[REVIEW]: pysr3: A Python Package for Sparse Relaxed Regularized Regression

[editorialbot]

Submitting author: @aksholokhov (Aleksei Sholokhov)
Repository: https://github.com/aksholokhov/pysr3
Branch with paper.md (empty if default branch):
Version: v0.3.5
Editor: @plaplant
Reviewers: @blakeaw, @mhu48
Archive: 10.5281/zenodo.7839335

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/67ea0de9a219ad072073a2304f11f820/status.svg)](https://joss.theoj.org/papers/67ea0de9a219ad072073a2304f11f820)

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

@blakeaw & @mhu48, 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 @plaplant 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 @mhu48

📝 Checklist for @blakeaw

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.14 s (322.9 files/s, 72286.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          22           1174           3387           3537
Markdown                         4            141              0            334
TeX                              1             14              0            147
YAML                             5             16             16            142
Jupyter Notebook                 3              0            673            121
XML                              5              0              0             52
DOS Batch                        1              8              1             26
Bourne Shell                     1              1              0             11
reStructuredText                 1              9              9             11
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            44           1367           4093           4390
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 787

[mhu48]

Review checklist for @mhu48

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/aksholokhov/pysr3?
• 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 (@aksholokhov) 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?

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.1007/s10182-019-00359-z is OK
- 10.1088/1361-6420/aba417 is OK
- 10.1007/s00162-020-00529-9 is OK

MISSING DOIs

- 10.1109/access.2018.2886528 may be a valid DOI for title: A unified framework for sparse relaxed regularized regression: SR3
- 10.1109/tsp.2019.2946029 may be a valid DOI for title: Basis pursuit denoise with nonsmooth constraints

INVALID DOIs

- None

[blakeaw]

Review checklist for @blakeaw

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/aksholokhov/pysr3?
• 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 (@aksholokhov) 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?

[plaplant]

@mhu48 @blakeaw thanks very much for your input to the review so far! Just checking in to see how the reviews are going. If you have any questions, please let me know!

[blakeaw]

Hi @plaplant and @aksholokhov, thank you for your patience. I've been traveling the last couple of weeks, so I was a bit delayed in finishing up my review. I've completed my initial review with my comments at aksholokhov/pysr3#11

[plaplant]

@blakeaw thanks for your review! @aksholokhov please begin addressing the comments in the review, and reply to this issue when you feel that you've addressed them.

@mhu48 I see that you've filled out your review checklist. Do you have issues that you feel need to be addressed? If so, please make an issue on the upstream repository: https://github.com/aksholokhov/pysr3. If not, then please reply to this issue stating you feel it is ready for acceptance.

[mhu48]

@plaplant Thanks for the update! I see I didn't post under the correct place earlier. The comments are submitted as a new issue under aksholokhov/pysr3#12

[plaplant]

@mhu48 thanks for your review! @aksholokhov please begin addressing the comments in this review as well.

[blakeaw]

Hi @plaplant, @aksholokhov has addressed all of my comments and I have completed my review checklist.

[plaplant]

@blakeaw thanks very much for your review!

@mhu48 are there issues that you feel still need to be addressed?

[mhu48]

@plaplant: Thanks for reaching out! I will reply to @aksholokhov <https://github.com/aksholokhov> in his email to me and cc you as well.

…

On Sun, Apr 9, 2023 at 11:24 AM Paul La Plante ***@***.***> wrote: @blakeaw <https://github.com/blakeaw> thanks very much for your review! @mhu48 <https://github.com/mhu48> are there issues that you feel still need to be addressed? — Reply to this email directly, view it on GitHub <#5155 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKGGVY4YRT5RW7CGIHIIZYTXAL5EZANCNFSM6AAAAAAU5GDL54> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Mingzhao Hu Phone: (608) 338-2571 Dept of Statistics & Applied Probability Univ of California ***@***.*** ***@***.***> Santa Barbara, CA 93106

[mhu48]

@plaplant: I have finished the review for the paper by @aksholokhov and have cc'ed you in the response email. The separate issue has been closed. My questions have been sufficiently addressed. Thank you for the opportunity to review.

[plaplant]

@mhu48 thanks very much for your review!

@aksholokhov both reviewers have recommended acceptance of the submission, so we can move forward with the final acceptance checks. If the software has changed in the course of the review, please make a new tagged release of the repository. After that, please archive it (on Zenodo, figshare, or some other long-term hosting platform). Once those are done, please post the version number and DOI of the archive in this thread. Let me know if you have any questions!

