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[REVIEW]: compboost: Modular Framework for Component-Wise Boosting #967

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whedon opened this Issue Sep 21, 2018 · 37 comments

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whedon commented Sep 21, 2018

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

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/94cfdbbfdfc8796c5bdb1a74ee59fcda"><img src="http://joss.theoj.org/papers/94cfdbbfdfc8796c5bdb1a74ee59fcda/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/94cfdbbfdfc8796c5bdb1a74ee59fcda/status.svg)](http://joss.theoj.org/papers/94cfdbbfdfc8796c5bdb1a74ee59fcda)

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:

  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.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

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?
  • Version: Does the release version given match the GitHub release (v0.1.0)?
  • Authorship: Has the submitting author (@schalkdaniel) 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 function 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

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
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whedon commented Sep 21, 2018

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 🎉.

⭐️ 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
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whedon commented Sep 21, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Sep 21, 2018

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brainstorm commented Sep 21, 2018

@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 :)

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moonso commented Sep 21, 2018

@whedon commands

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whedon commented Sep 21, 2018

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Compile the paper
@whedon generate pdf

🚧 🚧 🚧 Experimental Whedon features 🚧 🚧 🚧

# Compile the paper from a custom git branch
@whedon generate pdf from branch custom-branch-name

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moonso commented Sep 24, 2018

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

  1. 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?

  2. 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!

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brainstorm commented Sep 24, 2018

  1. Yes, that's right @moonso, your overall task (TL;DR'd) here is to validate the operation/usefulness/completeness of this package.

  2. 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! ;)

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schalkdaniel commented Sep 25, 2018

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).

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brainstorm commented Sep 26, 2018

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?

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schalkdaniel commented Sep 26, 2018

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.

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brainstorm commented Sep 27, 2018

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! ;)

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schalkdaniel commented Sep 27, 2018

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. :)

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moonso commented Sep 27, 2018

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

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schalkdaniel commented Sep 27, 2018

Hi @moonso, thanks for your effort. 👍

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

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?

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moonso commented Sep 27, 2018

I understand. It's a question for @brainstorm

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brainstorm commented Sep 28, 2018

@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! 👍

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arfon commented Sep 28, 2018

@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

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brainstorm commented Oct 1, 2018

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

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schalkdaniel commented Oct 1, 2018

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

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brainstorm commented Oct 8, 2018

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

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schalkdaniel commented Oct 8, 2018

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brainstorm commented Oct 9, 2018

@whedon set 10.2402/compboost.0.1.0 as archive

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whedon commented Oct 9, 2018

OK. 10.2402/compboost.0.1.0 is the archive.

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brainstorm commented Oct 9, 2018

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whedon commented Oct 9, 2018

OK. 10.2402/compboost.0.1.0 is the archive.

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arfon commented Oct 9, 2018

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

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schalkdaniel commented Oct 11, 2018

@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.

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schalkdaniel commented Oct 12, 2018

@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.

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arfon commented Oct 12, 2018

@whedon set 10.5281/zenodo.1460435 as archive

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whedon commented Oct 12, 2018

OK. 10.5281/zenodo.1460435 is the archive.

@arfon arfon added the accepted label Oct 12, 2018

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arfon commented Oct 12, 2018

@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 ⚡️ 🚀 💥

@arfon arfon closed this Oct 12, 2018

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whedon commented Oct 12, 2018

🎉🎉🎉 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](http://joss.theoj.org/papers/10.21105/joss.00967/status.svg)](https://doi.org/10.21105/joss.00967)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00967">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00967/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.00967/status.svg
   :target: https://doi.org/10.21105/joss.00967

This is how it will look in your documentation:

DOI

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schalkdaniel commented Oct 31, 2018

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!

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arfon commented Oct 31, 2018

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.

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schalkdaniel commented Oct 31, 2018

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

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arfon commented Oct 31, 2018

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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