[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: v1.1.0
Editor: @danielskatz
Reviewers: @dfm, @hawkinsp, @wsmoses
Archive: 10.5281/zenodo.12191214

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/e14ff58162889e474192301c8801dcba"><img src="https://joss.theoj.org/papers/e14ff58162889e474192301c8801dcba/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/e14ff58162889e474192301c8801dcba/status.svg)](https://joss.theoj.org/papers/e14ff58162889e474192301c8801dcba)

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

@dfm & @hawkinsp & @wsmoses, 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:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @danielskatz 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 @dfm

📝 Checklist for @hawkinsp

📝 Checklist for @wsmoses

[editorialbot]

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:

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (987.0 files/s, 148997.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          13            413            310           1282
TeX                              2             82             34            591
Markdown                         2             70              0            270
YAML                             3              3              0            100
C++                              1             21             17             80
TOML                             1              3              0             45
-------------------------------------------------------------------------------
SUM:                            22            592            361           2368
-------------------------------------------------------------------------------

Commit count by author:

   106	Gordian Edenhofer
    95	Jakob Roth
    36	Martin Reinecke

[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]

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

[editorialbot]

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

[danielskatz]

👋 @dfm, @hawkinsp, and @wsmoses - Thanks for agreeing to review this submission.
This is the review thread for the paper. All of our communications will happen here from now on.

As you can see above, you each should use the command @editorialbot generate my checklist to create your review checklist. @editorialbot commands need to be the first thing in a new comment.

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, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6532 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 reviews to be completed within about 2-4 weeks. Please let me know if either of you require some more time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@danielskatz) if you have any questions/concerns.

[dfm]

Review checklist for @dfm

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 https://github.com/NIFTy-PPL/JAXbind?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@roth-jakob) 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
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

• 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: Do the authors clearly state 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: 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?
• 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?

[danielskatz]

👋 @hawkinsp & @wsmoses - This is just a quick ping to ask you to use the command @editorialbot generate my checklist to create your review checklist, and to check off the CoI and CoC items, just to make sure all the permissions are working correctly.. @editorialbot commands need to be the first thing in a new comment. Thanks!

[hawkinsp]

Review checklist for @hawkinsp

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 https://github.com/NIFTy-PPL/JAXbind?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@roth-jakob) 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
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

• 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: Do the authors clearly state 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: 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?
• 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?

[wsmoses]

Review checklist for @wsmoses

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 https://github.com/NIFTy-PPL/JAXbind?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@roth-jakob) 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
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

• 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: Do the authors clearly state 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: 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?
• 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?

[danielskatz]

👋 @hawkinsp & @wsmoses - I see you both have started, at least to some extent. Is there anything blocking you?

[danielskatz]

👋 @hawkinsp & @wsmoses - I just wanted to check on your progress again. Can you let me know how you are doing on this?

[roth-jakob]

@editorialbot generate pdf

[editorialbot]

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

[roth-jakob]

Thanks to dfm's feedback, we have improved the paper. Please look at the new version I just created.

[dfm]

Thanks for your work on this @roth-jakob!

@danielskatz — I have completed my checklist and I'm happy to recommend this submission for publication.

[roth-jakob]

@dfm thank you for your review! Your comments really helped to clarify the documentation and the paper.

[editorialbot]

Done! version is now v1.1.0

[danielskatz]

@editorialbot set 10.5281/zenodo.12191214 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.12191214

[danielskatz]

@roth-jakob - I see the license in the archive is CC-BY - you might want to change it to match the software license, which you should be able to do in the metadata without creating a new deposit

[danielskatz]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[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
- 10.21105/joss.06593 is OK
- 10.1145/3620665.3640366 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
- No DOI given, and none found for title:  TensorFlow: Large-Scale Machine Learning on Heter...

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/csism-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#5520, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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: Roth
  given-names: Jakob
  orcid: "https://orcid.org/0000-0002-8873-8215"
- family-names: Reinecke
  given-names: Martin
- family-names: Edenhofer
  given-names: Gordian
  orcid: "https://orcid.org/0000-0003-3122-4894"
doi: 10.5281/zenodo.12191214
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Roth
    given-names: Jakob
    orcid: "https://orcid.org/0000-0002-8873-8215"
  - family-names: Reinecke
    given-names: Martin
  - family-names: Edenhofer
    given-names: Gordian
    orcid: "https://orcid.org/0000-0003-3122-4894"
  date-published: 2024-06-21
  doi: 10.21105/joss.06532
  issn: 2475-9066
  issue: 98
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6532
  title: "JAXbind: Bind any function to JAX"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06532"
  volume: 9
title: "`JAXbind`: Bind any function to JAX"

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]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 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.06532 joss-papers#5521
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06532
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 @roth-jakob (Jakob Roth) and co-authors on your publication!!

And thanks to @dfm, @hawkinsp, and @wsmoses for reviewing!
JOSS depends on volunteers and we couldn't do this without you

[editorialbot]

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

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.06532/status.svg)](https://doi.org/10.21105/joss.06532)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06532">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06532/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06532/status.svg
   :target: https://doi.org/10.21105/joss.06532

This is how it will look in your documentation:

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The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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[roth-jakob]

Many thanks to everyone for taking the time to review the paper and do editorial work!

[danielskatz]

👋 @roth-jakob - I see some problems in the suggested citation and the presentation of the paper on the JOSS cite

Can I ask that you remove the backquotes in the title in the .md file?
Then I will proceed to reaccept the paper, which will clean up these issues.

[roth-jakob]

Thanks for noticing that! The backquotes are removed.

[danielskatz]

@editorialbot re-accept

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[danielskatz]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[editorialbot]

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#5522

[danielskatz]

Thanks @roth-jakob - this now looks right to me