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[REVIEW]: CoSApp: a Python library to create, simulate and design complex systems #6292

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editorialbot opened this issue Jan 28, 2024 · 93 comments
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accepted HTML JavaScript 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 Jan 28, 2024

Submitting author: @elac-safran (Étienne Lac)
Repository: https://gitlab.com/cosapp/cosapp
Branch with paper.md (empty if default branch): joss-article
Version: v0.15.4
Editor: @HaoZeke
Reviewers: @jbussemaker, @chenxinye
Archive: 10.5281/zenodo.10722403

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/8621ea617b053ca80846478d4bde45ce"><img src="https://joss.theoj.org/papers/8621ea617b053ca80846478d4bde45ce/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/8621ea617b053ca80846478d4bde45ce/status.svg)](https://joss.theoj.org/papers/8621ea617b053ca80846478d4bde45ce)

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

@jbussemaker & @chenxinye, 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 @HaoZeke 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 @chenxinye

📝 Checklist for @jbussemaker

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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

- 10.1007/s00158-019-02211-z is OK
- 10.2514/6.2018-0657 is OK
- 10.4173/mic.2020.4.1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.71 s (637.4 files/s, 157932.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         283          12380          11854          50856
SVG                             40              3              3           8110
JavaScript                      19            710            352           4585
CSS                             14            641             37           3966
Jupyter Notebook                33              0           8942           3770
JSON                            21              1              0           1138
Markdown                        11            400              0            964
HTML                             6             81              4            674
reStructuredText                13            210            508            308
YAML                             5             41             45            223
DOS Batch                        1             29              1            213
INI                              1             29              0            201
make                             1             28              6            143
TeX                              1              2              0             29
C#                               1              0              0             10
-------------------------------------------------------------------------------
SUM:                           450          14555          21752          75190
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1639

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

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HaoZeke commented Jan 28, 2024

👋🏼 @elac-safran @jbussemaker & @chenxinye this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains 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 the URL openjournals/joss-reviews#6292. 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 reviews to be completed within about 2-4 weeks (with a maximum of around 6 weeks). Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@HaoZeke) if you have any questions/concerns.

Additional notes

Since this is for Gitlab repo, links will not be automatically created from this issue, so I'd like to request @jbussemaker & @chenxinye to leave a summary comment when your review is complete with the issues opened.

@elac-safran it might be useful to have a JOSS-Review label for issues related to the review in the repository.

@chenxinye
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chenxinye commented Jan 28, 2024

Review checklist for @chenxinye

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/cosapp/cosapp?
  • 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 (@elac-safran) 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?

@jbussemaker
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jbussemaker commented Jan 28, 2024

Review checklist for @jbussemaker

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/cosapp/cosapp?
  • 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 (@elac-safran) 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?

@elac-safran
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elac-safran commented Jan 28, 2024

@jbussemaker, @chenxinye, I have added the label JOSS-Review in the project repository.

@chenxinye
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@editorialbot commands

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Hello @chenxinye, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

@chenxinye
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@editorialbot check references

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

OK DOIs

- 10.1007/s00158-019-02211-z is OK
- 10.2514/6.2018-0657 is OK
- 10.4173/mic.2020.4.1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@chenxinye
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@editorialbot check repository

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.93 s (481.6 files/s, 119324.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         283          12380          11854          50856
SVG                             40              3              3           8110
JavaScript                      19            710            352           4585
CSS                             14            641             37           3966
Jupyter Notebook                33              0           8942           3770
JSON                            21              1              0           1138
Markdown                        11            400              0            964
HTML                             6             81              4            674
reStructuredText                13            210            508            308
YAML                             5             41             45            223
DOS Batch                        1             29              1            213
INI                              1             29              0            201
make                             1             28              6            143
TeX                              1              2              0             29
C#                               1              0              0             10
-------------------------------------------------------------------------------
SUM:                           450          14555          21752          75190
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1639

@chenxinye
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I've completed my review; the only remaining issues on my part are: the authors may upload their release in Zenodo and upload a plain text CITATION.cff file to the default branch of the repository.

After that I have no further issues ;-)

The software as well as the document and paper are well-written! I believe this is a novel software contribution to the community.

@elac-safran
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elac-safran commented Feb 1, 2024

Hello @HaoZeke.

I have a few questions concerning the review process:

What is the best practice, regarding the paper, if changes are made to the code per reviewer's request?
Should I tag and deploy a new version, and then rebase the joss-article branch?
Is the paper is linked to a specific tag?

@HaoZeke
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HaoZeke commented Feb 1, 2024

Hello @HaoZeke.

I have a few questions concerning the review process:

What is the best practice, regarding the paper, if changes are made to the code per reviewer's request? Should I tag and deploy a new version, and then rebase the joss-article branch? Is the paper is linked to a specific tag?

Excellent question @elac-safran.

Please feel free to continue development as usual. At the end of the review, after all the comments are in and acceptance is recommended, I will request a new tagged release and archive (e.g. on Zenodo, figshare, or others).

After that, I'll set the archive to the same.

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HaoZeke commented Feb 12, 2024

@jbussemaker just checking in, has @elac-safran been able to address your concerns about the paper? I see there was a discussion on this issue?

@jbussemaker
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@HaoZeke they are work-in-progress as far as I know. Can you confirm @elac-safran ?

@elac-safran
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@HaoZeke @jbussemaker I have been very busy at work in the past two weeks. I will submit a revised version of the manuscript as soon as possible. I apologize for the delay.

