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[REVIEW]: DataInterpolations.jl: Fast Interpolations of 1D data #6917

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editorialbot opened this issue Jun 22, 2024 · 44 comments
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[REVIEW]: DataInterpolations.jl: Fast Interpolations of 1D data #6917

editorialbot opened this issue Jun 22, 2024 · 44 comments
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accepted Julia published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics

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editorialbot commented Jun 22, 2024

Submitting author: @sathvikbhagavan (Sathvik Bhagavan)
Repository: https://github.com/SciML/DataInterpolations.jl
Branch with paper.md (empty if default branch):
Version: v5.1.0
Editor: @arfon
Reviewers: @carstenbauer, @dawbarton
Archive: 10.5281/zenodo.13384954

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/0524eb55e69a6aed3f029e637da62b0a"><img src="https://joss.theoj.org/papers/0524eb55e69a6aed3f029e637da62b0a/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/0524eb55e69a6aed3f029e637da62b0a/status.svg)](https://joss.theoj.org/papers/0524eb55e69a6aed3f029e637da62b0a)

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

@carstenbauer & @dawbarton, 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 @arfon 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 @dawbarton

📝 Checklist for @carstenbauer

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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

- 10.1137/141000671 is OK
- 10.1145/3511528.3511535 is OK
- 10.48550/arXiv.2103.05244 is OK
- 10.5194/amt-14-7909-2021 is OK
- 10.1007/978-1-4899-0433-1_17 is OK
- 10.1016/0021-9045(72)90080-9 is OK
- 10.1145/321607.321609 is OK
- 10.1007/978-1-4899-0433-1_1 is OK

MISSING DOIs

- No DOI given, and none found for title: On the stability of inverse problems
- No DOI given, and none found for title: Lectures on elementary mathematics, by Joseph Loui...

INVALID DOIs

- None

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1278.6 files/s, 131997.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           23            414            352           2898
Markdown                         8            167              0            500
YAML                            10             16              5            183
TeX                              1              9              0            127
TOML                             4              7              0             71
-------------------------------------------------------------------------------
SUM:                            46            613            357           3779
-------------------------------------------------------------------------------

Commit count by author:

    96	Christopher Rackauckas
    95	Sathvik Bhagavan
    47	shubham maddhashiya
    35	Andreas Noack
    22	dependabot[bot]
    18	Diogo Netto
    12	Anshul Singhvi
    12	Arno Strouwen
    12	Jonathan Stickel
    11	Daniel González
    11	Glen Hertz
     8	Chris Rackauckas
     8	avik-pal
     8	github-actions[bot]
     7	user.email
     6	Tim Kim
     6	Venkateshprasad
     5	Avik Pal
     5	Pepijn de Vos
     4	Fredrik Bagge Carlson
     3	Anant Thazhemadam
     3	Yingbo Ma
     3	contradict
     3	mleseach
     3	xzackli
     2	Dilum Aluthge
     2	Lucas Pacheco
     1	ArnoStrouwen
     1	David Widmann
     1	Eeshan Gupta
     1	Helge Eichhorn
     1	Julia TagBot
     1	Kristoffer Carlsson
     1	KristofferC
     1	Lilith Orion Hafner
     1	Lyndon White
     1	Steven G. Johnson
     1	lassepe

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Paper file info:

📄 Wordcount for paper.md is 408

✅ The paper includes a Statement of need section

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License info:

✅ License found: MIT License (Valid open source OSI approved license)

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

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arfon commented Jun 22, 2024

@carstenbauer, @dawbarton, @sathvikbhagavan – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing:

@editorialbot generate my checklist

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 https://github.com/openjournals/joss-reviews/issues/6917 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 make a start well 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.

@dawbarton
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dawbarton commented Jun 22, 2024

Review checklist for @dawbarton

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/SciML/DataInterpolations.jl?
  • 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 (@sathvikbhagavan) 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?

@sathvikbhagavan
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@carstenbauer, @dawbarton - A gentle reminder to start the review process.

@carstenbauer
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carstenbauer commented Jul 16, 2024

Review checklist for @carstenbauer

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/SciML/DataInterpolations.jl?
  • 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 (@sathvikbhagavan) 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?

@carstenbauer
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I've made my pass over my checklist, the package source code/documentation, and the short paper. Here are my comments and questions. All of them should be straightforward to integrate and answer, respectively.

  • The comparison to other interpolation packages in Julia (most notably Interpolations.jl) could be improved. First of all, these other options should be mentioned explicitly with links (at least Interpolations.jl). Secondly, what are the differences? The paper mentions that other packages require uniformly spaced data but at least according to the README.md of Interpolations.jl they also support irregular grids.
  • The target audience could be clarified more clearly (perhaps even addressed explicitly) in the statement of need section. A single sentence is sufficient.
  • The final sentences of the statement of need sections of the paper - especially the part about the symbiosis with Symbolics.jl and ModelingToolkit.jl - would perhaps be better suited in the summary section.
  • There is no statement of need section in the documentation. I'm fine with the documentation as is but the JOSS checklist asks for it, which is why I bring it up here.

Bonus:

  • It would be neat if the example would also highlight interoperability with Symbolics.jl, especially because this feature is mentioned in the text and could be a distinguishing factor of the package in comparison to other packages (in Julia and other languages).
  • The quality of writing is okay, but could probably be improved a little with little effort.

