon]

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

[whedon]

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

[tmigot]

@kthyng Sorry, I think there was something strange with the version name on github, should be ok now.

[whedon]

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

[jbytecode]

@tmigot have you changed anything between two pdf generation attempts?

[tmigot]

Yes, for some reason the version title was v0.2.6-cff (meaning the one you see on github's interface) while the version name was v0.2.6-alpha. So, I fixed the title to be v0.2.6-alpha.

[jbytecode]

@kthyng I think we don't need to change the version and the archive DOI, right?

[kthyng]

@jbytecode my understanding was that @tmigot wanted to incorporate the last few changes into the zenodo archive and also needed that update to change the title/authors. @tmigot did I understand correctly? Which zenodo archive and version do you want associated with your JOSS paper?

[tmigot]

The v0.2.6 and v0.2.6-alpha are the same. Since you suggest changing the title and author, we decided to do this automatically by adding a CITATION.cff file in the repository.
So, if you can do v0.2.6-alpha for Zenodo and v0.2.6 for the repo (as the v0.2.6-alpha is not a Julia version) that would be perfect.

[jbytecode]

could you please report the final version and doi for consistency?

[tmigot]

The doi for the v0.2.6 can be set as 10.5281/zenodo.6040222

[kthyng]

@whedon set 10.5281/zenodo.6040222 as archive

[whedon]

OK. 10.5281/zenodo.6040222 is the archive.

[kthyng]

@whedon set v0.2.6 as version

[whedon]

OK. v0.2.6 is the version.

[kthyng]

Ok I think we're good to go now!

[kthyng]

@whedon accept deposit=true from branch joss-paper-branch

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03991 joss-papers#2949
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03991
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kthyng]

Congratulations on your new publication @tmigot! Many thanks to editor @jbytecode and reviewers @odow and @jbcaillau for your time, hard work, and expertise!!

[whedon]

🎉🎉🎉 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://joss.theoj.org/papers/10.21105/joss.03991/status.svg)](https://doi.org/10.21105/joss.03991)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03991">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03991/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03991/status.svg
   :target: https://doi.org/10.21105/joss.03991

This is how it will look in your documentation:

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[tmigot]

Thanks @kthyng @jbytecode @odow @jbcaillau it's the first time I submitted to JOSS and it was a great experience!

[jbytecode]

@tmigot do not forget to add the new citation info in your repo, and great hopes you to have infinite number of cites to your paper! :) thank you all @odow and @jbcaillau

[jbcaillau]

Thanks @jbytecode for the patient editing, and congrats @tmigot et al for the paper!

[jbytecode]

@jbcaillau and @odow great thanks are for you just because you consumed your valuable time for reviewing!

I feel lucky to share the same space and time with you!

hope we will work together in later submissions and works!

It was nice to stand on the shoulders of giants with you all!