[REVIEW]: One4All: An Open Source Portal to Validate and Share Microplastics Data and Beyond

editorialbot commented 4 months ago

Submitting author: !--author-handle-->@hsherrod2019@kanishkan91<!--end-editor-- Reviewers: @hahsan1, @stephpenn1 Archive: 10.5281/zenodo.12747059

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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

@hahsan1 & @@stephpenn1 & @stephpenn1, 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:

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @kanishkan91 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 @hahsan1

📝 Checklist for @stephpenn1

hahsan1 commented 2 months ago

@hahsan1 , I just downloaded it from the CRAN version and I'm getting the same error as well (with only valid_example.xlsx). I also downloaded the github version and that is working so I recommend downloading the package through github. Please let me know if you are still facing the 'rules_broken' error through the github version. I will look into it in the meantime as well!

I installed the github version and now get the files you mentioned. So I uploaded the data.xlsx and extra_files.zip, and it gives me a warning and an error under "samples". The error is "Checking for duplicate entries", but when I select it, it doesn't show up on the issues selected window. A message pops up saying "Column being assessed by the rule is not in the dataset". Is this an expected behavior?

Also, I did try the rules_broken function, but still get the same error. It seems like it's not compatible with the list output from the validate_data function.

hsherrod2019 commented 2 months ago

Hi, @hsherrod2019 and @kanishkan91, I wanted to confirm before I complete my review that the paper should only be describing the validator app. I know that the other two apps have been integrated into the package but are listed in the Future Goals section of the paper. Thanks!

Hi @stephpenn1 , the paper is mainly focused on the validator tool and package, with the exception of the other two tools in the Future Goals section. However, the pkgdown (https://moore-institute-4-plastic-pollution-res.github.io/One4All/) has vignettes for each of the tools + package which we were hoping to be reviewed as well. Thank you!

hsherrod2019 commented 2 months ago

@hahsan1 , I just downloaded it from the CRAN version and I'm getting the same error as well (with only valid_example.xlsx). I also downloaded the github version and that is working so I recommend downloading the package through github. Please let me know if you are still facing the 'rules_broken' error through the github version. I will look into it in the meantime as well!

I installed the github version and now get the files you mentioned. So I uploaded the data.xlsx and extra_files.zip, and it gives me a warning and an error under "samples". The error is "Checking for duplicate entries", but when I select it, it doesn't show up on the issues selected window. A message pops up saying "Column being assessed by the rule is not in the dataset". Is this an expected behavior?

Also, I did try the rules_broken function, but still get the same error. It seems like it's not compatible with the list output from the validate_data function.

Hi @hahsan1 , I'm currently working through these errors and will get back to you as soon as I can! Thank you!

kanishkan91 commented 2 months ago

Hi, @hsherrod2019 and @kanishkan91, I wanted to confirm before I complete my review that the paper should only be describing the validator app. I know that the other two apps have been integrated into the package but are listed in the Future Goals section of the paper. Thanks!

Hi @stephpenn1 , the paper is mainly focused on the validator tool and package, with the exception of the other two tools in the Future Goals section. However, the pkgdown (https://moore-institute-4-plastic-pollution-res.github.io/One4All/) has vignettes for each of the tools + package which we were hoping to be reviewed as well. Thank you!

@hsherrod2019 Quick clarifying question on this. Based on our discussion earlier, since these new applications are now integrated into the same repository, the paper would need to be updated to reflect the same rather than mentioned as "future directions", correct? If so, I would recommend you make the requisite additions to the paper.

hsherrod2019 commented 2 months ago

Hi, @hsherrod2019 and @kanishkan91, I wanted to confirm before I complete my review that the paper should only be describing the validator app. I know that the other two apps have been integrated into the package but are listed in the Future Goals section of the paper. Thanks!

Hi @stephpenn1 , the paper is mainly focused on the validator tool and package, with the exception of the other two tools in the Future Goals section. However, the pkgdown (https://moore-institute-4-plastic-pollution-res.github.io/One4All/) has vignettes for each of the tools + package which we were hoping to be reviewed as well. Thank you!

@hsherrod2019 Quick clarifying question on this. Based on our discussion earlier, since these new applications are now integrated into the same repository, the paper would need to be updated to reflect the same rather than mentioned as "future directions", correct? If so, I would recommend you make the requisite additions to the paper.

