[REVIEW]: FAT Forensics: A Python Toolbox for Implementing and Deploying Fairness, Accountability and Transparency Algorithms in Predictive Systems

[whedon]

Submitting author: @So-Cool (Kacper Sokol)
Repository: https://github.com/fat-forensics/fat-forensics
Version: 0.0.1
Editor: @arokem
Reviewer: @bernease, @osolari
Archive: 10.5281/zenodo.3833199

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/070c8b6b705bb47d1432673a1eb03f0c"><img src="https://joss.theoj.org/papers/070c8b6b705bb47d1432673a1eb03f0c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/070c8b6b705bb47d1432673a1eb03f0c/status.svg)](https://joss.theoj.org/papers/070c8b6b705bb47d1432673a1eb03f0c)

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

@bernease & @osolari, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @bernease

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 repository url?
• 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 (@So-Cool) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

Review checklist for @osolari

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 repository url?
• 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 (@So-Cool) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @bernease, @ @osolari it looks like you're currently assigned to review this paper 🎉.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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

@whedon commands

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

@whedon generate pdf

[whedon]

Attempting to check references...

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

PDF failed to compile for issue #1904 with the following error:

pandoc-citeproc: reference osolari not found
Error producing PDF.
! TeX capacity exceeded, sorry [input stack size=5000].
\reserved@a ->\def \reserved@a
*{\let @xs@assign @xs@expand@and@detokenize...
l.324 }

Looks like we failed to compile the PDF

[danielskatz]

👋 @arokem - I can't quite understand the status of this review - can you let me know where it is?

[danielskatz]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1904 with the following error:

pandoc-citeproc: reference osolari not found
Error producing PDF.
! TeX capacity exceeded, sorry [input stack size=5000].
\reserved@a ->\def \reserved@a
*{\let @xs@assign @xs@expand@and@detokenize...
l.324 }

Looks like we failed to compile the PDF

[danielskatz]

👋 @arfon - something seems messed up here - the reference that pandoc mentions isn't in the paper, I don't think, but is one of the reviewers (?!) And the reviewer info in the first comment in this issue seems to have an extra @ - Any ideas?

[arfon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[arfon]

👋 @arfon - something seems messed up here - the reference that pandoc mentions isn't in the paper, I don't think, but is one of the reviewers (?!) And the reviewer info in the first comment in this issue seems to have an extra @ - Any ideas?

Very weird. I'm not sure what's going on here. I've manually fixed up the review issue at the top. Also, the compilation error is related to the extra @ which was then being fed into Pandoc (as we now include reviewer names in the compiled papers).

[danielskatz]

Thanks @arfon

[danielskatz]

👋 @arokem - this is now ready for you to start the review process

[arokem]

Thanks!

@bernease, @osolari: have you had a chance to take a look at the software?

The paper pdf should be ready for your review as well now.

[arokem]

@bernease, @osolari: where does this review currently stand? Have you had a chance to take a look?

[osolari]

I am currently finishing my review.

[osolari]

Hi, I wasn't able to install the package. Did others manage to install it using simple pip?

[osolari]

@whedon @arokem I finished my review, but could not install the package using pip. Have you given it a try?

[osolari]

@bernease I finished my review, but could not install the package using pip. Have you given it a try?

[So-Cool]

@osolari, have you tried pip install fat-forensics?

[osolari]

yes!

[So-Cool]

@osolari, could you please paste here the log of executing this command?

[So-Cool]

Hi @arokem,
I added the missing DOIs and referenced scikit-learn; thank you for the pointers. The arXiv preprint is an extended version of the JOSS paper with usage examples and more thorough discussion of the relevant literature. We will be revising it in the coming months and submitting it to either a journal or a conference.

If any other revisions are needed, just let me know.

[arokem]

Thank you. Before we proceed, could you please:

• Make a tagged release of your software, and list the version tag of the archived version here.
• Archive the reviewed software in Zenodo or a similar service (e.g. figshare, an institutional repository)
• Check the archival deposit (e.g., in Zenodo) has the correct metadata, this includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it); you may also add the authors' ORCID.
• Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

[arokem]

Hi @So-Cool : have you had a chance to complete these steps? Any questions?

[So-Cool]

Hi @arokem, I'm merging two more PRs before creating the release, hence the delay. I should wrap it up soon. I hope that's OK with you.

[arokem]

Yup. Just let me know here when it settles.

[arfon]

Dear authors and reviewers

We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.

Thanks in advance for your understanding.

Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team.

[arfon]

👋 @So-Cool, just a friendly check-in to see how things are going with those last few steps outlined by @arokem?

[So-Cool]

Thanks @arfon. We've had a bit of a delay but the things are heading in the right direction now and we should wrap it up relatively soon.

[So-Cool]

Hi @arfon and @arokem,
apologies for the delay. The release tag is 0.1.0. The DOI of the release is 10.5281/zenodo.3833199.

[arfon]

@whedon set 10.5281/zenodo.3833199 as archive

[whedon]

OK. 10.5281/zenodo.3833199 is the archive.

[arfon]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.18653/v1/n16-3020 is OK
- 10.1214/aos/1013203451 is OK
- 10.1080/10618600.2014.907095 is OK
- 10.5281/zenodo.1423046 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1452

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1452, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[arfon]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.01904 joss-papers#1453
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01904
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

[arfon]

@bernease, @osolari - many thanks for your reviews here and to @arokem for editing this submission ✨

@So-Cool - your paper is now accepted into JOSS ⚡🚀💥

[whedon]

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

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