[REVIEW]: SBArchOpt: Surrogate-Based Architecture Optimization

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@jbussemaker@vissarion<!--end-editor-- Reviewers: @athulpg007, @SichengHe Archive: 10.5281/zenodo.8318765

Status

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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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

Wordcount for paper.md is 1213

editorialbot commented 1 year ago

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 commented 1 year ago

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

athulpg007 commented 1 year ago

Review checklist for @athulpg007

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/jbussemaker/SBArchOpt?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 1 year ago

Review checklist for @SichengHe

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/jbussemaker/SBArchOpt?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 1 year ago

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

jbussemaker commented 1 year ago

@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 commented 1 year ago

@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 commented 1 year ago

@jbussemaker please take a look: https://github.com/jbussemaker/SBArchOpt/issues/4, https://github.com/jbussemaker/SBArchOpt/issues/5, https://github.com/jbussemaker/SBArchOpt/issues/6.

athulpg007 commented 1 year ago

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

A few minor suggestions:

Please update the PyPI release to the latest version which includes the recent bug fixes.
'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 commented 1 year ago

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

Thank you too for your valuable feedback!

jbussemaker commented 10 months ago

@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 commented 10 months ago

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

SichengHe commented 10 months ago

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

SichengHe commented 10 months ago

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

jbussemaker commented 10 months ago

And thank you for your review :)

vissarion commented 10 months ago

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 commented 10 months ago

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

vissarion commented 10 months ago

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

jbussemaker commented 10 months ago

@vissarion done 👍

vissarion commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

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

vissarion commented 10 months ago

@editorialbot set 10.5281/zenodo.8318765 as archive

editorialbot commented 10 months ago

Done! archive is now 10.5281/zenodo.8318765

vissarion commented 10 months ago

@editorialbot set v1.2.0 as version

editorialbot commented 10 months ago

Done! version is now v1.2.0

vissarion commented 10 months ago

@editorialbot check references

editorialbot commented 10 months ago

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

- 10.1002/iis2.13020 may be a valid DOI for title: Function-Based Architecture Optimization: An Application to Hybrid-Electric Propulsion Systems
- 10.1002/iis2.12935 may be a valid DOI for title: From System Architecting to System Design and Optimization: A Link Between MBSE and MDAO

INVALID DOIs

- None

jbussemaker commented 10 months ago

@editorialbot generate pdf

jbussemaker commented 10 months ago

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

- 10.1002/iis2.13020 may be a valid DOI for title: Function-Based Architecture Optimization: An Application to Hybrid-Electric Propulsion Systems
- 10.1002/iis2.12935 may be a valid DOI for title: From System Architecting to System Design and Optimization: A Link Between MBSE and MDAO

INVALID DOIs

- None

I have added the DOIs. Somehow they didn't work previously...

editorialbot commented 10 months ago

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

jbussemaker commented 10 months ago

@editorialbot check references

editorialbot commented 10 months ago

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
- 10.1109/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

vissarion commented 10 months ago

@editorialbot check references

editorialbot commented 10 months ago

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
- 10.1109/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

vissarion commented 10 months ago

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

vissarion commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

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

vissarion commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

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

vissarion commented 10 months ago

@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 commented 10 months ago

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

vissarion commented 10 months ago

@editorialbot recommend-accept

editorialbot commented 10 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 10 months ago

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 commented 10 months ago

:wave: @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4532, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 10 months ago

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

danielskatz commented 10 months ago

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

openjournals / joss-reviews