[REVIEW]: surtvep: An R package for estimating time-varying effects #5688

editorialbot · 2023-07-24T14:42:46Z

Submitting author: @LingfengLuo0510 (Lingfeng Luo)
Repository: https://github.com/UM-KevinHe/surtvep
Branch with paper.md (empty if default branch): JOSS
Version: v1.0.0
Editor: @osorensen
Reviewers: @adibender, @turgeonmaxime
Archive: 10.5281/zenodo.12575049

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📝 Checklist for @adibender

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

editorialbot · 2023-07-24T14:42:49Z

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editorialbot · 2023-07-24T14:42:50Z

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "title" (NAME) [#<BibTeX::Bibliography data=[8]>, "@", #<BibTeX::Entry >, "%"]

editorialbot · 2023-07-24T14:42:51Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.10 s (720.9 files/s, 190900.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            31           1137            263           6636
C++                              3            310            446           2410
XML                              2              0            133           1877
R                               14            231           1458           1485
CSS                              3             98             52            442
JavaScript                       3             64             32            256
TeX                              2             29              9            225
Markdown                         4             91              0            215
Rmd                              5            302            617            113
YAML                             3              6              2            109
SVG                              1              0              1             11
C/C++ Header                     1              2              0              5
-------------------------------------------------------------------------------
SUM:                            72           2270           3013          13784
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-07-24T14:42:53Z

Wordcount for paper.md is 1759

editorialbot · 2023-07-24T14:42:54Z

Failed to discover a valid open source license

editorialbot · 2023-07-24T14:44:31Z

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

turgeonmaxime · 2023-07-24T14:47:19Z

Review checklist for @turgeonmaxime

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/UM-KevinHe/surtvep?
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 (@LingfengLuo0510) 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?

adibender · 2023-07-25T09:00:25Z

Review checklist for @adibender

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/UM-KevinHe/surtvep?
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 (@LingfengLuo0510) 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?

adibender · 2023-07-25T09:03:49Z

@osorensen I work in the field and have a package which provides similar functionality. Not sure if this is conflict of interest, but I don't think it will affect review. Just wanted to mention it here

osorensen · 2023-07-25T09:12:16Z

@adibender, I agree. I see this as a strength rather than a conflict of interest, but thanks for mentioning it.

turgeonmaxime · 2023-08-10T19:28:48Z

@LingfengLuo0510 I just read the manuscript for the first time, and I have a few questions/comments.

I noticed that Figure 1 (the function flowchart) doesn't appear in the PDF. In its place, it looks like the caption is repeated twice. Please fix.
In Figure 2, the confidence bands don't cover the same range as the curve estimate. Why is that?
On line 119, you write: "We estimate cancer stage of kidney, lung, and breast." That's incorrect, you're estimating hazard ratios. The cancer stages are part of the data.
For the section "Data Example", would it be possible to share your code?
In the manuscript, could you clarify when a user should opt for a penalized approach? Does it depend on the number of covariates, or the number of basis functions?

I'm sure I'll have further comments/questions as I keep reviewing the package, but I'll put them in a different comment!

turgeonmaxime · 2023-08-10T19:41:34Z

Also, I haven't been able to install the package using the instructions in the manuscript. Here is the error message I got.

r$> remotes::install_github('UM-KevinHe/surtvep')
Downloading GitHub repo UM-KevinHe/surtvep@HEAD
── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
   checking for file ‘/private/var/folders/hb/r5l2r5b12gg5y2zxyg4l7nh80000gn/T/Rtmp42cwos/remotes1030ea884ab0/UM-KevinHe-surtvep-31f9fd4/DESC✔  checking for file ‘/private/var/folders/hb/r5l2r5b12gg5y2zxyg4l7nh80000gn/T/Rtmp42cwos/remotes1030ea884ab0/UM-KevinHe-surtvep-31f9fd4/DESCRIPTION’
─  preparing ‘surtvep’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘surtvep_1.0.0.tar.gz’

