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

whedon commented 4 years ago

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

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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:

Make sure you're logged in to your GitHub account
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?

arokem commented 4 years ago

@whedon check references

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.5281/zenodo.1423046 is OK

MISSING DOIs

- https://doi.org/10.18653/v1/n16-3020 may be missing for title: "Why Should I Trust You?": Explaining the Predictions of Any Classifier
- https://doi.org/10.1080/10618600.2014.907095 may be missing for title: Peeking inside the black box: Visualizing statistical learning with plots of individual conditional expectation

INVALID DOIs

- None

arokem commented 4 years ago

@So-Cool : could you please add the DOIs mentioned above?

Two other comments about references:

Since scikit learn is mentioned so prominently, it would be appropriate to cite their 2011 JMLR paper about the software: http://www.jmlr.org/papers/v12/pedregosa11a.html
What is the difference between this paper and the arXiv preprint referenced? Is that preprint already published elsewhere?

Thanks!

So-Cool commented 4 years ago

@whedon check references

whedon commented 4 years ago

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

So-Cool commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

So-Cool commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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

So-Cool commented 4 years ago

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 commented 4 years ago

Yup. Just let me know here when it settles.

arfon commented 4 years ago

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 commented 4 years ago

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

So-Cool commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

@whedon set 10.5281/zenodo.3833199 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3833199 is the archive.

arfon commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

arfon commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

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 commented 4 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1452

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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 commented 4 years ago

@whedon accept deposit=true

whedon commented 4 years ago

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

whedon commented 4 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 4 years 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/1453
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01904
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

arfon commented 4 years ago

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

@So-Cool - your paper is now accepted into JOSS :zap::rocket::boom:

whedon commented 4 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01904/status.svg)](https://doi.org/10.21105/joss.01904)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01904">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01904/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01904/status.svg
   :target: https://doi.org/10.21105/joss.01904

This is how it will look in your documentation:

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