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[REVIEW]: modelStudio: Interactive Studio with Explanations for ML Predictive Models #1798

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whedon opened this issue Oct 10, 2019 · 85 comments
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@whedon whedon commented Oct 10, 2019

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

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/9eec8c9d1969fbd44b3ea438a74af911"><img src="https://joss.theoj.org/papers/9eec8c9d1969fbd44b3ea438a74af911/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/9eec8c9d1969fbd44b3ea438a74af911/status.svg)](https://joss.theoj.org/papers/9eec8c9d1969fbd44b3ea438a74af911)

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:

  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 @terrytangyuan know.

Please try and complete your review in the next two weeks

Review checklist for @acolum

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

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 (@hbaniecki) 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 @expectopatronum

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

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 (@hbaniecki) 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?
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@whedon whedon commented Oct 10, 2019

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 🎉.

⭐️ 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:

watching

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

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
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@whedon whedon commented Oct 10, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Oct 10, 2019

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@hbaniecki hbaniecki commented Oct 10, 2019

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).

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@hbaniecki hbaniecki commented Oct 16, 2019

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@acolum acolum commented Oct 18, 2019

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

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@hbaniecki hbaniecki commented Oct 19, 2019

@whedon generate pdf

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@whedon whedon commented Oct 19, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Oct 19, 2019

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@hbaniecki hbaniecki commented Oct 19, 2019

@whedon generate pdf

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@whedon whedon commented Oct 19, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Oct 19, 2019

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@acolum acolum commented Oct 20, 2019

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."

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@expectopatronum expectopatronum commented Oct 21, 2019

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

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@hbaniecki hbaniecki commented Oct 21, 2019

@whedon generate pdf

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@whedon whedon commented Oct 21, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Oct 21, 2019

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@hbaniecki hbaniecki commented Oct 22, 2019

@whedon generate pdf

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@whedon whedon commented Oct 22, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Oct 22, 2019

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@hbaniecki hbaniecki commented Oct 22, 2019

@whedon generate pdf

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@whedon whedon commented Oct 22, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Oct 22, 2019

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@hbaniecki hbaniecki commented Oct 22, 2019

Hopefully it is clean now.

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@whedon whedon commented Nov 4, 2019

Check final proof 👉 openjournals/joss-papers#1084

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1084, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@terrytangyuan terrytangyuan commented Nov 4, 2019

This paper looks good to me now! Handing over to @openjournals/joss-eics!

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@kyleniemeyer kyleniemeyer commented Nov 5, 2019

Hi @hbaniecki, I made a few edits to the paper and references, if you could merge these:
ModelOriented/modelStudio#31 and ModelOriented/modelStudio#32

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@hbaniecki hbaniecki commented Nov 5, 2019

Hi @kyleniemeyer, I merged your PR.

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@kyleniemeyer kyleniemeyer commented Nov 5, 2019

@whedon generate pdf

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@whedon whedon commented Nov 5, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 5, 2019

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@kyleniemeyer kyleniemeyer commented Nov 5, 2019

@hbaniecki sorry, one last fix I noticed when reviewing: ModelOriented/modelStudio#33

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@hbaniecki hbaniecki commented Nov 5, 2019

@kyleniemeyer np. I merged.

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@kyleniemeyer kyleniemeyer commented Nov 5, 2019

@whedon generate pdf

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@whedon whedon commented Nov 5, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 5, 2019

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@kyleniemeyer kyleniemeyer commented Nov 5, 2019

@whedon accept

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@whedon whedon commented Nov 5, 2019

Attempting dry run of processing paper acceptance...
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@kyleniemeyer kyleniemeyer commented Nov 5, 2019

@whedon accept

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@whedon whedon commented Nov 5, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Nov 5, 2019


OK DOIs

- 10.18653/v1/n16-3020 is OK
- 10.32614/RJ-2018-072 is OK
- 10.21105/joss.01444 is OK
- 10.21105/joss.00786 is OK
- 10.32614/rj-2017-016 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Nov 5, 2019

Check final proof 👉 openjournals/joss-papers#1090

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1090, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@kyleniemeyer kyleniemeyer commented Nov 5, 2019

@whedon accept deposit=true

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@whedon whedon commented Nov 5, 2019

Doing it live! Attempting automated processing of paper acceptance...
@whedon whedon added the accepted label Nov 5, 2019
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@whedon whedon commented Nov 5, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Nov 5, 2019

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#1091
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01798
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

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@kyleniemeyer kyleniemeyer commented Nov 5, 2019

Congrats @hbaniecki on your article's publication in JOSS! Many thanks to @acolum and @expectopatronum for reviewing this, and @terrytangyuan for editing.

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@whedon whedon commented Nov 5, 2019

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

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.01798/status.svg)](https://doi.org/10.21105/joss.01798)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01798">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01798/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01798/status.svg
   :target: https://doi.org/10.21105/joss.01798

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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@hbaniecki hbaniecki commented Nov 5, 2019

wow even after so many reviews i can see a typo. @kyleniemeyer is it possible to fix the paper after the publication?

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@kyleniemeyer kyleniemeyer commented Nov 5, 2019

Oh no! Um, I think so. Can you fix the source file and let us know? (@arfon?)

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@hbaniecki hbaniecki commented Nov 5, 2019

I feel ashamed but hope that it can be updated. Fixed paper.md.

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@arfon arfon commented Nov 5, 2019

Oh no! Um, I think so. Can you fix the source file and let us know? (@arfon?)

No problem. Paper updated based on the latest paper.md in master. FWIW, the new PDF might not show up for a few hours as there's caching in place for the PDFs on the JOSS site.

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