[REVIEW]: Annotate-Lab: Simplifying Image Annotation #7210

editorialbot · 2024-09-10T10:30:21Z

Submitting author: @sumn2u (Suman Kunwar)
Repository: https://github.com/sumn2u/annotate-lab
Branch with paper.md (empty if default branch): paper
Version: 2.0.3
Editor: @boisgera
Reviewers: @jpcbertoldo, @PetervanLunteren
Archive: 10.5281/zenodo.14147025

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/7d9f9acf52f04d124399f26b37e6ab1a/status.svg)](https://joss.theoj.org/papers/7d9f9acf52f04d124399f26b37e6ab1a)

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

@jpcbertoldo & @PetervanLunteren, 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 @boisgera 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 @PetervanLunteren

📝 Checklist for @jpcbertoldo

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-09-10T10:30:24Z

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editorialbot · 2024-09-10T10:30:39Z

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

✅ OK DOIs

- 10.1145/3343031.3350535 is OK
- 10.5281/ZENODO.11543564 is OK
- 10.1109/I2C2.2017.8321819 is OK
- 10.1007/s11042-022-12100-1 is OK
- 10.48550/ARXIV.2401.01454 is OK
- 10.48550/ARXIV.2304.02643 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-09-10T10:30:45Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.14 s (1067.4 files/s, 242558.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                             3              0              0          18828
JSX                             45            360             64           6152
JavaScript                      76            512            189           5362
Python                           8            303            138           1605
Markdown                         7            204              0            745
YAML                             4             14              4             93
TeX                              1              7              0             81
HTML                             1              3             22             21
TOML                             1              0              0             20
Dockerfile                       2             14              0             18
CSS                              1              0              0              6
CSV                              4              0              0              4
-------------------------------------------------------------------------------
SUM:                           153           1417            417          32935
-------------------------------------------------------------------------------

Commit count by author:

   293	sumn2u
   192	seveibar
    71	Severin Ibarluzea
    47	semantic-release-bot
    13	Oleh Yasenytsky
    11	Suman Kunwar
    10	snyk-bot
     7	Henry LIANG
     7	Tamay Eser Uysal
     6	Emiliano Castellano
     5	DQ4443
     5	sreevardhanreddi
     3	Mews
     3	Mykyta Holubakha
     3	OmG2011
     3	dependabot[bot]
     2	Josep de Cid
     2	Katsuhisa Yuasa
     2	Mohammed Eldadah
     2	linyers
     1	HoangHN
     1	Hummer12007
     1	Joey Figaro
     1	Puskuruk
     1	Shahidul Islam Majumder
     1	ThibautGeriz
     1	beru
     1	harith-hacky03

editorialbot · 2024-09-10T10:30:49Z

Paper file info:

📄 Wordcount for paper.md is 1018

✅ The paper includes a Statement of need section

editorialbot · 2024-09-10T10:30:51Z

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot · 2024-09-10T10:31:47Z

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

editorialbot · 2024-09-16T15:30:54Z

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

✅ OK DOIs

- 10.1145/3343031.3350535 is OK
- 10.5281/ZENODO.11543564 is OK
- 10.1109/I2C2.2017.8321819 is OK
- 10.1007/s11042-022-12100-1 is OK
- 10.48550/ARXIV.2401.01454 is OK
- 10.48550/ARXIV.2304.02643 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

PetervanLunteren · 2024-10-09T11:18:25Z

Review checklist for @PetervanLunteren

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/sumn2u/annotate-lab?
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 (@sumn2u) 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?

PetervanLunteren · 2024-10-09T12:44:33Z

Hi @sumn2u,

I’ve taken a close look at your tool, and I want to commend you on the impressive work and extensive documentation. I have gone through the reviewer’s checklist and the Review criteria, and I noticed a few minor points that I would appreciate some clarification on:

Annotation project options: At the start of an annotation project, users can choose between “Image classification” and “Image segmentation.” I’d like to point out that “Image classification” typically refers to assigning a single label to an entire image, while the functionality of placing bounding boxes, circles, or polygons is more accurately described as “Object detection.” Would it be possible to revise this terminology to better reflect this distinction?
User experience for annotating multiple images: In scenarios where users want to annotate multiple images, particularly in bulk (potentially thousands), implementing shortcut keys could significantly enhance the user experience. During my testing, I found that the only way to move to the next image was by clicking on it in the list. Did I overlook any existing shortcuts, or is there a plan to introduce this feature in future updates?
Comparison with similar tools: In the manuscript, you mention other similar software tools such as Label Studio, VGG, COCO Annotator, Super Annotate, and CVAT. However, I found it challenging to pinpoint the main differences between your tool and these others. Is the primary distinguishing factor that your tool is open-source and community-driven? It might be helpful to elaborate on this in the manuscript to highlight what sets your tool apart.

Thank you for your time, and I look forward to your responses!

sumn2u · 2024-10-09T14:20:31Z

Hi @PetervanLunteren , Thank you for your review and for your kind words! I truly appreciate your thoughtful feedback on both the tool and its documentation. Here's answer to your questions:

Annotation project options: At the start of an annotation project, users can choose between “Image classification” and “Image segmentation.” I’d like to point out that “Image classification” typically refers to assigning a single label to an entire image, while the functionality of placing bounding boxes, circles, or polygons is more accurately described as “Object detection.” Would it be possible to revise this terminology to better reflect this distinction?

It makes sense to update the terminology, as it better conveys the intended functionality. I’ve made the necessary changes and updated the repository, documentation, and manuscript accordingly. It looks like this now.

User experience for annotating multiple images: In scenarios where users want to annotate multiple images, particularly in bulk (potentially thousands), implementing shortcut keys could significantly enhance the user experience. During my testing, I found that the only way to move to the next image was by clicking on it in the list. Did I overlook any existing shortcuts, or is there a plan to introduce this feature in future updates?

We don’t have this feature yet, but we plan to add it in the near future.

Comparison with similar tools: In the manuscript, you mention other similar software tools such as Label Studio, VGG, COCO Annotator, Super Annotate, and CVAT. However, I found it challenging to pinpoint the main differences between your tool and these others. Is the primary distinguishing factor that your tool is open-source and community-driven? It might be helpful to elaborate on this in the manuscript to highlight what sets your tool apart.

Yes, our tool is indeed open-source and community-driven. Moreover, our client-server architecture enhances flexibility and scalability, which distinguishes us from other annotation tools. I have added this section in our manuscript to provide a clearer comparison and to emphasize the unique features of our tool.

Please let me know if anything is unclear.

sumn2u · 2024-10-09T14:21:13Z

@editorialbot generate pdf

editorialbot · 2024-10-09T14:22:48Z

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

PetervanLunteren · 2024-10-10T12:17:32Z

@sumn2u Thank you for the quick response! In my opinion, with the revisions and answers, the submission meets the acceptance criteria.

boisgera · 2024-10-16T20:48:38Z

Thanks a lot for your great review @PetervanLunteren! 🙏

And thank you @sumn2u for your reactivity 👍

@jpcbertoldo should be able to start his own review pretty soon.

sumn2u · 2024-10-30T10:48:46Z

Hi @boisgera, Do you happen to know when the next review will begin? I was under the impression that the entire review process would start in about seven weeks.

jpcbertoldo · 2024-10-30T10:52:39Z

Hi @boisgera, Do you happen to know when the next review will begin? I was under the impression that the entire review process would start in about seven weeks.

Hi @sumn2u, I apologize for delaying this, I had some other things to prioritize, but I will be able to deal with this in a few days. So sorry for taking long @boisgera !

sumn2u · 2024-11-06T13:01:49Z

Hi @jpcbertoldo, when you have a moment, would you be able to review this? Thanks!

jpcbertoldo · 2024-11-07T20:50:54Z

Hi @jpcbertoldo, when you have a moment, would you be able to review this? Thanks!

doing it tomorrow!

jpcbertoldo · 2024-11-08T16:44:18Z

Review checklist for @jpcbertoldo

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/sumn2u/annotate-lab?
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 (@sumn2u) 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?

sumn2u · 2024-11-08T20:47:52Z

Thank you, @jpcbertoldo, for the thorough review. @boisgera, I believe we're now ready to move on to the next step.

editorialbot · 2024-11-13T16:50:04Z

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

boisgera · 2024-11-13T17:21:49Z

Hi @sumn2u,

I made a final pass on your paper draft and except for a very small typo, I have no comment to make. 👍

Could you adress the "Additional Author Tasks" in your post-review list?

I'll address the rest of my own tasks as soon as you give me your archive DOI and version number.

Best regards,

Sébastien

sumn2u · 2024-11-13T17:39:03Z

@boisgera I checked all points. Here are the information:

Double check authors and affiliations (including ORCIDs).
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Release Version: 2.0.3
Archive the release on Zenodo/figshare/etc. and post the DOI here.
Ensure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Verify that the license listed for the archive is the same as the software license.

boisgera · 2024-11-13T18:04:53Z

Hi again @sumn2u!

Could you please edit your Zenodo repo. to:

make the title match exactly the title of your JOSS paper ("Annotate-Lab: Simplifying Image Annotation")
list only yourself as the author (instead of I guess all contributors to the project; there is an other field for contributors that you can use AFAICT),
register your ORCID id with Zenodo (it should appear as a green badge)
make your Zenodo license matches your GitHub project license (MIT).

