[REVIEW]: Learning from Crowds with Crowd-Kit

[editorialbot]

Submitting author: @dustalov (Dmitry Ustalov)
Repository: https://github.com/Toloka/crowd-kit
Branch with paper.md (empty if default branch):
Version: v1.2.1
Editor: @arfon
Reviewers: @jorgedch, @Mind-the-Cap, @mitchellg
Archive: 10.5281/zenodo.10934189

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/2684e43cf35482812ae02396b3312fad/status.svg)](https://joss.theoj.org/papers/2684e43cf35482812ae02396b3312fad)

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

@jorgedch, 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 @arfon 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 @Mind-the-Cap

📝 Checklist for @mitchellg

📝 Checklist for @jorgedch

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.16 s (632.8 files/s, 188051.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          78           1703           2247           6615
Jupyter Notebook                 6              0          15669           2141
YAML                            10              5              3            737
TeX                              1             37              0            425
Markdown                         5            120              0            310
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                           101           1865          17919          10231
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2354

[editorialbot]

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

OK DOIs

- 10.1145/1866029.1866078 is OK
- 10.2307/2334029 is OK
- 10.1145/2433396.2433420 is OK
- 10.1609/aaai.v35i7.16730 is OK
- 10.2307/2346806 is OK
- 10.1109/ASRU.1997.659110 is OK
- 10.1162/neco.1997.9.8.1735 is OK
- 10.1287/opre.2013.1235 is OK
- 10.18653/v1/D19-5904 is OK
- 10.1145/3397271.3401239 is OK
- 10.1007/978-3-319-10602-1_48 is OK
- 10.17863/CAM.45912 is OK
- 10.1109/ICASSP.2010.5494979 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.1609/aaai.v32i1.11506 is OK
- 10.1007/s11263-016-0940-3 is OK
- 10.1609/hcomp.v1i1.13088 is OK
- 10.14778/3055540.3055547 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[arfon]

@jorgedch – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing:

@editorialbot generate my checklist

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/6227 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

Also, noting here that @jorgedch believes it will take them more like 6-8 weeks to complete their review.

[arfon]

@NeoTheThird @Mind-the-Cap - 👋 would you be willing to review this submission for JOSS? The submission under consideration is Learning from Crowds with Crowd-Kit

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. You can learn more about the process in these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Based on your experience, we think you might be able to provide a great review of this submission. Please let me know if you think you can help us out!

Many thanks
Arfon

[Mind-the-Cap]

Hi, very happy to review this submission, which is connected to my own research!

[arfon]

@editorialbot add @Mind-the-Cap as reviewer

@Mind-the-Cap – amazing, thank you! I'll go ahead and add you as a reviewer now, please take a look at the instructions at the top of the thread to get you started.

[editorialbot]

@Mind-the-Cap added to the reviewers list!

[Mind-the-Cap]

Review checklist for @Mind-the-Cap

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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/Toloka/crowd-kit?
• 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 (@dustalov) 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?

[Mind-the-Cap]

Hi @dustalov, I see Boris Tseitlin in the paper authors list but I don't see his account in the contributors list https://github.com/Toloka/crowd-kit/graphs/contributors

I suspect some code has been copied from an internal repo, would you be able to confirm that or to give me the explanation? Many thanks!

[dustalov]

Hi @Mind-the-Cap, Boris and Nikita worked on crowd-kit[learning] subpackage together in an internal repo at Toloka (Yandex Toloka at the time). Then, the corresponding code was open-sourced by Nikita.

[mitchellg]

@arfon has asked me to affirm here that I'm willing to be a reviewer. I affirm!

[arfon]

@editorialbot add @mitchellg as reviewer

[editorialbot]

@mitchellg added to the reviewers list!

[arfon]

@mitchellg – apologies for dropping the ball here and not getting you added sooner. Please see the instructions above and let me know if you have any questions. Thanks again!

[mitchellg]

Review checklist for @mitchellg

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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/Toloka/crowd-kit?
• 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 (@dustalov) 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?

[mitchellg]

This is mostly looking good! The one area in the checklist that I couldn't find was "clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support".

[dustalov]

Hi @mitchellg, thank you!

1. We have a CONTRIBUTING.md document inside the repository, but README.md does not mention it (however, it is present in issue/PR templates). We can state and link it explicitly.

2 & 3. We accept feature requests and issue reports and offer help via GitHub Issues. I'll make an update to the documentation.

Would these steps address your comments?

[mitchellg]

Thanks! Yup that seems like enough to check the box. Done!

[dustalov]

Thank you!

[arfon]

@dustalov – looks like we're very close to being done here. I will circle back here next week, but in the meantime, please give your own paper a final read to check for any potential typos etc.

After that, could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

• The title of the archive is the same as the JOSS paper title
• That the authors of the archive are the same as the JOSS paper authors
• I can then move forward with accepting the submission.

[dustalov]

@arfon: sure, will do. I'll post an update here when we're ready.

[dustalov]

@editorialbot generate pdf

[editorialbot]

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

[dustalov]

@editorialbot generate pdf

[dustalov]

@arfon: we read the paper, released the new version to PyPI, and uploaded the source archive to Zenodo.

