[REVIEW]: icepyx: querying, obtaining, analyzing, and manipulating ICESat-2 datasets #4912

editorialbot · 2022-11-07T16:45:32Z

Submitting author: @JessicaS11 (Jessica Scheick)
Repository: https://github.com/icesat2py/icepyx
Branch with paper.md (empty if default branch): pubs/joss
Version: v0.6.4_JOSS
Editor: @kthyng
Reviewers: @dimejimudele, @VaasuDevanS
Archive: https://doi.org/10.5281/zenodo.7806097

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/a355344b24ffa5fda7a04a5067e8be1f"><img src="https://joss.theoj.org/papers/a355344b24ffa5fda7a04a5067e8be1f/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/a355344b24ffa5fda7a04a5067e8be1f/status.svg)](https://joss.theoj.org/papers/a355344b24ffa5fda7a04a5067e8be1f)

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Reviewer instructions & questions

@dimejimudele & @VaasuDevanS, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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@editorialbot generate my checklist

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✨ 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 @VaasuDevanS

📝 Checklist for @dimejimudele

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

editorialbot · 2022-11-07T16:45:33Z

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:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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editorialbot · 2022-11-07T16:45:42Z

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "for" (NAME) [#<BibTeX::Bibliography data=[1]>, "@", #<BibTeX::Entry >, {:author=>["Scheick, Jessica and Bisson, Kelsey and Li, Tian and Leong, Wei Ji and Arendt, Anthony"], :note=>["Abstract and poster (presented by Wei Ji Leong). American Geophysical Union Fall Meeting, New Orleans, LA, USA. 13-17 December 2021."], :title=>["Collaborative Computational Resource Development around {ICESat-2} Data: the {icepyx} Community and Library"], :journal=>["Earth and Space Science Open Archive"], :pages=>["9"], :year=>["2022"]}, ",", "%"]

editorialbot · 2022-11-07T16:45:43Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.17 s (635.2 files/s, 127874.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              5              0            120           5951
Python                          37           1356           2571           5293
reStructuredText                41            727            417           1074
Jupyter Notebook                 7              0           3305            422
YAML                            10             34             48            215
Markdown                         3             54              0            192
TeX                              1             12              4            142
XML                              1              0              0             74
CSS                              1             18              2             53
DOS Batch                        1              8              1             26
make                             1              4              7              9
INI                              1              0              0              6
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                           110           2213           6475          13458
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-11-07T16:45:44Z

Wordcount for paper.md is 859

editorialbot · 2022-11-07T16:46:51Z

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

VaasuDevanS · 2022-11-07T16:47:55Z

Review checklist for @VaasuDevanS

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/icesat2py/icepyx?
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 (@JessicaS11) 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?

kthyng · 2022-11-07T16:48:23Z

👋🏼 @JessicaS11 @dimejimudele, @VaasuDevanS this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains 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 openjournals/joss-reviews#4912 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 reviews to be completed within about 2-4 weeks, or 4-6 weeks if needed. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@kthyng) if you have any questions/concerns.

kthyng · 2022-11-07T16:50:56Z

@JessicaS11 Have you put out your new release yet?

Also, please address the bib issue above.

dimejimudele · 2022-11-07T17:25:32Z

Review checklist for @dimejimudele

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/icesat2py/icepyx?
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 (@JessicaS11) 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?

weiji14 · 2022-11-07T18:44:33Z

@JessicaS11 Have you put out your new release yet?

Just a quick note: new icepyx version 0.6.4 has been released on 31 Oct 2022, see https://github.com/icesat2py/icepyx/releases/tag/v0.6.4

Also, please address the bib issue above.

BibTeX should be fixed in icesat2py/icepyx@88e5116.

Was causing issues with editorialbot at openjournals/joss-reviews#4912 (comment)

kthyng · 2022-11-07T18:59:35Z

@editorialbot generate pdf

editorialbot · 2022-11-07T19:01:30Z

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

kthyng · 2022-11-07T19:02:21Z

Seems like the paper works now.

kthyng · 2022-11-30T18:13:35Z

Hi all! Just want to see how the review is going for everyone. Please let me know if you have any questions.

