[REVIEW]: modelStudio: Interactive Studio with Explanations for ML Predictive Models

whedon commented 4 years ago

Submitting author: @hbaniecki (Hubert Baniecki) Repository: https://github.com/ModelOriented/modelStudio Version: v0.1.9 Editor: @terrytangyuan Reviewer: @acolum, @expectopatronum Archive: 10.5281/zenodo.3527770

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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

@acolum & @expectopatronum, 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 @terrytangyuan know.

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

Review checklist for @acolum

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 (@hbaniecki) 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 @expectopatronum

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 (@hbaniecki) 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?

whedon commented 4 years ago

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

:star: Important :star:

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@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

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

hbaniecki commented 4 years ago

Great! I am aware that i need to fix paper.bib file to properly code references. I will probably shorten the example. Then Figure 1 should fit one page earlier (same with Figure 2).

hbaniecki commented 4 years ago

@expectopatronum

acolum commented 4 years ago

Everything in the software and documentation looks good, but in the paper, there's some spelling, grammar, and citation errors.

hbaniecki commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

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

hbaniecki commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

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

acolum commented 4 years ago

The references and citations look great, but I'm still noticing a few spelling errors in the first paragraph under "Introduction" and the paragraph under "Conclusions."

expectopatronum commented 4 years ago

Yes, I also found several typos / missing articles. I marked them in the PDF: 10.21105.joss.01798_typos.pdf

hbaniecki commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

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

hbaniecki commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

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

hbaniecki commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

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

hbaniecki commented 4 years ago

Hopefully it is clean now.

hbaniecki commented 4 years ago

Hi! I would like to answer any further questions or resolve remarks to finish the review process (hopefully, by the end of the week) . 🔜 🔚 @acolum @expectopatronum

acolum commented 4 years ago

@hbaniecki Everything looks great, but there's still a few typos in the paper. In the second sentence under "Introduction," can you correct the spelling of "beeing" to "being" and "lead" to "leads"? After these are fixed, I'd be happy to approve everything for publication.

expectopatronum commented 4 years ago

Same here, after the typos are fixed, I can accept the paper.

hbaniecki commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

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

acolum commented 4 years ago

Looks great to me! I'm finished with my review and can now recommend this package and paper for publication.

expectopatronum commented 4 years ago

Same here!

hbaniecki commented 4 years ago

@terrytangyuan

terrytangyuan commented 4 years ago

Thanks everyone!

@hbaniecki At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

The title of the archive is the same as the JOSS paper title That the authors of the archive are the same as the JOSS paper authors I can then move forward with accepting the submission.

hbaniecki commented 4 years ago

Hi @terrytangyuan ! I am sorry, that it took so long but I had to wait for the finalized new version. It will be v0.1.9 and here is the link: https://zenodo.org/record/3527770.

hbaniecki commented 4 years ago

@whedon set v0.1.9 as version

whedon commented 4 years ago

I'm sorry @hbaniecki, I'm afraid I can't do that. That's something only editors are allowed to do.

hbaniecki commented 4 years ago

well, it will be v0.1.9 and 10.5281/zenodo.3527770

terrytangyuan commented 4 years ago

@whedon set v0.1.9 as version

whedon commented 4 years ago

OK. v0.1.9 is the version.

terrytangyuan commented 4 years ago

@whedon set 10.5281/zenodo.3527770 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3527770 is the archive.

terrytangyuan commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1083

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1083, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

whedon commented 4 years ago


OK DOIs

- 10.21105/joss.01444 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/10.32614/rj-2018-072 may be missing for title: Explanations of model predictions with live and breakDown packages
- https://doi.org/10.21105/joss.00786 may be missing for title: iml: An R package for Interpretable Machine Learning
- https://doi.org/10.32614/rj-2017-016 may be missing for title: pdp: An R Package for Constructing Partial Dependence Plots

INVALID DOIs

- None

terrytangyuan commented 4 years ago

@hbaniecki Could you fix the missing DOIs listed above?

hbaniecki commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

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

openjournals / joss-reviews