[REVIEW]: pycellga: A Python package for improved cellular genetic algorithms

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@sevgiakten@JBorrow<!--end-editor-- Reviewers: @jmejia8, @jbussemaker Archive: Pending

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @JBorrow know.

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Checklists

📝 Checklist for @jmejia8

📝 Checklist for @jbussemaker

editorialbot commented 1 month ago

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editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.10 s (1835.6 files/s, 123845.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         156           1777           4254           4248
reStructuredText                16            348            667            386
Markdown                         3             97              0            191
TeX                              1             11              0            113
YAML                             2             13              0             47
DOS Batch                        1              8              1             26
make                             2              5              7             13
-------------------------------------------------------------------------------
SUM:                           181           2259           4929           5024
-------------------------------------------------------------------------------

Commit count by author:

   116  SevgiAkten
    81  sevgiakten
    27  mhsatman@gmail.com
    15  Mehmet Hakan Satman
     5  jbytecode
     2  Sevgi AKTEN KARAKAYA
     2  Sevgi Akten

editorialbot commented 1 month ago

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

✅ OK DOIs

- 10.5860/choice.27-0936 is OK
- 10.1016/b978-0-08-050684-5.50008-2 is OK
- 10.1007/978-3-662-03315-9 is OK
- 10.1007/978-3-662-44874-8 is OK
- 10.1007/978-0-387-77610-1_1 is OK
- 10.26468/trakyasobed.452095 is OK
- 10.17093/alphanumeric.576919 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: An Improved Cellular Genetic Algorithm with Machin...
- No DOI given, and none found for title: Machine coded genetic algorithms for real paramete...
- No DOI given, and none found for title: Adaptation in Natural and Artificial Systems
- No DOI given, and none found for title: The Genetic Algorithm and the Structure of the Fit...
- No DOI given, and none found for title: Cellular genetic algorithms

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 1202

✅ 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)

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:

jmejia8 commented 1 month ago

Review checklist for @jmejia8

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/SevgiAkten/pycellga?
[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 (@sevgiakten) 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?
[ ] 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?
[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)?
[ ] 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?
[ ] 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?

JBorrow commented 1 month ago

Hi, a couple of reference notes:

9780262581110 is published by MIT Press, not Michigan (https://mitpress.mit.edu/9780262581110/adaptation-in-natural-and-artificial-systems/)
Proc. 4th Int. Conf. on Genetic Algorithms, 1991 is from 1991 not 1989
Please rationalise the text for 'Proceedings of the 5th International Conference on Genetic Algorithms' with the one for the 4th. They should not look so different when they are the same conference two y ears apart.

SevgiAkten commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

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

✅ OK DOIs

- 10.5860/choice.27-0936 is OK
- 10.1016/b978-0-08-050684-5.50008-2 is OK
- 10.1007/978-3-662-03315-9 is OK
- 10.1007/978-3-662-44874-8 is OK
- 10.1007/978-0-387-77610-1_1 is OK
- 10.26468/trakyasobed.452095 is OK
- 10.17093/alphanumeric.576919 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: An Improved Cellular Genetic Algorithm with Machin...
- No DOI given, and none found for title: Machine coded genetic algorithms for real paramete...
- No DOI given, and none found for title: Adaptation in Natural and Artificial Systems
- No DOI given, and none found for title: The Genetic Algorithm and the Structure of the Fit...
- No DOI given, and none found for title: Cellular Genetic Algorithms

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

SevgiAkten commented 1 month ago

@editorialbot generate pdf

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:

SevgiAkten commented 1 month ago

Hello @JBorrow, thank you for the detailed feedback.

I’ve implemented the requested changes and ensured the ICGA references are now consistent.

jbussemaker commented 3 weeks ago

Review checklist for @jbussemaker

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/SevgiAkten/pycellga?
[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 (@sevgiakten) 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?
[ ] 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

[x] 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?
[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?

SevgiAkten commented 3 weeks ago

@editorialbot generate pdf

editorialbot commented 3 weeks ago

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

SevgiAkten commented 1 week ago

@editorialbot generate pdf

editorialbot commented 1 week ago

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

SevgiAkten commented 1 week ago

Dear @jbussemaker, Thank you for your thoughtful and constructive feedback. I have carefully addressed each of your comments and made the necessary revisions to both the code and the manuscript. I kindly invite you to review the updated manuscript and code, and let me know if there are any remaining issues or further suggestions. Your insights are invaluable, and I am happy to make additional adjustments as needed. Thank you again for your guidance and support. I look forward to your feedback.

jmejia8 commented 1 day ago

Dear @SevgiAkten, The following are my comments.

Regarding the paper:

[ ] It is not clear for me whether CGA is a contribution from this paper and software, the confusion raises due to lines 16-17. This is later clarified in Section "Statement of need" (line 107), but it could be added in "Summary" as well.

The integration of cellular automata with genetic algorithms in pycellga represents a significant advancement in the field of evolutionary computation, offering increased flexibility and adaptability compared to traditional methods

[ ] I suggest to the authors to discuss why other libraries in Python (and other languages) are not including CGA variants in their list of implemented algorithms, considering that "... The integration of cellular automata with genetic algorithms in pycellga represents a significant advancement". This could be addressed in Section "State of the field"

Regarding the software:

[ ] Experiments and installation proceed as stated in paper.
[ ] The documentation is clear and with some illustrative examples. However, no examples are given to customize the methods and operators.
[ ] Installation is intuitive via PIP package manager, but slow. Perhaps pycellga has many requirements (dependencies), and it seems that many of them are not strictly necessary (e.g., geographiclib, geopy, pymoo, among others). Could you verify or clarify this?
[ ] In general, the codebase is well-structured and documented, extensible and easy to understand. However, guidelines for testing the software are missing.

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