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[REVIEW]: Chi: A Python package for treatment response modelling #5925

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editorialbot opened this issue Oct 4, 2023 · 99 comments
Closed

[REVIEW]: Chi: A Python package for treatment response modelling #5925

editorialbot opened this issue Oct 4, 2023 · 99 comments
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accepted published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials

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editorialbot commented Oct 4, 2023

Submitting author: @DavAug (David Augustin)
Repository: https://github.com/DavAug/chi
Branch with paper.md (empty if default branch): joss-publication
Version: 1.0.0
Editor: @ppxasjsm
Reviewers: @shahmoradi, @ns-rse
Archive: 10.5281/zenodo.10510572

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/ab102a087414584c19a7aeccc85fe3b2"><img src="https://joss.theoj.org/papers/ab102a087414584c19a7aeccc85fe3b2/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/ab102a087414584c19a7aeccc85fe3b2/status.svg)](https://joss.theoj.org/papers/ab102a087414584c19a7aeccc85fe3b2)

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

@shahmoradi, 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 @ppxasjsm 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 @ns-rse

📝 Checklist for @shahmoradi

@editorialbot editorialbot added Python review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Oct 4, 2023
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Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

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

@editorialbot generate pdf

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.73 s (130.1 files/s, 54335.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          39           5856          10146          20465
HTML                            10              0              0            710
reStructuredText                26            345            423            678
XML                              5             15              0            401
YAML                             8             43             11            228
TeX                              1             14              0            152
Markdown                         3             36              0            108
DOS Batch                        1              8              1             27
make                             1              4              6             10
CSS                              1              0              1              3
-------------------------------------------------------------------------------
SUM:                            95           6321          10588          22782
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 494

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

OK DOIs

- 10.1371/journal.pcbi.1011135 is OK
- 10.1038/nrd.2017.244 is OK
- 10.1101/2023.07.31.551404 is OK
- 10.5334/jors.252 is OK

MISSING DOIs

- 10.1038/psp.2013.24 may be a valid DOI for title: Modeling and simulation workbench for NONMEM: tutorial on Pirana, PsN, and Xpose
- 10.1007/s11095-021-03065-1 may be a valid DOI for title: Scipion PKPD: an Open-Source Platform for Biopharmaceutics, Pharmacokinetics and Pharmacodynamics Data Analysis
- 10.1101/2020.11.28.402297 may be a valid DOI for title: Accelerated predictive healthcare analytics with pumas, a high performance pharmaceutical modeling and simulation platform
- 10.1093/aje/kwt245 may be a valid DOI for title: Maximum likelihood, profile likelihood, and penalized likelihood: a primer
- 10.1007/s11222-013-9416-2 may be a valid DOI for title: Understanding predictive information criteria for Bayesian models
- 10.1101/2022.03.19.483454 may be a valid DOI for title: Treatment response prediction: Is model selection unreliable?

INVALID DOIs

- https://doi.org/10.1016/j.ddtec.2016.11.005 is INVALID because of 'https://doi.org/' prefix

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

@Kevin-Mattheus-Moerman
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@ppxasjsm note that over in the pre-review issue @ns-rse said they could help review too.

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ppxasjsm commented Oct 9, 2023

Thanks! I somehow missed this. @ns-rse I'll add you as a reviewer, please let me know if you cannot review anymore.

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ppxasjsm commented Oct 9, 2023

@editorialbot add @ns-rse as reviewer

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@ns-rse added to the reviewers list!

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ppxasjsm commented Oct 9, 2023

@DavAug could you take a look at the missing DOIs flagged by editorial bot and fix them please?

@DavAug
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DavAug commented Oct 9, 2023

@DavAug could you take a look at the missing DOIs flagged by editorial bot and fix them please?

Of course! No problem 😊

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ns-rse commented Oct 9, 2023

Review checklist for @ns-rse

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the https://github.com/DavAug/chi?
  • 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 (@DavAug) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

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DavAug commented Oct 9, 2023

@editorialbot generate pdf

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DavAug commented Oct 9, 2023

@DavAug could you take a look at the missing DOIs flagged by editorial bot and fix them please?

