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[REVIEW]: ewstools: A Python package for early warning signals of bifurcations in time series data #5038

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editorialbot opened this issue Jan 5, 2023 · 54 comments
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[REVIEW]: ewstools: A Python package for early warning signals of bifurcations in time series data #5038

editorialbot opened this issue Jan 5, 2023 · 54 comments
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accepted published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics

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editorialbot commented Jan 5, 2023 •
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Submitting author: @ThomasMBury (Thomas M Bury)
Repository: https://github.com/ThomasMBury/ewstools
Branch with paper.md (empty if default branch):
Version: v2.1.1
Editor: @osorensen
Reviewers: @mhu48, @mikesha2, @ranzhengcode
Archive: 10.5281/zenodo.7630022

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/72d1a4bf216c2a4b22edab3b8f1feae0"><img src="https://joss.theoj.org/papers/72d1a4bf216c2a4b22edab3b8f1feae0/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/72d1a4bf216c2a4b22edab3b8f1feae0/status.svg)](https://joss.theoj.org/papers/72d1a4bf216c2a4b22edab3b8f1feae0)

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

@mhu48 & @mikesha2 & @ranzhengcode, 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 @mikesha2

📝 Checklist for @ranzhengcode

📝 Checklist for @mhu48
@editorialbot editorialbot added Python review TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Jan 5, 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

@editorialbot editorialbot mentioned this issue Jan 5, 2023
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Software report:

github.com/AlDanial/cloc v 1.88  T=0.16 s (197.1 files/s, 139470.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           9            862           1251           1230
XML                              6              0              0            605
Markdown                         3             92              0            234
Jupyter Notebook                 4              0          17125            162
TeX                              1             22              4            148
YAML                             4             10              5             45
reStructuredText                 2             34             20             36
DOS Batch                        1              8              1             26
make                             1              4              6              9
-------------------------------------------------------------------------------
SUM:                            31           1032          18412           2495
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 845

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

OK DOIs

- 10.1038/nature08227 is OK
- 10.1111/ele.12948 is OK
- 10.1098/rsif.2020.0482 is OK
- 10.1073/pnas.2106140118 is OK
- 10.1371/journal.pone.0041010 is OK
- 10.1111/2041-210X.13058 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.5281/zenodo.15681 is OK
- 10.25080/Majora-92bf1922-011 is OK
- 10.1038/s41592-020-0772-5 is OK
- 10.48550/arXiv.1605.08695 is OK

MISSING DOIs

- 10.1163/1574-9347_bnp_e612900 may be a valid DOI for title: Keras

INVALID DOIs

- None

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

@mikesha2
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mikesha2 commented Jan 5, 2023 •
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Review checklist for @mikesha2

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/ThomasMBury/ewstools?
  • 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 (@ThomasMBury) 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?

@ranzhengcode
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ranzhengcode commented Jan 5, 2023 via email

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ranzhengcode commented Jan 5, 2023 •
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Review checklist for @ranzhengcode

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/ThomasMBury/ewstools?
  • 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 (@ThomasMBury) 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?

@mhu48
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mhu48 commented Jan 6, 2023 •
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Review checklist for @mhu48

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/ThomasMBury/ewstools?
  • 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 (@ThomasMBury) 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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👋 @mhu48

I notice there are a number of unchecked boxes in your review checklists. Are these related to issues which the authors should fix? If so, could you please elaborate here or by opening issues in the source repository?

@mhu48
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mhu48 commented Feb 10, 2023

@osorensen Thanks for the reminder! Apparently I made a mistake when I did the checklist. It should be updated correctly now? Please let me know if there is any further actions needed at this step.

