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[REVIEW]: Jury: A Comprehensive Evaluation Toolkit #6452

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editorialbot opened this issue Mar 7, 2024 · 78 comments
Closed

[REVIEW]: Jury: A Comprehensive Evaluation Toolkit #6452

editorialbot opened this issue Mar 7, 2024 · 78 comments
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accepted published Papers published in JOSS Python 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 Mar 7, 2024

Submitting author: @devrimcavusoglu (Devrim Çavuşoğlu)
Repository: https://github.com/obss/jury
Branch with paper.md (empty if default branch): joss-paper
Version: v2.3.1
Editor: @crvernon
Reviewers: @evamaxfield, @KennethEnevoldsen
Archive: 10.5281/zenodo.11170894

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/a41a840a782ead74b46ac05699ce6eed"><img src="https://joss.theoj.org/papers/a41a840a782ead74b46ac05699ce6eed/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/a41a840a782ead74b46ac05699ce6eed/status.svg)](https://joss.theoj.org/papers/a41a840a782ead74b46ac05699ce6eed)

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

@evamaxfield & @KennethEnevoldsen, 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 @crvernon 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 @evamaxfield

📝 Checklist for @KennethEnevoldsen

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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 1.90  T=0.09 s (1606.5 files/s, 135681.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         109           1402           2189           5368
JSON                            22              0              0           1713
Markdown                         4            101              0            279
TeX                              1              7              0            140
Jupyter Notebook                 1              0            399            111
YAML                             2             15              1             81
TOML                             1              1              0             17
-------------------------------------------------------------------------------
SUM:                           140           1526           2589           7709
-------------------------------------------------------------------------------

Commit count by author:

    62	Devrim
    19	devrimcavusoglu
     7	fcakyon
     5	Ulaş "Sophylax" Sert
     1	Ikko Eltociear Ashimine
     1	Nish
     1	Zafer Cavdar
     1	cemilcengiz
     1	devrim.cavusoglu

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

OK DOIs

- 10.18653/v1/W18-5446 is OK
- 10.18653/v1/N19-1423 is OK
- 10.18653/v1/2021.emnlp-demo.21 is OK
- 10.3115/1073083.1073135 is OK

MISSING DOIs

- No DOI given, and none found for title: Relevance of Unsupervised Metrics in Task-Oriented...
- No DOI given, and none found for title: Findings of the 2020 Conference on Machine Transla...
- No DOI given, and none found for title: XLNet: Generalized Autoregressive Pretraining for ...

INVALID DOIs

- None

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Paper file info:

📄 Wordcount for paper.md is 771

✅ The paper includes a Statement of need section

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License info:

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

@crvernon
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crvernon commented Mar 7, 2024

👋 @devrimcavusoglu , @evamaxfield , and @KennethEnevoldsen - 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.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. 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 #6452 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.

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

@evamaxfield
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evamaxfield commented Mar 8, 2024

Review checklist for @evamaxfield

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/obss/jury?
  • 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 (@devrimcavusoglu) 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?

@evamaxfield
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@crvernon I will start checking these off tomorrow and likely finish next week unless I run into any major issues.

@KennethEnevoldsen
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KennethEnevoldsen commented Mar 8, 2024

Review checklist for @KennethEnevoldsen

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/obss/jury?
  • 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 (@devrimcavusoglu) 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?

@KennethEnevoldsen
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@devrimcavusoglu this looks like a wonderful work, which I am sure will be beneficial to many people (seems like it already is). Overall I was able to run both the examples, tests and installation without issues and found that almost all of the information (required and desired) was available.

I have a few things I was hoping you could clear up:

  • it seems like there are no guidelines for how to report issues or seek support. I would add those in (it can simply be a table e.g. as seen here.
  • Have the metrics been evaluated against the implementation of e.g. Huggingface metrics (where meaningful)?

@evamaxfield
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@devrimcavusoglu seconding that this is really great and I will likely start using it in some of my own work :)

Some comments:

  1. (Not required but I tend to think its nice) I tried BERTScore in addition to the defaults and it asked me to install bert-score which I completely understand not including as a default install. I generally like it when packages provide an extra install for the required extra dependency(ies). For example pip install jury[bertscore]. It also allows you to put version pins on the extra dependencies to make sure that the version also works with your software.
  2. Also seconding that I didn't see any community guidelines or other documentation specifically around how to contribute or ways to contribute. Please add those.
  3. I am fine with not having a full documentation page or website but I do think it would be nice to have. At the very least can you include a link to the examples notebook somewhere in the README as "See more examples here" or something. (Although I guess this might be a question for @crvernon -- there is API docs in the code but to my knowledge I didn't see a documentation website where those API docs can be easily seen, is this an issue? I am fine with it because I am fine with digging through the source code but for others / general dev experience it may be a nice to add.)