VaasuDevanS · 2022-12-05T16:40:56Z

Sure. @kthyng Thanks.

dimejimudele · 2022-12-05T16:44:50Z

@kthyng Should get through with this before the closing work for the year. Scheduled to work on this in the coming weekend.

dimejimudele · 2022-12-05T16:45:05Z

@kthyng Thanks for checking

dimejimudele · 2022-12-14T18:34:15Z

Just a question for @kthyng, I could not find paper.md in the joss branch of the project repository, but I have performed my review responsibilities so far using the pdf linked here.

Any help?

kthyng · 2022-12-14T18:44:16Z

@dimejimudele The JOSS paper is in a branch called joss. Within that it is pretty buried though! I found it here: https://github.com/icesat2py/icepyx/blob/joss/doc/source/tracking/paper.md

dimejimudele · 2022-12-15T16:12:09Z

I have completed my review of this publication and the connected software tool.

I should say it is an impressive project that has taken a lot of collaboration and time to deliver up to its current state.

icepyx is a Python library for loading and processing ICESat-2 datasets. ICESat-2 is part of NASA's Earth Observing System and it provides data measuring ice sheet elevation and sea ice thickness, as well as land topography, vegetation characteristics, and clouds.

This tool enables faster workflows in many scientific domains.

The authors provided easy-to-follow examples
The installation guide (both through PyPI and Conda) works as provided in the documentation.
Sufficient documentation has already been provided for this library
There are sufficient use cases for this library
It has taken beyond substantial scholarly effort to get this project to its current state

A minor clarification the authors might need to make is about the difference between icesat2py and icepyx. It appears to be the case that the former is a previous name for the latter.

I do strongly recommend that this submission be published in JOSS.

@kthyng

kthyng · 2022-12-15T23:30:22Z

Thank you for your review @dimejimudele!

JessicaS11 · 2023-04-06T16:27:22Z

Hello @kthyng! I have completed all five of the tasks in the author checklist (I am unable to check them off).
Software release/tag (v0.6.4_JOSS): https://github.com/icesat2py/icepyx/tree/v0.6.4_JOSS
Zenodo link/doi: https://doi.org/10.5281/zenodo.7806097
Thanks for your hard work as lead editor!

kthyng · 2023-04-11T13:56:45Z

@editorialbot set https://doi.org/10.5281/zenodo.7806097 as archive

editorialbot · 2023-04-11T13:56:47Z

Done! Archive is now https://doi.org/10.5281/zenodo.7806097

kthyng · 2023-04-11T13:57:04Z

@editorialbot set v0.6.4_JOSS as version

editorialbot · 2023-04-11T13:57:06Z

Done! version is now v0.6.4_JOSS

kthyng · 2023-04-11T13:57:55Z

@JessicaS11 maybe I have to check off the list items? sorry for that confusion!

kthyng · 2023-04-11T13:58:42Z

@editorialbot check references

editorialbot · 2023-04-11T13:58:50Z

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

OK DOIs

- 10.5281/zenodo.6462479 is OK
- 10.1002/essoar.10511316.1 is OK
- 10.5281/zenodo.3966463 is OK
- 10.1002/essoar.10501423.1 is OK
- 10.1029/2021GL095051 is OK
- 10.1007/978-3-030-87013-3_13 is OK
- 10.5194/tc-14-3629-2020 is OK
- 10.1016/j.rse.2016.12.029 is OK
- 10.3390/rs14205158 is OK
- 10.5281/zenodo.7705009 is OK
- 10.1007/s12145-020-00520-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

kthyng · 2023-04-11T14:03:35Z

List of paper comments:

need a space between reference and parenthetical citation for several in the paper (like OpenAltimetry and its parenthetical reference)
Lindsey Heagy is the correct spelling
Make sure of proper capitalization in your references with {} around strings in your .bib file. For example, Li et al seems to not be properly capitalized.

