[REVIEW]: nimCSO: A Nim package for Compositional Space Optimization

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@amkrajewski@RMeli<!--end-editor-- Reviewers: @atzberg, @Henrium, @bdice Archive: Pending

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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

@atzberg & @Henrium & @bdice, 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 @RMeli 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 @Henrium

📝 Checklist for @bdice

editorialbot commented 1 month ago

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editorialbot commented 1 month ago

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

OK DOIs

- 10.1002/adem.200300567 is OK
- 10.1016/j.msea.2003.10.257 is OK
- 10.1145/512274.512284 is OK
- 10.20517/jmi.2021.05 is OK
- 10.1016/j.ijrmhm.2024.106673 is OK
- 10.1557/jmr.2018.153 is OK
- 10.48550/arXiv.2402.03528 is OK
- 10.5860/choice.27-0936 is OK
- 10.48550/arXiv.2402.00572 is OK

MISSING DOIs

- No DOI given, and none found for title: Nim Programming Language v2.0.0
- No DOI given, and none found for title: The Art of Computer Programming, Volume 4, Fascicl...
- No DOI given, and none found for title: Arraymancer v0.7.24: A fast, ergonomic and portabl...

INVALID DOIs

- None

editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (1775.2 files/s, 178954.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Nim                             14            222            393            925
TeX                              2             65             21            681
YAML                             9             31              0            259
Markdown                         3             89              0            207
Python                           2             16              0             76
CSV                              3              0              0             38
JSON                             1              1              0             27
Jupyter Notebook                 1              0            561             10
Dockerfile                       1              1              0              6
-------------------------------------------------------------------------------
SUM:                            36            425            975           2229
-------------------------------------------------------------------------------

Commit count by author:

   182  amkrajewski
   160  Adam M. Krajewski
     3  Zi-Kui Liu
     3  zikuiliu
     1  Arindam
     1  Arindam Debnath
     1  dovahkiin0022
     1  lukeamyers

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 1923

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

RMeli commented 1 month ago

This review is paused until June (see #6455 for the discussion).

editorialbot commented 1 month ago

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

Henrium commented 1 month ago

Review checklist for @Henrium

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/amkrajewski/nimCSO?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@amkrajewski) 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?
[ ] 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?
[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?
[ ] 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)?
[ ] 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?

Henrium commented 1 month ago

I have tested in both GitHub Codespaces and Linux, the package is easy to install and works as claimed. I have a few minor comments regarding the remaining checklist items:

Summary: I suggest the following to make it more accessible to "diverse, non-specialist audience": (1) introduce the background first, then what nimCSO is and what it does; (2) elaborate on the purpose and challenges.
State of field: What are some other approaches to compositional space optimization; are there relevant software? References should be added if applicable. It's not necessary to compare with them, but good to make the paper informative.
In quickstart.ipynb: the routine mostCommon is clear at first, but got confusing when it comes to "removing elements". What's the optimization objective of removing elements?
The "Algorithm-Based Search" method relies on an assumption, "elements present in already expanded ...", is it supported by any rationale, experiments, prior studies, etc.?
I didn't find "community guidelines", though it doesn't seem necessary here. Consider adding one?

amkrajewski commented 1 month ago

@Henrium Thank you for starting the review quickly and providing great feedback! I appreciate that.

I've opened an issue in the code/paper repository (https://github.com/amkrajewski/nimCSO/issues/2), where I will address your comments one by one.

RMeli commented 2 weeks ago

Hi all, since we are now in June I'll remove the "waitlisted" tag. Please let me know if you need any help during the review.

RMeli commented 6 days ago

👋 @amkrajewski, @atzberg, @Henrium, and @bdice

Could you all please provide a short few sentences/bullet points on how things are going with this review?

Thanks and keep up the great work!

amkrajewski commented 5 days ago

Hi @RMeli ! I got a nice constructive review from @Henrium, and I'm waiting for the two other reviewers. It would be great to get them sometime within two or three weeks, but there is no pressure.

bdice commented 5 days ago

Review checklist for @bdice

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/amkrajewski/nimCSO?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@amkrajewski) 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

[ ] Installation: Does installation proceed as outlined in the documentation?
[x] 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.
[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?
[ ] 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?

bdice commented 4 days ago

Thanks for the ping!

Status update: I started a review above. For any boxes I have not checked above, I have comments in this issue https://github.com/amkrajewski/nimCSO/issues/3. For some comments, I am proposing changes in this PR: https://github.com/amkrajewski/nimCSO/pull/4

I will return to this later -- my review is about 60% complete at the moment.

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