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[REVIEW]: PyNumDiff: A Python package for numerical differentiation of noisy time-series data #4078

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40 tasks done
whedon opened this issue Jan 20, 2022 · 73 comments
Closed
40 tasks done

[REVIEW]: PyNumDiff: A Python package for numerical differentiation of noisy time-series data #4078

whedon opened this issue Jan 20, 2022 · 73 comments
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@pmli @billtubbs @christinahedges
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accepted published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review TeX

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@whedon
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whedon commented Jan 20, 2022 •
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Submitting author: @florisvb (Floris van Breugel)
Repository: https://github.com/florisvb/PyNumDiff
Branch with paper.md (empty if default branch):
Version: v0.1.2.4
Editor: @christinahedges
Reviewers: @pmli, @billtubbs
Archive: 10.5281/zenodo.6374098

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/102257ee4b0142bf49bc18d7c810e9d5"><img src="https://joss.theoj.org/papers/102257ee4b0142bf49bc18d7c810e9d5/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/102257ee4b0142bf49bc18d7c810e9d5/status.svg)](https://joss.theoj.org/papers/102257ee4b0142bf49bc18d7c810e9d5)

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

@pmli & @billtubbs, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

Review checklist for @pmli

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
  • 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 (@florisvb) 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

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 and who the target audience is?
  • 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?

Review checklist for @billtubbs

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
  • 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 (@florisvb) 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

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 and who the target audience is?
  • 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?
@whedon whedon mentioned this issue Jan 20, 2022
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@whedon
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whedon commented Jan 20, 2022

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @pmli, @billtubbs it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

@whedon
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whedon commented Jan 20, 2022

Wordcount for paper.md is 799

@whedon
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whedon commented Jan 20, 2022 

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.11 s (683.5 files/s, 85918.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          41           1207           1912           2326
Jupyter Notebook                 3              0           2959            414
TeX                              1             24              0            193
Markdown                         2             53              0            184
reStructuredText                27             94             98            147
DOS Batch                        1              8              1             26
YAML                             1              3              0             10
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            77           1393           4977           3309
-------------------------------------------------------------------------------


Statistical information for the repository '2155460c82d03f71216fb25d' was
gathered on 2022/01/20.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Floris van Breugel              55          8297           1093           11.67
floris                           4             8             21            0.04
luckystarufo                    18         34640          36398           88.29

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Floris van Breugel          762            9.2          5.2                6.17
Yuying                     4683          100.0          7.2               16.10

@whedon
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whedon commented Jan 20, 2022 

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

OK DOIs

- 10.1109/access.2020.3034077 is OK
- 10.1515/9783110226157.263 is OK
- 10.1073/pnas.1517384113 is OK
- 10.1016/j.cpc.2007.03.009 is OK
- 10.1109/msp.2011.941097 is OK
- 10.1021/ac60214a047 is OK
- 10.1109/9780470544334.ch9 is OK
- 10.1017/S000192400001232X is OK
- 10.1016/j.automatica.2017.08.011 is OK
- 10.1016/0167-2789(92)90242-f is OK
- 10.5402/2011/164564 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.21105/joss.00530 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@whedon
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whedon commented Jan 20, 2022

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

@christinahedges
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@florisvb, @pmli , @billtubbs – This is the review thread for the PyNumDiff paper. Please don't hesitate to message me here if you have questions (use @christinahedges). ✉️

Please read the "Reviewer instructions & questions" in the first comment above to get started. If you get lost, you can also see the reviewer guidelines.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. To review for JOSS, @pmli and @billtubbs will step through that checklist for PyNumDiff and assess the package. As you go over the submission, please check any items that you feel have been satisfied. If you are concerned about a requirement, please discuss it here on this thread 🧵 . Feel free to post about questions/concerns as they come up as you go through your review. Discussion between the authors/reviewers and myself is encouraged!

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 this issue (#4078) so that a link is created to this thread (and I can keep an eye on what is happening).

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. When you're finished with your checklist, leave a comment and @ me to let everyone know your review is complete.

For this submission, don't forget there is a published journal article discussing the PyNumDiff algorithm. The JOSS editors have agreed that this JOSS submission is a separate and allowable submission given this published article. I'm leaving it here in case the reviewers find it useful during their review.

@pmli pmli mentioned this issue Jan 31, 2022
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@whedon
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whedon commented Feb 3, 2022

👋 @pmli, please update us on how your review is going (this is an automated reminder).

@whedon
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whedon commented Feb 3, 2022

👋 @billtubbs, please update us on how your review is going (this is an automated reminder).

@billtubbs
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billtubbs commented Feb 3, 2022 •
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@whedon , sorry, haven't had time to start on this yet. I will set some time aside this weekend. Thanks for the reminder.

