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[REVIEW]: PIVC: A C/C++ Program for Particle Image Velocimetry Vector Computation #3736

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whedon opened this issue Sep 18, 2021 · 116 comments
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accepted C++ C Makefile published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review Track: 7 (CSISM) Computer science, Information Science, and Mathematics

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@whedon
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whedon commented Sep 18, 2021

Submitting author: @fibreglass2 (Kadeem)
Repository: https://gitlab.com/fibreglass/pivc
Branch with paper.md (empty if default branch):
Version: v1.2-b
Editor: @Kevin-Mattheus-Moerman
Reviewers: @clarka34, @quynhneo
Archive: 10.5281/zenodo.7556040

⚠️ 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/9e69f9bdc717641df7cb41c3590f0ae4"><img src="https://joss.theoj.org/papers/9e69f9bdc717641df7cb41c3590f0ae4/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/9e69f9bdc717641df7cb41c3590f0ae4/status.svg)](https://joss.theoj.org/papers/9e69f9bdc717641df7cb41c3590f0ae4)

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

@timdewhirst & @clarka34 & @quynhneo, 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 @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

Review checklist for @timdewhirst

✨ 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 (@fibreglass2) 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 @clarka34

✨ 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 (@fibreglass2) 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 @quynhneo

✨ 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 (@fibreglass2) 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
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whedon commented Sep 18, 2021

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @timdewhirst, @clarka34, @quynhneo 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 Sep 18, 2021

Wordcount for paper.md is 938

@whedon
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whedon commented Sep 18, 2021

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.03 s (400.7 files/s, 47586.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                              4             72             78            794
TeX                              1             32              0            260
Markdown                         3             49              0            176
C/C++ Header                     4             15              1             59
make                             1              1              0              7
-------------------------------------------------------------------------------
SUM:                            13            169             79           1296
-------------------------------------------------------------------------------


Statistical information for the repository 'b544fa72933c272acc8be899' was
gathered on 2021/09/18.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
fibreglass                      14          1387            368          100.00

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
fibreglass                 1019           73.5          0.0                7.75

@whedon
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whedon commented Sep 18, 2021

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

OK DOIs

- 10.1007/s003489900085 is OK
- 10.1007/s00348-016-2173-1 is OK
- 10.5334/jors.334 is OK
- 10.5334/jors.bl is OK
- 10.1088/0169-5983/47/3/035509 is OK
- 10.1016/j.ijthermalsci.2013.11.001 is OK
- 10.1016/j.ijheatfluidflow.2013.12.005 is OK
- 10.1016/j.ijthermalsci.2014.11.026 is OK
- 10.1063/1.1375144 is OK
- 10.1016/j.expthermflusci.2020.110286 is OK
- 10.1016/j.est.2019.100825 is OK
- 10.1016/j.ijheatfluidflow.2021.108839 is OK
- 10.1016/j.ijheatfluidflow.2008.01.003 is OK
- 10.1063/1.2185709 is OK
- 10.1007/s00231-005-0072-8 is OK
- 10.1063/1.3054153 is OK
- 10.1088/0957-0233/18/1/012 is OK
- 10.1017/s0022112006003892 is OK
- 10.1016/j.ijthermalsci.2015.05.003 is OK
- 10.1016/j.jweia.2021.104605 is OK
- 10.1002/we.1895 is OK
- 10.1007/s10236-008-0132-y is OK
- 10.1016/j.solener.2010.02.008 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@whedon
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whedon commented Sep 18, 2021

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

@Kevin-Mattheus-Moerman
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Kevin-Mattheus-Moerman commented Sep 18, 2021

Reproducing @timdewhirst 's comments from the pre-review issue (#3603):

I've raised a few issues; links are at the bottom of this comment.

As I understand it there were two main questions around the code: does the use of OpenMP help take advantage of multicore processors, and is the code well structured and a suitable foundation for a collaborative project implementing various PIV processing algorithms?

On OpenMP: this appears to work as expected.

On code structure: this is my main area of concern; the code need work to follow best practices in structure, legibility, efficiency and testing. Very little C++ is used, and this is a shame; modern C++ has powerful features for generic and functional style programming which would allow the code to be cleaner, more legible, and just as efficient. Currently, I don't believe it's in good enough shape to act as a foundation for significant collaborative development.

issues:

@Kevin-Mattheus-Moerman
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Kevin-Mattheus-Moerman commented Sep 18, 2021

@timdewhirst, @clarka34, @quynhneo this is where the actual review takes place. Thank you all for you help!
Please have a look at the information at the top of this issue and the check-boxes that will guide the review.
Let me know if you have any questions.

@Kevin-Mattheus-Moerman
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@quynhneo to answer your query over at #3603, have a look at our review guidelines. Let me know if you have questions.

@clarka34
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I have added some more issues:

At this stage, my main concerns are the lack of real-word examples for users that are not very familiar with PIV. Additionally, the documentation could be extended and improved to make it easier for future collaboration/use of the software. It would be difficult for a person who is not familiar with PIV to understand the grid spacing options and what to do with the result files.

@Kevin-Mattheus-Moerman
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@fibreglass2 as you may have seen there are a number of issues open that were raised by the reviewers. ☝️. Can you start to address these? Let me know if you have any questions.

@clarka34
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Sorry, my phone has had a mind of its own this morning. It seems like I have unassigned @timdewhirst and closed this. I reopened but could not figure out how to reassign. @Kevin-Mattheus-Moerman can you do this?

