[REVIEW]: DAPPER: Data Assimilation with Python: a Package for Experimental Research #5150

editorialbot · 2023-02-13T19:09:28Z

Submitting author: @patnr (Patrick Nima Raanes)
Repository: https://github.com/nansencenter/DAPPER
Branch with paper.md (empty if default branch): paper_joss
Version: v1.6.0
Editor: @Fei-Tao
Reviewers: @sara-02, @Shreyas911
Archive: 10.5281/zenodo.10710355

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/bb5284cf4b025308352da7544a9f6001/status.svg)](https://joss.theoj.org/papers/bb5284cf4b025308352da7544a9f6001)

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

@sara-02 & @Shreyas911, 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 @Fei-Tao 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 @sara-02

📝 Checklist for @Shreyas911

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

editorialbot · 2023-02-13T19:09:30Z

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

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editorialbot · 2023-02-13T19:09:32Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.21 s (772.7 files/s, 137858.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         128           3622           6718           8594
SVG                              1              0             70           5726
Fortran 90                      10            251            310           1317
Markdown                        10            235              0            815
TeX                              2             62              0            571
XML                              1              0              0            228
YAML                             5             25             31            195
TOML                             1             17             27             99
Jupyter Notebook                 2              0            528             44
make                             1             14              4             37
Bourne Shell                     1              9             12             27
Jinja Template                   3              3              1             22
CSS                              1              0              0              4
-------------------------------------------------------------------------------
SUM:                           166           4238           7701          17679
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-02-13T19:09:32Z

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

OK DOIs

- 10.1007/978-3-030-77722-7_1 is OK
- 10.1007/s11004-021-09937-x is OK
- 10.5194/npg-26-325-2019 is OK
- 10.1002/qj.3386 is OK
- 10.1016/j.jocs.2020.101171 is OK
- 10.1137/1.9781611974546 is OK
- 10.1002/qj.2236 is OK
- 10.1175/2010MWR3253.1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-02-13T19:09:33Z

Wordcount for paper.md is 425

editorialbot · 2023-02-13T19:11:05Z

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

sara-02 · 2023-02-14T06:56:42Z

Review checklist for @sara-02

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/nansencenter/DAPPER?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@patnr) 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?

Fei-Tao · 2023-02-17T16:08:32Z

Hi @Shreyas911, would you please generate your checklist at your convenience? Thanks for your time.

patnr · 2023-02-17T16:40:54Z

Dear all,

Thank you for agreeing to review this software.

I await your comments and will try to be responsive!

Shreyas911 · 2023-02-19T01:55:52Z

@Fei-Tao and @patnr, please bear with me till this Thursday, after that I will be much more active.

Fei-Tao · 2023-02-19T02:57:32Z

@Shreyas911 Thanks for your prompt response. Take your time.

Shreyas911 · 2023-02-23T16:47:10Z

Review checklist for @Shreyas911

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/nansencenter/DAPPER?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@patnr) 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?

Fei-Tao · 2023-06-02T14:24:25Z

Hi @sara-02 and @Shreyas911, any updates on the review? Please let us know if you need any help. Thanks again for your time.

Shreyas911 · 2023-08-02T22:59:19Z

Hi @patnr,

Sorry for the delay, here's what I think so far. I have not run the examples yet.

Functionality

Installation: Does installation proceed as outlined in the documentation?

I get the following error when I create the conda environment dapper-env on our Linux machine for Python 3.16 as suggested in your README.

Traceback (most recent call last): File "/home/shreyas/DAPPER/examples/basic_1.py", line 10, in <module> from mpl_tools import is_notebook_or_qt as nb ModuleNotFoundError: No module named 'mpl_tools'

I tried my own conda environments with Python 3.10 or above and still had the same error. I guess mpl_tools needs to be specifically added to the environment

Functionality: Have the functional claims of the software been confirmed?

I will verify these soon if I can get this mpl_tools issue sorted.

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?

The target audience is not explicitly specified in the documentation, I think.

Installation instructions: Is there a clearly-stated list of dependencies? Ideally, these should be handled with an automated package management solution.

A list of dependencies should be stated, including conda/mamba along with a minimum version and maybe mpl_tools if that is to be separately added.

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

This is not explicitly stated. I do see a dev section, however, it would be great to include in the README.md file explicitly how to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support.

Software Paper

State of the field: Do the authors describe how this software compares to other commonly-used packages?

This section is missing from the paper. I do see it in the README, so maybe add that to the paper as well.

Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?

A few minor suggestions -

In the Statement of Need section, it is confusing to read (a) (b) (a) (b) (c) (d) (c) (d). Maybe change one of them to numbers or some other formatting.
In the Acknowledgements sections, end the paragraph with a full stop instead of a comma.

patnr · 2023-08-03T08:00:24Z

Thank you @Shreyas911 for the feedback.