Provided that these points are taken into account by the authors, I am happy to recommend the paper for publication.

@arfon
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arfon commented Jul 26, 2024

@dawbarton – I see you've started your review (thanks 😄), do you think you might be able to complete it soon?

@sathvikbhagavan
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@editorialbot generate pdf

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

@sathvikbhagavan
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Thanks @carstenbauer for the review!

I have addressed 1, 2, 3 points in the paper. I have addressed 4 - added statement of need in the documentation. I have also added a tutorial for using DataInterpolations with Symbolics and referenced that in the paper.
Do take a look if any other further changes are needed.

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@dawbarton – I see you've started your review (thanks 😄), do you think you might be able to complete it soon?

Sorry for the delay, I’ll try to get it done this week but it might slip into early next week.

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Sorry for the delay with this. Overall, it looks good to me, particularly with carstenbauer's comments.

A few minor comments on the paper:

  1. Missing a space between the first and second sentences of the Summary.
  2. Missing a reference for Symbolics.jl in the Summary.
  3. First sentence of the Example could do with rewording. Maybe "The following tutorials are provided in the documentation. Tutorial 1 provides.... Tutorial 2 provides.... Tutorial 3 provides...".

As a side note, it might be worth a mention somewhere in the documentation that vectors-of-vectors can be used for the input to get multiple outputs from DataInterpolations. (This wasn't obvious to me and it doesn't accept a matrix as an input.)

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@editorialbot generate pdf

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

@dawbarton
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Looks good to me.

@sathvikbhagavan
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Thanks!
@carstenbauer, do you have any other comments/concerns regarding the paper?

@carstenbauer
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No, I think the authors have done a good job of integrating my comments. Happy to suggest the paper for publication.

@sathvikbhagavan
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@arfon, is there anything else here to be done for the paper? Both the reviewers are satisfied with it.

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arfon commented Aug 26, 2024

@sathvikbhagavan – apologies for the delay, I was OoO on the 🏖 😎

It looks like we're very close to being done here. I will circle back here next week, but in the meantime, please give your own paper a final read to check for any potential typos etc.

After that, could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

  • The title of the archive is the same as the JOSS paper title
  • That the authors of the archive are the same as the JOSS paper authors
  • I can then move forward with accepting the submission.

@sathvikbhagavan
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Thanks!

We have released the package and here is the zenodo archive: https://zenodo.org/records/13384954

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arfon commented Sep 4, 2024

@editorialbot set 10.5281/zenodo.13384954 as archive

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Done! archive is now 10.5281/zenodo.13384954

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arfon commented Sep 4, 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

- 10.1137/141000671 is OK
- 10.1145/3511528.3511535 is OK
- 10.48550/arXiv.2103.05244 is OK
- 10.5194/amt-14-7909-2021 is OK
- 10.1007/978-1-4899-0433-1_17 is OK
- 10.1016/0021-9045(72)90080-9 is OK
- 10.1145/321607.321609 is OK
- 10.1007/978-1-4899-0433-1_1 is OK
- 10.1137/0905021 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: On the stability of inverse problems
- No DOI given, and none found for title: Lectures on elementary mathematics, by Joseph Loui...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

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👋 @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#5849, 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 Sep 4, 2024
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arfon commented Sep 5, 2024

@editorialbot accept

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

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⚠️ Couldn't acccept/publish paper. An error happened.

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tarleb commented Sep 5, 2024

@editorialbot generate pdf

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

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arfon commented Sep 5, 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: Bhagavan
  given-names: Sathvik
  orcid: "https://orcid.org/0000-0003-0785-3586"
- family-names: Koning
  given-names: Bart
  name-particle: de
  orcid: "https://orcid.org/0009-0005-6134-6608"
- family-names: Maddhashiya
  given-names: Shubham
- family-names: Rackauckas
  given-names: Christopher
  orcid: "https://orcid.org/0000-0001-5850-0663"
contact:
- family-names: Bhagavan
  given-names: Sathvik
  orcid: "https://orcid.org/0000-0003-0785-3586"
doi: 10.5281/zenodo.13384954
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Bhagavan
    given-names: Sathvik
    orcid: "https://orcid.org/0000-0003-0785-3586"
  - family-names: Koning
    given-names: Bart
    name-particle: de
    orcid: "https://orcid.org/0009-0005-6134-6608"
  - family-names: Maddhashiya
    given-names: Shubham
  - family-names: Rackauckas
    given-names: Christopher
    orcid: "https://orcid.org/0000-0001-5850-0663"
  date-published: 2024-09-05
  doi: 10.21105/joss.06917
  issn: 2475-9066
  issue: 101
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6917
  title: "DataInterpolations.jl: Fast Interpolations of 1D data"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06917"
  volume: 9
title: "DataInterpolations.jl: Fast Interpolations of 1D data"

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.06917 joss-papers#5853
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06917
  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 Sep 5, 2024
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arfon commented Sep 5, 2024

@carstenbauer, @dawbarton – 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 ✨

@sathvikbhagavan – your paper is now accepted and published in JOSS ⚡🚀💥

@arfon arfon closed this as completed Sep 5, 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.06917/status.svg)](https://doi.org/10.21105/joss.06917)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06917">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06917/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06917/status.svg
   :target: https://doi.org/10.21105/joss.06917

This is how it will look in your documentation:

DOI

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