@elac-safran
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@editorialbot check references

@danielskatz
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@elac-safran - can you add a country for the QuantStack affiliation in your metadata? I've also suggested a few small changes in https://gitlab.com/cosapp/cosapp/-/merge_requests/277 - please merge this or let me know what you disagree with.

@danielskatz
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@openjournals/dev - is #6292 (comment) going to be a problem?

Judging by the pdf proofs, it does not appear to be a problem.

I'm also concerned about the JATS compiled submission. I would prefer not to submit until I better understand the impact of this warning.

@elac-safran
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@danielskatz

@openjournals/dev - is #6292 (comment) going to be a problem?

Judging by the pdf proofs, it does not appear to be a problem.

I'm also concerned about the JATS compiled submission. I would prefer not to submit until I better understand the impact of this warning.

I understand. I can try to find an alternative notation, but this is already standard LaTeX, so I figured it would be accepted as is.

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@danielskatz

@openjournals/dev - is #6292 (comment) going to be a problem?

Judging by the pdf proofs, it does not appear to be a problem.

I'm also concerned about the JATS compiled submission. I would prefer not to submit until I better understand the impact of this warning.

I understand. I can try to find an alternative notation, but this is already standard LaTeX, so I figured it would be accepted as is.

Let's just wait a little bit on this and see what I find out from the JOSS developer team.

@danielskatz
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@elac-safran - another editor suggests

I'd personally replace it with \text{...}, i.e. for example p_\text{atm} which should work fine.

Can you try this?

@elac-safran
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@elac-safran - another editor suggests

I'd personally replace it with \text{...}, i.e. for example p_\text{atm} which should work fine.

Can you try this?

Yup, I can definitely try this. However, from my LaTeX years, I remember this syntax requires package amssymb or amsmath.

@elac-safran
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@editorialbot generate pdf

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

@elac-safran
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@danielskatz the newly generated pdf appears to be correct.

Can you please re-run the checks on your end to confirm that everything is fine now?

@danielskatz
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Yes, but can you also make the other changes if you haven't yet, so we can do all of this at once? (the PR and affiliation country from #6292 (comment))

@elac-safran
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Yes, but can you also make the other changes if you haven't yet, so we can do all of this at once? (the PR and affiliation country from #6292 (comment))

Sorry, I missed that. I will make the changes right away.

@elac-safran
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@editorialbot generate pdf

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

@danielskatz
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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

- 10.1007/s00158-019-02211-z is OK
- 10.2514/6.2018-0657 is OK
- 10.4173/mic.2020.4.1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@danielskatz
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@elac-safran - I think this looks fine (the proof). Do you agree? I'm also checking to make sure there are no warnings in the trail acceptance.

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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#5077, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@elac-safran
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@elac-safran - I think this looks fine (the proof). Do you agree? I'm also checking to make sure there are no warnings in the trail acceptance.

Everything looks good to me. Thank you very much.

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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: Lac
  given-names: Étienne
  orcid: "https://orcid.org/0000-0002-6964-0044"
- family-names: Spiegeleer
  given-names: Guy
  name-particle: De
  orcid: "https://orcid.org/0009-0005-9828-0550"
- family-names: Delsalle
  given-names: Adrien
  orcid: "https://orcid.org/0009-0001-8126-4045"
- family-names: Collonval
  given-names: Frédéric
  orcid: "https://orcid.org/0009-0000-3579-3424"
- family-names: Lê
  given-names: Duc-Trung
  orcid: "https://orcid.org/0009-0000-0415-8399"
- family-names: Malandain
  given-names: Mathias
  orcid: "https://orcid.org/0000-0001-9740-4914"
contact:
- family-names: Lac
  given-names: Étienne
  orcid: "https://orcid.org/0000-0002-6964-0044"
doi: 10.5281/zenodo.10722403
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Lac
    given-names: Étienne
    orcid: "https://orcid.org/0000-0002-6964-0044"
  - family-names: Spiegeleer
    given-names: Guy
    name-particle: De
    orcid: "https://orcid.org/0009-0005-9828-0550"
  - family-names: Delsalle
    given-names: Adrien
    orcid: "https://orcid.org/0009-0001-8126-4045"
  - family-names: Collonval
    given-names: Frédéric
    orcid: "https://orcid.org/0009-0000-3579-3424"
  - family-names: Lê
    given-names: Duc-Trung
    orcid: "https://orcid.org/0009-0000-0415-8399"
  - family-names: Malandain
    given-names: Mathias
    orcid: "https://orcid.org/0000-0001-9740-4914"
  date-published: 2024-02-29
  doi: 10.21105/joss.06292
  issn: 2475-9066
  issue: 94
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6292
  title: "CoSApp: a Python library to create, simulate and design
    complex systems."
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06292"
  volume: 9
title: "CoSApp: a Python library to create, simulate and design complex
  systems."

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.06292 joss-papers#5079
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06292
  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 Feb 29, 2024
@danielskatz
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Congratulations to @elac-safran (Étienne Lac) and co-authors on your publication!!

And thanks to @jbussemaker and @chenxinye for reviewing, and to @HaoZeke 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.06292/status.svg)](https://doi.org/10.21105/joss.06292)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06292">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06292/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06292/status.svg
   :target: https://doi.org/10.21105/joss.06292

This is how it will look in your documentation:

DOI

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