[REVIEW]: Re-Envisioning Numerical Information Field Theory (NIFTy.re): A Library for Gaussian Processes and Variational Inference #6593
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Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks. For a list of things I can do to help you, just type: For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type: |
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@Abinashbunty, @apizzuto — This is the review thread for the paper. All of our correspondence will happen here from now on. Thanks again for agreeing to participate! 👉 Please read the "Reviewer instructions & questions" in the first comment above, and generate your checklists by commenting 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 We aim for the review process to be completed within about 4-6 weeks but please try to make a start ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule. Please get your review started as soon as possible! |
Review checklist for @AbinashbuntyConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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Review checklist for @apizzutoConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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Hello authors — thank you for a lovely piece of software! I enjoyed installing and playing around with this tool. Overall, I found the paper to be extremely clear, the API docs and installation directions were well done, and the tutorials were a really nice introduction to solving real problems with the software. I left a couple of tiny nits as issues in the repository, they are pretty much all documentation based, so hopefully they won't be hard to address. The only remaining technical parts of my review involve reproducing plots from the paper, which I will try to do in the next few days. I will only benchmark a few performance metrics just to make sure that things seem to line up with your performance plot. I will circle back once I've completed those parts (and I'll check off the remaining boxes in my review once the issues I opened up are addressed). Cheers! |
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Many thanks for the review! I am very happy to hear that you enjoyed playing around with NIFTy.re! :) Thanks for filing these issues! They are all things that definitely still should be improved! I am currently in the midst of putting the finishing touches on my PhD thesis but I'll work on these issues as soon as possible, hopefully resolving them within the next week or so. Regarding the performance validation, feel free to use the [benchmarking script in the repo])https://github.com/NIFTy-PPL/NIFTy/blob/paper/paper/minimal_benchmark.py) to validate the results. I used it together with this visualization script to create the figure in the paper. |
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Thanks for the constructive feedback! I incorporated all of your comments into the code :) |
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@Abinashbunty Do you now approximately when you'll be able to review NIFTy.re? :) |
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@Edenhofer Hi! Perhaps 2 more days. I'm executing some parts of the package and then the review will be over. 👍🏻 |
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All of your fixes for the issues I opened were great, and I have completed the last items on my checklist. Everything looks good from my end. |
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@Abinashbunty — I'll check in here too. Let me know if you have any blockers to finishing your review. (@Edenhofer — Please let me do the reviewer reminders in the future!) |
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Hello @Abinashbunty, here are the things you can ask me to do: |
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@dfm I have verified all the aspects necessary for completing the review. Excellent paper! Kudos to the authors. Well documented with proper flow of execution and examples. I enjoyed installing and working on it for a while. 😄 I just have to check off the last remaining part related to missing DOIs which the bot mentions. The issue for the same has been created. Once that is resolved, my review is complete. 👍🏻 |
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@Abinashbunty, @apizzuto — Thanks for your thorough and constructive reviews!! @Edenhofer — I've opened a small PR with some minor edits to the manuscript, please take a look and merge or let me know what you think. Please also incorporate the DOIs identified by @Abinashbunty when you have a chance. Once you've done that:
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Thanks @apizzuto and @Abinashbunty for reviewing the submission and for providing valuable and constructive feedback! Thanks also @dfm for guiding us through the review process and for your fixes! I'm currently on vacation without my Laptop for one more week but will incorporate the feedback and finalize the submission at the end of next week. |
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Thanks for your all of your feedback! I've updated the references accordingly. Note, I left out the DOI if the journal paper doesn't have one even if there is a arXiv paper with a DOI. I left out the DOI as the cited paper technically has no unique identifier and the arXiv paper might be slightly different and/or outdated. I'm happy to add them in if the consensus is to include DOIs for arXiv papers in this case. I tagged the most recent release with v8.5.1 and pushed a release to zenodo (DOI 10.5281/zenodo.11441976). |
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Hi @dfm I approve of the citing of the references to the respective research papers that do not have a DOI apart from the one in arXiv. And hence also approve of the changes implemented by the authors. I'm just going to run the bot command for checking references as a final report generation. 👍🏻 |
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@editorialbot check references |
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@editorialbot set 10.5281/zenodo.11441976 as archive |
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Done! archive is now 10.5281/zenodo.11441976 |
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@editorialbot set v8.5.1 as version |
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Done! version is now v8.5.1 |
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@editorialbot generate pdf |
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👋 @openjournals/aass-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#5505, then you can now move forward with accepting the submission by compiling again with the command |
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@Abinashbunty, @apizzuto — Many thanks for your reviews here! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you!! @Edenhofer — Your paper is now accepted and published in JOSS! ⚡🚀💥 |
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Submitting author: @Edenhofer (Gordian Edenhofer)
Repository: https://github.com/nifty-ppl/nifty
Branch with paper.md (empty if default branch): paper
Version: v8.5.1
Editor: @dfm
Reviewers: @Abinashbunty, @apizzuto
Archive: 10.5281/zenodo.11441976
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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
@Abinashbunty & @apizzuto, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @dfm know.
✨ 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 ✨
Checklists
📝 Checklist for @Abinashbunty
📝 Checklist for @apizzuto
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