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[REVIEW]: snSMART: An R Package for Small Sample, Sequential, Multiple Assignment, Randomized Trial Data Analysis #6971

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editorialbot opened this issue Jul 10, 2024 · 60 comments
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accepted published Papers published in JOSS R recommend-accept Papers recommended for acceptance in JOSS. review Rez TeX Track: 4 (SBCS) Social, Behavioral, and Cognitive Sciences waitlisted Submissions in the JOSS backlog due to reduced service mode.

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editorialbot commented Jul 10, 2024

Submitting author: @sidiwang (Sidi Wang)
Repository: https://github.com/sidiwang/snSMART
Branch with paper.md (empty if default branch): JOSS
Version: 0.2.4
Editor: @osorensen
Reviewers: @aghaynes, @ezraporter
Archive: 10.5281/zenodo.13370298

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/119f9b14b157f475c25f737aca4a166e"><img src="https://joss.theoj.org/papers/119f9b14b157f475c25f737aca4a166e/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/119f9b14b157f475c25f737aca4a166e/status.svg)](https://joss.theoj.org/papers/119f9b14b157f475c25f737aca4a166e)

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

@aghaynes & @ezraporter, 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 @osorensen 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 @aghaynes

📝 Checklist for @ezraporter

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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

- 10.1016/j.cct.2020.105989 is OK
- 10.1002/sim.7900 is OK
- 10.1080/10543406.2020.1815032 is OK
- 10.1002/sim.8813 is OK
- 10.1002/sim.8776 is OK
- 10.1016/S0140-6736(02)07283-5 is OK
- 10.1186/s13063-020-04285-3 is OK
- 10.2307/2348770 is OK
- 10.1111/1467-985X.00154 is OK
- 10.1002/sim.2022 is OK
- 10.1093/biostatistics/kxr016 is OK
- 10.32614/CRAN.package.geepack is OK
- 10.18637/jss.v015.i02 is OK
- 10.1002/sim.1650 is OK
- 10.2307/2531248 is OK
- 10.32614/CRAN.package.EnvStats is OK
- 10.32614/CRAN.package.rjags is OK

MISSING DOIs

- No DOI given, and none found for title: geepack: Yet Another Package for Generalized Estim...
- No DOI given, and none found for title: JAGS: A Program for Analysis of Bayesian Graphical...

INVALID DOIs

- 10.1111/rssc.1246 is INVALID

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (993.3 files/s, 250890.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               10            436            929           2128
Markdown                         3            132              0            699
TeX                              1             33              1            195
YAML                             4             17              9            102
Rmd                              1             18             63             37
-------------------------------------------------------------------------------
SUM:                            19            636           1002           3161
-------------------------------------------------------------------------------

Commit count by author:

   117	Sidi Wang
    31	sidiwang
    13	Michael Kleinsasser
     1	Michael (Mike) Kleinsasser

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Paper file info:

📄 Wordcount for paper.md is 1205

✅ The paper includes a Statement of need section

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License info:

🟡 License found: GNU General Public License v2.0 (Check here for OSI approval)

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

@aghaynes
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aghaynes commented Jul 16, 2024

Review checklist for @aghaynes

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/sidiwang/snSMART?
  • 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 (@sidiwang) 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?

@aghaynes
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I have made some comments in the issue here which address the unchecked points above as well as some other points and (non-mandatory) recommendations

@osorensen
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Thanks for your review @aghaynes. @sidiwang, you are welcome to start addressing these issues right away. Please report here when done, or if you have any questions.

@aghaynes
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aghaynes commented Aug 8, 2024

@editorialbot generate pdf

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

@aghaynes
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aghaynes commented Aug 8, 2024

@sidiwang has addressed the vaste majority of my comments and has just one or two minor things to do.

@osorensen
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👋 @ezraporter could you please update us on how it's going with your review?

@ezraporter
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Sorry for the delay! I'm working on it now and expect to be done tomorrow

@ezraporter
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ezraporter commented Aug 9, 2024

Review checklist for @ezraporter

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/sidiwang/snSMART?
  • 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 (@sidiwang) 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?

@ezraporter
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My comments have been addressed by @sidiwang. All good on my end

@osorensen
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@editorialbot generate pdf

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

@osorensen
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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.cct.2020.105989 is OK
- 10.1111/rssc.12406 is OK
- 10.1002/sim.7900 is OK
- 10.1080/10543406.2020.1815032 is OK
- 10.1002/sim.8813 is OK
- 10.1002/sim.8776 is OK
- 10.1016/S0140-6736(02)07283-5 is OK
- 10.1186/s13063-020-04285-3 is OK
- 10.2307/2348770 is OK
- 10.1111/1467-985X.00154 is OK
- 10.1002/sim.2022 is OK
- 10.1093/biostatistics/kxr016 is OK
- 10.32614/CRAN.package.geepack is OK
- 10.18637/jss.v015.i02 is OK
- 10.1002/sim.1650 is OK
- 10.2307/2531248 is OK
- 10.32614/CRAN.package.EnvStats is OK
- 10.32614/CRAN.package.rjags is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: geepack: Yet Another Package for Generalized Estim...
- No DOI given, and none found for title: JAGS: A Program for Analysis of Bayesian Graphical...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

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

Element tbody content does not follow the DTD, expecting (tr)+, got ()

@osorensen
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@openjournals/dev can you help us with the issue above?

@arfon
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arfon commented Aug 29, 2024

Looks like there's some issue with the generated JATS file: https://github.com/openjournals/joss-papers/blob/bcb1737a9ecc52b458bd1019dd24fa82f36d10e6/joss.06971/paper.jats/10.21105.joss.06971.jats

I think it's the table in the document. @sidiwang – could you please try updating your table to be strictly Markdown formatted one?

