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[REVIEW]: Imbalance: A comprehensive multi-interface Julia toolbox to address class imbalance #6310

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editorialbot opened this issue Jan 31, 2024 · 73 comments
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accepted Julia published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning

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editorialbot commented Jan 31, 2024

Submitting author: @EssamWisam (Essam )
Repository: https://github.com/JuliaAI/Imbalance.jl
Branch with paper.md (empty if default branch): paper
Version: v0.1.6
Editor: @jbytecode
Reviewers: @sylvaticus, @ArneTillmann
Archive: 10.5281/zenodo.10823254

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/0b2c4dc93c666b0809bfe3443ea7f640"><img src="https://joss.theoj.org/papers/0b2c4dc93c666b0809bfe3443ea7f640/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/0b2c4dc93c666b0809bfe3443ea7f640/status.svg)](https://joss.theoj.org/papers/0b2c4dc93c666b0809bfe3443ea7f640)

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

@sylvaticus & @ArneTillmann, 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 @jbytecode 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 @sylvaticus

📝 Checklist for @ArneTillmann

@editorialbot editorialbot added Julia review TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning waitlisted Submissions in the JOSS backlog due to reduced service mode. labels Jan 31, 2024
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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=0.37 s (333.6 files/s, 114745.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           67           1563            806           6301
Markdown                        21           1434              0           3196
Jupyter Notebook                20              0          27731           1342
TeX                              1             22              0            145
YAML                             7              3              6            143
TOML                             4              5              0            106
Sass                             1             26              0             80
Python                           1             15             10             43
Bourne Shell                     1              0              0              9
JSON                             1              0              0              6
CSS                              1              0              8              1
-------------------------------------------------------------------------------
SUM:                           125           3068          28561          11372
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1448

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

OK DOIs

- 10.1007/978-3-540-75171-7_2 is OK

MISSING DOIs

- 10.1109/icoacs.2016.7563084 may be a valid DOI for title: Effective prediction of three common diseases by combining SMOTE with Tomek links technique for imbalanced medical data
- 10.1109/tsmcb.2008.2007853 may be a valid DOI for title: Exploratory Undersampling for Class-Imbalance Learning
- 10.46586/tches.v2019.i1.209-237 may be a valid DOI for title: The Curse of Class Imbalance and Conflicting Metrics with Machine Learning for Side-channel Evaluations
- 10.1613/jair.953 may be a valid DOI for title: SMOTE: Synthetic Minority Over-sampling Technique
- 10.1007/11538059_91 may be a valid DOI for title: Borderline-SMOTE: A New Over-Sampling Method in Imbalanced Data Sets Learning
- 10.1016/j.inffus.2013.12.003 may be a valid DOI for title: RWO-Sampling: A random walk over-sampling approach to imbalanced data classification
- 10.1007/s10618-012-0295-5 may be a valid DOI for title: Training and assessing classification rules with imbalanced data
- 10.1109/tit.1968.1054155 may be a valid DOI for title: The condensed nearest neighbor rule (Corresp.)
- 10.1016/j.knosys.2013.01.018 may be a valid DOI for title: Analysing the classification of imbalanced data-sets with multiple classes: Binarization techniques and ad-hoc approaches

INVALID DOIs

- https://doi.org/10.1016/j.neucom.2019.06.100 is INVALID because of 'https://doi.org/' prefix

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

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@sylvaticus, @ArneTillmann - thank you for accepting our invitation. Please, firstly create your checklist before starting your review. Thank you in advance

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sylvaticus commented Jan 31, 2024

Review checklist for @sylvaticus

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/JuliaAI/Imbalance.jl?
  • 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 (@EssamWisam) 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?

@jbytecode
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@sylvaticus, @ArneTillmann - Dear reviewers, how is your review going? I would be appreciated if you have a chance to update your status. Thank you in advance!

