[REVIEW]: Enlsip.jl: A Julia optimization package to solve constrained nonlinear least-squares problems

[editorialbot]

Submitting author: @pierre-borie (Pierre Borie)
Repository: https://github.com/UncertainLab/Enlsip.jl.git
Branch with paper.md (empty if default branch): joss-paper
Version: v0.9.7
Editor: @jbytecode
Reviewers: @tmigot, @odunbar
Archive: 10.5281/zenodo.11206280

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/f3a0b42a11b3169298278bd857c4075d/status.svg)](https://joss.theoj.org/papers/f3a0b42a11b3169298278bd857c4075d)

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) by leaving comments 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

@tmigot & @odunbar, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @jbytecode know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @odunbar

📝 Checklist for @tmigot

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (929.7 files/s, 197679.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                            9            838            590           2297
Markdown                         5            159              0            331
TeX                              1             12              0            119
YAML                             4              2              2             89
TOML                             2              5              0             21
-------------------------------------------------------------------------------
SUM:                            21           1016            592           2857
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1099

[editorialbot]

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

OK DOIs

- 10.1007/BF02591997 is OK
- 10.1137/141000671 is OK
- 10.1137/15M1020575 is OK
- 10.5281/zenodo.2558627 is OK
- 10.1145/355958.355965 is OK
- 10.1007/s10589-020-00201-2 is OK
- 10.1017/S0962492902000132 is OK
- 10.1137/1.9781611971200 is OK
- 10.1007/978-3-642-48320-2 is OK
- 10.1007/978-0-387-40065-5 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[jbytecode]

@tmigot, @odunbar - thank you for accepting our invitation. Please, firstly create your checklist before starting your review. Thank you in advance

[odunbar]

Review checklist for @odunbar

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 https://github.com/UncertainLab/Enlsip.jl.git?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@pierre-borie) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[tmigot]

Review checklist for @tmigot

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 https://github.com/UncertainLab/Enlsip.jl.git?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@pierre-borie) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[jbytecode]

@pierre-borie - Our reviewers have created issues in the software directory, have you seen them? Could you please update your status? Please consider changing/adding the suggestions pointed out by our reviewers. Thank you in advance.

[jbytecode]

@odunbar, @tmigot - Since the corresponding author hasn't responded in both the repo issues and here, I suggest you to pause your review. Please do not consume your valuable time until we receive a response from the author for the first round. Thank you in advance.

[pierre-borie]

@jbytecode - I thought that the checklist completions were still on progress and did not see the comments associated with it. My apologies for not having responded till today, I am aware of the time and effort put by you. and the reviewers into this.
@odunbar @tmigot thank you for your comments and suggestions. I will start to make modifications and come back to you asap. Once again, I am really sorry for my misunderstanding.

[jbytecode]

I am now removing the paused tag. @pierre-borie reviews in JOSS are interactive, so reviewers, the author and the editor can always interact each other during the process whenever needed. Please consider the changes stated in the issues and ping us again. Thank you!

[jbytecode]

@pierre-borie - Could you please update your status and inform us how is your set of corrections/additions going? Thank you in advance.

[pierre-borie]

@jbytecode So far I pushed corrections to the documentation. I also added formal corrections to the paper but I want to include an industrial application of our package before submitting another draft. I am currently working on this and still need to fix what we are allowed to show or not wiht the industrial partner in question.

[jbytecode]

@pierre-borie - How is your work going? Could you please update your status and inform us?

[pierre-borie]

@jbytecode For the past weeks I have encountered difficulties in the process of having access to an industrial application that can be described in the paper. Thoses issues have been fixed so I should be able to submit a new draft next week.

Concerning the package, I added and corrected some functionalities following advices from the reviewers. Documentation has been modified accordingly to thoses changes.

[pierre-borie]

@jbytecode - It took a few more days than I thought it would but I pushed a revised version of the paper on the joss-paper branch.

[jbytecode]

@editorialbot generate pdf

[jbytecode]

@pierre-borie - Could you please merge the PR?

@xuanxu - Thank you so much, indeed, that was very helpful!

[pierre-borie]

Hi @jbytecode - I merged the PR. Sorry for the error, I did not think this would cause an issue.
Thanks @xuanxu for your help!

[jbytecode]

@editorialbot generate pdf

[editorialbot]

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

[jbytecode]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1109/PES.2006.1709029 is OK
- 10.1007/BF02591997 is OK
- 10.1137/141000671 is OK
- 10.1137/15M1020575 is OK
- 10.5281/zenodo.2558627 is OK
- 10.1145/355958.355965 is OK
- 10.1007/s101070100263 is OK
- 10.1007/s10589-020-00201-2 is OK
- 10.1017/S0962492902000132 is OK
- 10.1137/S1052623498345075 is OK
- 10.1007/s10107-004-0559-y is OK
- 10.1137/1.9781611971200 is OK
- 10.1007/978-0-387-40065-5 is OK
- 10.1007/978-3-642-48320-2 is OK
- 10.1007/978-0-387-40065-5 is OK
- 10.5281/zenodo.3991143 is OK

MISSING DOIs

- No DOI given, and none found for title: Gauss-Newton based algorithms for constrained nonl...
- No DOI given, and none found for title: Sparse and Partially Separable Test Problems for U...