I fixed the Invalid DOI and manually checked the "Missing" ones. They all link to the correct publication on https://www.doi.org/

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

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DavAug commented Oct 9, 2023

@editorialbot commands

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Hello @DavAug, 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

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DavAug commented Oct 9, 2023

@editorialbot check references

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

OK DOIs

- 10.1371/journal.pcbi.1011135 is OK
- 10.1038/nrd.2017.244 is OK
- 10.1016/j.ddtec.2016.11.005 is OK
- 10.1101/2023.07.31.551404 is OK
- 10.5334/jors.252 is OK

MISSING DOIs

- 10.1038/psp.2013.24 may be a valid DOI for title: Modeling and simulation workbench for NONMEM: tutorial on Pirana, PsN, and Xpose
- 10.1007/s11095-021-03065-1 may be a valid DOI for title: Scipion PKPD: an Open-Source Platform for Biopharmaceutics, Pharmacokinetics and Pharmacodynamics Data Analysis
- 10.1101/2020.11.28.402297 may be a valid DOI for title: Accelerated predictive healthcare analytics with pumas, a high performance pharmaceutical modeling and simulation platform
- 10.1093/aje/kwt245 may be a valid DOI for title: Maximum likelihood, profile likelihood, and penalized likelihood: a primer
- 10.1007/s11222-013-9416-2 may be a valid DOI for title: Understanding predictive information criteria for Bayesian models
- 10.1101/2022.03.19.483454 may be a valid DOI for title: Treatment response prediction: Is model selection unreliable?

INVALID DOIs

- None

@DavAug
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DavAug commented Oct 19, 2023

One of the articles that we are referencing just got published, so I am just replacing the reference to the preprint by the reference to the peer-reviewed publication.

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DavAug commented Oct 19, 2023

@editorialbot generate pdf

@DavAug
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DavAug commented Oct 19, 2023

@editorialbot check references

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

OK DOIs

- 10.1371/journal.pcbi.1011135 is OK
- 10.1038/nrd.2017.244 is OK
- 10.1016/j.ddtec.2016.11.005 is OK
- 10.3389/fphar.2023.1270443 is OK
- 10.5334/jors.252 is OK
- 10.1016/j.pbiomolbio.2015.12.008 is OK

MISSING DOIs

- 10.1038/psp.2013.24 may be a valid DOI for title: Modeling and simulation workbench for NONMEM: tutorial on Pirana, PsN, and Xpose
- 10.1007/s11095-021-03065-1 may be a valid DOI for title: Scipion PKPD: an Open-Source Platform for Biopharmaceutics, Pharmacokinetics and Pharmacodynamics Data Analysis
- 10.1101/2020.11.28.402297 may be a valid DOI for title: Accelerated predictive healthcare analytics with pumas, a high performance pharmaceutical modeling and simulation platform
- 10.1093/aje/kwt245 may be a valid DOI for title: Maximum likelihood, profile likelihood, and penalized likelihood: a primer
- 10.1007/s11222-013-9416-2 may be a valid DOI for title: Understanding predictive information criteria for Bayesian models
- 10.1101/2022.03.19.483454 may be a valid DOI for title: Treatment response prediction: Is model selection unreliable?

INVALID DOIs

- None

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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

- 10.1093/bioinformatics/btg015 is OK
- 10.1371/journal.pcbi.1011135 is OK
- 10.1208/s12248-014-9716-2 is OK
- 10.1038/nrd.2017.244 is OK
- 10.1016/j.ddtec.2016.11.005 is OK
- 10.3389/fphar.2023.1270443 is OK
- 10.5334/jors.252 is OK
- 10.1038/psp.2013.24 is OK
- 10.1007/s10928-017-9562-9 is OK
- 10.1007/s11095-021-03065-1 is OK
- 10.1101/2020.11.28.402297 is OK
- 10.1093/aje/kwt245 is OK
- 10.1007/s11222-013-9416-2 is OK
- 10.1101/2022.03.19.483454 is OK
- 10.1016/j.pbiomolbio.2015.12.008 is OK
- 10.1038/s41592-019-0686-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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⚠️ Error preparing paper acceptance. The generated XML metadata file is invalid.

Element isbn: [facet 'minLength'] The value has a length of '9'; this underruns the allowed minimum length of '10'.

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@Kevin-Mattheus-Moerman can you help with this error? I don't know what to make of this.

@DavAug
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DavAug commented Feb 3, 2024

@editorialbot generate pdf

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

@DavAug
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DavAug commented Feb 3, 2024

@editorialbot check references

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

OK DOIs

- 10.1093/bioinformatics/btg015 is OK
- 10.1371/journal.pcbi.1011135 is OK
- 10.1208/s12248-014-9716-2 is OK
- 10.1038/nrd.2017.244 is OK
- 10.1016/j.ddtec.2016.11.005 is OK
- 10.3389/fphar.2023.1270443 is OK
- 10.5334/jors.252 is OK
- 10.1038/psp.2013.24 is OK
- 10.1007/s10928-017-9562-9 is OK
- 10.1007/s11095-021-03065-1 is OK
- 10.1101/2020.11.28.402297 is OK
- 10.1093/aje/kwt245 is OK
- 10.1007/s11222-013-9416-2 is OK
- 10.1101/2022.03.19.483454 is OK
- 10.1016/j.pbiomolbio.2015.12.008 is OK
- 10.1038/s41592-019-0686-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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DavAug commented Feb 3, 2024