@sylvaticus
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Fine for me, just minor points that I put in the issues in the repository but the project is mature, well documented and working as described.

@jbytecode jbytecode removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Feb 26, 2024
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@ArneTillmann - Could you please update your review status? It seems you haven't created you checklist, yet. Could you please create it and start your review?

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ArneTillmann commented Feb 26, 2024

Review checklist for @ArneTillmann

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/JuliaAI/Imbalance.jl?
  • 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 (@EssamWisam) 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?

@ArneTillmann
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@ArneTillmann - Could you please update your review status? It seems you haven't created you checklist, yet. Could you please create it and start your review?

As I have said before, I am now able to start the review process. I expect to finish it by the end of the week.

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@ArneTillmann - Thank you for the response. Your deadline is okay to us. I've just reminded you. Thank you in advance.

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

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Hello @ArneTillmann, 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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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/978-3-540-75171-7_2 is OK

MISSING DOIs

- 10.1109/icoacs.2016.7563084 may be a valid DOI for title: Effective prediction of three common diseases by combining SMOTE with Tomek links technique for imbalanced medical data
- 10.1109/tsmcb.2008.2007853 may be a valid DOI for title: Exploratory Undersampling for Class-Imbalance Learning
- 10.46586/tches.v2019.i1.209-237 may be a valid DOI for title: The Curse of Class Imbalance and Conflicting Metrics with Machine Learning for Side-channel Evaluations
- 10.1613/jair.953 may be a valid DOI for title: SMOTE: Synthetic Minority Over-sampling Technique
- 10.1007/11538059_91 may be a valid DOI for title: Borderline-SMOTE: A New Over-Sampling Method in Imbalanced Data Sets Learning
- 10.1016/j.inffus.2013.12.003 may be a valid DOI for title: RWO-Sampling: A random walk over-sampling approach to imbalanced data classification
- 10.1007/s10618-012-0295-5 may be a valid DOI for title: Training and assessing classification rules with imbalanced data
- 10.1109/tit.1968.1054155 may be a valid DOI for title: The condensed nearest neighbor rule (Corresp.)
- 10.1016/j.knosys.2013.01.018 may be a valid DOI for title: Analysing the classification of imbalanced data-sets with multiple classes: Binarization techniques and ad-hoc approaches

INVALID DOIs

- https://doi.org/10.1016/j.neucom.2019.06.100 is INVALID because of 'https://doi.org/' prefix

@ArneTillmann
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I am very happy with the quality of the submitted project and left my comments. As I am neither familiar with Julia, nor with the implementation of presented algorithms I rely somewhat on @sylvaticus review. If you, @jbytecode, are not satisfied with my review, please let me know as this is my first time :) Thank you very much

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@ArneTillmann - Thank you for your review. Please set on all of the tasks (check boxes) when the corresponding job is completed.

@EssamWisam - Please address all of the issues created in the target repository. After finishing your work, please ask the corresponding reviewers if it is okay to close the issue. Please ping me after you've done with all of the stuff.

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Done! version is now v0.1.6

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@editorialbot set 10.5281/zenodo.10823254 as archive

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Done! archive is now 10.5281/zenodo.10823254

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jbytecode commented Mar 17, 2024

@EssamWisam - The Zenodo archive is related to the v1 but the reported tag is v1.0.6. Please fix the zenodo entry.

@EssamWisam
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@jbytecode Fixed it.

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Now please have a full proof read of the manuscript and fix any issue if exists. Please, ping me when you have done with it.

@EssamWisam
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EssamWisam commented Mar 17, 2024

@jbytecode Done with that. Fixed a few very minor English issues and added a missing citation for the MLJ package.