JessicaS11 · 2023-04-11T16:14:09Z

Thanks @kthyng! Does JOSS have a recommended approach for applying these edits? I cannot update the files once they are on Zenodo (unless they agree to make an exception because I'm still within the one week window), and updating the repo won't port the changes over to Zenodo unless I create a new release (and thus change the release tag and and archive/DOI). Just want to make this as easy as possible for everyone!

kthyng · 2023-04-11T16:59:35Z

I'd say just update the paper and don't do anything else — it doesn't impact the software so isn't critical for the version nor archive to be exact for the paper wording.

JessicaS11 · 2023-04-11T20:31:40Z

@editorialbot set pubs/joss as branch

editorialbot · 2023-04-11T20:31:42Z

Done! branch is now pubs/joss

JessicaS11 · 2023-04-11T20:32:28Z

@editorialbot generate pdf

editorialbot · 2023-04-11T20:34:36Z

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

JessicaS11 · 2023-04-11T20:39:41Z

@kthyng Thanks for those edits - they should be all set!

kthyng · 2023-04-12T13:54:07Z

Great! We're all finished now.

kthyng · 2023-04-12T13:54:13Z

@editorialbot accept

editorialbot · 2023-04-12T13:54:15Z

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

editorialbot · 2023-04-12T13:56:41Z

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: Scheick
  given-names: Jessica
  orcid: "https://orcid.org/0000-0002-3421-4459"
- family-names: Leong
  given-names: Wei Ji
  orcid: "https://orcid.org/0000-0003-2354-1988"
- family-names: Bisson
  given-names: Kelsey
  orcid: "https://orcid.org/0000-0003-4230-3467"
- family-names: Arendt
  given-names: Anthony
  orcid: "https://orcid.org/0000-0003-0429-6905"
- family-names: Bhushan
  given-names: Shashank
  orcid: "https://orcid.org/0000-0003-3712-996X"
- family-names: Fair
  given-names: Zachary
  orcid: "https://orcid.org/0000-0002-6047-1723"
- family-names: Hagen
  given-names: Norland Raphael
  orcid: "https://orcid.org/0000-0003-1994-1153"
- family-names: Henderson
  given-names: Scott
  orcid: "https://orcid.org/0000-0003-0624-4965"
- family-names: Knuth
  given-names: Friedrich
  orcid: "https://orcid.org/0000-0003-1645-1984"
- family-names: Li
  given-names: Tian
  orcid: "https://orcid.org/0000-0002-1577-4004"
- family-names: Liu
  given-names: Zheng
  orcid: "https://orcid.org/0000-0003-4132-8136"
- family-names: Piunno
  given-names: Romina
  orcid: "https://orcid.org/0009-0000-1144-0915"
- family-names: Ravinder
  given-names: Nitin
- family-names: Setiawan
  given-names: Landung "Don"
  orcid: "https://orcid.org/0000-0002-1624-2667"
- family-names: Sutterley
  given-names: Tyler
  orcid: "https://orcid.org/0000-0002-6964-1194"
- family-names: Swinski
  given-names: JP
- family-names: Anubhav
  orcid: "https://orcid.org/0000-0003-4017-2862"
contact:
- family-names: Scheick
  given-names: Jessica
  orcid: "https://orcid.org/0000-0002-3421-4459"
doi: "https://doi.org/10.5281/zenodo.7806097"
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Scheick
    given-names: Jessica
    orcid: "https://orcid.org/0000-0002-3421-4459"
  - family-names: Leong
    given-names: Wei Ji
    orcid: "https://orcid.org/0000-0003-2354-1988"
  - family-names: Bisson
    given-names: Kelsey
    orcid: "https://orcid.org/0000-0003-4230-3467"
  - family-names: Arendt
    given-names: Anthony
    orcid: "https://orcid.org/0000-0003-0429-6905"
  - family-names: Bhushan
    given-names: Shashank
    orcid: "https://orcid.org/0000-0003-3712-996X"
  - family-names: Fair
    given-names: Zachary
    orcid: "https://orcid.org/0000-0002-6047-1723"
  - family-names: Hagen
    given-names: Norland Raphael
    orcid: "https://orcid.org/0000-0003-1994-1153"
  - family-names: Henderson
    given-names: Scott
    orcid: "https://orcid.org/0000-0003-0624-4965"
  - family-names: Knuth
    given-names: Friedrich
    orcid: "https://orcid.org/0000-0003-1645-1984"
  - family-names: Li
    given-names: Tian
    orcid: "https://orcid.org/0000-0002-1577-4004"
  - family-names: Liu
    given-names: Zheng
    orcid: "https://orcid.org/0000-0003-4132-8136"
  - family-names: Piunno
    given-names: Romina
    orcid: "https://orcid.org/0009-0000-1144-0915"
  - family-names: Ravinder
    given-names: Nitin
  - family-names: Setiawan
    given-names: Landung "Don"
    orcid: "https://orcid.org/0000-0002-1624-2667"
  - family-names: Sutterley
    given-names: Tyler
    orcid: "https://orcid.org/0000-0002-6964-1194"
  - family-names: Swinski
    given-names: JP
  - family-names: Anubhav
    orcid: "https://orcid.org/0000-0003-4017-2862"
  date-published: 2023-04-12
  doi: 10.21105/joss.04912
  issn: 2475-9066
  issue: 84
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 4912
  title: "icepyx: querying, obtaining, analyzing, and manipulating
    ICESat-2 datasets"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.04912"
  volume: 8
title: "icepyx: querying, obtaining, analyzing, and manipulating
  ICESat-2 datasets"