* installing *source* package ‘surtvep’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using C++11
using SDK: ‘MacOSX13.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include     -fPIC  -falign-functions=64 -Wall -g -O2  -c PenalizeStopCpp.cpp -o PenalizeStopCpp.o
PenalizeStopCpp.cpp:4:10: fatal error: 'omp.h' file not found
#include <omp.h>
         ^~~~~~~
1 error generated.
make: *** [PenalizeStopCpp.o] Error 1
ERROR: compilation failed for package ‘surtvep’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/surtvep’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/surtvep’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/hb/r5l2r5b12gg5y2zxyg4l7nh80000gn/T//Rtmp42cwos/file1030e79df6e36/surtvep_1.0.0.tar.gz’ had non-zero exit status

I did notice that the instructions in the README.md file are slightly different, as they point to the branch openmp. When I follow those instructions (i.e. remotes::install_github("UM-KevinHe/surtvep", ref = "openmp")), then the installation proceeds without error.

For reference, here's my session information:

r$> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

time zone: America/Edmonton
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
 [1] processx_3.8.2    compiler_4.3.0    R6_2.5.1          rprojroot_2.0.3   cli_3.6.1         prettyunits_1.1.1 tools_4.3.0
 [8] curl_5.0.1        crayon_1.5.2      remotes_2.4.2     desc_1.4.2        callr_3.7.3       ps_1.7.5          pkgbuild_1.4.2

turgeonmaxime · 2023-08-10T22:44:20Z

@LingfengLuo0510 One more thing: I ran devtools::check() on the openmp branch, and it highlighted many issues with the documentation of your package (among other things). I suggest you ran devtools::check() yourself and fix the warnings, and consider fixing the notes too.

osorensen · 2023-08-12T05:32:22Z

Thanks a lot for you comments @turgeonmaxime!

editorialbot · 2023-08-22T19:47:33Z

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

osorensen · 2023-08-24T12:35:47Z

@LingfengLuo0510, I just wanted to add to the comments from @turgeonmaxime that although we don't require R package submissions to be on CRAN, they should in general pass R CMD check with no NOTEs, WARNINGs, or ERRORs, unless there are very good arguments for not doing so. However, since this is an R package that needs compilation, I would also strongly recommend uploading it to CRAN, as it makes the installation process much easier for most users.

osorensen · 2023-09-02T12:31:16Z

@LingfengLuo0510, you're welcome to start addressing the points raised by @turgeonmaxime. Please keep us updated about any progress.

LingfengLuo0510 · 2023-09-03T20:13:55Z

@osorensen Thanks a lot for the instructions. I am submitting this project to CRAN now. I will update when it is successfully uploaded.
@turgeonmaxime The installation issues come from the fact that OpenMP feature is naturally supported in the Mac OS m1 chip system. I am uploading the package to CRAN and trying to fix the issue. I will reply to the points soon. Thanks a lot for the comments!

adibender · 2023-10-12T19:00:08Z

@LingfengLuo0510 some things that are currently missing from your package:

LICENSE file
automated tests (e.g. using testthat package)
Community guidelines (how to contribute)

osorensen · 2023-10-13T12:24:24Z

Thanks @adibender.

@LingfengLuo0510, any updates on fixing the issues pointed out be @turgeonmaxime or on the CRAN submission?

LingfengLuo0510 · 2023-10-13T18:29:12Z

Thank you for your comments. The package is currently under CRAN review. I’ve addressed CRAN's feedback and resubmitted the updated package for approval. I will provide an update once the review process is complete.

crvernon · 2024-06-28T17:16:19Z

👋 @LingfengLuo0510 - thanks for all of your hard work on this. Your paper is very clean and that is much appreciated! I just need you to address a few final things before we accept this for publication:

Please edit the metadata in your Zenodo archive to make the license match what you use in your repository. Currently your license in the archive is specified as Creative Commons Attribution 4.0 International.
Please match the author order in your Zenodo archive to what is in your paper.

