[REVIEW]: Re-Envisioning Numerical Information Field Theory (NIFTy.re): A Library for Gaussian Processes and Variational Inference

editorialbot commented 5 months ago

Submitting author: !--author-handle-->@Edenhofer@dfm<!--end-editor-- Reviewers: @Abinashbunty, @apizzuto Archive: 10.5281/zenodo.11441976

Status

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Markdown: [![status](https://joss.theoj.org/papers/9e0b78f8d981abdec4fc84605e46786a/status.svg)](https://joss.theoj.org/papers/9e0b78f8d981abdec4fc84605e46786a)

Reviewers and authors:

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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:

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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

editorialbot commented 5 months ago

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editorialbot commented 5 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.30 s (900.1 files/s, 177379.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         246           7215          11172          28144
TeX                              2            160             37           2283
SVG                              3              3              3           1067
Markdown                         4            227              0            885
reStructuredText                 8            330            237            605
YAML                             1             25              0            175
Dockerfile                       1              3              9             15
Bourne Shell                     1              4              0             12
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                           267           7967          11458          33189
-------------------------------------------------------------------------------

Commit count by author:

  1765  Martin Reinecke
  1457  Philipp Arras
  1129  Gordian Edenhofer
   279  Theo Steininger
   191  Reimar Leike
   186  theos
   131  Lukas Platz
   113  Marco Selig
   112  Vincent Eberle
   112  pfrank
   105  Philipp Frank
    93  Massin Guerdi
    79  Jait Dixit
    79  dpumpe
    57  Knollmueller, Jakob (kjako)
    52  csongor
    51  Ultima
    47  Jakob Roth
    39  veberle
    38  Mihai Baltac
    38  ultimanet
    30  Philipp Haim
    23  Jakob Knollmüller
    21  Philipp Frank (pfrank)
    21  Rouven Lemmerz
    16  Torsten Ensslin
    16  matteani
    12  Ensslin, Torsten (ensslint)
    11  Julia Stadler
    11  Matevz, Sraml (sraml)
    10  Julian Rüstig
    10  kjako
     9  Christoph Lienhard
     9  Hutschenreuter, Sebastian (hutsch)
     8  Steininger, Theo (theos)
     8  Ultimanet
     5  wmarg
     4  Andrija Kostic
     4  Lukas Scheel-Platz
     4  Simon Ding
     3  Kostic, Andrija (akostic)
     3  Matteo Guardiani
     3  Matteo.Guardiani
     3  Reimar
     3  mattteani
     3  natalia
     2  Newrzella, Max-Niklas (maxn)
     2  Pumpe, Daniel (dpumpe)
     2  clienhar
     1  David Gorbunov
     1  David Outland
     1  Harth-Kitzerow Johannes
     1  Johannes Buchner
     1  Platz, Lukas (lplatz)
     1  Silvan Streit
     1  ru87him
     1  vkainz

editorialbot commented 5 months ago

Paper file info:

📄 Wordcount for paper.md is 3244

✅ The paper includes a Statement of need section

editorialbot commented 5 months ago

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

editorialbot commented 5 months ago

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

OK DOIs

- 10.21105/joss.00695 is OK
- 10.1046/j.1365-8711.2002.05881.x is OK
- 10.3847/1538-4365/ac4df7 is OK
- 10.1051/0004-6361/202141570 is OK
- 10.1051/0004-6361/202141249 is OK
- 10.48550/arXiv.2208.00211 is OK
- 10.48550/arXiv.2206.06143 is OK
- 10.48550/arXiv.2206.06205 is OK
- 10.3847/1538-4365/aafbea is OK
- 10.1086/498708 is OK
- 10.1088/0004-6256/140/6/1868 is OK
- 10.3847/1538-4357/ac1f96 is OK
- 10.1051/0004-6361/201935093 is OK
- 10.1051/0004-6361/202038169 is OK
- 10.48550/ARXIV.2206.10634 is OK
- 10.48550/arXiv.2308.01295 is OK
- 10.1371/journal.pone.0275011 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.48550/ARXIV.1901.11033 is OK
- 10.3390/e23070853 is OK
- 10.3390/psf2022005006 is OK
- 10.1109/TPAMI.2015.2448083 is OK
- 10.3847/1538-3881/aa9332 is OK
- 10.5281/zenodo.10463641 is OK
- 10.18637/jss.v076.i01 is OK
- 10.7717/peerj-cs.55 is OK
- 10.1086/670067 is OK
- 10.1093/mnras/staa278 is OK
- 10.5281/zenodo.8408702 is OK
- 10.48550/arXiv.1912.11554 is OK
- 10.1002/andp.201800290 is OK
- 10.1051/0004-6361/202243319 is OK
- 10.1051/0004-6361/202142846 is OK
- 10.1051/0004-6361/201834695 is OK
- 10.1051/0004-6361/201832832 is OK
- 10.1051/0004-6361/201730831 is OK
- 10.1093/mnras/sty3341 is OK
- 10.1051/0004-6361/202038708 is OK
- 10.1051/0004-6361/201833284 is OK
- 10.3847/2041-8213/ac67db is OK
- 10.1051/0004-6361/201628885 is OK
- 10.1051/0004-6361/202244784 is OK
- 10.1051/0004-6361/202141298 is OK
- 10.48550/arXiv.2204.11715 is OK
- 10.3847/1538-4357/ab5362 is OK
- 10.1093/mnras/sty1008 is OK
- 10.48550/arXiv.2303.03420 is OK
- 10.1051/0004-6361/201935765 is OK
- 10.1051/0004-6361/202142369 is OK
- 10.48550/arXiv.2303.09926 is OK
- 10.1051/0004-6361/201323195 is OK
- 10.48550/arXiv.2206.06710 is OK
- 10.1038/s41586-019-1874-z is OK
- 10.3847/1538-4365/abe465 is OK
- 10.3847/1538-3881/ab99c8 is OK
- 10.48550/arXiv.2206.05796 is OK
- 10.1038/s41550-021-01548-0 is OK
- 10.3847/1538-4357/ab2388 is OK
- 10.1051/0004-6361/202346851 is OK
- 10.48550/arXiv.2304.12350 is OK
- 10.1051/0004-6361/202346423 is OK
- 10.3847/1538-3881/acabc1 is OK
- 10.1051/0004-6361/202140486 is OK
- 10.1051/0004-6361/202243326 is OK
- 10.21105/joss.00695 is OK
- 10.21105/joss.01298 is OK
- 10.1086/427976 is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.1051/0004-6361/201322068 is OK
- 10.1051/0004-6361/202243819 is OK
- 10.1103/PhysRevE.96.052104 is OK
- 10.1088/1475-7516/2021/04/071 is OK
- 10.48550/arXiv.2308.09176 is OK
- 10.3390/e25040652 is OK
- 10.3390/psf2022005033 is OK
- 10.1051/0004-6361/201935555 is OK

MISSING DOIs

- No DOI given, and none found for title: Physics of the Interstellar and Intergalactic Medi...
- No DOI given, and none found for title: The Pan-STARRS1 Surveys
- No DOI given, and none found for title: Variational Inference with Normalizing Flows
- No DOI given, and none found for title: The No-U-Turn Sampler: Adaptively Setting Path Len...
- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: DUCC: Distinctly Useful Code Collection
- No DOI given, and none found for title: Equinox: neural networks in JAX via callable PyTre...
- No DOI given, and none found for title: Efficient and Modular Implicit Differentiation
- No DOI given, and none found for title: The DeepMind JAX Ecosystem
- No DOI given, and none found for title: Scalable Variational Gaussian Process Classificati...
- No DOI given, and none found for title: GPflow: A Gaussian Process Library Using Tensorflo...
- No DOI given, and none found for title: Pyro: Deep Universal Probabilistic Programming
- No DOI given, and none found for title: Blackjax: A sampling library for JAX
- No DOI given, and none found for title: NIFTY: A versatile Python library for signal infer...
- No DOI given, and none found for title: NIFTy5: Numerical Information Field Theory v5
- No DOI given, and none found for title: Re-Envisioning Numerical Information Field Theory ...
- Entry without DOI or title found

INVALID DOIs

- None

dfm commented 5 months ago

@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 @editorialbot generate my checklist on this issue ASAP. 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#6593 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 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!

editorialbot commented 5 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Abinashbunty commented 5 months ago

Review checklist for @Abinashbunty

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/nifty-ppl/nifty?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@Edenhofer) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] 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?

apizzuto commented 5 months ago

Review checklist for @apizzuto

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/nifty-ppl/nifty?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@Edenhofer) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

apizzuto commented 4 months ago

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!