@billtubbs
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Hi @whedon. I read the reviewer guidelines. But I can't edit the checklist above. When I clicked on the accept invitation URL it says it has expired (not sure if I already did this before). Anyway, I will start the review.

@danielskatz
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@whedon re-invite @billtubbs as reviewer

if this doesn't work, please let me know - there's sometimes a timing issue

@whedon
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whedon commented Feb 5, 2022

OK, the reviewer has been re-invited.

@billtubbs please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

@billtubbs
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@pmli I accidentally clicked on some of the checkboxes in your section of the review! I tried unclicking them but can't remember exactly which ones I changed so you better check all of them. Sorry about that.

@pmli
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pmli commented Feb 8, 2022

@billtubbs No problem, looks good.

This was referenced Feb 11, 2022
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This was referenced Feb 25, 2022
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@pmli
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pmli commented Mar 4, 2022

I believe I'm done with the review. All of the issues I opened are closed.

@florisvb
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florisvb commented Mar 4, 2022 via email

@florisvb
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florisvb commented Mar 9, 2022 via email

@editorialbot
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My name is now @editorialbot

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

OK DOIs

- 10.1109/access.2020.3034077 is OK
- 10.1515/9783110226157.263 is OK
- 10.1073/pnas.1517384113 is OK
- 10.1016/j.cpc.2007.03.009 is OK
- 10.1109/msp.2011.941097 is OK
- 10.1021/ac60214a047 is OK
- 10.1109/9780470544334.ch9 is OK
- 10.1017/S000192400001232X is OK
- 10.1016/j.automatica.2017.08.011 is OK
- 10.1016/0167-2789(92)90242-f is OK
- 10.5402/2011/164564 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.21105/joss.00530 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@editorialbot
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👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#3077

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3077, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@danielskatz
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sorry @florisvb - I also see some bib changes that are needed - in florisvb/PyNumDiff#28. And once this is done, I think I will need to talk to @arfon about some bugs in our processing of some of these elements...

@florisvb
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florisvb commented Mar 21, 2022 via email

@danielskatz
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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.1109/access.2020.3034077 is OK
- 10.1515/9783110226157.263 is OK
- 10.1073/pnas.1517384113 is OK
- 10.1016/j.cpc.2007.03.009 is OK
- 10.1109/msp.2011.941097 is OK
- 10.1021/ac60214a047 is OK
- 10.1109/9780470544334.ch9 is OK
- 10.1017/S000192400001232X is OK
- 10.1016/j.automatica.2017.08.011 is OK
- 10.1016/0167-2789(92)90242-f is OK
- 10.5402/2011/164564 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.21105/joss.00530 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@editorialbot
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👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#3078

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3078, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@danielskatz
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Thanks @florisvb - now we just need to fix a bug in our processing of a couple of these entries

@danielskatz
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@editorialbot recommend-accept

checking to see if our change has been implemented

@editorialbot
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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.1109/access.2020.3034077 is OK
- 10.1515/9783110226157.263 is OK
- 10.1073/pnas.1517384113 is OK
- 10.1016/j.cpc.2007.03.009 is OK
- 10.1109/msp.2011.941097 is OK
- 10.1021/ac60214a047 is OK
- 10.1109/9780470544334.ch9 is OK
- 10.1017/S000192400001232X is OK
- 10.1016/j.automatica.2017.08.011 is OK
- 10.1016/0167-2789(92)90242-f is OK
- 10.5402/2011/164564 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.21105/joss.00530 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@editorialbot
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👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#3085

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3085, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@danielskatz
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@editorialbot accept

(our problems are fixed)

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

@editorialbot
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🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

@editorialbot
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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.04078 joss-papers#3087
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04078
  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, 2022
@florisvb
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florisvb commented Mar 22, 2022 via email

@danielskatz
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Congratulations to @florisvb (Floris van Breugel) and co-authors!!

And thanks to @pmli and @billtubbs for reviewing, and to @christinahedges for editing!
We couldn't do this without you

@danielskatz danielskatz reopened this Mar 22, 2022
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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.04078/status.svg)](https://doi.org/10.21105/joss.04078)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04078">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04078/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04078/status.svg
   :target: https://doi.org/10.21105/joss.04078

This is how it will look in your documentation:

DOI

We need your help!

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:

1 similar comment
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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.04078/status.svg)](https://doi.org/10.21105/joss.04078)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04078">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04078/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04078/status.svg
   :target: https://doi.org/10.21105/joss.04078

This is how it will look in your documentation:

DOI

We need your help!

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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florisvb commented Oct 11, 2022 via email

@editorialbot editorialbot mentioned this issue Jul 24, 2024
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@editorialbot editorialbot mentioned this issue Oct 11, 2024
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@editorialbot editorialbot mentioned this issue Oct 24, 2024
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