[REVIEW]: SBArchOpt: Surrogate-Based Architecture Optimization

[editorialbot]

Submitting author: @jbussemaker (Jasper Bussemaker)
Repository: https://github.com/jbussemaker/SBArchOpt
Branch with paper.md (empty if default branch): joss-paper
Version: v1.2.0
Editor: @vissarion
Reviewers: @athulpg007, @SichengHe
Archive: 10.5281/zenodo.8318765

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/0b2b765c04d31a4cead77140f82ecba0/status.svg)](https://joss.theoj.org/papers/0b2b765c04d31a4cead77140f82ecba0)

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

@athulpg007 & @SichengHe, 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 @vissarion 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 @athulpg007

📝 Checklist for @SichengHe

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.13 s (596.5 files/s, 114627.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          61           2956           2075           7831
Markdown                        12            223              0            823
Jupyter Notebook                 1              0            450            531
TeX                              1             16              0            162
YAML                             3             16             13             82
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            79           3211           2538           9432
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1213

[editorialbot]

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

OK DOIs

- 10.1007/978-1-4020-4399-4 is OK
- 10.1007/978-3-030-27486-3_36-1 is OK
- 10.2514/6.2021-3095 is OK
- 10.1007/s00500-017-2965-0 is OK
- 10.1017/9781108348973 is OK
- 10.48550/ARXIV.2302.08436 is OK
- 10.1109/access.2020.2990567 is OK
- 10.1016/j.ast.2019.03.041 is OK
- 10.2514/6.2022-3899 is OK
- 10.1115/detc2021-71399 is OK
- 10.2514/6.2021-3078 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[athulpg007]

Review checklist for @athulpg007

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/jbussemaker/SBArchOpt?
• 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 (@jbussemaker) 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?

[SichengHe]

Review checklist for @SichengHe

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/jbussemaker/SBArchOpt?
• 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 (@jbussemaker) 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?

[athulpg007]

Hi @jbussemaker, I tried to step through the tutorial notebook here and ran into two issues. Details can be found in jbussemaker/SBArchOpt#1 and jbussemaker/SBArchOpt#2.

[jbussemaker]

@athulpg007 thank you for catching these problems. I have corrected them, in addition to adding unit tests to also test the tutorial notebooks.

I also corrected another small mistake I made with one of the dependencies I use: if you're starting from a previously-prepared Python environment, ensure you have numba installed: pip install numba

Thank you for your time reviewing the library!

[vissarion]

@athulpg007 thanks for the review details!

Let me share one comment. Please, next time try opening one (or more) issue(s) to the reviewing repository with the details and mention the issue link in the tread. This will keep review more organized and focused. Thanks again!

[athulpg007]

@jbussemaker please take a look: jbussemaker/SBArchOpt#4, jbussemaker/SBArchOpt#5, jbussemaker/SBArchOpt#6.

[athulpg007]

Hi @jbussemaker, thank you for addressing my comments. I have completed my review and am happy to accept this paper.

A few minor suggestions:

1. Please update the PyPI release to the latest version which includes the recent bug fixes.
2. 'An accompanying publication will be prepared in the near future detailing more about the implemented optimization features.' I suggest to remove this line from the paper, as it is making a promise of future work that is not yet done at this time. Once the mentioned publication is available, it can be linked to in the documentation page. This will allow users who want to gain a more in depth understanding of the features to refer to it. You can also consider linking any other published articles which used the library.

Thank you for this valuable contribution to the field of systems architecture optimization.

[jbussemaker]

@athulpg007 I have updated the latest PyPI release and removed the line in the paper

Thank you too for your valuable feedback!

[jbussemaker]

@SichengHe there have been quite some improvements to the code since athulpg007 provided feedback. I kindly request you to update your checklist. Feel free to contact me (through an issue in the repo) if there are any further questions.

@vissarion

[vissarion]

@SichengHe could you please update us on the progress of your review?

[SichengHe]

@jbussemaker @vissarion Sorry for the late response. I will finish tomorrow BEOD.

[SichengHe]

Sorry for the late response @vissarion . The edited version passed all the tests. Thanks for putting effort into this @jbussemaker !

