[PRE REVIEW]: PySLSQP: A transparent Python package for the SLSQP optimization algorithm modernized with utilities for visualization and post-processing

[editorialbot]

Submitting author: !--author-handle-->@anugrahjo<!--end-author-handle-- (Anugrah Jo Joshy) Repository: https://github.com/anugrahjo/PySLSQP Branch with paper.md (empty if default branch): Version: v0.1.0 Editor: !--editor-->@prashjha<!--end-editor-- Reviewers: @hariharanragothaman, @saaikrishnan Managing EiC: Daniel S. Katz

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Thanks for submitting your paper to JOSS @anugrahjo. Currently, there isn't a JOSS editor assigned to your paper.

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[editorialbot]

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[editorialbot]

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

✅ OK DOIs

- None

🟡 SKIP DOIs

- No DOI given, and none found for title: A software package for sequential quadratic progra...
- No DOI given, and none found for title: The NLopt nonlinear-optimization package
- No DOI given, and none found for title: A MODular development environment and library for ...

❌ MISSING DOIs

- 10.1145/192115.192124 may be a valid DOI for title: Algorithm 733: TOMP–Fortran modules for optimal co...

❌ INVALID DOIs

- https://doi.org/10.1137/S0036144504446096 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/s41592-019-0686-2 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.21105/joss.02564 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1007/s00158-011-0666-3 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

:warning: An error happened when generating the pdf. Problem with ORCID (0000-0000-0000-0000) for Anugrah Joshy. Invalid ORCID.

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1141.3 files/s, 207485.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          14            405            817           1604
Fortran 77                       1            384            691           1115
Markdown                        14            191              0            812
YAML                             5             58            105            247
TeX                              2             10              0             96
Jupyter Notebook                 2              0           1021             75
TOML                             1              8             13             65
Meson                            2              8              3             34
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            43           1076           2658           4083
-------------------------------------------------------------------------------

Commit count by author:

    28  anugrahjo

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 2707

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

[danielskatz]

👋 @anugrahjo - note that your paper does not compile. Please follow the example paper and note that you can click on the error above to find out more about it. (In this case, you have an invalid DOI. If there is no DOI for an author, remove the DOI line.) In addition, you could work on the possibly missing DOI that editorialbot suggests, but note that it may be incorrect, as well as fixing the DOIs with the extra prefix. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf after making changes to the .md file or when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

Also, your paper is 2700 words long, and JOSS papers are intended to be 250-1000 words, so you will have to substantially cut your paper. Again, see the example paper and the JOSS documentation for what a JOSS paper should be.

Finally, looking at the code itself, it appears the Fortran code here is not an original contribution, but the Python code is. Is this correct?

[anugrahjo]

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[editorialbot]

Hello @anugrahjo, here are the things you can ask me to do:

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@editorialbot check repository

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@editorialbot generate pdf

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@editorialbot generate preprint

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[anugrahjo]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[anugrahjo]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[editorialbot]

Five most similar historical JOSS papers:

PyCUTEst: an open source Python package of optimization test problems Submitting author: @jfowkes Handling editor: @diehlpk (Active) Reviewers: @stsievert, @jonjoncardoso Similarity score: 0.7378

BayesO: A Bayesian optimization framework in Python Submitting author: @jungtaekkim Handling editor: @drvinceknight (Active) Reviewers: @salrm8, @thomaspinder Similarity score: 0.7277

Enlsip.jl: A Julia optimization package to solve constrained nonlinear least-squares problems Submitting author: @pierre-borie Handling editor: @jbytecode (Active) Reviewers: @tmigot, @odunbar Similarity score: 0.7243

FitBenchmarking: an open source Python package comparing data fitting software Submitting author: @tyronerees Handling editor: @dhhagan (Retired) Reviewers: @johnsamuelwrites, @djmitche Similarity score: 0.7240

PySensors: A Python package for sparse sensor placement Submitting author: @briandesilva Handling editor: @pdebuyl (Active) Reviewers: @jordanperr, @tuelwer Similarity score: 0.7224

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[anugrahjo]

👋 @danielskatz Thank you for the feedback. I have made the changes to the references and the paper compiles now.

Sorry about the length of the paper. One of the JOSS papers in our list of references was of similar length so we thought the 250-1000 word length was a suggestion. We can reduce the length if necessary.

