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[REVIEW]: RingsPy: A Python package for Voronoi mesh generation of cellular solids with radial growth pattern #4945

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editorialbot opened this issue Nov 18, 2022 · 67 comments
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accepted published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials

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editorialbot commented Nov 18, 2022

Submitting author: @kingyin3613 (Hao Yin)
Repository: https://github.com/kingyin3613/RingsPy
Branch with paper.md (empty if default branch):
Version: v1.0.2
Editor: @Kevin-Mattheus-Moerman
Reviewers: @niallmadden, @mahtab-vafaee
Archive: 10.5281/zenodo.7703344

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/3dd05ca1103829e7620731845b0d2472"><img src="https://joss.theoj.org/papers/3dd05ca1103829e7620731845b0d2472/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/3dd05ca1103829e7620731845b0d2472/status.svg)](https://joss.theoj.org/papers/3dd05ca1103829e7620731845b0d2472)

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

@niallmadden & @yg42 & @mahtab-vafaee, 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 @Kevin-Mattheus-Moerman 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 @yg42

📝 Checklist for @mahtab-vafaee

📝 Checklist for @niallmadden

@editorialbot editorialbot added Python review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Nov 18, 2022
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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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Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (255.2 files/s, 93599.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           7            603           1639           3050
Markdown                         2             61              0            233
TeX                              1             10              0            132
YAML                             4             10              4             96
INI                              1              3              0             18
TOML                             1              1              0              8
-------------------------------------------------------------------------------
SUM:                            16            688           1643           3537
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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

OK DOIs

- 10.1017/CBO9781139878326 is OK
- 10.3390/cells9071658 is OK
- 10.1017/CBO9781139878326 is OK
- 10.1073/pnas.1111557108 is OK
- 10.15252/embj.201592374 is OK
- 10.1145/2897824.2925922 is OK
- 10.1017/CBO9781139878326 is OK
- 10.1017/CBO9781139878326 is OK
- 10.1126/science.abn1459 is OK
- 10.1007/s13595-016-0613-y is OK
- 10.1007/s00332-019-09531-w is OK
- 10.1016/j.pmatsci.2010.06.001 is OK
- 10.3390/designs3010019 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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Wordcount for paper.md is 968

@Kevin-Mattheus-Moerman
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@niallmadden, @yg42, @mahtab-vafaee thanks for agreeing to review this work for JOSS!!!!!!!!! This is where the review takes place which you may now commence. You can comment @editorialbot generate my checklist here to generate your checklist which will guide you through the review process. There is more information at the top of this issue ☝️ as well. Let me know if you have any questions.

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

@yg42
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yg42 commented Nov 18, 2022

Review checklist for @yg42

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/kingyin3613/RingsPy?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@kingyin3613) 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?

@kingyin3613
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Dear all, thanks for agreeing to review my paper! May I request, to review version v0.3.4 (latest version) of RingsPy? In that version, I attached a few new functionalities including saving/reading generated Voronoi cell nuclei, etc. I appreciate that in advance! (@Kevin-Mattheus-Moerman what else should I do in order to update the software version in the reviewing process?)

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@editorialbot set v0.3.4 as version

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Done! version is now v0.3.4

@Kevin-Mattheus-Moerman
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@kingyin3613 I've changed the version tag and since you've alerted the reviewers we should be all set. Let me know if the tag chances again during this review.

@kingyin3613
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@kingyin3613 I've changed the version tag and since you've alerted the reviewers we should be all set. Let me know if the tag chances again during this review.

Thanks!

@mahtab-vafaee
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mahtab-vafaee commented Nov 21, 2022

Review checklist for @mahtab-vafaee

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/kingyin3613/RingsPy?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@kingyin3613) 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?

@Kevin-Mattheus-Moerman
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@niallmadden, @yg42, @mahtab-vafaee thanks again for agreeing to review this submission for JOSS. Could you provide an update on how you are getting on, or if you have not started yet, when you think you'll pick this up? thanks

@mahtab-vafaee
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@kevin, I'll start working on it next week. I'll create an issue if anything come up. Thanks.

@niallmadden
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@Kevin-Mattheus-Moerman I've set some time aside for it next week too.

@niallmadden
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niallmadden commented Dec 16, 2022

Review checklist for @niallmadden

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/kingyin3613/RingsPy?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@kingyin3613) 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?

@niallmadden
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This does not work for me: "pip install" without error, but tests fail - No module named 'RingsPy'
kingyin3613/ringspy#1 (comment)

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@editorialbot remove @yg42 as reviewer

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@yg42 removed from the reviewers list!

