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[REVIEW]: Mantik: A Workflow Platform for the Development of Artificial Intelligence on High-Performance Computing Infrastructures #6136

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editorialbot opened this issue Dec 9, 2023 · 89 comments
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accepted Dockerfile Jupyter Notebook published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review Shell Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning

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editorialbot commented Dec 9, 2023

Submitting author: @rico-berner (Rico Berner)
Repository: https://gitlab.com/mantik-ai/mantik
Branch with paper.md (empty if default branch):
Version: 0.4.2
Editor: @arfon
Reviewers: @zhaozhang, @gflofst
Archive: 10.5281/zenodo.11196516

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/31e03b578e512eb5565baca1a21fe268"><img src="https://joss.theoj.org/papers/31e03b578e512eb5565baca1a21fe268/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/31e03b578e512eb5565baca1a21fe268/status.svg)](https://joss.theoj.org/papers/31e03b578e512eb5565baca1a21fe268)

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

@zhaozhang, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest

Checklists

📝 Checklist for @zhaozhang

📝 Checklist for @gflofst

📝 Checklist for @acrlakshman

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Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

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

@editorialbot generate pdf

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

OK DOIs

- 10.5194/egusphere-egu21-9632 is OK
- 10.1145/3399579.3399867 is OK
- 10.1109/ACCESS.2023.3262138 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.19 s (1435.1 files/s, 113942.3 lines/s)
---------------------------------------------------------------------------------------
Language                             files          blank        comment           code
---------------------------------------------------------------------------------------
Python                                 194           2451           1303          12424
Markdown                                47           1184              0           2909
YAML                                     5             50             10            526
JSON                                     9              5              0            219
TOML                                     4             28              4            188
make                                     2             18              4             71
Jupyter Notebook                         1              0            106             57
TeX                                      1              2              0             32
HTML                                     1              0              0             29
reStructuredText                         2             27             34             27
CSS                                      1              1              0             24
SVG                                      3              0              0              9
Bourne Shell                             2              0              1              7
Dockerfile                               1              1              0              2
Windows Module Definition                1              0              0              2
---------------------------------------------------------------------------------------
SUM:                                   274           3767           1462          16526
---------------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1410

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

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arfon commented Dec 9, 2023

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

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

@editorialbot generate my checklist

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/6136 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

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arfon commented Dec 9, 2023

@dghoshal-lbl @cc-a @ian-taylor @gflofst @thurber @acrlakshman – 👋 would you be willing to review this submission for JOSS? The submission under consideration is Mantik: A Workflow Platform for the Development of Artificial Intelligence on High-Performance Computing Infrastructures

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. You can learn more about the process in these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Based on your experience, and past submissions to JOSS, we think you might be able to provide a great review of this submission. Please let me know if you think you can help us out!

Many thanks
Arfon

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gflofst commented Dec 10, 2023 via email

@acrlakshman
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@dghoshal-lbl @cc-a @ian-taylor @gflofst @thurber @acrlakshman – 👋 would you be willing to review this submission for JOSS? The submission under consideration is Mantik: A Workflow Platform for the Development of Artificial Intelligence on High-Performance Computing Infrastructures

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. You can learn more about the process in these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Based on your experience, and past submissions to JOSS, we think you might be able to provide a great review of this submission. Please let me know if you think you can help us out!

Many thanks
Arfon

Sure.

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arfon commented Dec 12, 2023

@editorialbot add @gflofst as reviewer

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@gflofst added to the reviewers list!

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arfon commented Dec 12, 2023

@editorialbot add @acrlakshman as reviewer

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@acrlakshman added to the reviewers list!

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arfon commented Dec 12, 2023

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

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

@editorialbot generate my checklist

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/6136 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

@gflofst
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gflofst commented Dec 12, 2023

Review checklist for @gflofst

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://gitlab.com/mantik-ai/mantik?
  • 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 (@rico-berner) 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?

@arfon
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arfon commented Jan 6, 2024

👋 @acrlakshman – just checking in here. Do you think you might be able to start your review soon?

@acrlakshman
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👋 @acrlakshman – just checking in here. Do you think you might be able to start your review soon?