@sidiwang
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sidiwang commented Sep 2, 2024

@arfon @osorensen Thank you for the feedback. I just made some changes. Could you take a look and see whether it works now? Thanks a lot.

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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.cct.2020.105989 is OK
- 10.1111/rssc.12406 is OK
- 10.1002/sim.7900 is OK
- 10.1080/10543406.2020.1815032 is OK
- 10.1002/sim.8813 is OK
- 10.1002/sim.8776 is OK
- 10.1016/S0140-6736(02)07283-5 is OK
- 10.1186/s13063-020-04285-3 is OK
- 10.2307/2348770 is OK
- 10.1111/1467-985X.00154 is OK
- 10.1002/sim.2022 is OK
- 10.1093/biostatistics/kxr016 is OK
- 10.32614/CRAN.package.geepack is OK
- 10.18637/jss.v015.i02 is OK
- 10.1002/sim.1650 is OK
- 10.2307/2531248 is OK
- 10.32614/CRAN.package.EnvStats is OK
- 10.32614/CRAN.package.rjags is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: geepack: Yet Another Package for Generalized Estim...
- No DOI given, and none found for title: JAGS: A Program for Analysis of Bayesian Graphical...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

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👋 @openjournals/sbcs-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#5843, 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 Sep 3, 2024
@samhforbes
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@editorialbot check references

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

✅ OK DOIs

- 10.1016/j.cct.2020.105989 is OK
- 10.1111/rssc.12406 is OK
- 10.1002/sim.7900 is OK
- 10.1080/10543406.2020.1815032 is OK
- 10.1002/sim.8813 is OK
- 10.1002/sim.8776 is OK
- 10.1016/S0140-6736(02)07283-5 is OK
- 10.1186/s13063-020-04285-3 is OK
- 10.2307/2348770 is OK
- 10.1111/1467-985X.00154 is OK
- 10.1002/sim.2022 is OK
- 10.1093/biostatistics/kxr016 is OK
- 10.32614/CRAN.package.geepack is OK
- 10.18637/jss.v015.i02 is OK
- 10.1002/sim.1650 is OK
- 10.2307/2531248 is OK
- 10.32614/CRAN.package.EnvStats is OK
- 10.32614/CRAN.package.rjags is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: geepack: Yet Another Package for Generalized Estim...
- No DOI given, and none found for title: JAGS: A Program for Analysis of Bayesian Graphical...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

@samhforbes
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Hi @sidiwang I noticed your software licence doesn't match the licence in your archive. Can you update to make sure both use a OSI approved licence and that it matches please?

@sidiwang
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sidiwang commented Sep 6, 2024

Hi @samhforbes I just updated the license in my archive. Hopefully, I did it the right way! Thank you!

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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.cct.2020.105989 is OK
- 10.1111/rssc.12406 is OK
- 10.1002/sim.7900 is OK
- 10.1080/10543406.2020.1815032 is OK
- 10.1002/sim.8813 is OK
- 10.1002/sim.8776 is OK
- 10.1016/S0140-6736(02)07283-5 is OK
- 10.1186/s13063-020-04285-3 is OK
- 10.2307/2348770 is OK
- 10.1111/1467-985X.00154 is OK
- 10.1002/sim.2022 is OK
- 10.1093/biostatistics/kxr016 is OK
- 10.32614/CRAN.package.geepack is OK
- 10.18637/jss.v015.i02 is OK
- 10.1002/sim.1650 is OK
- 10.2307/2531248 is OK
- 10.32614/CRAN.package.EnvStats is OK
- 10.32614/CRAN.package.rjags is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: geepack: Yet Another Package for Generalized Estim...
- No DOI given, and none found for title: JAGS: A Program for Analysis of Bayesian Graphical...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

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👋 @openjournals/sbcs-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#5876, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@samhforbes
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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: Wang
  given-names: Sidi
  orcid: "https://orcid.org/0000-0003-4838-0842"
- family-names: Fang
  given-names: Fang
  orcid: "https://orcid.org/0000-0002-7089-3591"
- family-names: Tamura
  given-names: Roy
- family-names: Braun
  given-names: Thomas
  orcid: "https://orcid.org/0000-0002-7113-6998"
- family-names: Kidwell
  given-names: Kelley M
  orcid: "https://orcid.org/0000-0002-1717-4483"
doi: 10.5281/zenodo.13370298
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Wang
    given-names: Sidi
    orcid: "https://orcid.org/0000-0003-4838-0842"
  - family-names: Fang
    given-names: Fang
    orcid: "https://orcid.org/0000-0002-7089-3591"
  - family-names: Tamura
    given-names: Roy
  - family-names: Braun
    given-names: Thomas
    orcid: "https://orcid.org/0000-0002-7113-6998"
  - family-names: Kidwell
    given-names: Kelley M
    orcid: "https://orcid.org/0000-0002-1717-4483"
  date-published: 2024-09-12
  doi: 10.21105/joss.06971
  issn: 2475-9066
  issue: 101
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6971
  title: "snSMART: An R Package for Small Sample, Sequential, Multiple
    Assignment, Randomized Trial Data Analysis"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06971"
  volume: 9
title: "snSMART: An R Package for Small Sample, Sequential, Multiple
  Assignment, Randomized Trial Data Analysis"

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.06971 joss-papers#5877
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06971
  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 Sep 12, 2024
@samhforbes
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Congrats @sidiwang on a very nice package.
Thanks to our reviewers @aghaynes, @ezraporter for taking the time, and of course to @osorensen for editing this submission.

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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.06971/status.svg)](https://doi.org/10.21105/joss.06971)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06971">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06971/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06971/status.svg
   :target: https://doi.org/10.21105/joss.06971

This is how it will look in your documentation:

DOI

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