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Kevin-Mattheus-Moerman commented Jan 24, 2023

@niallmadden @mahtab-vafaee thanks again for your help here. Can you provide an update on review progress? Thanks.

@Kevin-Mattheus-Moerman
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@niallmadden @mahtab-vafaee 👋

@mahtab-vafaee
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@Kevin-Mattheus-Moerman I had a problem with the installation. It's now working and I'm running/checking the codes.

@niallmadden
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niallmadden commented Feb 3, 2023

@Kevin-Mattheus-Moerman I had a problem with the installation. It's now working and I'm running/checking the codes.

Same here, and informed the authors. kingyin3613/ringspy#1
Working now, though the standard convention of using only lower-case for module names is not followed.

Will finish the review Tuesday.

@mahtab-vafaee
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@kingyin3613 Thanks for the update.
@Kevin-Mattheus-Moerman With all the boxes checked, I confirm my acceptance recommendation.

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@editorialbot generate pdf

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

@kingyin3613
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@niallmadden @mahtab-vafaee thanks for the constructive and timely reviews, as well as the final recommendation for acceptance! and @Kevin-Mattheus-Moerman thanks for helping out here with everything!

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@editorialbot check references

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

OK DOIs

- 10.1017/CBO9781139878326 is OK
- 10.3390/cells9071658 is OK
- 10.1017/CBO9781139878326 is OK
- 10.1073/pnas.1111557108 is OK
- 10.15252/embj.201592374 is OK
- 10.1145/2897824.2925922 is OK
- 10.1017/CBO9781139878326 is OK
- 10.1017/CBO9781139878326 is OK
- 10.1126/science.abn1459 is OK
- 10.1007/s13595-016-0613-y is OK
- 10.1007/s00332-019-09531-w is OK
- 10.1016/j.pmatsci.2010.06.001 is OK
- 10.3390/designs3010019 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@Kevin-Mattheus-Moerman
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Kevin-Mattheus-Moerman commented Mar 6, 2023

@kingyin3613 now that both reviewers are happy we'll process this work for acceptance in JOSS. Below are some steps that require your attention.

  • Please spell out USA as United States of America.

After you've completed the above ☝️, Please work on the following:

  • Please archive a copy of the software on ZENODO. You can do this manually, or you may follow these automated steps: https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content
  • Once you have the above archive, please report back here with the archive DOI.
  • Please ensure that the ZENODO archive has the same title and author list (and order) as the paper, and the same license (it might list "Other(open)" by default) as your software. You may need to manually edit these aspects.
  • Please let me know if v0.4.1 is still the current version tag for the JOSS publication. It may have altered during review or be incremented during archiving. Note that the version listed on ZENODO, should match the version listed here, and should also be a release tag on your repository.

@kingyin3613
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Thanks @Kevin-Mattheus-Moerman! I have corrected the nation name in the paper and the software has been archived. The archive DOI is: 10.5281/zenodo.7703344. The version tag now should be v1.0.2.

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@editorialbot set 10.5281/zenodo.7703344 as archive

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Done! Archive is now 10.5281/zenodo.7703344

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@editorialbot set v1.0.2 as version

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Done! version is now v1.0.2

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@editorialbot generate pdf

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

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@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

- 10.1017/CBO9781139878326 is OK
- 10.3390/cells9071658 is OK
- 10.1017/CBO9781139878326 is OK
- 10.1073/pnas.1111557108 is OK
- 10.15252/embj.201592374 is OK
- 10.1145/2897824.2925922 is OK
- 10.1017/CBO9781139878326 is OK
- 10.1017/CBO9781139878326 is OK
- 10.1126/science.abn1459 is OK
- 10.1007/s13595-016-0613-y is OK
- 10.1007/s00332-019-09531-w is OK
- 10.1016/j.pmatsci.2010.06.001 is OK
- 10.3390/designs3010019 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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👋 @openjournals/bcm-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#4020, 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 Mar 7, 2023
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@editorialbot accept

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

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🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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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.04945 joss-papers#4028
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04945
  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 Mar 7, 2023
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@kingyin3613 congratulations on this publication in JOSS! 🥳

A special thanks goes to the reviewers @niallmadden and @mahtab-vafaee !!!! 🎉

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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.04945/status.svg)](https://doi.org/10.21105/joss.04945)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04945">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04945/status.svg" alt="DOI badge" >
</a>

reStructuredText:
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   :target: https://doi.org/10.21105/joss.04945

This is how it will look in your documentation:

DOI

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