[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

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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

@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

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

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

Review checklist for @osolari

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

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: 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?
• [x] 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 :tada:.

:star: Important :star:

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:

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

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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]

:point_right: Check article proof :page_facing_up: :point_left:

[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?

[osolari]

ERROR: Could not find a version that satisfies the requirement fat-forensics (from versions: none) ERROR: No matching distribution found for fat-forensics

[osolari]

nvm. I tried it on my own machine and it was installed. sorry!

[So-Cool]

Are you trying to install it on Windows? At the moment only Linux and MacOS are supported. You may try to install it directly from sources (which may or may not work):

pip install git+https://github.com/fat-forensics/fat-forensics.git

[osolari]

both machines were Macs. Solved thanks!

Btw, should I just ping @whedon when I'm done?

[osolari]

@whedon @arfon @arokem I'm done with the review!

[arokem]

Hi @osolari, Thanks for your review! I see that there are still two boxes left unchecked in your review (functionality and references). Is this because you still have issues with these two items? If these are not properly addressed right now, could you please make some comments about the changes you believe need to be made?

[osolari]

Sorry I forgot to check functionality.

About the other two though. I think a brief literature review of the field with more references would help me understand the importance of the work better. Currently the report only references FATFORENSIC itself.

[osolari]

*by check I meant "check off".

[osolari]

@arokem I was wondering if I would receive an email indicating that I have completed my review service. :-)

[arokem]

Hey @osolari : have your previously-raised concerns (here) been addressed?

[osolari]

@arokem no it hasn't. :-)

[arokem]

Hey @bernease : have you had a chance to take a look at this? Thanks!

[osolari]

@arokem Would someone please confirm that I have submitted the review?

[arokem]

Hi @osolari : I believe that the authors are currently still waiting for comments from @bernease to proceed with their revision. I will ping her by email to see when she might have the chance to take a look.

[bernease]

Sorry for letting this fall off my radar. I can have the feedback into you by EOD Thursday conservatively, perhaps earlier if I'm able to clear some time later today.

[bernease]

I have completed the review to the best of my ability.

I have some concerns about the lack of references to related work as well as discussion of related software in the field, leading me keep these two fields unchecked for now. There is a singular reference to a pre-print manuscript describing the FATForensics software package in depth, Sokol, Santos-Rodriguez, and Flach (2019).

At minimum, would like to see directly comparative software packages in Python (e.g., eli5, AI Fairness 360) referenced and compared to FATForensics in JOSS submission. As the article stands, it is difficult to see where this work fits into the landscape of software without consulting the other manuscript from the authors. Should that be sufficient, I will mark these two criteria as met.

[So-Cool]

Thank you for the review, @bernease. I'll address your and @osolari's comments over the weekend and update the paper. I'll make sure to let you know when this is done.

[So-Cool]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[So-Cool]

We revised the paper taking into consideration your feedback and comments. @osolari and @bernease, please let us know if you find something that we can improve.

[bernease]

I have updated (and completed all marks) based on the updates provided by the author.

[arokem]

@whedon check DOI

[whedon]

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

@whedon commands

[arokem]

@whedon commands

[whedon]

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