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[REVIEW]: HW2D: A reference implementation of the Hasegawa-Wakatani model for plasma turbulence in fusion reactors #5959
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👋 @the-rccg @archermarx @Uddiptaatwork the review will take place here |
Review checklist for @archermarxConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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Review checklist for @UddiptaatworkConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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I have completed most of my review, except for actually running the software. Overall, I think this is a very nice contribution. I have two main comments:
I will try and run the software tomorrow. |
@archermarx I added an example for the CLI interface with an explanation for the kwargs used. There is also an additional paragraph on the accelerators that clearly labels available accelerators (currently only Numba). Others should be ready soon, and will be added to the readme and installation. For a full workflow example, a more thorough framework would be needed like a Google Colab Notebook, which is planned for the future. |
Great! I've now run the code and it mostly works. However, I encounter an error using the following input
The code runs to completion and generates a (very nice looking) movie. However, in the "Plotting properties" step, I get this error:
And no image is produced. |
@archermarx I updated the error handling to give graceful explanations and handling of this case. The issue was that end_time=100 is not inside of the saturated turbulent phase, so all statistical properties would be meaningless for the turbulent system. It now provides a warning and includes a picture of the non-converged data. |
Excellent! In that case, I think I can mark my review as completed. Very cool work! |
@archermarx Thank you very much for your time and effort in finding these issues and reviewing the submission! Really appreciate it. |
I have now concluded my review. The code works great and the tests ran smoothly without any errors.
The documentation pertaining to the API is very well done and appears highly useful for any new user of the code. The article is succinct with analytical descriptions and citations where necessary. Overall, I would like to congratulate the author for a very well written code and article. |
Thank you, @Uddiptaatwork. @the-rccg, is that suggestion on a home page for the documentation something you could address? |
@Uddiptaatwork Thank you very much for the review. I have added a dynamic link for the top-level that includes the README.md dynamically in documentation creation upon commit. pdoc3 currently has some issues with latex formulas in include and does no support for GitHub Flavored Markdown (GFM), therefore some things are not properly displayed at this time. I have opened an issue with pdoc3 and will try to get the support implemented myself to make sure it displays properly. Preview of the ReadMe in the docs: https://the-rccg.github.io/hw2d/index.html |
@the-rccg in the past, I think I converted my Markdown README to ReST and then used that for the docs generation to avoid some issues like that, but may have been with Sphinx. This looks like a good solution, though |
@kyleniemeyer After a lot of back and forth, I have now moved from pdoc3 to pdoc. Images and equations now work and all information is pulled dynamically from the readme. |
That looks great! At this point, I think the review is complete. |
Post-Review Checklist for Editor and AuthorsAdditional Author Tasks After Review is Complete
Editor Tasks Prior to Acceptance
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OK, all looks great @the-rccg! |
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The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.
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👋 @openjournals/pe-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#4832, then you can now move forward with accepting the submission by compiling again with the command |
Can the Tex warnings be safely ignored or do I need to removethe \space and \small from it still? |
@the-rccg let's try removing As for |
@kyleniemeyer removed all \small, \normalsize, and \space and replaces some with more explicit spacings. |
@editorialbot generate pdf |
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👋 @openjournals/pe-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#4833, then you can now move forward with accepting the submission by compiling again with the command |
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All looks good. Once again, thank you all for helping in the review process! |
Congratulations @the-rccg on your article's publication in JOSS! Please consider signing up as a reviewer if you haven't already. Many thanks to @archermarx and @Uddiptaatwork for reviewing this. We can't do it without your support. |
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Submitting author: @the-rccg (Robin Greif)
Repository: https://github.com/the-rccg/hw2d
Branch with paper.md (empty if default branch): main
Version: 1.0.0
Editor: @kyleniemeyer
Reviewers: @archermarx, @Uddiptaatwork
Archive: 10.5281/zenodo.10365012
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