@crvernon
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@evamaxfield to your question:

I am fine with not having a full documentation page or website but I do think it would be nice to have. At the very least can you include a link to the examples notebook somewhere in the README as "See more examples here" or something. (Although I guess this might be a question for @crvernon -- there is API docs in the code but to my knowledge I didn't see a documentation website where those API docs can be easily seen, is this an issue? I am fine with it because I am fine with digging through the source code but for others / general dev experience it may be a nice to add.)

We don't require documentation to be hosted separately; though it is a nice complement that many reviewers have started to point out. I would say this falls under the category of suggestion but not requirement as long as the codebase has the necessary documentation that is visible to the user. Thanks!

@evamaxfield
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Sounds good! Then my comment resolves to simply adding a link to the examples notebook.

@devrimcavusoglu
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@KennethEnevoldsen @evamaxfield Thank you for the reviews and feedback. Apologizes for a late response. I will try to respond to items that you mentioned.

Response to @KennethEnevoldsen:

  • it seems like there are no guidelines for how to report issues or seek support. I would add those in (it can simply be a table e.g. as seen here.

We did not actually documented this as we think for most of the open-source software the Github platform is the de facto standard for raising issues, bug reports, discussions and etc. If we were using another platform for those stuff we could've mentioned it which is reasonable; however, utilizing the standard does not necessitate this as it is the standard and easy to be grasped by all users. Nonetheless, we particularly included templates for the issues (e.g. bug reports, feature/metric request).

  • Have the metrics been evaluated against the implementation of e.g. Huggingface metrics (where meaningful)?

Yes, there is a comparison in the paper, particularly Fig. 2. Jury is compared to HF metrics package in two different perspectives, input size and number of metrics.

Response to @evamaxfield:

Sounds good! Then my comment resolves to simply adding a link to the examples notebook.

Actually, we do have link to the notebook as a Google Colab link although it's not expressed and written down, for example, in a table in README. This way we think is more user friendly as the users can directly engage with the package and play around.

image

(Not required but I tend to think its nice) I tried BERTScore in addition to the defaults and it asked me to install bert-score which I completely understand not including as a default install. I generally like it when packages provide an extra install for the required extra dependency(ies). For example pip install jury[bertscore]. It also allows you to put version pins on the extra dependencies to make sure that the version also works with your software.

That is a really good suggestion, we may definitely plan to add this feature in upcoming versions.

@KennethEnevoldsen
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We did not actually documented this as we think for most of the open-source software the Github platform is the de facto standard for raising issues, bug reports, discussions and etc. If we were using another platform for those stuff we could've mentioned it which is reasonable; however, utilizing the standard does not necessitate this as it is the standard and easy to be grasped by all users. Nonetheless, we particularly included templates for the issues (e.g. bug reports, feature/metric request).

I am perfectly fine with this as long as the editors (@crvernon) agree. I will leave it unchecked on the checklist.

Yes, there is a comparison in the paper, particularly Fig. 2. Jury is compared to HF metrics package in two different perspectives, input size and number of metrics.

Thanks for the clarification

I believe this clarifies all my points.

@evamaxfield
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I definitely missed the open in collab button. I will check that off and the contributing section.

All good from my review :)

@crvernon
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Per @KennethEnevoldsen 's comment...

We did not actually documented this as we think for most of the open-source software the Github platform is the de facto standard for raising issues, bug reports, discussions and etc. If we were using another platform for those stuff we could've mentioned it which is reasonable; however, utilizing the standard does not necessitate this as it is the standard and easy to be grasped by all users. Nonetheless, we particularly included templates for the issues (e.g. bug reports, feature/metric request).

I am perfectly fine with this as long as the editors (@crvernon) agree. I will leave it unchecked on the checklist.

I do believe there needs to be a bit more here to meet the guidelines for:

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

Even though I do agree that many users may be aware of what issues and pull requests are, our papers go out to a general audience. Thus, questions and contributions may not always come in the form of code modifications/additions from engineers, but from program managers, etc. who seek clarity on the purpose of the software in the context of their mission. These audiences often do not have familiarity with how GitHub works. So I do advise @devrimcavusoglu to be more descriptive for how to contribute. Feel free to check out previous JOSS publications for some examples. Thanks!

@devrimcavusoglu
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Even though I do agree that many users may be aware of what issues and pull requests are, our papers go out to a general audience. Thus, questions and contributions may not always come in the form of code modifications/additions from engineers, but from program managers, etc. who seek clarity on the purpose of the software in the context of their mission. These audiences often do not have familiarity with how GitHub works. So I do advise @devrimcavusoglu to be more descriptive for how to contribute. Feel free to check out previous JOSS publications for some examples. Thanks!

@crvernon I see the point, thanks for clarfying. I will make appropriate updates in the repo ASAP and will ping you then.

@crvernon
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crvernon commented Apr 3, 2024

👋 @devrimcavusoglu, @evamaxfield, and @KennethEnevoldsen

I'm just checking in to see how things are going. I believe @evamaxfield has finished their review and there were a few things left to do pertaining to the review from @KennethEnevoldsen. Will you please provide a short update to how things are going? Thanks!

@KennethEnevoldsen
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With the addition of community guidelines I don't believe there is any additions I want to add. I believe it is a good paper/package which provides solid tools for developers.

@crvernon
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crvernon commented Apr 3, 2024

Great, thanks @KennethEnevoldsen!

@devrimcavusoglu let me know when you have the community guidelines element addressed and are ready for me to take my final look.

@devrimcavusoglu
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@crvernon I updated the repo for regarding changes. You can access to the community guidline in the repo.

Thank you for review and fruitful discussion. @KennethEnevoldsen @evamaxfield @crvernon

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crvernon commented Apr 5, 2024

@editorialbot generate pdf

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Done! version is now v2.3.1

@crvernon
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@devrimcavusoglu no need to do another release, but please edit the authors in the Zenodo record metadata to match the authors and order of those who appear in your paper.

Also...please ensure that the title of the Zenodo record matches exactly with what is in the paper.

Please let me know when this is done so we can move forward.

@devrimcavusoglu
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@crvernon I updated the zenodo version, as you suggested under the same version, I updated the metadata.

@crvernon
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crvernon commented May 20, 2024

@devrimcavusoglu the titles still do not match.

  • Please fix the title
    What is in your paper: Jury: A Comprehensive Evaluation Toolkit
    The title of your archive: Jury: A Comprehensive NLP Evaluation toolkit

  • Also, the author order is still incorrect in your archive as compared to what it is in the paper.

Please fix both issue to match what is in the paper.

@devrimcavusoglu
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@crvernon sorry for the inconvenience, I updated the zenodo version with the proper name and corrected author order.

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@editorialbot check references

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

OK DOIs

- 10.18653/v1/W18-5446 is OK
- 10.18653/v1/N19-1423 is OK
- 10.18653/v1/2021.emnlp-demo.21 is OK
- 10.3115/1073083.1073135 is OK

MISSING DOIs

- No DOI given, and none found for title: Relevance of Unsupervised Metrics in Task-Oriented...
- No DOI given, and none found for title: Findings of the 2020 Conference on Machine Transla...
- No DOI given, and none found for title: XLNet: Generalized Autoregressive Pretraining for ...

INVALID DOIs

- None

@crvernon
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@editorialbot set 10.5281/zenodo.11170894 as archive

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Done! archive is now 10.5281/zenodo.11170894

@crvernon
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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

- 10.18653/v1/W18-5446 is OK
- 10.18653/v1/N19-1423 is OK
- 10.18653/v1/2021.emnlp-demo.21 is OK
- 10.3115/1073083.1073135 is OK

MISSING DOIs

- No DOI given, and none found for title: Relevance of Unsupervised Metrics in Task-Oriented...
- No DOI given, and none found for title: Findings of the 2020 Conference on Machine Transla...
- No DOI given, and none found for title: XLNet: Generalized Autoregressive Pretraining for ...

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#5360, 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 May 20, 2024
@crvernon
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Alright @devrimcavusoglu, take a final look at the proof above and make sure all is well from your side and let me know when you are satisfied with it. Then I'll accept this one for publication in full.

@devrimcavusoglu
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@crvernon I just checked the proof, LGTM 👍 I didn't want to provide a link to the arxiv, but I don't know we can do such thing. If joss allow, I can cite/provide our arxiv paper as well. If not, we can proceed with this latest proof.

@crvernon
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@devrimcavusoglu - We have no problems with the preprint. See https://joss.readthedocs.io/en/latest/submitting.html#preprint-policy

Just let me know if you alter the paper and I'll recheck. If not, just let me know and we can move forward. Thanks!

@devrimcavusoglu
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@crvernon I rechecked it and I think there's no need for any revision. We can proceed with this version.

@crvernon
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@editorialbot accept

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

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

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

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

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Cavusoglu
  given-names: Devrim
- family-names: Sen
  given-names: Secil
- family-names: Sert
  given-names: Ulas
- family-names: Altinuc
  given-names: Sinan
contact:
- family-names: Cavusoglu
  given-names: Devrim
doi: 10.5281/zenodo.11170894
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Cavusoglu
    given-names: Devrim
  - family-names: Sen
    given-names: Secil
  - family-names: Sert
    given-names: Ulas
  - family-names: Altinuc
    given-names: Sinan
  date-published: 2024-05-20
  doi: 10.21105/joss.06452
  issn: 2475-9066
  issue: 97
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6452
  title: "Jury: A Comprehensive Evaluation Toolkit"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06452"
  volume: 9
title: "Jury: A Comprehensive Evaluation Toolkit"

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.06452 joss-papers#5363
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06452
  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 May 20, 2024
@crvernon
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🥳 Congratulations on your new publication @devrimcavusoglu! Many thanks to @evamaxfield and @KennethEnevoldsen for your time, hard work, and expertise in reviewing!! 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

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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.06452/status.svg)](https://doi.org/10.21105/joss.06452)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06452">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06452/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06452/status.svg
   :target: https://doi.org/10.21105/joss.06452

This is how it will look in your documentation:

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