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[REVIEW]: checkpoint_schedules: schedules for incremental of adjoint simulations #6148

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editorialbot opened this issue Dec 14, 2023 · 70 comments
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accepted published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review Track: 7 (CSISM) Computer science, Information Science, and Mathematics

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editorialbot commented Dec 14, 2023

Submitting author: @Ig-dolci (Daiane Iglesia Dolci)
Repository: https://github.com/firedrakeproject/checkpoint_schedules
Branch with paper.md (empty if default branch): main
Version: v1.0.3
Editor: @diehlpk
Reviewers: @matt-graham, @KYANJO
Archive: 10.5281/zenodo.10817312

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/89bd54d1204e0297bec46740ee23e2ff"><img src="https://joss.theoj.org/papers/89bd54d1204e0297bec46740ee23e2ff/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/89bd54d1204e0297bec46740ee23e2ff/status.svg)](https://joss.theoj.org/papers/89bd54d1204e0297bec46740ee23e2ff)

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

@matt-graham, 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 @diehlpk 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 @matt-graham

📝 Checklist for @KYANJO

📝 Checklist for @KYANJO

@editorialbot editorialbot added Python review Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Dec 14, 2023
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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 (545.1 files/s, 107411.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          19            751           1548           2629
TeX                              1             19              0            181
Jupyter Notebook                 1              0            793            144
Markdown                         2             19              0            144
YAML                             4             14             19            142
reStructuredText                 4             66             66             74
TOML                             1              7              0             29
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            34            888           2434           3378
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 857

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

OK DOIs

- 10.1145/347837.347846 is OK
- 10.1111/j.1365-246X.2006.02978.x is OK
- 10.1137/20M1326209 is OK
- 10.1016/j.compfluid.2010.09.039 is OK
- 10.1145/347837.347846 is OK
- 10.1145/3378672 is OK
- 10.1137/080718036 is OK
- 10.48550/arXiv.2305.09568 is OK
- 10.1137/18M1209465 is OK
- 10.1016/j.procs.2016.05.444 is OK
- 10.1080/10556788.2016.1230612 is OK
- 10.1029/2020JC016370 is OK
- 10.1016/j.jocs.2022.101913 is OK
- 10.21105/joss.01292 is OK
- 10.25561/104839 is OK
- 10.11588/ans.2015.100.20553 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

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matt-graham commented Dec 14, 2023

Review checklist for @matt-graham

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/firedrakeproject/checkpoint_schedules?
  • 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 (@Ig-dolci) 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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diehlpk commented Dec 20, 2023

@editorialbot generate pdf

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

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diehlpk commented Jan 5, 2024

@matt-graham how is your review going?

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diehlpk commented Jan 5, 2024

hi @KYANJO please let me know if you have questions about your first review?

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KYANJO commented Jan 5, 2024 via email

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KYANJO commented Jan 5, 2024 via email

@KYANJO
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KYANJO commented Jan 17, 2024

Review checklist for @KYANJO

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/firedrakeproject/checkpoint_schedules?
  • 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 (@Ig-dolci) 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?

@KYANJO
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KYANJO commented Jan 17, 2024

I am through with my first review, and I have included comments in the pdf it's self. Find attached.
10.21105.joss.06148.pdf

PS; If there is a better way i can upload the document please let me know, Is it better to create a pull request instead?

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diehlpk commented Jan 18, 2024

@Ig-dolci please take a look at the comments.

@Ig-dolci
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@diehlpk Yes. I am aware.

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diehlpk commented Jan 31, 2024

@Ig-dolci how are your changes going?

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Ig-dolci commented Feb 1, 2024

@diehlpk It is going well. Hopefully, I will return with the reviewer's responses in the coming week.

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diehlpk commented Feb 8, 2024

@Ig-dolci how are your changes going?

1 similar comment
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diehlpk commented Feb 14, 2024

@Ig-dolci how are your changes going?

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@diehlpk It is going well. Unfortunately, it has required more time due to personal unforeseen the last week.

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diehlpk commented Feb 23, 2024

@Ig-dolci When do you think you can have the new revision done?

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diehlpk commented Feb 29, 2024

@Ig-dolci When do you think you can have the new revision done?

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diehlpk commented Mar 12, 2024

@Ig-dolci Please finish these tasks, so we can proceed with the paper

  • Double check authors and affiliations (including ORCIDs)
  • Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
  • Archive the release on Zenodo/figshare/etc and post the DOI here.
  • Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
  • Make sure that the license listed for the archive is the same as the software license.

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@Ig-dolci Please finish these tasks, so we can proceed with the paper

  • Double check authors and affiliations (including ORCIDs)
  • Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
  • Archive the release on Zenodo/figshare/etc and post the DOI here.
  • Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
  • Make sure that the license listed for the archive is the same as the software license.