Let me know when these are done and I will move to accept.

LingfengLuo0510 · 2024-06-28T17:23:11Z

👋 @LingfengLuo0510 - thanks for all of your hard work on this. Your paper is very clean and that is much appreciated! I just need you to address a few final things before we accept this for publication:

Please edit the metadata in your Zenodo archive to make the license match what you use in your repository. Currently your license in the archive is specified as Creative Commons Attribution 4.0 International.

Please match the author order in your Zenodo archive to what is in your paper.

Let me know when these are done and I will move to accept.

@crvernon

Thanks a lot!
(1) I have updated the license. It matches what I use in my repository.
(2) I have adjusted the auther order. It matches the author order now.

Thanks again!

crvernon · 2024-06-28T17:29:27Z

@editorialbot accept

editorialbot · 2024-06-28T17:29:29Z

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

editorialbot · 2024-06-28T17:36:20Z

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: Luo
  given-names: Lingfeng
- family-names: Wu
  given-names: Wenbo
- family-names: Taylor
  given-names: Jeremy
- family-names: Kang
  given-names: Jian
- family-names: Kleinsasser
  given-names: Michael
- family-names: He
  given-names: Kevin
contact:
- family-names: He
  given-names: Kevin
doi: 10.5281/zenodo.12575049
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Luo
    given-names: Lingfeng
  - family-names: Wu
    given-names: Wenbo
  - family-names: Taylor
    given-names: Jeremy
  - family-names: Kang
    given-names: Jian
  - family-names: Kleinsasser
    given-names: Michael
  - family-names: He
    given-names: Kevin
  date-published: 2024-06-28
  doi: 10.21105/joss.05688
  issn: 2475-9066
  issue: 98
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5688
  title: "surtvep: An R package for estimating time-varying effects"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05688"
  volume: 9
title: "surtvep: An R package for estimating time-varying effects"

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 · 2024-06-28T17:36:24Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-06-28T17:36:24Z

🚨🚨🚨 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.05688 joss-papers#5550
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05688
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

crvernon · 2024-06-28T17:39:05Z

🥳 Congratulations on your new publication @LingfengLuo0510! Many thanks to @osorensen for editing and @adibender and @turgeonmaxime 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 · 2024-06-28T17:39:07Z

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

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

Markdown:
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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.05688/status.svg" alt="DOI badge" >
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   :target: https://doi.org/10.21105/joss.05688

This is how it will look in your documentation:

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The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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LingfengLuo0510 · 2024-06-28T17:40:52Z

@crvernon I feel so sorry that may I ask if I can update the middle name of one of the authors? So sorry about this.

crvernon · 2024-06-28T17:43:10Z

Yes please do so. I am getting ready to board a flight but will reaccept this as soon as I can. Just let me know once you have made the change.

LingfengLuo0510 · 2024-06-28T17:44:25Z

@editorialbot generate pdf

editorialbot · 2024-06-28T17:45:36Z

⚠️ An error happened when generating the pdf.

LingfengLuo0510 · 2024-06-28T17:54:29Z

@editorialbot generate pdf

editorialbot · 2024-06-28T17:55:38Z

⚠️ An error happened when generating the pdf.

LingfengLuo0510 · 2024-06-28T19:08:49Z

@editorialbot generate pdf

editorialbot · 2024-06-28T19:10:23Z

⚠️ An error happened when generating the pdf.

LingfengLuo0510 · 2024-06-28T19:21:23Z

Yes please do so. I am getting ready to board a flight but will reaccept this as soon as I can. Just let me know once you have made the change.

