[PRE REVIEW]: JAXbind: Bind any function to JAX

[editorialbot]

Submitting author: @roth-jakob (Jakob Roth)
Repository: https://github.com/NIFTy-PPL/JAXbind
Branch with paper.md (empty if default branch):
Version: 0.1.0
Editor: @danielskatz
Reviewers: @dfm, @hawkinsp, @wsmoses
Managing EiC: Daniel S. Katz

Status

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Author instructions

Thanks for submitting your paper to JOSS @roth-jakob. Currently, there isn't a JOSS editor assigned to your paper.

@roth-jakob if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (957.2 files/s, 144404.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          13            413            310           1282
TeX                              2             82             34            589
Markdown                         2             70              0            270
YAML                             3              3              0            100
C++                              1             21             17             80
TOML                             1              3              0             45
-------------------------------------------------------------------------------
SUM:                            22            592            361           2366
-------------------------------------------------------------------------------

Commit count by author:

   105	Gordian Edenhofer
    94	Jakob Roth
    35	Martin Reinecke

[editorialbot]

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

OK DOIs

- 10.1145/3458817.3476165 is OK

MISSING DOIs

- 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: Enzyme-JAX
- No DOI given, and none found for title: Instead of Rewriting Foreign Code for Machine Lear...
- 10.1109/sc41404.2022.00065 may be a valid DOI for title: Scalable Automatic Differentiation of Multiple Par...
- No DOI given, and none found for title: RESOLVE
- No DOI given, and none found for title: Re-Envisioning Numerical Information Field Theory ...

INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1518

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: BSD 2-Clause "Simplified" License (Valid open source OSI approved license)

[editorialbot]

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

[danielskatz]

👋 @roth-jakob - thanks for your submission.

Could you work on the possibly missing DOI that editorialbot suggests, but note that this may be incorrect. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

[roth-jakob]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1145/3458817.3476165 is OK
- 10.1109/SC41404.2022.00065 is OK
- 10.48550/arXiv.2402.16683 is OK

MISSING DOIs

- 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: Enzyme-JAX
- No DOI given, and none found for title: Instead of Rewriting Foreign Code for Machine Lear...
- No DOI given, and none found for title: RESOLVE

INVALID DOIs

- None

[roth-jakob]

Thanks for instantly opening the review issue!

I added DOIs wherever possible. Some of the citations refer to software or proceedings and don't have a DOI.

[danielskatz]

thanks!

[danielskatz]

@editorialbot generate pdf

[editorialbot]

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

[roth-jakob]

Suitable reviewer in the list of people who already agreed to review might be:

• Saran-nns
• GarrettMerz
• WangKehan573

Not in the list of reviewers, but definitely with expertise on JAX automatic differentiation are:

• wsmoses
• dfm
• hawkinsp

[danielskatz]

@editorialbot assign me as editor

[editorialbot]

Assigned! @danielskatz is now the editor

[danielskatz]

@roth-jakob - Due to the relatively small amount of code, the editors will now discuss if it meets the substantial scholarly effort criterion for review by JOSS. You should hear back in a week or two.

If this passes, @dfm has agree to be a reviewer.

[danielskatz]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[roth-jakob]

Thank you for the update!

We are aware that the codebase of JAXbind is relatively small. Nevertheless, we believe it to be highly useful for various applications requiring custom functions in JAX. Binding custom functions to JAX without our JAXbind package is a big effort, as described for one example function in Dan Foreman-Mackey's repository: https://github.com/dfm/extending-jax

We are very happy that we managed to code general JAX bindings in a compact form, but of course, understand you have to check the JOSS guidelines. Regarding the age of the repository and the number of commits, please be aware that we previously worked on this project in other repositories. See, for example, the various branches in: https://gitlab.mpcdf.mpg.de/jroth/extending-jax-and-nifty

Great to hear that Dan Foreman-Mackey agreed to review!

[danielskatz]

@roth-jakob - this has passed the scope review, so we'll go ahead and get going. I'll add @dfm as a reviewer, and look for at least one more next.

[danielskatz]

@editorialbot add @dfm as reviewer

[editorialbot]

@dfm added to the reviewers list!

[danielskatz]

👋 @wsmoses & @hawkinsp - would one or both you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[roth-jakob]

I am happy to hear that our submission is accepted for review! Thanks for updating!

[hawkinsp]

@danielskatz I would be happy to review this.

[danielskatz]

Thanks @hawkinsp - I'll add you in the system, but wait to see if @wsmoses is also interested before we start the actual review.

[danielskatz]

@editorialbot add @hawkinsp as reviewer

[editorialbot]

@hawkinsp added to the reviewers list!

[roth-jakob]

Thank you @dfm and @hawkinsp for agreeing to review. Looking very much forward to your comments!

[wsmoses]

I'd be happy to review as well. For sake of scheduling, in what timeframe would you expect the review?

[danielskatz]

Great - thanks @wsmoses! I'll add you and we'll start. JOSS reviews are typically expected in about 4 weeks, but since they are iterative, this really depends on what reviewers think needs to be done and how the authors respond. The authors can work on items as soon as reviewers raise them, rather than waiting for a review to be fully completed.

[danielskatz]

@editorialbot add @wsmoses as reviewer

[editorialbot]

@wsmoses added to the reviewers list!

[danielskatz]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #6532.