Edenhofer commented 4 months ago

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.

Edenhofer commented 4 months ago

Thanks for the constructive feedback! I incorporated all of your comments into the code :)

Edenhofer commented 4 months ago

@Abinashbunty Do you now approximately when you'll be able to review NIFTy.re? :)

Abinashbunty commented 3 months ago

@Edenhofer Hi! Perhaps 2 more days. I'm executing some parts of the package and then the review will be over. 👍🏻

apizzuto commented 3 months ago

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.

dfm commented 3 months ago

@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!)

Abinashbunty commented 3 months ago

@editorialbot commands

editorialbot commented 3 months ago

Hello @Abinashbunty, here are the things you can ask me to do:


# List all available commands
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# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

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Abinashbunty commented 3 months ago

@editorialbot check references

editorialbot commented 3 months ago

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

OK DOIs

- 10.21105/joss.00695 is OK
- 10.1046/j.1365-8711.2002.05881.x is OK
- 10.3847/1538-4365/ac4df7 is OK
- 10.1051/0004-6361/202141570 is OK
- 10.1051/0004-6361/202141249 is OK
- 10.48550/arXiv.2208.00211 is OK
- 10.48550/arXiv.2206.06143 is OK
- 10.48550/arXiv.2206.06205 is OK
- 10.3847/1538-4365/aafbea is OK
- 10.1086/498708 is OK
- 10.1088/0004-6256/140/6/1868 is OK
- 10.3847/1538-4357/ac1f96 is OK
- 10.1051/0004-6361/201935093 is OK
- 10.1051/0004-6361/202038169 is OK
- 10.48550/ARXIV.2206.10634 is OK
- 10.48550/arXiv.2308.01295 is OK
- 10.1371/journal.pone.0275011 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.48550/ARXIV.1901.11033 is OK
- 10.3390/e23070853 is OK
- 10.3390/psf2022005006 is OK
- 10.1109/TPAMI.2015.2448083 is OK
- 10.3847/1538-3881/aa9332 is OK
- 10.5281/zenodo.10463641 is OK
- 10.18637/jss.v076.i01 is OK
- 10.7717/peerj-cs.55 is OK
- 10.1086/670067 is OK
- 10.1093/mnras/staa278 is OK
- 10.5281/zenodo.8408702 is OK
- 10.48550/arXiv.1912.11554 is OK
- 10.1002/andp.201800290 is OK
- 10.1051/0004-6361/202243319 is OK
- 10.1051/0004-6361/202142846 is OK
- 10.1051/0004-6361/201834695 is OK
- 10.1051/0004-6361/201832832 is OK
- 10.1051/0004-6361/201730831 is OK
- 10.1093/mnras/sty3341 is OK
- 10.1051/0004-6361/202038708 is OK
- 10.1051/0004-6361/201833284 is OK
- 10.3847/2041-8213/ac67db is OK
- 10.1051/0004-6361/201628885 is OK
- 10.1051/0004-6361/202244784 is OK
- 10.1051/0004-6361/202141298 is OK
- 10.48550/arXiv.2204.11715 is OK
- 10.3847/1538-4357/ab5362 is OK
- 10.1093/mnras/sty1008 is OK
- 10.48550/arXiv.2303.03420 is OK
- 10.1051/0004-6361/201935765 is OK
- 10.1051/0004-6361/202142369 is OK
- 10.48550/arXiv.2303.09926 is OK
- 10.1051/0004-6361/201323195 is OK
- 10.48550/arXiv.2206.06710 is OK
- 10.1038/s41586-019-1874-z is OK
- 10.3847/1538-4365/abe465 is OK
- 10.3847/1538-3881/ab99c8 is OK
- 10.48550/arXiv.2206.05796 is OK
- 10.1038/s41550-021-01548-0 is OK
- 10.3847/1538-4357/ab2388 is OK
- 10.1051/0004-6361/202346851 is OK
- 10.48550/arXiv.2304.12350 is OK
- 10.1051/0004-6361/202346423 is OK
- 10.3847/1538-3881/acabc1 is OK
- 10.1051/0004-6361/202140486 is OK
- 10.1051/0004-6361/202243326 is OK
- 10.21105/joss.00695 is OK
- 10.21105/joss.01298 is OK
- 10.1086/427976 is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.1051/0004-6361/201322068 is OK
- 10.1051/0004-6361/202243819 is OK
- 10.1103/PhysRevE.96.052104 is OK
- 10.1088/1475-7516/2021/04/071 is OK
- 10.48550/arXiv.2308.09176 is OK
- 10.3390/e25040652 is OK
- 10.3390/psf2022005033 is OK
- 10.1051/0004-6361/201935555 is OK

