[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: v0.9.1
Editor: @jbytecode
Reviewers: @tmigot, @odunbar
Archive: Pending

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.

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

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

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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

[editorialbot]

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

[odunbar]

Update on my end, I had another sweep through my checklist:
@pierre-borie has addressed the majority of my points. I think the softening of claims in the the paper, the more comprehensive state of field, and the numerical example together give a more accurate link between what is claimed and evidenced.

There are a few typos and minor comments outstanding etc. but I do not expect these to take a long time.

[jbytecode]

@tmigot - May I kindly ask you to update your review status? Thank you in advance.

[tmigot]

@jbytecode @pierre-borie sorry for the delay, I will update my status in the upcoming days.

[odunbar]

Hi @jbytecode,
@pierre-borie has now addressed the remaining points, I'd be happy to support the submission and have no further comments.

Thanks!

[jbytecode]

@odunbar - You have got still unchecked items in your task list. Are they okay? Could you please finish checking them?

[jbytecode]

@odunbar - sorry for pinging. It's my fault. You don't need to take any further actions.

[pierre-borie]

@jbytecode I pushed another revised version of the paper, correcting (hopefully) the lastest issues.

@odunbar Thanks for supporting the submission! The new version does not differ much from the previous one

• The comparison graph have been replaced with a performance profile obtained with a dedicated package
• Some sentences have been reformulated and citations of other least-squares packages added

[jbytecode]

@editorialbot generate pdf

[editorialbot]

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

[jbytecode]

@pierre-borie - Could you please update your status?

[pierre-borie]

@jbytecode - I created a pull request covering the last issues about the package.

Edit: I merged the above mentionned corrections and released a new version of the package. Also corrected typo in the paper.

[tmigot]

Hi @jbytecode

With the last PR now merged, @pierre-borie answered all my comments and I completed the check-list.
I am happy to recommend the publication of Enlsip in JOSS.

The nonlinear least squares problem is both important and very frequent in practice, so I think this algorithm will be an interesting addition to the Julia background. My only comment would be that modeling a problem for the solver is not an easy task. I would recommend relying on NLPModels.jl to interact with the model as it would open the door to several modeling and benchmarking tools, but that's a biased opinion and independent of this submission process.

Congrats @pierre-borie for the nice work!

[jbytecode]

@tmigot, @odunbar - Thank you so much!

[jbytecode]

@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
- 10.1007/978-0-387-40065-5 is OK
- 10.1007/978-3-642-48320-2 is OK
- 10.1007/978-0-387-40065-5 is OK

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...
- No DOI given, and none found for title: JSOSolvers.jl: JuliaSmoothOptimizers optimization ...

INVALID DOIs

- None

[jbytecode]

@editorialbot generate pdf

[editorialbot]

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

[tmigot]

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

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...
- No DOI given, and none found for title: JSOSolvers.jl: JuliaSmoothOptimizers optimization ...

INVALID DOIs

- None

DOI for JSOSolvers: https://github.com/JuliaSmoothOptimizers/JSOSolvers.jl/blob/main/CITATION.cff

[jbytecode]

@pierre-borie - could you please fix the missing DOI issue and ping me again, thank you in advance!

[pierre-borie]

@jbytecode - I added the DOI for JSOSolvers. For the other two papers, I could not find any. I also checked in papers/books citing them and they are referenced without DOI so I believe they don't have one (perhaps because they are technical reports).

[pierre-borie]

@tmigot - Thanks for approving the corrections and for your advices! The current modeling interface isn't the best one indeed and switching NLPModels.jl is definitely something I intend to work on.

[jbytecode]

@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
- 10.1007/978-0-387-40065-5 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

[jbytecode]

@editorialbot generate pdf

[editorialbot]

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