If you need an example, use e.g. https://doi.org/10.5281/zenodo.13922881

sumn2u · 2024-11-13T18:36:21Z

Sure @boisgera. I made all the requested changes.

make the title match exactly the title of your JOSS paper ("Annotate-Lab: Simplifying Image Annotation")
list only yourself as the author (instead of I guess all contributors to the project; there is an other field for contributors that you can use AFAICT),
register your ORCID id with Zenodo (it should appear as a green badge)
make your Zenodo license match your GitHub project license (MIT).

boisgera · 2024-11-14T10:06:23Z

@editorialbot set 10.5281/zenodo.14147025 as archive

editorialbot · 2024-11-14T10:06:26Z

Done! archive is now 10.5281/zenodo.14147025

boisgera · 2024-11-14T10:06:49Z

@editorialbot set 2.0.3 as version

editorialbot · 2024-11-14T10:06:52Z

Done! version is now 2.0.3

boisgera · 2024-11-14T10:08:50Z

@editorialbot generate pdf

editorialbot · 2024-11-14T10:10:28Z

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

boisgera · 2024-11-14T10:23:44Z

Great, this is coming along nicely! I am ready to recommend acceptance; the Editor in Chief will then take over the process.

Thanks a lot to Peter and João (@PetervanLunteren, @jpcbertoldo) for reviewing the project; your work is greatly appreciated! 🙏. And thanks to you Suman (@sumn2u) for this really nice project and your reactivity during the review. 🙏

👋

boisgera · 2024-11-14T10:24:00Z

@editorialbot recommend-accept

editorialbot · 2024-11-14T10:24:03Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-11-14T10:24:17Z

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

✅ OK DOIs

- 10.1145/3343031.3350535 is OK
- 10.5281/ZENODO.11543564 is OK
- 10.1109/I2C2.2017.8321819 is OK
- 10.1007/s11042-022-12100-1 is OK
- 10.48550/ARXIV.2401.01454 is OK
- 10.48550/ARXIV.2304.02643 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-11-14T10:25:53Z

👋 @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#6136, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

crvernon · 2024-11-14T13:01:02Z

editorialbot · 2024-11-14T13:02:59Z

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

crvernon · 2024-11-14T13:31:30Z

@editorialbot accept

editorialbot · 2024-11-14T13:31:32Z

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

editorialbot · 2024-11-14T13:38:31Z

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: Kunwar
  given-names: Suman
  orcid: "https://orcid.org/0000-0002-4345-1050"
doi: 10.5281/zenodo.14147025
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Kunwar
    given-names: Suman
    orcid: "https://orcid.org/0000-0002-4345-1050"
  date-published: 2024-11-14
  doi: 10.21105/joss.07210
  issn: 2475-9066
  issue: 103
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7210
  title: "Annotate-Lab: Simplifying Image Annotation"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07210"
  volume: 9
title: "Annotate-Lab: Simplifying Image Annotation"

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 · 2024-11-14T13:38:36Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-11-14T13:38:37Z

🦋🦋🦋 👉 Bluesky post for this paper 👈 🦋🦋🦋

editorialbot · 2024-11-14T13:38:37Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.07210 joss-papers#6138
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07210
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

crvernon · 2024-11-14T13:39:59Z

🥳 Congratulations on your new publication @sumn2u! Many thanks to @boisgera for editing and @jpcbertoldo and @PetervanLunteren for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Please consider becoming a reviewer for JOSS if you are not already: https://reviewers.joss.theoj.org/join

editorialbot · 2024-11-14T13:40:02Z

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

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

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.07210/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.07210/status.svg
   :target: https://doi.org/10.21105/joss.07210

This is how it will look in your documentation:

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editorialbot added JavaScript Python review TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning labels Sep 10, 2024

editorialbot assigned boisgera Sep 10, 2024

editorialbot mentioned this issue Sep 10, 2024

[PRE REVIEW]: Annotate-Lab: Simplifying Image Annotation #7065

Closed

This was referenced Nov 13, 2024

Download sumn2u/annotate-lab#206

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editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Nov 14, 2024

editorialbot added accepted published Papers published in JOSS labels Nov 14, 2024

crvernon closed this as completed Nov 14, 2024

[REVIEW]: Annotate-Lab: Simplifying Image Annotation #7210

[REVIEW]: Annotate-Lab: Simplifying Image Annotation #7210

Comments

editorialbot commented Sep 10, 2024 • edited Loading

Status

Reviewer instructions & questions

Checklists

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PetervanLunteren commented Oct 9, 2024 • edited Loading

Review checklist for @PetervanLunteren

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

PetervanLunteren commented Oct 9, 2024

sumn2u commented Oct 9, 2024 • edited Loading

sumn2u commented Oct 9, 2024

editorialbot commented Oct 9, 2024

PetervanLunteren commented Oct 10, 2024

boisgera commented Oct 16, 2024

sumn2u commented Oct 30, 2024

jpcbertoldo commented Oct 30, 2024

sumn2u commented Nov 6, 2024

jpcbertoldo commented Nov 7, 2024

jpcbertoldo commented Nov 8, 2024 • edited Loading

Review checklist for @jpcbertoldo

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

sumn2u commented Nov 8, 2024

editorialbot commented Nov 13, 2024

boisgera commented Nov 13, 2024

sumn2u commented Nov 13, 2024

boisgera commented Nov 13, 2024 • edited Loading

sumn2u commented Nov 13, 2024

boisgera commented Nov 14, 2024

editorialbot commented Nov 14, 2024

boisgera commented Nov 14, 2024

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boisgera commented Nov 14, 2024

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