[REVIEW]: Moead-framework : a modular MOEA/D python framework

[whedon]

Submitting author: @geoffreyp (Geoffrey Pruvost)
Repository: https://github.com/moead-framework/framework
Branch with paper.md (empty if default branch):
Version: 1.0
Editor: @melissawm
Reviewers: @sjvrijn, @chkoar
Archive: 10.5281/zenodo.7152178

⚠️ JOSS reduced service mode ⚠️

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Status

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Markdown: [![status](https://joss.theoj.org/papers/a81ea21d0358e013000b0b3b926bd4ba/status.svg)](https://joss.theoj.org/papers/a81ea21d0358e013000b0b3b926bd4ba)

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

@sjvrijn & @chkoar, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ 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 ✨

Review checklist for @sjvrijn

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 repository url?
• 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 (@geoffreyp) 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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

Review checklist for @chkoar

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 repository url?
• 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 (@geoffreyp) 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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @sjvrijn, @chkoar it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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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:

@whedon generate pdf

[whedon]

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

OK DOIs

- 10.1109/TEVC.2008.925798 is OK
- 10.1109/TEVC.2007.892759 is OK
- 10.1109/CEC.2009.4982949 is OK
- 10.1145/3377930.3390149 is OK
- 10.1007/978-3-030-43680-3_9 is OK
- 10.18637/jss.v092.i06 is OK
- 10.1109/ACCESS.2020.2990567 is OK
- 10.21105/joss.02338 is OK
- 10.1145/2739482.2768462 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[melissawm]

👋🏼 @geoffreyp @sjvrijn @chkoar this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#2974 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@melissawm) if you have any questions/concerns.

[melissawm]

Hello, folks! @chkoar @sjvrijn @geoffreyp I see some progress in the checkboxes, let me know if there's anything I can help you with. Thanks!

[whedon]

👋 @sjvrijn, please update us on how your review is going.

[whedon]

👋 @chkoar, please update us on how your review is going.

[chkoar]

Hey @melissawm, I hope that by Monday I will have completed the review.

[chkoar]

Hey @melissawm, I created a couple of issues in the software repo.
I'll wait the authors response in order to continue my review report.

[geoffreyp]

@whedon generate pdf

[whedon]

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

[geoffreyp]

Hello @chkoar and @sjvrijn,
I answered your issues and push the new release(0.5.8) of the framework with your comments and tips, thank you!

I move the documentation in the same repository, the new URL is: https://moead-framework.github.io/framework/

[chkoar]

@geoffreyp please try to address the raised issues atomically. Unrelated changes might slow down the review process. Thanks.

[geoffreyp]

@editorialbot generate pdf

[editorialbot]

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

[geoffreyp]

Hello @melissawm, here are the requested information :

• doi archive : 10.5281/zenodo.7152178 and the url : https://zenodo.org/record/7152178
• The release : https://github.com/moead-framework/framework/releases/tag/1.0

[melissawm]

@editorialbot set 10.5281/zenodo.7152178 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7152178

[melissawm]

@editorialbot set 1.0 as version

[editorialbot]

Done! version is now 1.0

[melissawm]

@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

- 10.1109/TEVC.2008.925798 is OK
- 10.1109/TEVC.2007.892759 is OK
- 10.1109/CEC.2009.4982949 is OK
- 10.1145/3377930.3390149 is OK
- 10.1007/978-3-030-43680-3_9 is OK
- 10.18637/jss.v092.i06 is OK
- 10.1109/ACCESS.2020.2990567 is OK
- 10.21105/joss.02338 is OK
- 10.1145/2739482.2768462 is OK
- 10.1109/SSCI.2016.7850138 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/joss-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#3625, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@geoffreyp – I found a couple of minor typos in your paper here: moead-framework/framework#79

[arfon]

@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

- 10.1109/TEVC.2008.925798 is OK
- 10.1109/TEVC.2007.892759 is OK
- 10.1109/CEC.2009.4982949 is OK
- 10.1145/3377930.3390149 is OK
- 10.1007/978-3-030-43680-3_9 is OK
- 10.18637/jss.v092.i06 is OK
- 10.1109/ACCESS.2020.2990567 is OK
- 10.21105/joss.02338 is OK
- 10.1145/2739482.2768462 is OK
- 10.1109/SSCI.2016.7850138 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[geoffreyp]

Thanks @arfon, it is fixed

[editorialbot]

👋 @openjournals/joss-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#3629, 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]

🐦🐦🐦 👉 Tweet 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.02974 joss-papers#3630
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.02974
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]

@sjvrijn, @chkoar – many thanks for your reviews here and to @melissawm 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 ✨

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

[editorialbot]

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

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