[jbussemaker]

And thank you for your review :)

[vissarion]

When a submission is ready to be accepted, we ask that the authors issue a new tagged release of the software (if changed), and archive it (see this guide).

@jbussemaker Please do this and post the version number and archive DOI here.

[jbussemaker]

@vissarion thank you.
The release is v1.2.0 and is archived at 10.5281/zenodo.8318765

[vissarion]

Thanks @jbussemaker, please change the title and author list of the zenodo archive to match the title of your JOSS paper.

[jbussemaker]

@vissarion done 👍

[vissarion]

@editorialbot generate pdf

[vissarion]

@jbussemaker thanks! I have opened an issue with few comments regarding references.

[vissarion]

@editorialbot generate pdf

[editorialbot]

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

[vissarion]

@editorialbot generate pdf

[editorialbot]

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

[vissarion]

@jbussemaker thanks for all the efforts and for writing this useful paper!
@athulpg007, @SichengHe thanks for the constructive reviews!

I will know ping the Track Editor in Chief for final processing.

@editorialbot recommend-accept

[jbussemaker]

@vissarion thank you very much for the coordination!
@athulpg007 @SichengHe thank you for your time reviewing the paper and software!

[vissarion]

@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

- 10.1007/978-1-4020-4399-4 is OK
- 10.1007/978-3-030-27486-3_36-1 is OK
- 10.2514/6.2021-3095 is OK
- 10.1007/s00500-017-2965-0 is OK
- 10.1017/9781108348973 is OK
- 10.1002/iis2.13020 is OK
- 10.1002/iis2.12935 is OK
- 10.48550/ARXIV.2302.08436 is OK
- 10.1613/jair.1.13643 is OK
- 10.1109/access.2020.2990567 is OK
- 10.1016/j.ast.2019.03.041 is OK
- 10.2514/6.2022-3899 is OK
- 10.1115/detc2021-71399 is OK
- 10.2514/6.2021-3078 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/csism-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#4532, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@jbussemaker - as the track chair, I'll now proofread the draft and let you know the next steps

[danielskatz]

I have a bunch of suggested changes, as indicated in jbussemaker/SBArchOpt#8 - please merge this, or let me know what you disagree with, then we can proceed.

[jbussemaker]

@danielskatz I have merged the pull request, thank you for the suggestions 👍

[danielskatz]

@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

- 10.1007/978-1-4020-4399-4 is OK
- 10.1007/978-3-030-27486-3_36-1 is OK
- 10.2514/6.2021-3095 is OK
- 10.1007/s00500-017-2965-0 is OK
- 10.1017/9781108348973 is OK
- 10.1002/iis2.13020 is OK
- 10.1002/iis2.12935 is OK
- 10.48550/ARXIV.2302.08436 is OK
- 10.1613/jair.1.13643 is OK
- 10.1109/access.2020.2990567 is OK
- 10.1016/j.ast.2019.03.041 is OK
- 10.2514/6.2022-3899 is OK
- 10.1115/detc2021-71399 is OK
- 10.2514/6.2021-3078 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/csism-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#4533, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@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: Bussemaker
  given-names: Jasper H.
  orcid: "https://orcid.org/0000-0002-5421-6419"
doi: 10.5281/zenodo.8318765
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Bussemaker
    given-names: Jasper H.
    orcid: "https://orcid.org/0000-0002-5421-6419"
  date-published: 2023-09-07
  doi: 10.21105/joss.05564
  issn: 2475-9066
  issue: 89
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5564
  title: "SBArchOpt: Surrogate-Based Architecture Optimization"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05564"
  volume: 8
title: "SBArchOpt: Surrogate-Based Architecture Optimization"

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.05564 joss-papers#4534
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05564
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...

[danielskatz]

Congratulations to @jbussemaker (Jasper Bussemaker) on your publication!!

And thanks to @athulpg007, @SichengHe for reviewing, and to @vissarion for editing.
JOSS is fully dependent on volunteers and we couldn't do this without you

[editorialbot]

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

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[athulpg007]

Congratulations @jbussemaker!