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[REVIEW]: `datastructures`: An R package for organisation and storage of data #910

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whedon opened this Issue Aug 22, 2018 · 23 comments

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whedon commented Aug 22, 2018

Submitting author: @dirmeier (Simon Dirmeier)
Repository: https://github.com/dirmeier/datastructures
Version: v0.2.7
Editor: @karthik
Reviewer: @fabian-s
Archive: 10.5281/zenodo.1404281

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/393deb8b3b02d221559bf82bf2c4f108"><img src="http://joss.theoj.org/papers/393deb8b3b02d221559bf82bf2c4f108/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/393deb8b3b02d221559bf82bf2c4f108/status.svg)](http://joss.theoj.org/papers/393deb8b3b02d221559bf82bf2c4f108)

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

@fabian-s, 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 @karthik know.

Please try and complete your review in the next two weeks

Review checklist for @fabian-s

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 (v0.2.7)?
  • Authorship: Has the submitting author (@dirmeier) 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 Aug 22, 2018

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Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @fabian-s 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

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For a list of things I can do to help you, just type:

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whedon commented Aug 22, 2018

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @fabian-s 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 Aug 22, 2018

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Attempting PDF compilation. Reticulating splines etc...
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whedon commented Aug 22, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Aug 22, 2018

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fabian-s Aug 27, 2018

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@whedon generate pdf

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fabian-s commented Aug 27, 2018

@whedon generate pdf

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fabian-s Aug 27, 2018

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@dirmeier "generate pdf" might be an author command --
can you try to get whedon to re-generate your updated paper so I can check the missing checkmarks ;)

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fabian-s commented Aug 27, 2018

@dirmeier "generate pdf" might be an author command --
can you try to get whedon to re-generate your updated paper so I can check the missing checkmarks ;)

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dirmeier Aug 27, 2018

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@whedon generate pdf

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dirmeier commented Aug 27, 2018

@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...
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whedon commented Aug 27, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Aug 27, 2018

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fabian-s Aug 27, 2018

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well damn! that worked!

@karthik: this is done (and very well done, too, @dirmeier!) except the fact that the version is off by one (says 0.2.7 in my checklist above, is now at 0.2.8) -- does that matter? can you correct from your side?

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fabian-s commented Aug 27, 2018

well damn! that worked!

@karthik: this is done (and very well done, too, @dirmeier!) except the fact that the version is off by one (says 0.2.7 in my checklist above, is now at 0.2.8) -- does that matter? can you correct from your side?

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dirmeier Aug 27, 2018

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and very well done, too, @dirmeier!

thanks :). I incremented the version after the review, to keep track of the changes. Thanks for the time and effort reviewing, Fabian. That definitely improved the package a lot.

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dirmeier commented Aug 27, 2018

and very well done, too, @dirmeier!

thanks :). I incremented the version after the review, to keep track of the changes. Thanks for the time and effort reviewing, Fabian. That definitely improved the package a lot.

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karthik Aug 27, 2018

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@fabian-s The Whedon commands are only for the editors. Thanks for checking in regarding the version issue. That is not a problem and generally to be expected. Authors will submit a version, but in the process of revisions end up bumping to something higher. That is typically what we expect.

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karthik commented Aug 27, 2018

@fabian-s The Whedon commands are only for the editors. Thanks for checking in regarding the version issue. That is not a problem and generally to be expected. Authors will submit a version, but in the process of revisions end up bumping to something higher. That is typically what we expect.

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karthik Aug 27, 2018

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@dirmeier The next step is for you to archive this software on Zenodo. Please follow instructions there (making sure to input all metadata) and then update this thread with your DOI. Once I have that, I can proceed with acceptance.

And thanks so much @fabian-s for a timely review! We really appreciate it. 🙏

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karthik commented Aug 27, 2018

@dirmeier The next step is for you to archive this software on Zenodo. Please follow instructions there (making sure to input all metadata) and then update this thread with your DOI. Once I have that, I can proceed with acceptance.

And thanks so much @fabian-s for a timely review! We really appreciate it. 🙏

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dirmeier Aug 27, 2018

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Hello @karthik , the DOI is 10.5281/zenodo.1404281. Thanks for everything.

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dirmeier commented Aug 27, 2018

Hello @karthik , the DOI is 10.5281/zenodo.1404281. Thanks for everything.

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karthik Aug 27, 2018

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@whedon set 10.5281/zenodo.1404281 as archive

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karthik commented Aug 27, 2018

@whedon set 10.5281/zenodo.1404281 as archive

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whedon Aug 27, 2018

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OK. 10.5281/zenodo.1404281 is the archive.

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whedon commented Aug 27, 2018

OK. 10.5281/zenodo.1404281 is the archive.

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@whedon generate pdf

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karthik commented Aug 27, 2018

@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...
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whedon commented Aug 27, 2018

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@dirmeier Congrats, your paper has been accepted! @fabian-s Thanks so much for the prompt review, we really appreciate it.

@arfon this is ready to process.

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karthik commented Aug 27, 2018

@dirmeier Congrats, your paper has been accepted! @fabian-s Thanks so much for the prompt review, we really appreciate it.

@arfon this is ready to process.

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dirmeier Aug 27, 2018

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Cool, that's great. Thanks @karthik and thanks for the review again @fabian-s

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dirmeier commented Aug 27, 2018

Cool, that's great. Thanks @karthik and thanks for the review again @fabian-s

@karthik karthik added the accepted label Aug 27, 2018

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@fabian-s many thanks for your review here and to @karthik for editing this submission

@dirmeier - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00910 ⚡️ 🚀 💥

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arfon commented Aug 27, 2018

@fabian-s many thanks for your review here and to @karthik for editing this submission

@dirmeier - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00910 ⚡️ 🚀 💥

@arfon arfon closed this Aug 27, 2018

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🎉🎉🎉 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.00910/status.svg)](https://doi.org/10.21105/joss.00910)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00910">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00910/status.svg" alt="DOI badge" >
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This is how it will look in your documentation:

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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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whedon commented Aug 27, 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.00910/status.svg)](https://doi.org/10.21105/joss.00910)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00910">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00910/status.svg" alt="DOI badge" >
</a>

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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danielskatz Aug 28, 2018

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just a note that one of the items in the review is not checked, though this has been accepted.

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danielskatz commented Aug 28, 2018

just a note that one of the items in the review is not checked, though this has been accepted.

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