[REVIEW]: LGP: A robust Linear Genetic Programming implementation on the JVM using Kotlin.

[whedon]

Submitting author: @JedS6391 (Jed Simson)
Repository: https://github.com/JedS6391/LGP
Version: 5.1
Editor: @gkthiruvathukal
Reviewer: @homonecloco
Archive: 10.5281/zenodo.3519400

Status

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Markdown: [![status](http://joss.theoj.org/papers/a3f8ca9f3d7c7a7c1b02dc04c49154c2/status.svg)](http://joss.theoj.org/papers/a3f8ca9f3d7c7a7c1b02dc04c49154c2)

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) 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

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

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @gkthiruvathukal know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @homonecloco

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
• Version: 5.1
• Authorship: Has the submitting author (@JedS6391) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @homonecloco it looks like you're currently assigned as the reviewer for this paper 🎉.

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[arfon]

👋 @homonecloco - how are you getting along with your review?

[homonecloco]

Hi,
I'm still figuring out how to do the reviews in here.

[kyleniemeyer]

@homonecloco other than filling out the checkboxes that you think the submission satisfies, you can submit any other feedback/comments here in the issue thread. You can do that all at once, or as you have comments—either is fine!

[homonecloco]

The documentation is extensive and detailed. However, the links to the API are broken. Reported as an issue in JedS6391/LGP#55

[homonecloco]

There is a link to the Thesis of the author, http://www.jedsimson.co.nz/static/assets/thesis/Open-Source%20Linear%20Genetic%20Programming.pdf Would it be appropriate to also include the supervisor as author?

[homonecloco]

I had issues running the program, as stated JedS6391/LGP#56 . I'll continue the review once this issue is resolved.

[homonecloco]

The installation consists on downloading the jars. There is also an option to do it from Maven.

[gkthiruvathukal]

@JedS6391 I'm not sure whether you saw the issues that have been reported by @homonecloco. Can you please follow up when you get a chance? Thanks.

[JedS6391]

Hi @gkthiruvathukal, JedS6391/LGP#55 and JedS6391/LGP#56 have been addressed. I am currently working on JedS6391/LGP#7, but it is taking a little while to write the unit tests before the issue can be closed.

[gkthiruvathukal]

Thanks, @JedS6391. Please let us know when you've had a chance to add unit tests.

[gkthiruvathukal]

Just a nudge here, @JedS6391. Any update on unit tests?

[gkthiruvathukal]

@JedS6391 Please provide an update on when you will be able to address unit tests.

[JedS6391]

Hi @gkthiruvathukal, apologies for the lack of updates. Unfortunately I have not had time recently to dedicate to the LGP project, and as such I am happy for this review to be cancelled and postponed until I can satisfy the requirements.

[gkthiruvathukal]

@JedS6391 I don't want you to withdraw the submission. You have been good about addressing 2/3 issues. Can you give me an idea of when you might be able to do it? I will work with your schedule and nudge you accordingly.

[JedS6391]

Much appreciated! I will able to start working on the remaining issues over the next few weekends.

[JedS6391]

Hi @gkthiruvathukal -- just wanted to give you a brief progress update.

I have implemented unit tests for a subset of the functionality in this PR. I hope to finish the remaining tests over the weekend.

I will let you know once all unit tests have been completed.

[gkthiruvathukal]

@JedS6391 Perfect. Let me know when you have a few more tests in place. I don't need 100% test coverage to proceed. I just did a quick look and it seems like something is failing, so I will wait until you get it sorted out. Thanks for moving on this!

[JedS6391]

Hi @gkthiruvathukal, the latest commit against the develop branch has a green build and has a subset of the tests.

At the moment, the line coverage is 20% and complexity coverage is 47%, but I intended to increase this going forward. If you are interested to see a breakdown of the areas covered, then that can be viewed here.

I will continue to add more tests and eventually close the initial issue.

[gkthiruvathukal]

@JedS6391 I find your efforts satisfactory as there is now a basis for doing further testing in future work. If our reviewer, @homonecloco, agrees, I would like to move toward accepting your submission. Once we hear from @homonecloco, you will need to create a Zenodo archive.

[gkthiruvathukal]

@homonecloco When you get a chance, can you let us know if your issues are all addressed so I can proceed with the next steps (recommending acceptance).

[homonecloco]

Hi, I haven't got a chance, I'd been travelling the last week. I'll aim to review before the end of this week.

[gkthiruvathukal]

@homonecloco No problem! Thanks for your quick response. End of week is fine.

[Kevin-Mattheus-Moerman]

@JedS6391 👋 ☝️

[gkthiruvathukal]

/ooo October 24 until October 27

[ooo]

👍 Marked @gkthiruvathukal as OOO from Thursday, October 24th 2019 to Sunday, October 27th 2019. 📆

[JedS6391]

Hi @Kevin-Mattheus-Moerman, I think something went wrong with the automatic upload to Zenodo from GitHub so I created the archive manually (see here). I have also updated the archive title + author list to be correct.

The new DOI is 10.5281/zenodo.3519400.

Apologies for the delay in getting this sorted.

[JedS6391]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[JedS6391]

I believe I need to change the DOI to the new one to get the paper to reflect the changes made?

[Kevin-Mattheus-Moerman]

@JedS6391 no you need to make the changes in your paper.md file (https://github.com/JedS6391/LGP/blob/develop/paper.md) and run '@whedon generate pdf'. Note the two changes I proposed above. Let me know if you have questions.

[JedS6391]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[JedS6391]

Hi @Kevin-Mattheus-Moerman, the generated PDF now has the reflected changes (I didn't realise whedon read from the develop branch). Please note that the correct DOI is as stated yesterday: 10.5281/zenodo.3519400.

[Kevin-Mattheus-Moerman]

@whedon set 10.5281/zenodo.3519400 as archive

[whedon]

OK. 10.5281/zenodo.3519400 is the archive.

[Kevin-Mattheus-Moerman]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

OK DOIs

- 10.1147/rd.21.0002 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Check final proof 👉 openjournals/joss-papers#1057

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1057, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[Kevin-Mattheus-Moerman]

@whedon accept deposit=true

[whedon]

Doing it live! Attempting automated processing of paper acceptance...

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.01337 joss-papers#1058
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01337
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...

[whedon]

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

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