Hi @kanishkan91 , the two tools had been added to the flowchart, and the Microplastics Data Portal is discussed in the Statement of Need. I will also add the two tools into the tutorial section to explain how they are related to the validator tool. Thank you for your patience!

hahsan1 commented 2 months ago

Hi @kanishkan91 and @hsherrod2019 , I want to note that I will be on vacation for three weeks starting Monday, so I want to provide some final comments so that I don't hold up the review. I've had a chance to look at all three tools. Overall the tools are very well made and generally easy to use. It seems that the validator app is quite versatile, if it allows the user to create their own rules sheet to validate data against. The other tools are specific for microplastic visualization and identification. A few questions/comments about the tools.

Validator: Is there a way to upload a custom rules sheet? I might have missed this in the tutorial. I believe you mentioned that there is a rules sheet already embedded in the tool.

Data visualization tool: The map isn’t populated with the microplastics data until a country is selected in the search bar. Would be nice to have them all there by default.

Microplastic Image Explorer: Just a minor comment. I found that clicking on an image opens an empty window.

hsherrod2019 commented 2 months ago

Hi @kanishkan91 and @hsherrod2019 , I want to note that I will be on vacation for three weeks starting Monday, so I want to provide some final comments so that I don't hold up the review. I've had a chance to look at all three tools. Overall the tools are very well made and generally easy to use. It seems that the validator app is quite versatile, if it allows the user to create their own rules sheet to validate data against. The other tools are specific for microplastic visualization and identification. A few questions/comments about the tools.

Validator: Is there a way to upload a custom rules sheet? I might have missed this in the tutorial. I believe you mentioned that there is a rules sheet already embedded in the tool.

Data visualization tool: The map isn’t populated with the microplastics data until a country is selected in the search bar. Would be nice to have them all there by default.

Microplastic Image Explorer: Just a minor comment. I found that clicking on an image opens an empty window.

Hi @hahsan1 and @kanishkan91 ,

Thank you so much for the feedback! The responses are below:

Validator: Yes, users can upload a custom rules sheet. I've added additional instructions on how to do this in the tutorial section of the paper. Users can define which rules sheet to use in the configuration file (field 'rules_to_use'), or they can hash out the field and upload the rules sheet directly in the app.

Data Visualization Tool: I just integrated those changes, the locations should now appear by default.

Image Explorer: Unfortunately, that appears to be an issue with the R browser. Clicking the image opens another browser and I don't think R itself is able to handle this, which is why it appears blank. However, if you open the tool in the web browser, this shouldn't be an issue!

Also, the 'check for duplicates' error is now resolved as well! Thank you.

hsherrod2019 commented 2 months ago

Hi, @hsherrod2019 and @kanishkan91, I wanted to confirm before I complete my review that the paper should only be describing the validator app. I know that the other two apps have been integrated into the package but are listed in the Future Goals section of the paper. Thanks!

Hi @stephpenn1 , the paper is mainly focused on the validator tool and package, with the exception of the other two tools in the Future Goals section. However, the pkgdown (https://moore-institute-4-plastic-pollution-res.github.io/One4All/) has vignettes for each of the tools + package which we were hoping to be reviewed as well. Thank you!

@hsherrod2019 Quick clarifying question on this. Based on our discussion earlier, since these new applications are now integrated into the same repository, the paper would need to be updated to reflect the same rather than mentioned as "future directions", correct? If so, I would recommend you make the requisite additions to the paper.

Hi @kanishkan91 , the two tools had been added to the flowchart, and the Microplastics Data Portal is discussed in the Statement of Need. I will also add the two tools into the tutorial section to explain how they are related to the validator tool. Thank you for your patience!

Hi @kanishkan91 I'm currently working on integrating these changes to the paper and will update it on github (along with the custom rules sheet update) as soon as possible. Thank you.

hsherrod2019 commented 2 months ago

Hi, @hsherrod2019 and @kanishkan91, I wanted to confirm before I complete my review that the paper should only be describing the validator app. I know that the other two apps have been integrated into the package but are listed in the Future Goals section of the paper. Thanks!

Hi @stephpenn1 , the paper is mainly focused on the validator tool and package, with the exception of the other two tools in the Future Goals section. However, the pkgdown (https://moore-institute-4-plastic-pollution-res.github.io/One4All/) has vignettes for each of the tools + package which we were hoping to be reviewed as well. Thank you!

@hsherrod2019 Quick clarifying question on this. Based on our discussion earlier, since these new applications are now integrated into the same repository, the paper would need to be updated to reflect the same rather than mentioned as "future directions", correct? If so, I would recommend you make the requisite additions to the paper.

