[REVIEW]: stacks: Stacked Ensemble Modeling with Tidy Data Principles

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@simonpcouch@osorensen<!--end-editor-- Reviewers: @mcavs, @rcannood Archive: 10.5281/zenodo.6800026

Status

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Markdown: [![status](https://joss.theoj.org/papers/53561aa0549d1080196072043212fa16/status.svg)](https://joss.theoj.org/papers/53561aa0549d1080196072043212fa16)

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

@mcavs & @rcannood, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @rcannood

📝 Checklist for @mcavs

editorialbot commented 2 years ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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:

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editorialbot commented 2 years ago

Software report:

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gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 1031

editorialbot commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.01686 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

rcannood commented 2 years ago

Review checklist for @rcannood

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 https://github.com/tidymodels/stacks?
[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 (@simonpcouch) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[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?

simonpcouch commented 2 years ago

@editorialbot generate pdf

Updating with changes in response to https://github.com/tidymodels/stacks/issues/135!

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

simonpcouch commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

editorialbot commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.01686 is OK
- 10.2202/1544-6115.1309 is OK

MISSING DOIs

- 10.1163/1574-9347_dnp_e612900 may be a valid DOI for title: Keras

INVALID DOIs

- None

simonpcouch commented 2 years ago

re: the reported missing DOI, the suggested DOI for Keras doesn't seem to point to the deep learning framework, and the bib entry for this paper uses the requested citation in Keras docs.

osorensen commented 2 years ago

Thanks for clarifying @simonpcouch. Let's count that missing DOI as a false positive.

rcannood commented 2 years ago

Hi @simonpcouch @osorensen!

As mentioned earlier, I think the paper is very well written and is definitely worthy of publication at JOSS.

I had a few minor comments (tidymodels/stacks#135), but @simonpcouch was able to resolve them quickly. I have no further remarks.

Looking forward to seeing @mcavs' comments :)

osorensen commented 2 years ago

Thanks a lot for your review, @rcannood!

osorensen commented 2 years ago

:wave: @mcavs can you please update us on how it's going with your review? Please let me know if you have any questions about the process.

mcavs commented 2 years ago

Review checklist for @mcavs

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 https://github.com/tidymodels/stacks?
[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 (@simonpcouch) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[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?

mcavs commented 2 years ago

I am about to complete my review. I will share in a few days @osorensen.

osorensen commented 2 years ago

Thanks @mcavs. I notice that you have completed the checklist, but I hope @simonpcouch can address the issue you opened in the source repository before we proceed with acceptance.

simonpcouch commented 2 years ago

Absolutely—will address https://github.com/tidymodels/stacks/issues/137 first thing next week! Thanks all for your work.

simonpcouch commented 2 years ago

@editorialbot generate pdf

Updating with changes in response to https://github.com/tidymodels/stacks/issues/137!

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

osorensen commented 2 years ago

Thanks @simonpcouch.

At this point could you:

[ ] 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.

In the meantime I will read through the paper once more and let you know if I have any further suggested changes.

simonpcouch commented 2 years ago

Thank you! Of course.

The tag for the archived release is v0.2.4. The DOI is 10.5281/zenodo.6800026.

osorensen commented 2 years ago

@editorialbot set version v0.2.4

editorialbot commented 2 years ago

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

@editorialbot commands

osorensen commented 2 years ago

@editorialbot set v0.2.4 as version

editorialbot commented 2 years ago

Done! version is now v0.2.4

osorensen commented 2 years ago

@editorialbot set 10.5281/zenodo.6800026 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6800026

osorensen commented 2 years ago

@editorialbot check references

osorensen commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.01686 is OK
- 10.2202/1544-6115.1309 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

simonpcouch commented 2 years ago

@editorialbot generate pdf

Updating with changes in response to https://github.com/tidymodels/stacks/issues/138 and https://github.com/tidymodels/stacks/issues/139!

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

osorensen commented 2 years ago

Thanks @simonpcouch. I discovered a few more formatting issues, and made a PR in the package repository. Once that is fixed, we can proceed with acceptance.

osorensen commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.01686 is OK
- 10.2202/1544-6115.1309 is OK
- 10.21105/joss.01903 is OK

MISSING DOIs

- None

INVALID DOIs

- None

simonpcouch commented 2 years ago

@editorialbot generate pdf

Thanks for that PR, @osorensen! Regenerating with those changes.

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

osorensen commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.01686 is OK
- 10.2202/1544-6115.1309 is OK
- 10.21105/joss.01903 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3355, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 2 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/3356
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04471
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz commented 2 years ago

Congratulations to @simonpcouch (Simon Couch) and co-author!!

And thanks to @mcavs and @rcannood for reviewing, and to @osorensen for editing! We couldn't do this without you

openjournals / joss-reviews