editorialbot commented 1 year ago

Submitting author: !--author-handle-->@brendanc490@osorensen<!--end-editor-- Reviewers: @codeling, @osorensen Archive: 10.5281/zenodo.10463335

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b7c917fb55a1743a539139a74229fdcf"><img src="https://joss.theoj.org/papers/b7c917fb55a1743a539139a74229fdcf/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b7c917fb55a1743a539139a74229fdcf/status.svg)](https://joss.theoj.org/papers/b7c917fb55a1743a539139a74229fdcf)

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

@codeling & @osorensen, 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 @osorensen 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 @codeling

📝 Checklist for @osorensen

editorialbot commented 1 year ago

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

For a list of things I can do to help you, just type:

@editorialbot commands

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

@editorialbot generate pdf

editorialbot commented 1 year ago

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

OK DOIs

- 10.1109/VR46266.2020.00108 is OK
- 10.1002/jsid.1208 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=1.34 s (1625.9 files/s, 308114.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                            12              5              0         210852
YAML                             7              1              9          97436
JavaScript                      47           8132           5941          41744
CSS                             28           5967            238          16478
SVG                           2023              0             15           8089
Sass                            19            556             72           6965
LESS                            18            552             72           6907
HTML                             5            106             51           1103
reStructuredText                 6             75             18            347
Markdown                         5             50              0            248
DOS Batch                        1              8              1             26
TeX                              1              1              0             16
Python                           1             14             31             10
TypeScript                       1              4              0             10
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                          2175          15475           6455         390240
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 964

editorialbot commented 1 year ago

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

codeling commented 1 year ago

Review checklist for @codeling

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/DIDSR/WebXR-tools.git?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@brendanc490) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

codeling commented 1 year ago

Regarding the license: as far as I can see, the Unlicense is applied so far only in the LICENSE file in the JOSS-Submission branch, but the LICENSE file in the main branch and the license setting of the repository (shown on the right side of the code on the repositories "code" tab) still reference the CC0-1.0 license. This might satisfy the conditions of this review (not sure there as well, since the JOSS branch is allowed to be deleted after submission); in any case, it could be confusing to future users.

osorensen commented 1 year ago

Thanks @codeling. The license should definitely by the same also for the master branch. @brendanc490, can you please fix this?

osorensen commented 1 year ago

Review checklist for @osorensen

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/DIDSR/WebXR-tools.git?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@brendanc490) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

osorensen commented 1 year ago

@brendanc490, now that both @codeling and myself have completed our first round of reviews, you're welcome to start addressing the issues. Please reach out if you have any further questions.

osorensen commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

osorensen commented 11 months ago

👋 @brendanc490, I wanted to raise the issue that you don't want the main branch of the repository to be part of the review. This is of relevance, e.g., here. It is absolutely fine that you use the JOSS review branch for development during the review, but unless you have very compelling arguments, I think the final revised version should be merged onto the main branch, so that the reviewed software becomes the default. Does that sound ok to you?

brendanc490 commented 11 months ago

Thanks for pointing this out, you're absolutely right. We will merge the JOSS review branch onto the main branch when the review is complete.

On Mon, Jan 1, 2024 at 12:04 PM Øystein Sørensen @.***> wrote:

👋 @brendanc490 https://github.com/brendanc490, I wanted to raise the issue that you don't want the main branch of the repository to be part of the review. This is of relevance, e.g., here https://github.com/DIDSR/WebXR-tools/issues/8. It is absolutely fine that you use the JOSS review branch for development during the review, but unless you have very compelling arguments, I think the final revised version should be merged onto the main branch, so that the reviewed software becomes the default. Does that sound ok to you?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6021#issuecomment-1873402281, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQJNVRBIEETTYH5I2CZ7VI3YMLUDRAVCNFSM6AAAAAA66RIH2OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNZTGQYDEMRYGE . You are receiving this because you were mentioned.Message ID: @.***>

osorensen commented 11 months ago

👋 @codeling, could you please update your checklist based on the changes made by the authors? If there are further issues that should be addressed, please let us know.

codeling commented 11 months ago

@osorensen thanks for the ping, everything looks good from my side, I have updated my checklist!

osorensen commented 11 months ago

Thanks @codeling!