Hi @ppxasjsm @Kevin-Mattheus-Moerman

Thank you so much for recommending the acceptance of my article. I really appreciate it! :)

I just had a quick look into the error message, and while I am not sure why the error occured, I noticed that it was related to "wrong" ISBN in one of my BibTeX entries. Since the ISBN is not actually included in the reference that appear on the rendered article, I simply removed it.

@ppxasjsm would you, perhaps, be able to trigger the acceptance again? I hope that this will remove the error (I saw that an article was successfully published yesterday, so the error does seem to be specific to my article).

Thank you so much and best wishes,
David

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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

- 10.1093/bioinformatics/btg015 is OK
- 10.1371/journal.pcbi.1011135 is OK
- 10.1208/s12248-014-9716-2 is OK
- 10.1038/nrd.2017.244 is OK
- 10.1016/j.ddtec.2016.11.005 is OK
- 10.3389/fphar.2023.1270443 is OK
- 10.5334/jors.252 is OK
- 10.1038/psp.2013.24 is OK
- 10.1007/s10928-017-9562-9 is OK
- 10.1007/s11095-021-03065-1 is OK
- 10.1101/2020.11.28.402297 is OK
- 10.1093/aje/kwt245 is OK
- 10.1007/s11222-013-9416-2 is OK
- 10.1101/2022.03.19.483454 is OK
- 10.1016/j.pbiomolbio.2015.12.008 is OK
- 10.1038/s41592-019-0686-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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👋 @openjournals/bcm-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#4979, 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 Feb 3, 2024
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DavAug commented Feb 6, 2024

👋 @openjournals/bcm-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#4979, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Hi @Kevin-Mattheus-Moerman , thank you so much for recommending the acceptance.

I just wanted to kindly confirm that accepting the submission is not in my mandate? I.e. we are not waiting for me to approve the final version of the article.

Best,
David

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Kevin-Mattheus-Moerman commented Feb 7, 2024

@DavAug As AEiC I will now help process this submission for acceptance in JOSS. I have just checked your repository, the archive link, this review, and the paper. Most seems in order. I do however have the below points that require your attention:

  • In your affiliation, please spell out UK as United Kingdom
  • Please edit the ZENODO archive version tag to be v1.0.0
  • Check methdological which should read methodological

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DavAug commented Feb 7, 2024

@DavAug As AEiC I will now help process this submission for acceptance in JOSS. I have just checked your repository, the archive link, this review, and the paper. Most seems in order. I do however have the below points that require your attention:

  • In your affiliation, please spell out UK as United Kingdom
  • Please edit the ZENODO archive version tag to be v1.0.0
  • Check methdological which should read methodological

Hi @Kevin-Mattheus-Moerman , Thank you so much for the thorough review! Requested updates are now completed.

  • In your affiliation, please spell out UK as United Kingdom
  • Please edit the ZENODO archive version tag to be v1.0.0
  • Check methdological which should read methodological

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DavAug commented Feb 7, 2024

@editorialbot generate pdf

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

@Kevin-Mattheus-Moerman
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@DavAug great, thanks, now all looks in order, ready to proceed.

@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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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: Augustin
  given-names: David
  orcid: "https://orcid.org/0000-0002-4885-1088"
contact:
- family-names: Augustin
  given-names: David
  orcid: "https://orcid.org/0000-0002-4885-1088"
doi: 10.5281/zenodo.10510572
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Augustin
    given-names: David
    orcid: "https://orcid.org/0000-0002-4885-1088"
  date-published: 2024-02-07
  doi: 10.21105/joss.05925
  issn: 2475-9066
  issue: 94
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5925
  title: "Chi: A Python package for treatment response modelling"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05925"
  volume: 9
title: "Chi: A Python package for treatment response modelling"

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.05925 joss-papers#4991
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05925
  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 7, 2024
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@DavAug congrats on this publication with JOSS!

Thanks for editing @ppxasjsm!

And a special thank you to the reviewers: @shahmoradi, @ns-rse!!

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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.05925/status.svg)](https://doi.org/10.21105/joss.05925)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05925">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05925/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05925/status.svg
   :target: https://doi.org/10.21105/joss.05925

This is how it will look in your documentation:

DOI

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