Hi @kanishkan91 , the two tools had been added to the flowchart, and the Microplastics Data Portal is discussed in the Statement of Need. I will also add the two tools into the tutorial section to explain how they are related to the validator tool. Thank you for your patience!

Hi @kanishkan91 I'm currently working on integrating these changes to the paper and will update it on github (along with the custom rules sheet update) as soon as possible. Thank you.

Hi @stephpenn1 and @kanishkan91 , the Data Visualization Tool and Microplastic Image Explorer have been integrated into the main section of the paper. Everything should be up to date now! Please let me know if you have any questions!

kanishkan91 commented 2 months ago

@hsherrod2019 Thanks so much! I'm looking through your responses to make sure @hahsan1's last issues are addressed.

@stephpenn1 - Would you mind taking a look at the paper?

kanishkan91 commented 1 month ago

I checked my share of the issues and found nothing major. I need to read through the paper though.

@stephpenn1 - Did you have any issues to discuss? If you think the repository is staisfactory, would you mind finishing up your checklist? Thanks in advance!

stephpenn1 commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

stephpenn1 commented 1 month ago

Hi @hsherrod2019 and @kanishkan91 , I have completed my review and have summarized comments below, including any new questions and those already addressed. Overall the package is very well documented and the UI is smooth! Nicely prepared and this was a pleasure to review.

Paper:

Thank you for updating the paper to include the other two apps within One4All, this new wording more accurately reflects your software. I think the paper reads well and looks good.

Software Functionality:

There was a minor bug in the run_app function (https://github.com/Moore-Institute-4-Plastic-Pollution-Res/One4All/issues/104) which has now been resolved and works as described in the paper.
When installing and running the package for the first time, I noticed you have a handy error message listing the packages that need to be installed. This is super optional but one suggestion would be to also list the packages in an error message that could be copied directly into the console (e.g. Please use install.packages(c(package1, package2)))
The data already integrated into your app - does this come from your own plastics data repository? And the validator app is for users looking to upload their own data?

Documentation:

Now that you have made some changes to the functions, do you plan on resubmitting to CRAN? If so, documentation is good as is. If not, it should be clear this paper focuses on the github version.

hsherrod2019 commented 1 month ago

Hi @stephpenn1 ,

Thank you so much for the comments!

Software Functionality:

Yes, the data already integrated comes from our own plastics data repository ('data.xlsx' and 'extra_files.zip'). Also yes, the validator app is for users looking to upload their own data.
I will update the error message to include the packages, early next week, and will let you and @kanishkan91 know once I have integrated those changes!

Documentation:

I resubmitted to CRAN last week after implementing changes to the package. The changes were approved and everything is up to date on CRAN now as well!

Thank you again.

kanishkan91 commented 1 month ago

👋 @hsherrod2019 - Once you address the comment above as you said and the repository is finalized, we need to set up the archive for your new release.

We want to make sure the archival has the correct metadata that JOSS requires. This includes a title that matches the paper title and a correct author list.

So after the last issues are resolved:

[x] Conduct a GitHub release of the current reviewed version of the software and archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository). Please ensure that the software archive uses the same license as the license you have posted on GitHub.
[x] Check the archival deposit (e.g., in Zenodo) to ensure it has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list matches the people and order in your paper). You may also add the authors' ORCID.
[x] Check that software archive exists and title and author list match JOSS paper (or purposefully do not).

Please respond with the 1) version and 2) DOI of the archived version here

hsherrod2019 commented 1 month ago

Hi @kanishkan91 ,

I have resolved the last issues!

1) 2.0 2) https://doi.org/10.5281/zenodo.12747059

kanishkan91 commented 1 month ago

@editorialbot set 10.5281/zenodo.12747059 as archive

editorialbot commented 1 month ago

Done! archive is now 10.5281/zenodo.12747059

kanishkan91 commented 1 month ago

@editorialbot set v2.0 as version

editorialbot commented 1 month ago

Done! version is now v2.0

kanishkan91 commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

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

OK DOIs

- 10.3390/microplastics2010010 is OK
- 10.1039/D2VA00275B is OK
- 10.1371/journal.pbio.3000932 is OK
- 10.1021/acs.analchem.1c00123 is OK
- 10.1016/j.envres.2022.112734 is OK
- 10.1029/2022CSJ000017 is OK
- 10.1016/j.envpol.2023.122938 is OK
- 10.1186/s43591-022-00035-1 is OK
- 10.3389/fenvs.2022.912107 is OK
- 10.1126/science.1213847 is OK
- 10.1002/etc.4371 is OK
- 10.1016/j.envpol.2021.118275 is OK
- 10.18637/jss.v097.i10 is OK
- 10.21105/joss.05136 is OK
- 10.1177/0003702820930292 is OK
- 10.1016/j.scitotenv.2021.146693 is OK