osorensen commented 11 months ago

@editorialbot generate pdf

osorensen commented 11 months ago

@editorialbot check references

editorialbot commented 11 months ago

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

OK DOIs

- 10.1109/VR46266.2020.00108 is OK
- 10.1002/jsid.1208 is OK

MISSING DOIs

- None

INVALID DOIs

- None

osorensen commented 11 months ago

@editorialbot generate post-review checklist

editorialbot commented 11 months ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

osorensen commented 11 months ago

@editorialbot commands

editorialbot commented 11 months ago

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


# List all available commands
@editorialbot commands

# Add to this issue's reviewers list
@editorialbot add @username as reviewer

# 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

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

# Perform checks on the repository
@editorialbot check repository

# 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 set 10.5281/zenodo.6861996 as archive

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

# 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

osorensen commented 11 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[x] Double check authors and affiliations (including ORCIDs)
[x] 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.
[x] Archive the release on Zenodo/figshare/etc and post the DOI here.
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a PR)
[x] Check the references in the paper for corrections (e.g. capitalization)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

editorialbot commented 11 months ago

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

osorensen commented 11 months ago

@brendanc490, could you please complete the tasks under the header "Additional Author Tasks After Review is Complete" in this checklist, and report back here when done?

In addition, please merge the JOSS branch onto the main branch now that the review is complete.

brendanc490 commented 11 months ago

I have completed the tasks in the checklist. The DOI from Zenodo is: 10.5281/zenodo.10463335. Also, the JOSS branch has been merged onto main. Please let me know if I missed anything.

osorensen commented 11 months ago

@editorialbot set 10.5281/zenodo.10463335 as archive

editorialbot commented 11 months ago

Done! archive is now 10.5281/zenodo.10463335

osorensen commented 11 months ago

@editorialbot set v1.0 as version

editorialbot commented 11 months ago

Done! version is now v1.0

osorensen commented 11 months ago

@editorialbot recommend-accept

editorialbot commented 11 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 11 months ago

Couldn't check the bibtex because branch name is incorrect: JOSS-Submission

editorialbot commented 11 months ago

:warning: Error preparing paper acceptance.

osorensen commented 11 months ago

@editorialbot set main as branch

editorialbot commented 11 months ago

Done! branch is now main

osorensen commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

osorensen commented 11 months ago

@editorialbot check references

editorialbot commented 11 months ago

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

OK DOIs

- 10.1109/VR46266.2020.00108 is OK
- 10.1002/jsid.1208 is OK

MISSING DOIs

- None

INVALID DOIs

- None

osorensen commented 11 months ago

@editorialbot recommend-accept

editorialbot commented 11 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 11 months ago

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

OK DOIs

- 10.1109/VR46266.2020.00108 is OK
- 10.1002/jsid.1208 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 11 months ago

:wave: @openjournals/bcm-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/4873, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 10 months ago

@brendanc490 I am the AEiC and here to help with final steps to process acceptance in JOSS. I have check this review, the archive link, your repository, and the paper. Most seems in order. I only have the below points that requires your attention:

[x] For your affiliations please add city, state, and country information. And please spell out the country name, e.g. Unites States of America.
[x] The sentence This is a contribution of the U.S. Food and Drug Administration and not subject to copyright, seems to lack a full stop at the end.

brendanc490 commented 10 months ago

Thanks for pointing this out. These have been addressed. Let me know if anything further is needed.

Thanks, Brendan

On Thu, Jan 11, 2024 at 12:03 PM Kevin Mattheus Moerman < @.***> wrote:

@brendanc490 https://github.com/brendanc490 I am the AEiC and here to help with final steps to process acceptance in JOSS. I have check this review, the archive link, your repository, and the paper. Most seems in order. I only have the below points that requires your attention:

For your affiliations please add city, state, and country information. And please spell out the country name, e.g. Unites States of America.

The sentence This is a contribution of the U.S. Food and Drug Administration and not subject to copyright, seems to lack a full stop at the end.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6021#issuecomment-1887587775, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQJNVRD5Y5PXEDLAP7LRYD3YOALNBAVCNFSM6AAAAAA66RIH2OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBXGU4DONZXGU . You are receiving this because you were mentioned.Message ID: @.***>

Kevin-Mattheus-Moerman commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

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

openjournals / joss-reviews

[REVIEW]: Open-Source Pattern Creation Tool for Medical Extended Reality Image Quality Assessment #6021

Status

Reviewer instructions & questions

Checklists

Review checklist for @codeling

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @osorensen

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance