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[REVIEW]: piggyback: Managing Larger Data on a GitHub Repository #971

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whedon opened this Issue Sep 22, 2018 · 16 comments

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whedon commented Sep 22, 2018

Submitting author: @cboettig (Carl Boettiger)
Repository: https://github.com/ropensci/piggyback
Version: v0.0.6
Editor: @arfon
Reviewer: @arfon
Archive: 10.5281/zenodo.1432527

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/5cfd756478838ef71796b6831efee8b5"><img src="http://joss.theoj.org/papers/5cfd756478838ef71796b6831efee8b5/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/5cfd756478838ef71796b6831efee8b5/status.svg)](http://joss.theoj.org/papers/5cfd756478838ef71796b6831efee8b5)

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

@arfon, 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 @arfon know.

Please try and complete your review in the next two weeks

Review checklist for @arfon

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 (v0.0.6)?
  • Authorship: Has the submitting author (@cboettig) 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 Sep 22, 2018

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

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whedon commented Sep 22, 2018

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @arfon 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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Attempting PDF compilation. Reticulating splines etc...
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whedon commented Sep 22, 2018

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

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annakrystalli Sep 22, 2018

This submission has been accepted to rOpenSci. The review thread can be found at ropensci/onboarding#220

annakrystalli commented Sep 22, 2018

This submission has been accepted to rOpenSci. The review thread can be found at ropensci/onboarding#220

@arfon arfon added the accepted label Sep 23, 2018

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Hey @cboettig - thanks for submitting this package. Do you think you could add a little more context to your paper including any examples of projects using this package?

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arfon commented Sep 23, 2018

Hey @cboettig - thanks for submitting this package. Do you think you could add a little more context to your paper including any examples of projects using this package?

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cboettig commented Sep 23, 2018

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I think the vignettes are a little too much like technical documentation for the paper. The submission guidelines list these as what your paper should contain:

  • A list of the authors of the software and their affiliations
  • A summary describing the high-level functionality and purpose of the software for a diverse, non-specialist audience
  • A clear statement of need that illustrates the purpose of the software
  • A list of key references including a link to the software archive
  • Mentions (if applicable) of any ongoing research projects using the software or recent scholarly publications enabled by it

... so a little bit more about high-level functionality, some use cases, and projects/research making use of this software already. Does that sound OK?

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arfon commented Sep 23, 2018

I think the vignettes are a little too much like technical documentation for the paper. The submission guidelines list these as what your paper should contain:

  • A list of the authors of the software and their affiliations
  • A summary describing the high-level functionality and purpose of the software for a diverse, non-specialist audience
  • A clear statement of need that illustrates the purpose of the software
  • A list of key references including a link to the software archive
  • Mentions (if applicable) of any ongoing research projects using the software or recent scholarly publications enabled by it

... so a little bit more about high-level functionality, some use cases, and projects/research making use of this software already. Does that sound OK?

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cboettig commented Sep 23, 2018

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cboettig Sep 24, 2018

@arfon Hey Arfon, I just took a stab at updating the paper.md along the lines you suggested (and tagged you in the commit). Let me know if that's better? Thanks for your patience and help on this, really appreciate the effort to get the right level of detail/content/focus in my paper.md's, both for this time and future reference.

cboettig commented Sep 24, 2018

@arfon Hey Arfon, I just took a stab at updating the paper.md along the lines you suggested (and tagged you in the commit). Let me know if that's better? Thanks for your patience and help on this, really appreciate the effort to get the right level of detail/content/focus in my paper.md's, both for this time and future reference.

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Thanks for the updates @cboettig - this is looking good!

Your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00971 ⚡️ 🚀 💥

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arfon commented Sep 24, 2018

Thanks for the updates @cboettig - this is looking good!

Your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00971 ⚡️ 🚀 💥

@arfon arfon closed this Sep 24, 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.00971/status.svg)](https://doi.org/10.21105/joss.00971)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00971">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00971/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.00971/status.svg
   :target: https://doi.org/10.21105/joss.00971

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:

Collaborator

whedon commented Sep 24, 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.00971/status.svg)](https://doi.org/10.21105/joss.00971)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00971">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00971/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.00971/status.svg
   :target: https://doi.org/10.21105/joss.00971

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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cboettig Sep 25, 2018

@arfon Thanks! Just a quick note: Looks like the "Software Archive" link at http://joss.theoj.org/papers/10.21105/joss.00971 is pointing back to the JOSS DOI, not the Zenodo DOI. Can we fix that?

cboettig commented Sep 25, 2018

@arfon Thanks! Just a quick note: Looks like the "Software Archive" link at http://joss.theoj.org/papers/10.21105/joss.00971 is pointing back to the JOSS DOI, not the Zenodo DOI. Can we fix that?

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@whedon set 10.5281/zenodo.1432527 as archive

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arfon commented Sep 25, 2018

@whedon set 10.5281/zenodo.1432527 as archive

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OK. 10.5281/zenodo.1432527 is the archive.

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whedon commented Sep 25, 2018

OK. 10.5281/zenodo.1432527 is the archive.

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@arfon Thanks! Just a quick note: Looks like the "Software Archive" link at http://joss.theoj.org/papers/10.21105/joss.00971 is pointing back to the JOSS DOI, not the Zenodo DOI. Can we fix that?

That should be fixed now.

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arfon commented Sep 25, 2018

@arfon Thanks! Just a quick note: Looks like the "Software Archive" link at http://joss.theoj.org/papers/10.21105/joss.00971 is pointing back to the JOSS DOI, not the Zenodo DOI. Can we fix that?

That should be fixed now.

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cboettig Sep 25, 2018

sweet, thanks @arfon and @whedon bot!

cboettig commented Sep 25, 2018

sweet, thanks @arfon and @whedon bot!

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