MISSING DOIs

- No DOI given, and none found for title: Physics of the Interstellar and Intergalactic Medi...
- No DOI given, and none found for title: The Pan-STARRS1 Surveys
- No DOI given, and none found for title: Variational Inference with Normalizing Flows
- No DOI given, and none found for title: The No-U-Turn Sampler: Adaptively Setting Path Len...
- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: DUCC: Distinctly Useful Code Collection
- No DOI given, and none found for title: Equinox: neural networks in JAX via callable PyTre...
- No DOI given, and none found for title: Efficient and Modular Implicit Differentiation
- No DOI given, and none found for title: The DeepMind JAX Ecosystem
- No DOI given, and none found for title: Scalable Variational Gaussian Process Classificati...
- No DOI given, and none found for title: GPflow: A Gaussian Process Library Using Tensorflo...
- No DOI given, and none found for title: Pyro: Deep Universal Probabilistic Programming
- No DOI given, and none found for title: Blackjax: A sampling library for JAX
- No DOI given, and none found for title: NIFTY: A versatile Python library for signal infer...
- No DOI given, and none found for title: NIFTy5: Numerical Information Field Theory v5
- No DOI given, and none found for title: Re-Envisioning Numerical Information Field Theory ...
- Entry without DOI or title found

INVALID DOIs

- None

Abinashbunty commented 3 months ago

@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. 👍🏻

dfm commented 3 months ago

@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:

Take one last read through the manuscript to make sure that you're happy with it (it's harder to make changes later!), especially the author names and affiliations. I've taken a pass and it looks good to me!
Increment the version number of the software and report that version number back here.
Create an archived release of that version of the software (using Zenodo or something similar). Please make sure that the metadata (title and author list) exactly match the paper. Then report the DOI of the release back to this thread.

Edenhofer commented 3 months ago

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.

Edenhofer commented 3 months ago

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).

Abinashbunty commented 2 months ago

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. 👍🏻

Abinashbunty commented 2 months ago

@editorialbot check references

editorialbot commented 2 months ago

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

OK DOIs

- 10.1051/0004-6361/201935555 is OK
- 10.1038/s41550-021-01548-0 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.18637/jss.v076.i01 is OK
- 10.3390/e25040652 is OK
- 10.3390/psf2022005033 is OK
- 10.48550/ARXIV.2206.10634 is OK
- 10.1051/0004-6361/202347628 is OK
- 10.1086/670067 is OK
- 10.3847/1538-3881/aa9332 is OK
- 10.5281/zenodo.10463641 is OK
- 10.1103/PhysRevE.96.052104 is OK
- 10.3390/e23070853 is OK
- 10.3390/psf2022005006 is OK
- 10.1086/427976 is OK
- 10.21105/joss.00695 is OK
- 10.1371/journal.pone.0275011 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1051/0004-6361/202140486 is OK
- 10.48550/arXiv.2304.12350 is OK
- 10.48550/ARXIV.1901.11033 is OK
- 10.5281/zenodo.8408702 is OK
- 10.1051/0004-6361/201935093 is OK
- 10.1051/0004-6361/202038169 is OK
- 10.48550/arXiv.2204.11715 is OK
- 10.1051/0004-6361/202243326 is OK
- 10.48550/arXiv.1912.11554 is OK
- 10.1051/0004-6361/202346851 is OK
- 10.3847/1538-3881/acabc1 is OK
- 10.7717/peerj-cs.55 is OK
- 10.1051/0004-6361/202243819 is OK
- 10.1051/0004-6361/201321236 is OK
- 10.1109/TPAMI.2015.2448083 is OK
- 10.1093/mnras/staa278 is OK
- 10.1002/andp.201800290 is OK
- 10.1051/0004-6361/202346423 is OK
- 10.1088/1475-7516/2021/04/071 is OK
- 10.48550/arXiv.2308.09176 is OK
- 10.21105/joss.01298 is OK

