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[REVIEW]: KerrGeoPy: A Python Package for Computing Timelike Geodesics in Kerr Spacetime #6587

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editorialbot opened this issue Apr 8, 2024 · 61 comments
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accepted Jupyter Notebook published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 1 (AASS) Astronomy, Astrophysics, and Space Sciences

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editorialbot commented Apr 8, 2024

Submitting author: @syp2001 (Seyong Park)
Repository: https://github.com/BlackHolePerturbationToolkit/KerrGeoPy
Branch with paper.md (empty if default branch): paper
Version: v0.9.3
Editor: @xuanxu
Reviewers: @Uddiptaatwork, @sterinaldi
Archive: 10.5281/zenodo.11386563

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/21ee313e418a9fed60099b33cafbd24b"><img src="https://joss.theoj.org/papers/21ee313e418a9fed60099b33cafbd24b/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/21ee313e418a9fed60099b33cafbd24b/status.svg)](https://joss.theoj.org/papers/21ee313e418a9fed60099b33cafbd24b)

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

@Uddiptaatwork & @sterinaldi, 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 @xuanxu 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 @sterinaldi

📝 Checklist for @Uddiptaatwork

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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:

@editorialbot commands

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

@editorialbot generate pdf

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5281/zenodo.8233425 is OK
- 10.1051/0004-6361/201935406 is OK
- 10.48550/arXiv.1903.03686 is OK
- 10.48550/arXiv.1907.06482 is OK
- 10.5281/zenodo.8108265 is OK
- 10.1103/PhysRevD.101.064007 is OK
- 10.1088/0264-9381/26/13/135002 is OK
- 10.1088/1361-6382/acf552 is OK
- 10.1103/PhysRevD.73.024027 is OK
- 10.1088/0264-9381/19/10/314 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (1039.5 files/s, 99045.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          17            724           1942           2712
Jupyter Notebook                 6              0           1716            438
Markdown                         2            133              0            288
TeX                              1             14              0            227
reStructuredText                65            409            395            149
YAML                             5             18             18            100
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            98           1310           4079           3949
-------------------------------------------------------------------------------

Commit count by author:

   104	Se Yong Park
    24	Seyong Park
    21	Seyong
     2	Zachary Nasipak

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Paper file info:

📄 Wordcount for paper.md is 1061

✅ The paper includes a Statement of need section

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License info:

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

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

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xuanxu commented Apr 8, 2024

👋 Hi @Uddiptaatwork and @sterinaldi, and thank you for agreeing to review this submission for KerrGeoPy !

The review will take place in this issue, and you can generate your individual reviewer checklists by asking editorialbot directly with @editorialbot generate my checklist

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 #6587 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.

As you go over the submission, please check any items on your reviewer checklist that you feel have been satisfied. If you aren't sure how to get started, please see the JOSS reviewer guidelines -- and of course, feel free to ping me (@xuanxu) with any questions !

We aim for reviews to be completed within four weeks, or six weeks at latest. 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.

If you any questions or concerns arise, please feel free to ask here or via email. And thank you again !

@sterinaldi
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Thanks @xuanxu! I'll start the review in the next few days.

@sterinaldi
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sterinaldi commented Apr 9, 2024

Review checklist for @sterinaldi

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/BlackHolePerturbationToolkit/KerrGeoPy?
  • 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 (@syp2001) 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?

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xuanxu commented Apr 24, 2024

👋 @Uddiptaatwork, @sterinaldi Can you update us on the progress of your review?

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xuanxu commented Apr 26, 2024

@Uddiptaatwork I've noticed you have not created your review checklist yet, please do so by running this command in a separate comment:

@editorialbot generate my checklist

@sterinaldi
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sterinaldi commented Apr 26, 2024

Hi @xuanxu, sorry for the late reply, I had a few hectic days. So far, I managed to install the code on a fresh environment, run the automated tests and played a bit with the code, which seems to work well so far. I think I'll be able to have a more thorough look at the documentation and the paper by the end of next week.

@Uddiptaatwork
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Uddiptaatwork commented May 2, 2024

Review checklist for @Uddiptaatwork

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/BlackHolePerturbationToolkit/KerrGeoPy?
  • 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 (@syp2001) 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?

@sterinaldi
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Hi @syp2001, I was looking for some indications about how to contribute to the code but I couldn't find any – could you please tell me whether if this is specified somewhere or it's still to be added?
Thanks!

@sterinaldi
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Hi @xuanxu, I completed the checklist. Caveat the contribution point (see comment above), I'm happy with the package and the paper and, as soon as that point is addressed, this submission has green light from my side.

@syp2001
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syp2001 commented May 8, 2024

Hi @sterinaldi, sorry for the late reply. There are currently no community guidelines specified, but I am working on writing them and they should hopefully be up within the next few days.