MISSING DOIs

- No DOI given, and none found for title: Policy Handbook Establishing a Standard Method of ...
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: shiny: Web Application Framework for R
- No DOI given, and none found for title: dplyr: A Grammar of Data Manipulation
- 10.32614/cran.package.digest may be a valid DOI for title: digest: Create Compact Hash Digests of R Objects
- No DOI given, and none found for title: data.table: Extension of ‘data.frame‘
- 10.32614/cran.package.ckanr may be a valid DOI for title: ckanr: Client for the Comprehensive Knowledge Arch...
- 10.32614/cran.package.openxlsx may be a valid DOI for title: openxlsx: Read, Write and Edit xlsx Files
- No DOI given, and none found for title: lexicon: Lexicon Data
- 10.32614/cran.package.readr may be a valid DOI for title: readr: Read Rectangular Text Data
- 10.32614/cran.package.readxl may be a valid DOI for title: readxl: Read Excel Files
- 10.32614/cran.package.tibble may be a valid DOI for title: tibble: Simple Data Frames
- 10.32614/cran.package.aws.s3 may be a valid DOI for title: aws.s3: AWS S3 Client Package
- 10.32614/cran.package.rlang may be a valid DOI for title: rlang: Functions for Base Types and Core R and ’Ti...
- No DOI given, and none found for title: The jsonlite Package: A Practical and Consistent M...
- 10.32614/cran.package.httr may be a valid DOI for title: httr: Tools for Working with URLs and HTTP
- No DOI given, and none found for title: ChatGPT: Large language model
- No DOI given, and none found for title: data.validator: Automatic Data Validation and Repo...

INVALID DOIs

- None

kanishkan91 commented 1 month ago

@editorialbot recommend-accept

@hsherrod2019 Thanks ! I have recommended this for acceptance now . The AEiC in this submission track will review shortly and if all goes well this will go live soon! Before I forget, big thank you to @stephpenn1 and @hahsan1 for reviewing this paper! Your expertise and insights have been invaluable to this process. JOSS relies heavily on reviewers such as yourself. I will leave a positive review for your reviewing efforts on the JOSS reviewer hub. (PS- The positive reviews may lead to more invitations to review for JOSS in the future! My apologies in advance)

@hsherrod2019 - I will now go through the paper and post some comments if I find any typos or anything.

editorialbot commented 1 month ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 month ago

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

OK DOIs

- 10.3390/microplastics2010010 is OK
- 10.1039/D2VA00275B is OK
- 10.1371/journal.pbio.3000932 is OK
- 10.1021/acs.analchem.1c00123 is OK
- 10.1016/j.envres.2022.112734 is OK
- 10.1029/2022CSJ000017 is OK
- 10.1016/j.envpol.2023.122938 is OK
- 10.1186/s43591-022-00035-1 is OK
- 10.3389/fenvs.2022.912107 is OK
- 10.1126/science.1213847 is OK
- 10.1002/etc.4371 is OK
- 10.1016/j.envpol.2021.118275 is OK
- 10.18637/jss.v097.i10 is OK
- 10.21105/joss.05136 is OK
- 10.1177/0003702820930292 is OK
- 10.1016/j.scitotenv.2021.146693 is OK

MISSING DOIs

- No DOI given, and none found for title: Policy Handbook Establishing a Standard Method of ...
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: shiny: Web Application Framework for R
- No DOI given, and none found for title: dplyr: A Grammar of Data Manipulation
- 10.32614/cran.package.digest may be a valid DOI for title: digest: Create Compact Hash Digests of R Objects
- No DOI given, and none found for title: data.table: Extension of ‘data.frame‘
- 10.32614/cran.package.ckanr may be a valid DOI for title: ckanr: Client for the Comprehensive Knowledge Arch...
- 10.32614/cran.package.openxlsx may be a valid DOI for title: openxlsx: Read, Write and Edit xlsx Files
- No DOI given, and none found for title: lexicon: Lexicon Data
- 10.32614/cran.package.readr may be a valid DOI for title: readr: Read Rectangular Text Data
- 10.32614/cran.package.readxl may be a valid DOI for title: readxl: Read Excel Files
- 10.32614/cran.package.tibble may be a valid DOI for title: tibble: Simple Data Frames
- 10.32614/cran.package.aws.s3 may be a valid DOI for title: aws.s3: AWS S3 Client Package
- 10.32614/cran.package.rlang may be a valid DOI for title: rlang: Functions for Base Types and Core R and ’Ti...
- No DOI given, and none found for title: The jsonlite Package: A Practical and Consistent M...
- 10.32614/cran.package.httr may be a valid DOI for title: httr: Tools for Working with URLs and HTTP
- No DOI given, and none found for title: ChatGPT: Large language model
- No DOI given, and none found for title: data.validator: Automatic Data Validation and Repo...