[aksholokhov]

@mhu48 @blakeaw thank you a lot again for your reviews and suggestions.

@plaplant done:
https://zenodo.org/record/7839335#.ZD4Dgy_MK-Y

Version number: 0.3.5
DOI: 10.5281/zenodo.7839335

[plaplant]

@aksholokhov thank you!

[plaplant]

@aksholokhov it looks like there might have been a mix-up in the ORCIDs of the co-authors on the paper. The paper (and Zenodo archive) have Aleksandr Aravkin's ORCID listed as 0000-0003-3313-215X, which goes to Peng Zheng's ORCID page, and vice versa. Please update the paper and Zenodo author list metadata accordingly. Thanks!

[aksholokhov]

My apologies and thank you for spotting the mix-up. The corrections have been made both on Zenodo and on Github.

[plaplant]

Thanks!

@editorialbot generate pdf

[danielskatz]

An @editorialbot command needs to be the first thing in a comment

[plaplant]

@editorialbot generate pdf

[editorialbot]

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

[plaplant]

@editorialbot set 10.5281/zenodo.7839335 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7839335

[plaplant]

@editorialbot set v0.3.5 as version

[editorialbot]

Done! version is now v0.3.5

[plaplant]

@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

- 10.1007/s10182-019-00359-z is OK
- 10.1109/ACCESS.2018.2886528 is OK
- 10.48550/arXiv.2205.06925 is OK
- 10.48550/arXiv.2209.10575 is OK
- 10.1109/tsp.2019.2946029 is OK
- 10.1016/S0140-6736(20)30752-2 is OK
- 10.1080/10618600.2013.773239 is OK
- 10.1109/TCYB.2020.2982445 is OK
- 10.1016/j.procs.2016.07.111 is OK
- 10.1007/s00162-020-00529-9 is OK
- 10.48550/arXiv.1911.05182 is OK
- 10.48550/arXiv.1309.0238 is OK
- 10.1111/j.1467-9469.2011.00740.x is OK

MISSING DOIs

- None

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#4166, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@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: Sholokhov
  given-names: Aleksei
  orcid: "https://orcid.org/0000-0001-8173-6236"
- family-names: Zheng
  given-names: Peng
  orcid: "https://orcid.org/0000-0003-3313-215X"
- family-names: Aravkin
  given-names: Aleksandr
  orcid: "https://orcid.org/0000-0002-1875-1801"
doi: 10.5281/zenodo.7839335
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Sholokhov
    given-names: Aleksei
    orcid: "https://orcid.org/0000-0001-8173-6236"
  - family-names: Zheng
    given-names: Peng
    orcid: "https://orcid.org/0000-0003-3313-215X"
  - family-names: Aravkin
    given-names: Aleksandr
    orcid: "https://orcid.org/0000-0002-1875-1801"
  date-published: 2023-04-23
  doi: 10.21105/joss.05155
  issn: 2475-9066
  issue: 84
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5155
  title: "pysr3: A Python Package for Sparse Relaxed Regularized
    Regression"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05155"
  volume: 8
title: "pysr3: A Python Package for Sparse Relaxed Regularized
  Regression"

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]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[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.05155 joss-papers#4173
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05155
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...

[arfon]

@blakeaw, @mhu48 – many thanks for your reviews here and to @plaplant for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@aksholokhov – your paper is now accepted and published in JOSS ⚡🚀💥

[editorialbot]

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

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[aksholokhov]

@arfon @plaplant Thank you so much! @saravkin, @ zhengp0, and I are thrilled that our paper is now published at JOSS and we are so grateful for all the work that you put into JOSS and in this review in particular.
@blakeaw @mhu48 Thanks a lot for your thorough and insightful reviews, they really helped me to improve the paper.

I am currently preparing for my graduation but starting June I would be happy to be on the list of possible reviewers for JOSS. It would be an honor for me to be a part of this community.

[plaplant]

@aksholokhov thank you very much for your kind words! This was my first editorial assignment, so I appreciate you bearing with me as I learned the ropes.

When you're ready, you can add yourself to the JOSS reviewer pool here: https://reviewers.joss.theoj.org/. You can select specific tracks and areas of expertise you'd like to be considered for. We'd be delighted to have you as a reviewer!