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5371, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[crvernon]

🔍 checking out the following:

• reviewer checklists are completed or addressed
• version set
• archive set
• archive names (including order) and title in archive matches those specified in the paper
• archive uses the same license as the repo and is OSI approved as open source
• archive DOI and version match or redirect to those set by editor in review thread
• paper is error free - grammar and typos
• paper is error free - test links in the paper and bib
• paper is error free - refs preserve capitalization where necessary
• paper is error free - no invalid refs without justification

[crvernon]

👋 @pierre-borie - this submission is looking really good! I only have the one issue for you to see to before I accept this for publication.

• The DOI in the following reference is pointing to the incorrect location:

Gill, P. E., Murray, W., & Wright, M. H. (1981). Practical optimization. Academic Press. https://doi.org/10.1007/978-0-387-40065-5

Instead it is pointing to the same DOI as this reference:

Nocedal, J., & Wright, S. J. (2006). Numerical optimization (Second edition). Springer. https://doi.org/10.1007/978-0-387-40065-5

Let me know when you have fixed this and we will move forward.

[pierre-borie]

@crvernon - Hi! Thanks for the feedback. I modified the wrong DOI in the bib file. Sorry about that!

[crvernon]

No problem @pierre-borie, thanks for the quick turnaround.

[crvernon]

@editorialbot generate pdf

[editorialbot]

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

[crvernon]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1109/PES.2006.1709029 is OK
- 10.1007/BF02591997 is OK
- 10.1137/141000671 is OK
- 10.1137/15M1020575 is OK
- 10.5281/zenodo.2558627 is OK
- 10.1145/355958.355965 is OK
- 10.1007/s101070100263 is OK
- 10.1007/s10589-020-00201-2 is OK
- 10.1017/S0962492902000132 is OK
- 10.1137/S1052623498345075 is OK
- 10.1007/s10107-004-0559-y is OK
- 10.1137/1.9781611971200 is OK
- 10.1137/1.9781611975604 is OK
- 10.1007/978-3-642-48320-2 is OK
- 10.1007/978-0-387-40065-5 is OK
- 10.5281/zenodo.3991143 is OK

MISSING DOIs

- No DOI given, and none found for title: Gauss-Newton based algorithms for constrained nonl...
- No DOI given, and none found for title: Sparse and Partially Separable Test Problems for U...

INVALID DOIs

- None

[crvernon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Borie
  given-names: Pierre
  orcid: "https://orcid.org/0009-0000-1043-5057"
- family-names: Marcotte
  given-names: Alain
  orcid: "https://orcid.org/0009-0009-5964-8892"
- family-names: Bastin
  given-names: Fabian
  orcid: "https://orcid.org/0000-0003-1323-6787"
- family-names: Dellacherie
  given-names: Stéphane
  orcid: "https://orcid.org/0009-0005-9043-9328"
doi: 10.5281/zenodo.11206280
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Borie
    given-names: Pierre
    orcid: "https://orcid.org/0009-0000-1043-5057"
  - family-names: Marcotte
    given-names: Alain
    orcid: "https://orcid.org/0009-0009-5964-8892"
  - family-names: Bastin
    given-names: Fabian
    orcid: "https://orcid.org/0000-0003-1323-6787"
  - family-names: Dellacherie
    given-names: Stéphane
    orcid: "https://orcid.org/0009-0005-9043-9328"
  date-published: 2024-05-22
  doi: 10.21105/joss.06226
  issn: 2475-9066
  issue: 97
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6226
  title: "Enlsip.jl: A Julia optimization package to solve constrained
    nonlinear least-squares problems"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06226"
  volume: 9
title: "Enlsip.jl: A Julia optimization package to solve constrained
  nonlinear least-squares problems"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 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.06226 joss-papers#5372
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06226
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...

[crvernon]

🥳 Congratulations on your new publication @pierre-borie! Many thanks to @jbytecode for editing and @tmigot and @odunbar for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Please consider becoming a reviewer for JOSS if you are not already: https://reviewers.joss.theoj.org/join

[editorialbot]

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

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

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.06226/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06226/status.svg
   :target: https://doi.org/10.21105/joss.06226

This is how it will look in your documentation:

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[pierre-borie]

Thanks a lot @jbytecode for the editing and @tmigot @odunbar for the reviews. The package and its documentation has clearly benefited from your comments!