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@editorialbot generate pdf

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

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@editorialbot check references

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

OK DOIs

- 10.1137/141000671 is OK
- 10.1007/978-3-540-75171-7_2 is OK
- 10.1109/ICOACS.2016.7563084 is OK
- 10.1109/TSMCB.2008.2007853 is OK
- 10.13154/tches.v2019.i1.209-237 is OK
- 10.1613/jair.953 is OK
- 10.1007/11538059_91 is OK
- 10.1016/j.inffus.2013.12.003 is OK
- 10.1007/s10618-012-0295-5 is OK
- 10.1016/j.ins.2017.05.008 is OK
- 10.1109/TIT.1968.1054155 is OK
- 10.1016/j.neucom.2019.06.100 is OK
- 10.1016/J.KNOSYS.2013.01.018 is OK
- 10.21105/joss.02704 is OK

MISSING DOIs

- No DOI given, and none found for title: Classification with class imbalance problem: A rev...
- No DOI given, and none found for title: Addressing the Curse of Imbalanced Training Sets: ...
- No DOI given, and none found for title: Imbalanced-learn: A Python Toolbox to Tackle the C...
- No DOI given, and none found for title: The Rise of Julia

INVALID DOIs

- None

@jbytecode
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@EssamWisam - I think we have nothing to do with those missing DOIs, right?

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@editorialbot generate pdf

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

@EssamWisam
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EssamWisam commented Mar 18, 2024

@EssamWisam - I think we have nothing to do with those missing DOIs, right?

Yes, unlike other articles, I couldn't find that they have a DOI.

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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

- 10.1137/141000671 is OK
- 10.1007/978-3-540-75171-7_2 is OK
- 10.1109/ICOACS.2016.7563084 is OK
- 10.1109/TSMCB.2008.2007853 is OK
- 10.13154/tches.v2019.i1.209-237 is OK
- 10.1613/jair.953 is OK
- 10.1007/11538059_91 is OK
- 10.1016/j.inffus.2013.12.003 is OK
- 10.1007/s10618-012-0295-5 is OK
- 10.1016/j.ins.2017.05.008 is OK
- 10.1109/TIT.1968.1054155 is OK
- 10.1016/j.neucom.2019.06.100 is OK
- 10.1016/J.KNOSYS.2013.01.018 is OK
- 10.21105/joss.02704 is OK

MISSING DOIs

- No DOI given, and none found for title: Classification with class imbalance problem: A rev...
- No DOI given, and none found for title: Addressing the Curse of Imbalanced Training Sets: ...
- No DOI given, and none found for title: Imbalanced-learn: A Python Toolbox to Tackle the C...
- No DOI given, and none found for title: The Rise of Julia

INVALID DOIs

- None

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5143, 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 Mar 18, 2024
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arfon commented Mar 18, 2024

@editorialbot accept

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

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

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

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

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Wisam
  given-names: Essam
  orcid: "https://orcid.org/0009-0009-1198-7166"
- family-names: Blaom
  given-names: Anthony
  orcid: "https://orcid.org/0000-0001-6689-886X"
doi: 10.5281/zenodo.10823254
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Wisam
    given-names: Essam
    orcid: "https://orcid.org/0009-0009-1198-7166"
  - family-names: Blaom
    given-names: Anthony
    orcid: "https://orcid.org/0000-0001-6689-886X"
  date-published: 2024-03-18
  doi: 10.21105/joss.06310
  issn: 2475-9066
  issue: 95
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6310
  title: "Imbalance: A comprehensive multi-interface Julia toolbox to
    address class imbalance"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06310"
  volume: 9
title: "Imbalance: A comprehensive multi-interface Julia toolbox to
  address class imbalance"

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.06310 joss-papers#5144
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06310
  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 Mar 18, 2024
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arfon commented Mar 18, 2024

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

@EssamWisam – your paper is now accepted and published in JOSS ⚡🚀💥

@arfon arfon closed this as completed Mar 18, 2024
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🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.06310/status.svg)](https://doi.org/10.21105/joss.06310)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06310">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06310/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06310/status.svg
   :target: https://doi.org/10.21105/joss.06310

This is how it will look in your documentation:

DOI

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