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Thanks @mhu48, everything looks good now

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@editorialbot check references

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@editorialbot generate pdf

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

OK DOIs

- 10.1038/nature08227 is OK
- 10.1111/ele.12948 is OK
- 10.1098/rsif.2020.0482 is OK
- 10.1073/pnas.2106140118 is OK
- 10.1371/journal.pone.0041010 is OK
- 10.1111/2041-210X.13058 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.5281/zenodo.15681 is OK
- 10.25080/Majora-92bf1922-011 is OK
- 10.1038/s41592-020-0772-5 is OK
- 10.48550/arXiv.1605.08695 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

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osorensen commented Feb 10, 2023 •
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@ThomasMBury, could you please replace the current pandas citation with those suggested here (preferably include both): https://pandas.pydata.org/about/citing.html

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@ThomasMBury, once you have fixed the pandas reference issue above, could you please

  • Make a tagged release of your software, and list the version tag of the archived version here.
  • Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
  • Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
  • Please list the DOI of the archived version here.

I can then move forward with recommending acceptance of the submission.

@ThomasMBury
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@editorialbot generate pdf

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

@ThomasMBury
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@editorialbot check references

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

OK DOIs

- 10.1038/nature08227 is OK
- 10.1111/ele.12948 is OK
- 10.1098/rsif.2020.0482 is OK
- 10.1073/pnas.2106140118 is OK
- 10.1371/journal.pone.0041010 is OK
- 10.1111/2041-210X.13058 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.15681 is OK
- 10.25080/Majora-92bf1922-011 is OK
- 10.1038/s41592-020-0772-5 is OK
- 10.48550/arXiv.1605.08695 is OK

MISSING DOIs

- 10.1163/1574-9347_bnp_e612900 may be a valid DOI for title: Keras

INVALID DOIs

- None

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@editorialbot commands

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Hello @ThomasMBury, 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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@editorialbot generate pdf

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

@ThomasMBury
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I'm afraid I couldn't find a DOI for the Keras API - I hope this is ok. The bot didn't seem to mind the first time I submitted.

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Ok, then I think it's fine.

@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

- 10.1038/nature08227 is OK
- 10.1111/ele.12948 is OK
- 10.1098/rsif.2020.0482 is OK
- 10.1073/pnas.2106140118 is OK
- 10.1371/journal.pone.0041010 is OK
- 10.1111/2041-210X.13058 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.15681 is OK
- 10.25080/Majora-92bf1922-011 is OK
- 10.1038/s41592-020-0772-5 is OK
- 10.48550/arXiv.1605.08695 is OK

MISSING DOIs

- 10.1163/1574-9347_dnp_e612900 may be a valid DOI for title: Keras

INVALID DOIs

- None

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👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3958, 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 11, 2023
@danielskatz
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👋 @ThomasMBury - I'm working on the next steps for this submission, and after proofreading it, I have some suggested changes, in ThomasMBury/ewstools#433 Please merge this, or let me know what you disagree with, then we can continue the process.

@ThomasMBury
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Thanks for proofreading @danielskatz. I approve of the changes and have merged the pull request.

@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

- 10.1038/nature08227 is OK
- 10.1111/ele.12948 is OK
- 10.1098/rsif.2020.0482 is OK
- 10.1073/pnas.2106140118 is OK
- 10.1371/journal.pone.0041010 is OK
- 10.1111/2041-210X.13058 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.15681 is OK
- 10.25080/Majora-92bf1922-011 is OK
- 10.1038/s41592-020-0772-5 is OK
- 10.48550/arXiv.1605.08695 is OK

MISSING DOIs

- 10.1163/1574-9347_dnp_e612900 may be a valid DOI for title: Keras

INVALID DOIs

- None

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👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3959, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

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@editorialbot accept

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

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🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05038 joss-papers#3960
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05038
  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 11, 2023
@danielskatz
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Congratulations to @ThomasMBury (Thomas M Bury)!!

And thanks to @mhu48, @mikesha2, and @ranzhengcode for reviewing, and to @osorensen for editing!
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.05038/status.svg)](https://doi.org/10.21105/joss.05038)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05038">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05038/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05038/status.svg
   :target: https://doi.org/10.21105/joss.05038

This is how it will look in your documentation:

DOI

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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:

@ThomasMBury
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Thank you everyone for your help in reviewing this paper :)

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