INVALID DOIs

- None

editorialbot commented 1 month ago

:wave: @openjournals/dsais-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5629, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

crvernon commented 1 month ago

🔍 checking out the following:

[x] reviewer checklists are completed or addressed
[x] version set
[x] archive set
[x] archive names (including order) and title in archive matches those specified in the paper
[x] archive uses the same license as the repo and is OSI approved as open source
[x] archive DOI and version match or redirect to those set by editor in review thread
[x] paper is error free - grammar and typos
[x] paper is error free - test links in the paper and bib
[x] paper is error free - refs preserve capitalization where necessary
[x] paper is error free - no invalid refs without justification

crvernon commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

crvernon commented 1 month ago

@hsherrod2019 - Things are looking good, I just need you to address the following before I accept this one:

[x] Some of the headers in the paper have a colon behind them. Please remove the colons to make things consistent throughout the paper.
[x] Please ensure items needing capitalization in the references in your bib file are maintained after the paper is compiled. You can do this by adding curly brackets around items needing to maintain formatting. For example, LINE 186 should have "r" capitalized. Please check to make sure there are not others that need to be fixed as well.

No need to conduct another release. Once these have been changed, I will move forward with acceptance.

hsherrod2019 commented 1 month ago

@crvernon Thank you!

I have removed the colons from the headers and ensured capitalization for the references. Both changes are pushed to GitHub now as well.

crvernon commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

crvernon commented 1 month ago

@editorialbot accept

editorialbot commented 1 month ago

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

editorialbot commented 1 month ago

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editorialbot commented 1 month ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 month ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/5632
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06715
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

crvernon commented 1 month ago

@editorialbot reaccept

editorialbot commented 1 month ago

Rebuilding paper!

editorialbot commented 1 month ago

🌈 Paper updated!

New PDF and metadata files :point_right: https://github.com/openjournals/joss-papers/pull/5633

kanishkan91 commented 1 month ago

@editorialbot commands

editorialbot commented 1 month ago

Hello @kanishkan91, here are the things you can ask me to do:


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# Remove from this issue's reviewers list
@editorialbot remove @username from reviewers

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Assign a user as the editor of this submission
@editorialbot assign @username as editor

# Remove the editor assigned to this submission
@editorialbot remove editor

# Remind an author, a reviewer or the editor to return to a review after a 
# certain period of time (supported units days and weeks)
@editorialbot remind @reviewer in 2 weeks

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for version
@editorialbot set v1.0.0 as version

# Set a value for branch
@editorialbot set joss-paper as branch

# Set a value for repository
@editorialbot set https://github.com/organization/repo as repository

# Set a value for the archive DOI
@editorialbot set 10.5281/zenodo.6861996 as archive

# Mention the EiCs for the correct track
@editorialbot ping track-eic

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Recommends the submission for acceptance
@editorialbot recommend-accept

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Flag submission with questionable scope
@editorialbot query scope

# Get a link to the complete list of reviewers
@editorialbot list reviewers

# Creates a post-review checklist with editor and authors tasks
@editorialbot create post-review checklist

# Open the review issue
@editorialbot start review

kanishkan91 commented 1 month ago

@editorialbot remove @@stephpenn1 from reviewers

editorialbot commented 1 month ago

@@stephpenn1 removed from the reviewers list!

kanishkan91 commented 1 month ago

@crvernon could you try re-accepting the paper? I seemed to have added an extra erroneous reviewer at the very beginning which I removed now.

kanishkan91 commented 1 month ago

@editorialbot generate pdf

crvernon commented 1 month ago

@editorialbot reaccept

@kanishkan91 no problem

editorialbot commented 1 month ago

Rebuilding paper!

openjournals / joss-reviews