@diehlpk below the latest release and Zenodo DOI.
Release version: v1.0.3
Zenodo DOI: 10817312

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diehlpk commented Mar 14, 2024

@editorialbot set v1.0.3 as version

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Done! version is now v1.0.3

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diehlpk commented Mar 14, 2024

@editorialbot set 10.5281/zenodo.10817312 as archive

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Done! archive is now 10.5281/zenodo.10817312

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diehlpk commented Mar 14, 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

- 10.1145/347837.347846 is OK
- 10.1111/j.1365-246X.2006.02978.x is OK
- 10.1137/20M1326209 is OK
- 10.1016/j.compfluid.2010.09.039 is OK
- 10.1145/347837.347846 is OK
- 10.1145/3378672 is OK
- 10.1137/080718036 is OK
- 10.48550/arXiv.2305.09568 is OK
- 10.1137/18M1209465 is OK
- 10.1016/j.procs.2016.05.444 is OK
- 10.1080/10556788.2016.1230612 is OK
- 10.1029/2020JC016370 is OK
- 10.1016/j.jocs.2022.101913 is OK
- 10.21105/joss.01292 is OK
- 10.25561/104839 is OK
- 10.11588/ans.2015.100.20553 is OK

MISSING DOIs

- No DOI given, and none found for title: Providing the ARCHER community with adjoint modell...

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#5132, 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 14, 2024
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@Ig-dolci - I'm the track editor who will finish the processing of this submission.

I've suggested some small changes in firedrakeproject/checkpoint_schedules#65. Please merge this, or let me know what you disagree with.

In addition, please add countries to all of the affiliations, though we don't need mailing address / postal codes. Usually, institution & country is enough, though department or similar is also fine.

Also in the paper, "in the frame of DASH" in the acknowledgements sounds awkward to me, but I'm not sure how to fix it, as I don't really know what this means.

Finally, in the references, the one for Pringle seems to be missing information about how to access it. Should it have a URL or something else?

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Ig-dolci commented Mar 15, 2024

@danielskatz Your pull request PR 65 has been merged.

In addition, I have opened PR 66, which includes the countries of all affiliations and a URL was added in the Pringle reference. Could you please verify if it sounds good for the final version of the JOSS paper?

The mention of "in the frame of DASH" in the acknowledgements section refers to a funding project. I verified this terminology is usual in other papers authored by one of our authors. So, we should keep it in this form.

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danielskatz commented Mar 15, 2024

Thanks - this looks good, though I'm not sure if the type for Pringle should be article or misc. We can try this and see how the PDF looks.

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I think misc is better for this case. I just changed from article to misc.

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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

- 10.1145/347837.347846 is OK
- 10.1111/j.1365-246X.2006.02978.x is OK
- 10.1137/20M1326209 is OK
- 10.1016/j.compfluid.2010.09.039 is OK
- 10.1145/347837.347846 is OK
- 10.1145/3378672 is OK
- 10.1137/080718036 is OK
- 10.48550/arXiv.2305.09568 is OK
- 10.1137/18M1209465 is OK
- 10.1016/j.procs.2016.05.444 is OK
- 10.1080/10556788.2016.1230612 is OK
- 10.1029/2020JC016370 is OK
- 10.1016/j.jocs.2022.101913 is OK
- 10.21105/joss.01292 is OK
- 10.25561/104839 is OK
- 10.11588/ans.2015.100.20553 is OK

MISSING DOIs

- No DOI given, and none found for title: Providing the ARCHER community with adjoint modell...

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#5162, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

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@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: Dolci
  given-names: Daiane I.
  orcid: "https://orcid.org/0000-0002-1435-9538"
- family-names: Maddison
  given-names: James R.
  orcid: "https://orcid.org/0000-0001-5742-4363"
- family-names: Ham
  given-names: David A.
  orcid: "https://orcid.org/0000-0001-9545-9110"
- family-names: Pallez
  given-names: Guillaume
  orcid: "https://orcid.org/0000-0001-8862-3277"
- family-names: Herrmann
  given-names: Julien
  orcid: "https://orcid.org/0000-0003-4935-2368"
doi: 10.5281/zenodo.10817312
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Dolci
    given-names: Daiane I.
    orcid: "https://orcid.org/0000-0002-1435-9538"
  - family-names: Maddison
    given-names: James R.
    orcid: "https://orcid.org/0000-0001-5742-4363"
  - family-names: Ham
    given-names: David A.
    orcid: "https://orcid.org/0000-0001-9545-9110"
  - family-names: Pallez
    given-names: Guillaume
    orcid: "https://orcid.org/0000-0001-8862-3277"
  - family-names: Herrmann
    given-names: Julien
    orcid: "https://orcid.org/0000-0003-4935-2368"
  date-published: 2024-03-22
  doi: 10.21105/joss.06148
  issn: 2475-9066
  issue: 95
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6148
  title: "checkpoint_schedules: schedules for incremental checkpointing
    of adjoint simulations"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06148"
  volume: 9
title: "checkpoint_schedules: schedules for incremental checkpointing of
  adjoint simulations"

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.06148 joss-papers#5163
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06148
  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 22, 2024
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Congratulations to @Ig-dolci (Daiane Iglesia Dolci) and co-authors on your publication!!

And thanks to @matt-graham and @KYANJO for reviewing, and to @diehlpk for editing!
JOSS depends on volunteers and we couldn't do this without you

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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.06148/status.svg)](https://doi.org/10.21105/joss.06148)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06148">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06148/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06148/status.svg
   :target: https://doi.org/10.21105/joss.06148

This is how it will look in your documentation:

DOI

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