[REVIEW]: Kinetic.jl: A lightweight finite volume toolbox in Julia

[whedon]

Submitting author: @vavrines (Tianbai Xiao)
Repository: https://github.com/vavrines/Kinetic.jl
Version: v0.7.5
Editor: @diehlpk
Reviewers: @rdeits, @jarvist
Archive: 10.5281/zenodo.4958132

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Status

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Markdown: [![status](https://joss.theoj.org/papers/65d56efef938caf92c2cc942d2c25ea4/status.svg)](https://joss.theoj.org/papers/65d56efef938caf92c2cc942d2c25ea4)

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

@jarvist & @rdeits, 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 @jarvist

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 (@vavrines) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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 @rdeits

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 (@vavrines) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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. @KristofferC, @rdeits 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.

⭐ Important ⭐

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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2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.05 s (1223.4 files/s, 97969.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                        42            257              0           1862
TOML                             4            260              1           1218
Julia                           13            170            237            972
YAML                             5              7             30            115
TeX                              1              0              0             76
-------------------------------------------------------------------------------
SUM:                            65            694            268           4243
-------------------------------------------------------------------------------


Statistical information for the repository 'e631d825b06217276c947127' was
gathered on 2021/02/23.
No commited files with the specified extensions were found.

[whedon]

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

OK DOIs

- None

MISSING DOIs

- 10.2307/3609795 may be a valid DOI for title: The mathematical theory of non-uniform gases: an account of the kinetic theory of viscosity, thermal conduction and diffusion in gases
- 10.1137/141000671 may be a valid DOI for title: Julia: A fresh approach to numerical computing
- 10.1016/j.jcp.2016.12.022 may be a valid DOI for title: A well-balanced unified gas-kinetic scheme for multiscale flow transport under gravitational field

INVALID DOIs

- https://doi.org/10.5281/zenodo.4025432 is INVALID because of 'https://doi.org/' prefix

[whedon]

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

[diehlpk]

@whedon remind @rdeits in 2 weeks

[whedon]

@rdeits doesn't seem to be a reviewer or author for this submission.

[diehlpk]

@whedon remind @KristofferC in 2 weeks

[whedon]

Reminder set for @KristofferC in 2 weeks

[whedon]

👋 @KristofferC, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @rdeits, please update us on how your review is going (this is an automated reminder).

[diehlpk]

Reminder set for @KristofferC in 2 weeks

[diehlpk]

@whedon remind @rdeits in 2 weeks

[whedon]

Reminder set for @rdeits in 2 weeks

[whedon]

👋 @KristofferC, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @rdeits, please update us on how your review is going (this is an automated reminder).

[rdeits]

I've submitted an issue to Kinetic.jl with some notes on the installation + setup process: vavrines/Kinetic.jl#12

[diehlpk]

@whedon remind @KristofferC in 2 weeks

[whedon]

Reminder set for @KristofferC in 2 weeks

[diehlpk]

@whedon remind @rdeits in 2 weeks

[whedon]

Reminder set for @rdeits in 2 weeks

[rdeits]

Thanks for the reminder. I'm still having trouble getting the basic example to run at all--I've updated the discussion here: vavrines/Kinetic.jl#12 (comment)

[vavrines]

@whedon generate pdf

[whedon]

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

[diehlpk]

@vavrines

vavrines/Kinetic.jl: Kinetic.jl: A portable finite volume toolbox for scientific and neural computing

The Zendo title does not match the title of the paper. Please update the title there as well. I recommend adding your DOI as well.

[diehlpk]

@whedon set 10.5281/zenodo.4958132 as archive

[whedon]

OK. 10.5281/zenodo.4958132 is the archive.

[vavrines]

Hi @diehlpk

I've changed the title (https://zenodo.org/record/4958132#.YMjN6y0RppQ).
The repository was given a Zenodo DOI before I did the submission to JOSS. According to their rules, it's not allowed to change anymore.

[diehlpk]

@vavrines Perfect, I can not recommend your paper for acceptance.

[diehlpk]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.2307/3609795 is OK
- 10.1017/CBO9780511800955 is OK
- 10.1016/j.cpc.2016.11.010 is OK
- 10.1137/141000671 is OK
- 10.5281/zenodo.4025432 is OK
- 10.1016/j.jcp.2016.12.022 is OK
- 10.1016/j.jcp.2020.109535 is OK
- 10.1016/j.camwa.2020.04.033 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2391

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2391, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[danielskatz]

@vavrines - While proofreading this paper before publishing it, I found a number of things that I suggested fixes for in vavrines/Kinetic.jl#15 Please merge this or let me know what you disagree with, then we can proceed with the final publication.

[vavrines]

@vavrines - While proofreading this paper before publishing it, I found a number of things that I suggested fixes for in vavrines/Kinetic.jl#15 Please merge this or let me know what you disagree with, then we can proceed with the final publication.

Hi @danielskatz

Thank you very much for the careful check and revision.
The patch has been merged into master branch.
Do I need to make another release on Zenodo for the latest change?

[danielskatz]

no, you don't need to make a new release for changes in the paper/bib

[danielskatz]

@whedon generate pdf

[whedon]

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

[danielskatz]

@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.03060 joss-papers#2392
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03060
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...

[danielskatz]

Congratulations to @vavrines (Tianbai Xiao)!!

And thanks to @rdeits and @jarvist for reviewing and @diehlpk for editing!

[whedon]

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

If you would like to include a link to your paper from your README use the following code snippets:

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HTML:
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