I shall be working on it this week and provide an update.

@zhaozhang
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zhaozhang commented Jan 9, 2024

Review checklist for @zhaozhang

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://gitlab.com/mantik-ai/mantik?
  • 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 (@rico-berner) 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?

@acrlakshman
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acrlakshman commented Jan 10, 2024

Review checklist for @acrlakshman

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://gitlab.com/mantik-ai/mantik?
  • 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 (@rico-berner) 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?

@acrlakshman
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@arfon I need to go through the technical details. At first glance, the submitting author (@rico-berner) did not make significant contributions to the software, however the author list looks complete and appropriately ordered. How would you prefer me handle the relevant checkbox in the general checks section.

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arfon commented May 18, 2024

@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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⚠️ Error preparing paper acceptance.

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arfon commented May 18, 2024

Seems like the clone from GitLab failed. Will try again.

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arfon commented May 18, 2024

@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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⚠️ Error preparing paper acceptance.

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arfon commented May 18, 2024

OK, looks like GitLab is being wonky right now. Will try later.

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OK, looks like GitLab is being wonky right now. Will try later.

@arfon Is there anything, we could help with?

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arfon commented Jun 2, 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

- 10.5194/egusphere-egu21-9632 is OK
- 10.1145/3399579.3399867 is OK
- 10.1109/ACCESS.2023.3262138 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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👋 @openjournals/dsais-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#5437, 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 Jun 2, 2024
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arfon commented Jun 2, 2024

@editorialbot accept

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

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Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Seidler
  given-names: Thomas
- family-names: Emmerich
  given-names: Fabian
- family-names: Ehlert
  given-names: Kristian
  orcid: "https://orcid.org/0000-0002-7094-6403"
- family-names: Berner
  given-names: Rico
  orcid: "https://orcid.org/0000-0003-4821-3366"
- family-names: Nagel-Kanzler
  given-names: Oliver
- family-names: Schultz
  given-names: Norbert
- family-names: Quade
  given-names: Markus
- family-names: Schultz
  given-names: Martin G.
  orcid: "https://orcid.org/0000-0003-3455-774X"
- family-names: Abel
  given-names: Markus
contact:
- family-names: Seidler
  given-names: Thomas
doi: 10.5281/zenodo.11196516
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Seidler
    given-names: Thomas
  - family-names: Emmerich
    given-names: Fabian
  - family-names: Ehlert
    given-names: Kristian
    orcid: "https://orcid.org/0000-0002-7094-6403"
  - family-names: Berner
    given-names: Rico
    orcid: "https://orcid.org/0000-0003-4821-3366"
  - family-names: Nagel-Kanzler
    given-names: Oliver
  - family-names: Schultz
    given-names: Norbert
  - family-names: Quade
    given-names: Markus
  - family-names: Schultz
    given-names: Martin G.
    orcid: "https://orcid.org/0000-0003-3455-774X"
  - family-names: Abel
    given-names: Markus
  date-published: 2024-06-02
  doi: 10.21105/joss.06136
  issn: 2475-9066
  issue: 98
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6136
  title: "Mantik: A Workflow Platform for the Development of Artificial
    Intelligence on High-Performance Computing Infrastructures"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06136"
  volume: 9
title: "Mantik: A Workflow Platform for the Development of Artificial
  Intelligence on High-Performance Computing Infrastructures"

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.06136 joss-papers#5438
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06136
  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 Jun 2, 2024
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arfon commented Jun 2, 2024

@zhaozhang, @gflofst – many thanks for your reviews here! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@rico-berner – your paper is now accepted and published in JOSS ⚡🚀💥

@arfon arfon closed this as completed Jun 2, 2024
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🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.06136/status.svg)](https://doi.org/10.21105/joss.06136)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06136">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06136/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06136/status.svg
   :target: https://doi.org/10.21105/joss.06136

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:

@rico-berner
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@zhaozhang, @gflofst – many thanks for your reviews here! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@rico-berner – your paper is now accepted and published in JOSS ⚡🚀💥

@zhaozhang, @gflofst Thank you for your time reviewing the paper as well as the software.

@arfon Thank you for handling the reviewing process so well.

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