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 · 2023-04-12T13:56:47Z

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editorialbot · 2023-04-12T13:56:48Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-04-12T13:56:49Z

🚨🚨🚨 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.04912 joss-papers#4120
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04912
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng · 2023-04-12T14:30:32Z

Congrats to @JessicaS11 on your new publication! Many thanks to reviewers @dimejimudele and @VaasuDevanS for your time, hard work, and expertise!!

editorialbot · 2023-04-12T14:30:34Z

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

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reStructuredText:
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JessicaS11 · 2023-04-12T20:13:23Z

Thanks to the reviewers and awesome editor @kthyng for all your hard work on this!

editorialbot added Python review Track: 6 (ESE) Earth Sciences and Ecology labels Nov 7, 2022

editorialbot assigned kthyng Nov 7, 2022

editorialbot mentioned this issue Nov 7, 2022

[PRE REVIEW]: icepyx: querying, obtaining, analyzing, and manipulating ICESat-2 datasets #4820

Closed

weiji14 mentioned this issue Nov 7, 2022

JOSS submission draft icesat2py/icepyx#361

Merged

weiji14 added a commit to icesat2py/icepyx that referenced this issue Nov 7, 2022

Remove comment on AGU Fall Meeting 2021 citation

88e5116

Was causing issues with editorialbot at openjournals/joss-reviews#4912 (comment)

dshean mentioned this issue Nov 7, 2022

[PRE REVIEW]: SlideRule: Enabling rapid, scalable, open science for the NASA ICESat-2 mission and beyond #4700

Closed

JessicaS11 mentioned this issue Jan 3, 2023

add icesat2py clarification note icesat2py/icepyx#395

Merged

editorialbot added accepted published Papers published in JOSS labels Apr 12, 2023

kthyng closed this as completed Apr 12, 2023

editorialbot mentioned this issue Oct 9, 2024

[PRE REVIEW]: IncrementalDebrisFlowVolumeAnalyzer: A Python tool for estimating volumes along a debris flow path #7336

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[REVIEW]: icepyx: querying, obtaining, analyzing, and manipulating ICESat-2 datasets #4912

[REVIEW]: icepyx: querying, obtaining, analyzing, and manipulating ICESat-2 datasets #4912

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editorialbot commented Nov 7, 2022 • edited Loading

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VaasuDevanS commented Nov 7, 2022 • edited Loading

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dimejimudele commented Nov 7, 2022 • edited Loading

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