@sterinaldi
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Thanks! I found this template pretty useful, myself: https://github.com/nayafia/contributing-template

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xuanxu commented May 20, 2024

@Uddiptaatwork any update on how your review is going?

@syp2001
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syp2001 commented May 21, 2024

Hi @sterinaldi, sorry again for the delay. I finally had time to write the guidelines and they are up at https://github.com/BlackHolePerturbationToolkit/KerrGeoPy/blob/main/CONTRIBUTING.md now.

@sterinaldi
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sterinaldi commented May 21, 2024

Thanks @syp2001! The guidelines looks fine with me, very nice work overall!
@xuanxu – Green light from my side.

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xuanxu commented May 22, 2024

Thanks @sterinaldi! can you confirm you recommend the submission for publication?

@sterinaldi
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Yes, I confirm that I recommend this paper for publication.

@Uddiptaatwork
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Apologies for the delay, we were going through a few closures at our institute due to extraneous (geopolitical) reasons.

I just finished going through the paper, documentation and currently running tests for a final sanity check.
The paper itself and the documentation looks great and definitely up to par. The installation on Linux and MacOS(intel) was seamless.

I will get back to you in an hour with the sanity checks.

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5281/zenodo.8233425 is OK
- 10.1051/0004-6361/201935406 is OK
- 10.48550/arXiv.1903.03686 is OK
- 10.48550/arXiv.1907.06482 is OK
- 10.5281/zenodo.8108265 is OK
- 10.1103/PhysRevD.101.064007 is OK
- 10.1088/0264-9381/26/13/135002 is OK
- 10.1088/1361-6382/acf552 is OK
- 10.1103/PhysRevD.73.024027 is OK
- 10.1088/0264-9381/19/10/314 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

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xuanxu commented May 31, 2024

Looking good!

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xuanxu commented May 31, 2024

@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5281/zenodo.8233425 is OK
- 10.1051/0004-6361/201935406 is OK
- 10.48550/arXiv.1903.03686 is OK
- 10.48550/arXiv.1907.06482 is OK
- 10.5281/zenodo.8108265 is OK
- 10.1103/PhysRevD.101.064007 is OK
- 10.1088/0264-9381/26/13/135002 is OK
- 10.1088/1361-6382/acf552 is OK
- 10.1103/PhysRevD.73.024027 is OK
- 10.1088/0264-9381/19/10/314 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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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#5414, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label May 31, 2024
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dfm commented Jun 1, 2024

@editorialbot generate pdf

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

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dfm commented Jun 1, 2024

@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5281/zenodo.8233425 is OK
- 10.1051/0004-6361/201935406 is OK
- 10.48550/arXiv.1903.03686 is OK
- 10.48550/arXiv.1907.06482 is OK
- 10.5281/zenodo.8108265 is OK
- 10.1103/PhysRevD.101.064007 is OK
- 10.1088/0264-9381/26/13/135002 is OK
- 10.1088/1361-6382/acf552 is OK
- 10.1103/PhysRevD.73.024027 is OK
- 10.1088/0264-9381/19/10/314 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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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#5428, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

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dfm commented Jun 1, 2024

@editorialbot accept

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

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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: Park
  given-names: Seyong
  orcid: "https://orcid.org/0009-0002-1152-9324"
- family-names: Nasipak
  given-names: Zachary
  orcid: "https://orcid.org/0000-0002-5109-9704"
doi: 10.5281/zenodo.11386563
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Park
    given-names: Seyong
    orcid: "https://orcid.org/0009-0002-1152-9324"
  - family-names: Nasipak
    given-names: Zachary
    orcid: "https://orcid.org/0000-0002-5109-9704"
  date-published: 2024-06-01
  doi: 10.21105/joss.06587
  issn: 2475-9066
  issue: 98
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6587
  title: "KerrGeoPy: A Python Package for Computing Timelike Geodesics
    in Kerr Spacetime"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06587"
  volume: 9
title: "`KerrGeoPy`: A Python Package for Computing Timelike Geodesics
  in Kerr Spacetime"

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.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06587 joss-papers#5429
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06587
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Jun 1, 2024
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dfm commented Jun 1, 2024

Many thanks to @Uddiptaatwork and @sterinaldi for reviewing and to @xuanxu for editing! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you!!

@syp2001 — Your paper is now accepted and published in JOSS! ⚡🚀💥

@dfm dfm closed this as completed Jun 1, 2024
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🎉🎉🎉 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.06587/status.svg)](https://doi.org/10.21105/joss.06587)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06587">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06587/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06587/status.svg
   :target: https://doi.org/10.21105/joss.06587

This is how it will look in your documentation:

DOI

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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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znasipak commented Jun 3, 2024

@editorialbot generate preprint

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📄 Preprint file created: Find it here in the Artifacts list 📄

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