Regarding the code contribution, yes, the Python code is the main contribution and the build workflows for autogenerating the precompiled binaries for the wrapped Fortran code. The Fortran code for SLSQP itself is open-source and in our case, it is sourced from the SciPy repository but is also available from many other sources.

[danielskatz]

Paper length is one of many things in JOSS that has gotten stricter over time...

Please let me know when you have a shorter paper. I'll mark this as paused for now.

[danielskatz]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1145/192115.192124 is OK
- 10.1137/S0036144504446096 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.21105/joss.02564 is OK
- 10.1007/s00158-011-0666-3 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: A software package for sequential quadratic progra...
- No DOI given, and none found for title: The NLopt nonlinear-optimization package
- No DOI given, and none found for title: A MODular development environment and library for ...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[danielskatz]

@editorialbot check repository

this command includes checking the length of the paper

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1167.3 files/s, 212233.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          14            405            817           1604
Fortran 77                       1            384            691           1115
Markdown                        14            191              0            812
YAML                             5             58            105            247
TeX                              2             10              0             97
Jupyter Notebook                 2              0           1021             75
TOML                             1              8             13             65
Meson                            2              8              3             34
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            43           1076           2658           4084
-------------------------------------------------------------------------------

Commit count by author:

    30  anugrahjo

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 2707

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

[danielskatz]

@anugrahjo - before you do any extra work (on shortening the paper), I'm going to ask the JOSS editors to take a look at this for scope, since the commit history here and in https://github.com/anugrahjo/PySLSQP_alpha just goes back about 3 months. There should be a decision on this in a week or two.

[danielskatz]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[anugrahjo]

@danielskatz - I want to let you know that even the PySLSQP_alpha repository was created only after the software reached a reasonably stable working state. There is an earlier private repository that predates PySLSQP_alpha, as well as weeks of local development prior to the creation of the initial repository.

[anugrahjo]

@editorialbot generate preprint

[editorialbot]

:page_facing_up: Preprint file created: Find it here in the Artifacts list :page_facing_up:

[danielskatz]

@danielskatz - I want to let you know that even the PySLSQP_alpha repository was created only after the software reached a reasonably stable working state. There is an earlier private repository that predates PySLSQP_alpha, as well as weeks of local development prior to the creation of the initial repository.

Can you provide information about that repo, since as the number of commits and the period in which they were made?

[anugrahjo]

@danielskatz - Sure. It's a private repository located at https://github.com/anugrahjo/python-slsqp. The first commit there was on March 20 and the last one on May 12. There were 27 commits there and those commits were made mainly to test the workflows as the development was mostly local even then.

[danielskatz]

Thanks - We'll take that into account

[anugrahjo]

Thank you.

[danielskatz]

@anugrahjo - This submission has passed our scope review. I'll next look for an editor

[danielskatz]

👋 @faroit - Would you be willing to edit this submission? I see you are at your maximum, but have at least one submission that is basically done.

[danielskatz]

@editorialbot invite @faroit as editor

[editorialbot]

Invitation to edit this submission sent!

[anugrahjo]

@danielskatz That's great! Thanks for the update.

[faroit]

@danielskatz I have capacity but this submission is out of my domain

[danielskatz]

👋 @prashjha - Would you be willing to edit this submission?

[danielskatz]

@editorialbot invite @prashjha as editor

[editorialbot]

Invitation to edit this submission sent!

[prashjha]

@danielskatz happy to edit this submission!

[prashjha]

@editorialbot assign me as editor

[editorialbot]

Assigned! @prashjha is now the editor

[prashjha]

Hi @anugrahjo, could you please look at the JOSS reviewer database and suggest a few names who can review your submission?

[anugrahjo]

Hi @prashjha, sure. Below are some potential reviewers (ordered according to the relevance of our submission to their topic areas): bbrelje, jbussemaker, andim, zhaowei0566, bleyerj, e-dub, benoitpaillard, kylebeggs, athulpg007

[hariharanragothaman]

1. @anugrahjo - I would like to participate and review this paper.
2. Can I get assigned to review this please? Thanks in advance.

[saaikrishnan]

@anugrahjo - Can I please get assigned to review this ? Thank you in advance.

[anugrahjo]

@prashjha - Could you check and assign the reviewers? Thanks.

[hariharanragothaman]

@prashjha - Just following up on this request. Could I get assigned to review this please?