@crvernon Than
Thanks a lot! I just updated the paper.md file
(1) Jeremy Taylor -> Jeremy M.G. Taylor
(2) Michael Kleinsasser -> Michael J. Kleinsasser

However, I'm encountering errors when generating the PDF, even after reverting to the previously accepted version. Could this be related to the paper's accepted status?

crvernon · 2024-06-28T22:14:58Z

@editorialbot generate pdf

editorialbot · 2024-06-28T22:16:16Z

⚠️ An error happened when generating the pdf.

crvernon · 2024-06-28T22:20:32Z

@editorialbot reaccept

editorialbot · 2024-06-28T22:20:34Z

Rebuilding paper!

editorialbot · 2024-06-28T22:22:43Z

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#5551

crvernon · 2024-06-28T22:26:24Z

@LingfengLuo0510 - the paper should now reflect your changes.

editorialbot · 2024-06-28T22:26:26Z

🎉🎉🎉 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:
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HTML:
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</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05688/status.svg
   :target: https://doi.org/10.21105/joss.05688

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

editorialbot added HTML R review TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning waitlisted Submissions in the JOSS backlog due to reduced service mode. labels Jul 24, 2023

editorialbot assigned osorensen Jul 24, 2023

editorialbot mentioned this issue Jul 24, 2023

[PRE REVIEW]: surtvep: An R package for estimating time-varying effects #5644

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editorialbot added the C++ label Jul 24, 2023

editorialbot added accepted published Papers published in JOSS labels Jun 28, 2024

crvernon closed this as completed Jun 28, 2024

crvernon reopened this Jun 28, 2024

crvernon closed this as completed Jun 28, 2024

[REVIEW]: surtvep: An R package for estimating time-varying effects #5688

[REVIEW]: surtvep: An R package for estimating time-varying effects #5688

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turgeonmaxime commented Jul 24, 2023 • edited Loading

Review checklist for @turgeonmaxime

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

adibender commented Jul 25, 2023 • edited Loading

Review checklist for @adibender

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

adibender commented Jul 25, 2023

osorensen commented Jul 25, 2023

turgeonmaxime commented Aug 10, 2023 • edited Loading

turgeonmaxime commented Aug 10, 2023 • edited Loading

turgeonmaxime commented Aug 10, 2023 • edited Loading

osorensen commented Aug 12, 2023

editorialbot commented Aug 22, 2023

osorensen commented Aug 24, 2023

osorensen commented Sep 2, 2023

LingfengLuo0510 commented Sep 3, 2023

adibender commented Oct 12, 2023

osorensen commented Oct 13, 2023

LingfengLuo0510 commented Oct 13, 2023

crvernon commented Jun 28, 2024

LingfengLuo0510 commented Jun 28, 2024

crvernon commented Jun 28, 2024

editorialbot commented Jun 28, 2024

editorialbot commented Jun 28, 2024

editorialbot commented Jun 28, 2024

editorialbot commented Jun 28, 2024

crvernon commented Jun 28, 2024

editorialbot commented Jun 28, 2024

LingfengLuo0510 commented Jun 28, 2024

crvernon commented Jun 28, 2024

LingfengLuo0510 commented Jun 28, 2024

editorialbot commented Jun 28, 2024

LingfengLuo0510 commented Jun 28, 2024

editorialbot commented Jun 28, 2024

LingfengLuo0510 commented Jun 28, 2024

editorialbot commented Jun 28, 2024

LingfengLuo0510 commented Jun 28, 2024

crvernon commented Jun 28, 2024

editorialbot commented Jun 28, 2024

crvernon commented Jun 28, 2024

editorialbot commented Jun 28, 2024

editorialbot commented Jun 28, 2024

crvernon commented Jun 28, 2024

editorialbot commented Jun 28, 2024

editorialbot commented Jul 24, 2023 •

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turgeonmaxime commented Jul 24, 2023 •

edited

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adibender commented Jul 25, 2023 •

edited

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turgeonmaxime commented Aug 10, 2023 •

edited

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turgeonmaxime commented Aug 10, 2023 •

edited

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turgeonmaxime commented Aug 10, 2023 •

edited

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