[REVIEW]: Redflag: machine learning safety by design

[editorialbot]

Submitting author: @kwinkunks (Matt Hall)
Repository: https://github.com/scienxlab/redflag
Branch with paper.md (empty if default branch): paper
Version: v0.4.1
Editor: @mbobra
Reviewers: @jsheunis, @kaurao
Archive: Pending

Status

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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

@jsheunis & @kaurao, 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 @mbobra 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 @jsheunis

📝 Checklist for @kaurao

[editorialbot]

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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (901.8 files/s, 202359.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          17            933           2034           1681
Markdown                        14            165              0            375
Jupyter Notebook                 5              0           4496            295
SVG                              2              2              2            261
YAML                             4             23              0            105
TOML                             1              9              2             68
CSS                              1              7              3             60
reStructuredText                 2             58             81             55
TeX                              1              2              0             34
make                             1              4              3             13
-------------------------------------------------------------------------------
SUM:                            48           1203           6621           2947
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 816

[editorialbot]

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

OK DOIs

- 10.3390/ijerph18126329 is OK
- 10.25080/Majora-92bf1922-00a is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[mbobra]

@jsheunis @kaurao Thank you so much for agreeing to review! You can find the article in the comment box above ⬆️ and the software repository linked in the first comment box on this issue. To generate your checklist, use the following command:

@editorialbot generate my checklist

I think you're good to go. Again, JOSS is an open review process and we encourage communication between the reviewers, the submitting author, and the editor. And please feel free to ask me questions, I'm always around.

Can you please respond here (or give a thumbs up) so I know you're in the right place and found all the materials?

[jsheunis]

Review checklist for @jsheunis

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/scienxlab/redflag?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@kwinkunks) 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?

[kwinkunks]

Thank you for the feedback @jsheunis - much appreciated - I plan to get to these over the next few days.

[kwinkunks]

@mbobra @jsheunis Thanks both for looking at this submission. I think I've improved things and addressed the issues raised; tagged a new version with the changes and the paper branch is up to date. I guess we're waiting for another review too, but I wasn't sure if there was a step I should take at this point?

@editorialbot generate pdf

[kaurao]

Review checklist for @kaurao

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/scienxlab/redflag?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@kwinkunks) 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?

[mbobra]

I wasn't sure if there was a step I should take at this point?

👋 @kwinkunks Nice, thanks! This was speedy. I think there are still some unchecked boxes on @jsheunis' review -- if you think you've addressed all remaining concerns, then feel free to ping them here. Otherwise, let's give the other reivewer some time to finish the review.

[kwinkunks]

Thank you for the review @kaurao - I will try to get to the issues this week, weekend for sure.

@mbobra I do think I got everything, but maybe I'll ping Stephan when I've revised for Kaustubh then we can see where we're at. Cheers!

[kwinkunks]

Just wanted to update everyone; I guess I got a bit derailed over the holiday period. I am working on improving the docs and will revert soon with a response to Kaustubh's suggestions. Cheers!

[mbobra]

Sounds good, thanks for the update @kwinkunks!

[mbobra]

👋 @kwinkunks How is it going? Do you need any help with this submission?

[kwinkunks]

Hello @mbobra -- thank you for checking in. Sorry to be so slow. I must admit, I got a bit crushed by item 4 in the 'final' issue scienxlab/redflag#97 -- probably I blew it out of proportion. If it's okay with you, I will review where I am and close that issue -- then I'll come back here ASAP.

[crvernon]

👋 @mbobra - could you check in on this one and let me know if we need to pause this submission? Thanks!