Concerning mpl-tools, I'm guessing you have not done pip install -e DAPPER in your dapper-env, as listed here. Could you please verify?

The target audience is not explicitly specified in the documentation, I think.

The README states

In summary, DAPPER is well suited for teaching and fundamental DA research. Also see its drawbacks.
DAPPER is aimed at research and teaching [...]
if you have an operational or real-world application, such as WRF, you should look into one of the alternatives [...]

Do you think its needs further clarification?

A list of dependencies should be stated, including conda/mamba along with a minimum version and maybe mpl_tools if that is to be separately added.

The dependencies, including mpl_tools are listed in setup.py, which is used by the installation, whose instructions also indicate a minimum version

This is not explicitly stated. I do see a dev section, however, it would be great to include in the README.md file explicitly how to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support.

Done, thank you.

State of the field: Do the authors describe how this software compares to other commonly-used packages?

This section is missing from the paper. I do see it in the README, so maybe add that to the paper as well.

Done, thank you.

In the Statement of Need section, it is confusing to read (a) (b) (a) (b) (c) (d) (c) (d). Maybe change one of them to numbers or some other formatting.

The 2nd occurrence of an item is supposed to reference the first (cause and effect), but I agree that it probably just comes off as confusing, so I removed it.

In the Acknowledgements sections, end the paragraph with a full stop instead of a comma.

Done, thanks.

Hopefully the following will update the paper.

@editorialbot generate pdf

Shreyas911 · 2023-09-11T22:58:46Z

@editorialbot generate pdf

editorialbot · 2023-09-11T22:59:57Z

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

Shreyas911 · 2023-09-11T23:22:53Z

@patnr @Fei-Tao ,

Sorry for the delay, I quite like the paper. I have checked all the boxes related to that. The State of the Field section could be separate, not just the second paragraph of the Statement of Need. I leave that up to your preference.

Otherwise, thanks to your instructions, I was able to install and run the software. I think all the requirements are adequately satisfied. I am able to mark the review as complete.

It is an amazing piece of Python code, and I personally learned a lot from its construction. Thanks for the opportunity to review such great software! :)

Fei-Tao · 2023-09-13T19:51:09Z

Hi @Shreyas911 thanks for your time reviewing this submission. Appreciate it.
@patnr would you please make the change following Shreyas's comments. I think that can help to highlight the contribution of this package.

Fei-Tao · 2023-09-13T19:52:09Z

Hi @sara-02, could you please start your review at your convenience? Please feel free to let me know if you need any help. Thanks in advance for your time.

patnr · 2023-09-14T07:57:06Z

Dear @Shreyas911 ,
Many thanks for your review, and the kind words.

I added a section "Statement of need" as per your suggestion.

patnr · 2023-09-14T08:00:08Z

@editorialbot generate pdf

Fei-Tao · 2024-02-26T15:29:56Z

@editorialbot check references

editorialbot · 2024-02-26T15:29:59Z

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

OK DOIs

- 10.1007/978-3-030-77722-7_1 is OK
- 10.1007/s11004-021-09937-x is OK
- 10.5194/npg-26-325-2019 is OK
- 10.1002/qj.3386 is OK
- 10.1016/j.jocs.2020.101171 is OK
- 10.1137/1.9781611974546 is OK
- 10.1002/qj.2236 is OK
- 10.1175/2010MWR3253.1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

Fei-Tao · 2024-02-26T15:34:18Z

Hi @patnr, can you check the Post-Review Checklist above? Please Archive the release on Zenodo/figshare/etc and post the DOI here after you complete it. Thanks for your time.

patnr · 2024-02-26T17:31:38Z

Thank you for the guidelines.

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.
v1.6.0
Archive the release on Zenodo/figshare/etc and post the DOI here.
10.5281/zenodo.10710355
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Make sure that the license listed for the archive is the same as the software license.

Fei-Tao · 2024-02-27T22:29:27Z

@editorialbot generate pdf

editorialbot · 2024-02-27T22:30:37Z

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

Fei-Tao · 2024-02-27T22:39:09Z

@editorialbot set 10.5281/zenodo.10710355 as archive

editorialbot · 2024-02-27T22:39:12Z

Done! archive is now 10.5281/zenodo.10710355

Fei-Tao · 2024-02-27T22:39:38Z

@editorialbot set v1.6.0 as version

editorialbot · 2024-02-27T22:39:41Z

Done! version is now v1.6.0

Fei-Tao · 2024-02-27T22:40:00Z

@editorialbot recommend-accept

editorialbot · 2024-02-27T22:40:02Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-02-27T22:40:04Z

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

OK DOIs

- 10.1007/978-3-030-77722-7_1 is OK
- 10.1007/s11004-021-09937-x is OK
- 10.5194/npg-26-325-2019 is OK
- 10.1002/qj.3386 is OK
- 10.1016/j.jocs.2020.101171 is OK
- 10.1137/1.9781611974546 is OK
- 10.1002/qj.2236 is OK
- 10.1175/2010MWR3253.1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-02-27T22:41:23Z

👋 @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#5061, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Fei-Tao · 2024-02-27T22:44:16Z

@sara-02 @Shreyas911 Thanks for your time for reviewing this submission.

@openjournals/dsais-eics, this submission looks good to me now. Could you take it from here? Thanks.

arfon · 2024-02-29T10:11:21Z

@patnr – one more thing, could you please add a section named # References at the end of your paper.md please?

patnr · 2024-02-29T10:19:12Z

@editorialbot generate pdf

editorialbot · 2024-02-29T10:56:34Z

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

arfon · 2024-02-29T19:03:37Z

@editorialbot accept

editorialbot · 2024-02-29T19:03:39Z

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

editorialbot · 2024-02-29T19:10:36Z

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: Raanes
  given-names: Patrick N.
  orcid: "https://orcid.org/0000-0001-5073-6786"
- family-names: Chen
  given-names: Yumeng
  orcid: "https://orcid.org/0000-0002-2319-6937"
- family-names: Grudzien
  given-names: Colin
  orcid: "https://orcid.org/0000-0002-3084-3178"
contact:
- family-names: Raanes
  given-names: Patrick N.
  orcid: "https://orcid.org/0000-0001-5073-6786"
doi: 10.5281/zenodo.10710355
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Raanes
    given-names: Patrick N.
    orcid: "https://orcid.org/0000-0001-5073-6786"
  - family-names: Chen
    given-names: Yumeng
    orcid: "https://orcid.org/0000-0002-2319-6937"
  - family-names: Grudzien
    given-names: Colin
    orcid: "https://orcid.org/0000-0002-3084-3178"
  date-published: 2024-02-29
  doi: 10.21105/joss.05150
  issn: 2475-9066
  issue: 94
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5150
  title: "DAPPER: Data Assimilation with Python: a Package for
    Experimental Research"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05150"
  volume: 9
title: "DAPPER: Data Assimilation with Python: a Package for
  Experimental Research"

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 · 2024-02-29T19:10:41Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-02-29T19:10:41Z

🚨🚨🚨 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.05150 joss-papers#5078
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05150
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon · 2024-03-01T08:09:24Z

@sara-02, @Shreyas911 – many thanks for your reviews here and to @Fei-Tao 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 ✨

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

editorialbot · 2024-03-01T08:13:07Z

🎉🎉🎉 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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  <img src="https://joss.theoj.org/papers/10.21105/joss.05150/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05150/status.svg
   :target: https://doi.org/10.21105/joss.05150

This is how it will look in your documentation:

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editorialbot added Fortran Makefile Python review Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning waitlisted Submissions in the JOSS backlog due to reduced service mode. labels Feb 13, 2023

editorialbot assigned Fei-Tao Feb 13, 2023

editorialbot mentioned this issue Feb 13, 2023

[PRE REVIEW]: DAPPER: Data Assimilation with Python: a Package for Experimental Research #5080

Closed

arfon removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Feb 19, 2023

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Feb 27, 2024

editorialbot added accepted published Papers published in JOSS labels Feb 29, 2024

arfon closed this as completed Mar 1, 2024

editorialbot mentioned this issue Sep 4, 2024

[PRE REVIEW]: ndbc-api: Accelerating oceanography and climate science research with Python #7182

Closed

[REVIEW]: DAPPER: Data Assimilation with Python: a Package for Experimental Research #5150

[REVIEW]: DAPPER: Data Assimilation with Python: a Package for Experimental Research #5150

Comments

editorialbot commented Feb 13, 2023 • edited Loading

Status

Reviewer instructions & questions

Checklists

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sara-02 commented Feb 14, 2023 • edited Loading

Review checklist for @sara-02

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Fei-Tao commented Feb 17, 2023

patnr commented Feb 17, 2023

Shreyas911 commented Feb 19, 2023

Fei-Tao commented Feb 19, 2023

Shreyas911 commented Feb 23, 2023 • edited Loading

Review checklist for @Shreyas911

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Fei-Tao commented Jun 2, 2023

Shreyas911 commented Aug 2, 2023 • edited Loading

Functionality

Documentation

Software Paper

patnr commented Aug 3, 2023

Shreyas911 commented Sep 11, 2023

editorialbot commented Sep 11, 2023

Shreyas911 commented Sep 11, 2023 • edited Loading

Fei-Tao commented Sep 13, 2023

Fei-Tao commented Sep 13, 2023

patnr commented Sep 14, 2023 • edited Loading

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editorialbot commented Feb 29, 2024

arfon commented Mar 1, 2024

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editorialbot commented Feb 13, 2023 •

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sara-02 commented Feb 14, 2023 •

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Shreyas911 commented Feb 23, 2023 •

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Shreyas911 commented Sep 11, 2023 •

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patnr commented Sep 14, 2023 •

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