MISSING DOIs

- No DOI given, and none found for title: NIFTy5: Numerical Information Field Theory v5
- No DOI given, and none found for title: Pyro: Deep Universal Probabilistic Programming
- No DOI given, and none found for title: Blackjax: A sampling library for JAX
- No DOI given, and none found for title: Efficient and Modular Implicit Differentiation
- No DOI given, and none found for title: The DeepMind JAX Ecosystem
- No DOI given, and none found for title: DUCC: Distinctly Useful Code Collection
- No DOI given, and none found for title: Scalable Variational Gaussian Process Classificati...
- No DOI given, and none found for title: The No-U-Turn Sampler: Adaptively Setting Path Len...
- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: Equinox: neural networks in JAX via callable PyTre...
- No DOI given, and none found for title: GPflow: A Gaussian Process Library Using Tensorflo...
- No DOI given, and none found for title: Variational Inference with Normalizing Flows

INVALID DOIs

- None

dfm commented 2 months ago

@editorialbot set 10.5281/zenodo.11441976 as archive

editorialbot commented 2 months ago

Done! archive is now 10.5281/zenodo.11441976

dfm commented 2 months ago

@editorialbot set v8.5.1 as version

editorialbot commented 2 months ago

Done! version is now v8.5.1

dfm commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

dfm commented 2 months ago

@editorialbot recommend-accept

editorialbot commented 2 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 months ago

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

OK DOIs

- 10.1051/0004-6361/201935555 is OK
- 10.1038/s41550-021-01548-0 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.18637/jss.v076.i01 is OK
- 10.3390/e25040652 is OK
- 10.3390/psf2022005033 is OK
- 10.48550/ARXIV.2206.10634 is OK
- 10.1051/0004-6361/202347628 is OK
- 10.1086/670067 is OK
- 10.3847/1538-3881/aa9332 is OK
- 10.5281/zenodo.10463641 is OK
- 10.1103/PhysRevE.96.052104 is OK
- 10.3390/e23070853 is OK
- 10.3390/psf2022005006 is OK
- 10.1086/427976 is OK
- 10.21105/joss.00695 is OK
- 10.1371/journal.pone.0275011 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1051/0004-6361/202140486 is OK
- 10.48550/arXiv.2304.12350 is OK
- 10.48550/ARXIV.1901.11033 is OK
- 10.5281/zenodo.8408702 is OK
- 10.1051/0004-6361/201935093 is OK
- 10.1051/0004-6361/202038169 is OK
- 10.48550/arXiv.2204.11715 is OK
- 10.1051/0004-6361/202243326 is OK
- 10.48550/arXiv.1912.11554 is OK
- 10.1051/0004-6361/202346851 is OK
- 10.3847/1538-3881/acabc1 is OK
- 10.7717/peerj-cs.55 is OK
- 10.1051/0004-6361/202243819 is OK
- 10.1051/0004-6361/201321236 is OK
- 10.1109/TPAMI.2015.2448083 is OK
- 10.1093/mnras/staa278 is OK
- 10.1002/andp.201800290 is OK
- 10.1051/0004-6361/202346423 is OK
- 10.1088/1475-7516/2021/04/071 is OK
- 10.48550/arXiv.2308.09176 is OK
- 10.21105/joss.01298 is OK

