[REVIEW]: compboost: Modular Framework for Component-Wise Boosting

whedon commented 6 years ago

Submitting author: @schalkdaniel (Daniel Schalk) Repository: https://github.com/schalkdaniel/compboost Version: v0.1.0 Editor: @brainstorm Reviewer: @moonso Archive: 10.5281/zenodo.1460435

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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) 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

@moonso, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @brainstorm know.

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

Review checklist for @moonso

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: Does the release version given match the GitHub release (v0.1.0)?
[x] Authorship: Has the submitting author (@schalkdaniel) 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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
[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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

whedon commented 6 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @moonso it looks like you're currently assigned as the reviewer for this paper :tada:.

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whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

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

brainstorm commented 6 years ago

@moonso, please read the instructions on this issue, you are now the reviewer for this JOSS paper, let me know if anything is unclear about how to proceed with it :)

moonso commented 6 years ago

@whedon commands

whedon commented 6 years ago

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moonso commented 6 years ago

Hi @brainstorm ! Thanks for asking me to review, I will do my best here. To start with I have a few questions:

The theory and real world use of this project are a bit over my expertise. When I read the reviewer guidelines it is mostly about testing the functionality of the package so I guess this is my focus?
When I post issues in the package should I use some special words to indicate that I am a reviewer? In this case the LICENCE does not follow any of the approved ones as far as I can tell. Not sure how to communicate that in the issue.

Thx!

brainstorm commented 6 years ago

Yes, that's right @moonso, your overall task (TL;DR'd) here is to validate the operation/usefulness/completeness of this package.
I already assigned you as a reviewer, so whedon, our friendly bot knows you already, no worries ;)

@schalkdaniel, as @moonso points out, you should use a valid, OSI approved LICENSE.

@moonso You can move on into reviewing the other points while the author addresses things. Thanks a lot for helping out JOSS! ;)

schalkdaniel commented 6 years ago

Hi @moonso @brainstorm, I have added another file LICENSE.md containing the plain text of the MIT license. The file LICENSE is required by CRAN and should just include the year and copyright holder (if I understood that correctly).

brainstorm commented 6 years ago

Weird, are you sure @schalkdaniel?:

https://cran.r-project.org/web/licenses/

According to:

https://cran.r-project.org/doc/contrib/Leisch-CreatingPackages.pdf

The format you mention seems to belong to DESCRIPTION?

schalkdaniel commented 6 years ago

But isn't that what I have done @brainstorm? Maybe I miss something, but my DESCRIPTION file contains

License: MIT + file LICENSE

and refers to the LICENSE file as specified in your link and also here. Some other repositories follow the same guidelines, e.g. iml, pdfsearch, or checkr.

brainstorm commented 6 years ago

Sure, I just find it confusing to have two LICENSE(.md) files, but fair enough, @moonso, proceed with the other aspects of this JOSS paper whenever you can, thanks again for the efforts! ;)

schalkdaniel commented 6 years ago

Ah, yes I see. Originally there were one LICENSE and the plain text of the MIT license was included in the Readme. The intention to include another LICENSE.md file came after looking at repositories from the tidyverse (e.g. dplyr) where they do it like this. :)

moonso commented 6 years ago

Hi @schalkdaniel @brainstorm . I'm done with the review now, nice job @schalkdaniel 😸 . The documentation is clear and comprehensive, examples could be followed. I went through a little installation hell, nice to see that it exists in R to 😛 , it had nothing to do with this package though. It was to install 'devtools' on my Mac OS.

My only remark is the contribution of the co-authors. Thomas Janek has contributed a fairly small part of the code compare to the main author. Also it is unclear how Bernd Bischl have contributed, I guess he is the PI but I think it should be stated somewhere how this person have contributed.

Again good job!

Best

/Måns

schalkdaniel commented 6 years ago

Hi @moonso, thanks for your effort. :+1:

Yeah, installing devtools is not that straight forward. But I hope the package is on CRAN soon and then (hopefully) easier to install. :smile:

Regarding the contribution of the authors: The project has started as master thesis and will probably go on and on. Janek and Bernd give much input on general principles like theory, software design, and many other important things that are not directly visible. Janek also developed main parts of the R API.

I don't know where it is best to mention their contribution. Do you have any preferences?

moonso commented 6 years ago

I understand. It's a question for @brainstorm

brainstorm commented 6 years ago

@arfon Do we have any established policies for contributions that are not reflected/seen on github?

Other than that, this is a thumbs up submission, thanks everyone! 👍

arfon commented 6 years ago

@arfon Do we have any established policies for contributions that are not reflected/seen on github?

Ultimately, authorship is left up to the authors but we have some guidelines here: https://joss.readthedocs.io/en/latest/review_criteria.html#authorship

brainstorm commented 6 years ago

Alright, nothing seems off as far as I can see regarding authorship then and the author stated publicly who contributed where.

schalkdaniel commented 6 years ago

@brainstorm I have added a file CONTRIBUTORS.md and linked on this file from the Readme.

brainstorm commented 6 years ago

@schalkdaniel Could you please make a tarball and push it on Zenodo so we can attach a DOI to it?

schalkdaniel commented 6 years ago

@brainstorm Sure, the link is https://zenodo.org/record/1451302#.W7sPNXUzan8

brainstorm commented 6 years ago

@whedon set 10.2402/compboost.0.1.0 as archive

whedon commented 6 years ago

OK. 10.2402/compboost.0.1.0 is the archive.

brainstorm commented 6 years ago

@whedon set https://doi.org/10.2402/compboost.0.1.0 as archive

whedon commented 6 years ago

OK. 10.2402/compboost.0.1.0 is the archive.

arfon commented 6 years ago

@schalkdaniel - it doesn't look like https://doi.org/10.2402/compboost.0.1.0 resolves yet?

schalkdaniel commented 6 years ago

@arfon - I have no idea why it does not work yet. I have asked the Zenodo support what I could do to get it work. I will let you know here as soon as I have a response.

schalkdaniel commented 5 years ago

@arfon - I have uploaded a new version. The archive is: https://doi.org/10.5281/zenodo.1460435

The problem was that zenodo does not register custom dois. Sorry for that.

arfon commented 5 years ago

@whedon set 10.5281/zenodo.1460435 as archive

whedon commented 5 years ago

OK. 10.5281/zenodo.1460435 is the archive.

arfon commented 5 years ago

@moonso - many thanks for your review here and to @brainstorm for editing this submission ✨

@schalkdaniel - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00967 :zap: :rocket: :boom:

whedon commented 5 years ago

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schalkdaniel commented 5 years ago

Hi @arfon, is it possible to make a small change to the paper? I (stupidly) used a wrong latex symbol and didn't recognize it during the review process. Instead of \geq it should be \gg.

It would be really great if I could update the paper with the correct symbol.

Thanks for your efforts!

arfon commented 5 years ago

It would be really great if I could update the paper with the correct symbol.

Sure thing. Please go ahead and push the fix to the master branch of your repository and we can recompile the paper.

schalkdaniel commented 5 years ago

Thanks! @arfon I have pushed the fix to the master. :-)

arfon commented 5 years ago

Thanks! @arfon I have pushed the fix to the master. :-)

OK, I've updated the paper. This sometimes take a few hours to update on the live site because of caching.

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