• https://pypi.org/project/crowd-kit/1.3.0/
• https://zenodo.org/records/10934189

[editorialbot]

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

[arfon]

@editorialbot set 10.5281/zenodo.10934189 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10934189

[arfon]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

👋 @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#5221, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[editorialbot]

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

OK DOIs

- 10.1145/1866029.1866078 is OK
- 10.2307/2334029 is OK
- 10.1145/2433396.2433420 is OK
- 10.1609/aaai.v35i7.16730 is OK
- 10.2307/2346806 is OK
- 10.1109/ASRU.1997.659110 is OK
- 10.1162/neco.1997.9.8.1735 is OK
- 10.1287/opre.2013.1235 is OK
- 10.18653/v1/D19-5904 is OK
- 10.1145/3397271.3401239 is OK
- 10.1007/978-3-319-10602-1_48 is OK
- 10.17863/CAM.45912 is OK
- 10.1109/ICASSP.2010.5494979 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.1609/aaai.v32i1.11506 is OK
- 10.1007/s11263-016-0940-3 is OK
- 10.1609/hcomp.v1i1.13088 is OK
- 10.1609/aaai.v37i13.26886 is OK
- 10.14778/3055540.3055547 is OK

MISSING DOIs

- No DOI given, and none found for title: Overview of the TREC 2010 Relevance Feedback Track...
- No DOI given, and none found for title: Aggregation of pairwise comparisons with reduction...
- No DOI given, and none found for title: Improving Web Ranking with Human-in-the-Loop: Meth...
- No DOI given, and none found for title: Learning Whom to Trust with MACE
- No DOI given, and none found for title: Quality Evaluation Methods for Crowdsourced Image ...
- No DOI given, and none found for title: Content Analysis: An Introduction to Its Methodolo...
- No DOI given, and none found for title: Learning Multiple Layers of Features from Tiny Ima...
- No DOI given, and none found for title: RoBERTa: A Robustly Optimized BERT Pretraining App...
- No DOI given, and none found for title: Adversarial Crowdsourcing Through Robust Rank-One ...
- No DOI given, and none found for title: Learning Word Vectors for Sentiment Analysis
- No DOI given, and none found for title: CrowdSpeech and Vox DIY: Benchmark Dataset for Cro...
- No DOI given, and none found for title: IMDB-WIKI-SbS: An Evaluation Dataset for Crowdsour...
- No DOI given, and none found for title: PyTorch: An Imperative Style, High-Performance Dee...
- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
- No DOI given, and none found for title: spark-crowd: A Spark Package for Learning from Cro...
- No DOI given, and none found for title: Very Deep Convolutional Networks for Large-Scale I...
- No DOI given, and none found for title: Toloka Public Datasets for Machine Learning and Da...
- No DOI given, and none found for title: Calculating Worker Agreement with Aggregate (Wawa)
- No DOI given, and none found for title: Whose Vote Should Count More: Optimal Integration ...
- No DOI given, and none found for title: CEKA: A Tool for Mining the Wisdom of Crowds

INVALID DOIs

- None

[arfon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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: Ustalov
  given-names: Dmitry
  orcid: "https://orcid.org/0000-0002-9979-2188"
- family-names: Pavlichenko
  given-names: Nikita
  orcid: "https://orcid.org/0000-0002-7330-393X"
- family-names: Tseitlin
  given-names: Boris
  orcid: "https://orcid.org/0000-0001-8553-4260"
contact:
- family-names: Ustalov
  given-names: Dmitry
  orcid: "https://orcid.org/0000-0002-9979-2188"
doi: 10.5281/zenodo.10934189
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Ustalov
    given-names: Dmitry
    orcid: "https://orcid.org/0000-0002-9979-2188"
  - family-names: Pavlichenko
    given-names: Nikita
    orcid: "https://orcid.org/0000-0002-7330-393X"
  - family-names: Tseitlin
    given-names: Boris
    orcid: "https://orcid.org/0000-0001-8553-4260"
  date-published: 2024-04-06
  doi: 10.21105/joss.06227
  issn: 2475-9066
  issue: 96
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6227
  title: Learning from Crowds with Crowd-Kit
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06227"
  volume: 9
title: Learning from Crowds with Crowd-Kit

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.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06227 joss-papers#5222
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06227
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@jorgedch, @Mind-the-Cap, @mitchellg – many thanks for your reviews here! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

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

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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

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[![DOI](https://joss.theoj.org/papers/10.21105/joss.06227/status.svg)](https://doi.org/10.21105/joss.06227)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.06227/status.svg" alt="DOI badge" >
</a>

reStructuredText:
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   :target: https://doi.org/10.21105/joss.06227

This is how it will look in your documentation:

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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:

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[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

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[dustalov]

@editorialbot generate preprint

[editorialbot]

📄 Preprint file created: Find it here in the Artifacts list 📄

[dustalov]

We have updated the references and citations in our repositories. Also, I updated the arXiv preprint.

@arfon, @jorgedch, @Mind-the-Cap, @mitchellg: thank you very much! I wish more journals follow the JOSS model.