MISSING DOIs

- No DOI given, and none found for title: NIFTy5: Numerical Information Field Theory v5
- No DOI given, and none found for title: Pyro: Deep Universal Probabilistic Programming
- No DOI given, and none found for title: Blackjax: A sampling library for JAX
- No DOI given, and none found for title: Efficient and Modular Implicit Differentiation
- No DOI given, and none found for title: The DeepMind JAX Ecosystem
- No DOI given, and none found for title: DUCC: Distinctly Useful Code Collection
- No DOI given, and none found for title: Scalable Variational Gaussian Process Classificati...
- No DOI given, and none found for title: The No-U-Turn Sampler: Adaptively Setting Path Len...
- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: Equinox: neural networks in JAX via callable PyTre...
- No DOI given, and none found for title: GPflow: A Gaussian Process Library Using Tensorflo...
- No DOI given, and none found for title: Variational Inference with Normalizing Flows

INVALID DOIs

- None

editorialbot commented 2 months ago

:wave: @openjournals/aass-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5505, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

dfm commented 2 months ago

@editorialbot accept

editorialbot commented 2 months ago

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

editorialbot commented 2 months ago

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Edenhofer given-names: Gordian orcid: "https://orcid.org/0000-0003-3122-4894" - family-names: Frank given-names: Philipp orcid: "https://orcid.org/0000-0001-5610-3779" - family-names: Roth given-names: Jakob orcid: "https://orcid.org/0000-0002-8873-8215" - family-names: Leike given-names: Reimar H. orcid: "https://orcid.org/0000-0002-1640-6772" - family-names: Guerdi given-names: Massin - family-names: Scheel-Platz given-names: Lukas I. orcid: "https://orcid.org/0000-0003-0809-9634" - family-names: Guardiani given-names: Matteo orcid: "https://orcid.org/0000-0002-4905-6692" - family-names: Eberle given-names: Vincent orcid: "https://orcid.org/0000-0002-5713-3475" - family-names: Westerkamp given-names: Margret orcid: "https://orcid.org/0000-0001-7218-8282" - family-names: Enßlin given-names: Torsten A. orcid: "https://orcid.org/0000-0001-5246-1624" contact: - family-names: Edenhofer given-names: Gordian orcid: "https://orcid.org/0000-0003-3122-4894" doi: 10.5281/zenodo.11441976 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Edenhofer given-names: Gordian orcid: "https://orcid.org/0000-0003-3122-4894" - family-names: Frank given-names: Philipp orcid: "https://orcid.org/0000-0001-5610-3779" - family-names: Roth given-names: Jakob orcid: "https://orcid.org/0000-0002-8873-8215" - family-names: Leike given-names: Reimar H. orcid: "https://orcid.org/0000-0002-1640-6772" - family-names: Guerdi given-names: Massin - family-names: Scheel-Platz given-names: Lukas I. orcid: "https://orcid.org/0000-0003-0809-9634" - family-names: Guardiani given-names: Matteo orcid: "https://orcid.org/0000-0002-4905-6692" - family-names: Eberle given-names: Vincent orcid: "https://orcid.org/0000-0002-5713-3475" - family-names: Westerkamp given-names: Margret orcid: "https://orcid.org/0000-0001-7218-8282" - family-names: Enßlin given-names: Torsten A. orcid: "https://orcid.org/0000-0001-5246-1624" date-published: 2024-06-15 doi: 10.21105/joss.06593 issn: 2475-9066 issue: 98 journal: Journal of Open Source Software publisher: name: Open Journals start: 6593 title: "Re-Envisioning Numerical Information Field Theory (NIFTy.re): A Library for Gaussian Processes and Variational Inference" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06593" volume: 9 title: "Re-Envisioning Numerical Information Field Theory (NIFTy.re): A Library for Gaussian Processes and Variational Inference" ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot commented 2 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 2 months ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/5506
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06593
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

dfm commented 2 months ago

@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! :zap::rocket::boom:

editorialbot commented 2 months ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.06593/status.svg)](https://doi.org/10.21105/joss.06593)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06593">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06593/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06593/status.svg
   :target: https://doi.org/10.21105/joss.06593

This is how it will look in your documentation:

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openjournals / joss-reviews