@Kevin-Mattheus-Moerman
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@openjournals/dev can you check if I need to fix anything? ☝️

@Kevin-Mattheus-Moerman
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@clarka34 no worries we'll sort it out

@clarka34
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@Kevin-Mattheus-Moerman thank you! again, I am sorry about this...

@fibreglass2
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@fibreglass2 as you may have seen there are a number of issues open that were raised by the reviewers. point_up. Can you start to address these? Let me know if you have any questions.

Thanks to the reviewers for the detailed feedback. I will be working to investigate and address issues raised.

@whedon
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whedon commented Oct 2, 2021

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

@whedon
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whedon commented Oct 2, 2021

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

@fibreglass2
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@editorialbot generate pdf

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

@fibreglass2
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Simply updated a citation in the paper. Thanks to the reviewers for their extensive and detailed feedback.

@fibreglass2
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@Kevin-Mattheus-Moerman Is this review completed?

@Kevin-Mattheus-Moerman
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@fibreglass2 yes it is. Apologies for the delay! I will now process this for acceptance as soon as possible. There may be come minor edits required from my end of the paper and it should move relatively quickly now.

@Kevin-Mattheus-Moerman
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@fibreglass2 I have read the paper and it looks good to me. A minor note, which you may or may not choose to work on, is that mostly we use open source rather than open-source (if you choose to change it, also change closed-source to closed source in the text). But this is not a requirement.

At this point can you work on the following:

  • Can you archive a copy of your software on ZENODO? You can do this manually or follow these steps: https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content
  • Can you report the DOI of the ZENODO archive?
  • Next check that the metadata for the ZENODO archive matches certain aspects of the paper, in particular the author list (default may be all contributors so edit if needed), the author order, the title (default is the repository name so change it to match the JOSS paper title). You can also add ORCIDs for all researchers on ZENODO there if you like.
  • Next inform me if the version tag (currently here set to v1.0.0) is still good or if during review or archiving you'd altered it.

@fibreglass2
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@editorialbot generate pdf

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

@fibreglass2
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fibreglass2 commented Jan 20, 2023

@Kevin-Mattheus-Moerman

  • Can you archive a copy of your software on ZENODO?

See archive here

  • Can you report the DOI of the ZENODO archive?

DOI: 10.5281/zenodo.7556040

  • Next check that the metadata for the ZENODO archive matches certain aspects of the paper, in particular the author list (default may be all contributors so edit if needed), the author order, the title (default is the repository name so change it to match the JOSS paper title). You can also add ORCIDs for all researchers on ZENODO there if you like.

Author name and title are correct on Zenodo.

  • Next inform me if the version tag (currently here set to v1.0.0) is still good or if during review or archiving you'd altered it.

Newest version is v1.2-b

The paper has been updated with corrected usage of "open source" and "closed source".

@Kevin-Mattheus-Moerman
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@editorialbot set 10.5281/zenodo.7556040 as archive

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Done! Archive is now 10.5281/zenodo.7556040

@Kevin-Mattheus-Moerman
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@editorialbot set v1.2-b as version

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Done! version is now v1.2-b

@Kevin-Mattheus-Moerman
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@editorialbot recommend accept

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I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

@Kevin-Mattheus-Moerman
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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

- 10.1016/j.expthermflusci.2022.110734 is OK
- 10.1007/s003489900085 is OK
- 10.1007/s00348-016-2173-1 is OK
- 10.5334/jors.334 is OK
- 10.5334/jors.bl is OK
- 10.1088/0169-5983/47/3/035509 is OK
- 10.1016/j.ijthermalsci.2013.11.001 is OK
- 10.1016/j.ijheatfluidflow.2013.12.005 is OK
- 10.1016/j.ijthermalsci.2014.11.026 is OK
- 10.1063/1.1375144 is OK
- 10.1016/j.expthermflusci.2020.110286 is OK
- 10.1016/j.est.2019.100825 is OK
- 10.1016/j.ijheatfluidflow.2021.108839 is OK
- 10.1016/j.euromechflu.2022.05.012 is OK
- 10.1016/j.ijheatfluidflow.2008.01.003 is OK
- 10.1063/1.2185709 is OK
- 10.1007/s00231-005-0072-8 is OK
- 10.1063/1.3054153 is OK
- 10.1088/0957-0233/18/1/012 is OK
- 10.1017/s0022112006003892 is OK
- 10.1016/j.ijthermalsci.2015.05.003 is OK
- 10.1016/j.jweia.2021.104605 is OK
- 10.1002/we.1895 is OK
- 10.1007/s10236-008-0132-y is OK
- 10.1016/j.solener.2010.02.008 is OK

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#3894, 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 Jan 21, 2023
@Kevin-Mattheus-Moerman
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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.03736 joss-papers#3895
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03736
  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 Jan 21, 2023
@Kevin-Mattheus-Moerman
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Congratulations on this publication @fibreglass2 !!! Our apologies for the longer than usual review process.

I'd like to thank the reviewers @clarka34, @quynhneo, and also @timdewhirst for their help here!!!

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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.03736/status.svg)](https://doi.org/10.21105/joss.03736)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03736">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03736/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03736/status.svg
   :target: https://doi.org/10.21105/joss.03736

This is how it will look in your documentation:

DOI

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