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[REVIEW]: workloopR: Analysis of work loops and other data from muscle physiology experiments in R #1856

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whedon opened this issue Nov 1, 2019 · 44 comments
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@whedon whedon commented Nov 1, 2019

Submitting author: @vbaliga (Vikram B. Baliga)
Repository: https://github.com/ropensci/workloopR/
Version: v1.1.1
Editor: @danielskatz
Reviewer: @danielskatz
Archive: 10.5281/zenodo.3523384

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/f0eca1d99dde4e02b414e65271cc24ca"><img src="https://joss.theoj.org/papers/f0eca1d99dde4e02b414e65271cc24ca/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/f0eca1d99dde4e02b414e65271cc24ca/status.svg)](https://joss.theoj.org/papers/f0eca1d99dde4e02b414e65271cc24ca)

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

@danielskatz, 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.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @danielskatz know.

Please try and complete your review in the next two weeks

Review checklist for @danielskatz

Conflict of interest

  • 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

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?
  • Contribution and authorship: Has the submitting author (@vbaliga) 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 functionality 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

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • 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?
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@whedon whedon commented Nov 1, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @danielskatz it looks like you're currently assigned to review 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

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf
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@whedon whedon commented Nov 1, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 1, 2019

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@danielskatz danielskatz commented Nov 1, 2019

Note: this package has been reviewed by rOpenSci: ropensci/software-review#326

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@danielskatz danielskatz commented Nov 1, 2019

@whedon accept

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@whedon whedon commented Nov 1, 2019

No archive DOI set. Exiting...

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@danielskatz danielskatz commented Nov 1, 2019

@whedon set 10.5281/zenodo.3523384 as archive

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@whedon whedon commented Nov 1, 2019

OK. 10.5281/zenodo.3523384 is the archive.

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@danielskatz danielskatz commented Nov 1, 2019

@whedon accept

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@whedon whedon commented Nov 1, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Nov 1, 2019


OK DOIs

- 10.1242/jeb.062752 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Nov 1, 2019

Check final proof 👉 openjournals/joss-papers#1069

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1069, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@danielskatz danielskatz commented Nov 1, 2019

@whedon set v1.1.1 as version

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@whedon whedon commented Nov 1, 2019

OK. v1.1.1 is the version.

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@danielskatz danielskatz commented Nov 1, 2019

@whedon accept

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@whedon whedon commented Nov 1, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Nov 1, 2019


OK DOIs

- 10.1242/jeb.062752 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Nov 1, 2019

Check final proof 👉 openjournals/joss-papers#1070

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1070, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@danielskatz danielskatz commented Nov 1, 2019

👋 @vbaliga - in the paper, can you please add commas after "e.g."s so that they look like, e.g., this.)
Also, please fix the cases in the first reference - the first word doesn't need to be all CAPS...

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@vbaliga vbaliga commented Nov 1, 2019

Hi @danielskatz - thanks for catching these. I pushed a new commit (ropensci/workloopR@0fc4be0) that takes care of both the comma issue and the CAPS issue. I did not create a new release, so the one I made yesterday (v1.1.1) is still the latest one in our Zenodo archive (https://doi.org/10.5281/zenodo.3523384), too. Please let me know if there's anything more I should do & thanks again for all your help

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@danielskatz danielskatz commented Nov 1, 2019

@whedon accept

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@whedon whedon commented Nov 1, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Nov 1, 2019


OK DOIs

- 10.1242/jeb.062752 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Nov 1, 2019

Check final proof 👉 openjournals/joss-papers#1075

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1075, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@danielskatz danielskatz commented Nov 1, 2019

@vbaliga - one more small change is needed - the first reference title should have a "-" in the middle: "How muscles function - the work loop technique"

vbaliga added a commit to ropensci/workloopR that referenced this issue Nov 1, 2019
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@vbaliga vbaliga commented Nov 1, 2019

@danielskatz - OK no problem. I just pushed a commit (ropensci/workloopR@6323524) that replaced the dash. I think that should take care of the issue.

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@danielskatz danielskatz commented Nov 1, 2019

@whedon accept

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@whedon whedon commented Nov 1, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Nov 1, 2019


OK DOIs

- 10.1242/jeb.062752 is OK

MISSING DOIs

- None

INVALID DOIs

- None
@whedon

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@whedon whedon commented Nov 1, 2019

Check final proof 👉 openjournals/joss-papers#1076

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1076, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@danielskatz danielskatz commented Nov 1, 2019

@whedon generate pdf

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@whedon whedon commented Nov 1, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 1, 2019

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@danielskatz danielskatz commented Nov 1, 2019

@whedon accept

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@whedon whedon commented Nov 1, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Nov 1, 2019


OK DOIs

- 10.1242/jeb.062752 is OK

MISSING DOIs

- None

INVALID DOIs

- None
@whedon

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@whedon whedon commented Nov 1, 2019

Check final proof 👉 openjournals/joss-papers#1077

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1077, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@danielskatz danielskatz commented Nov 1, 2019

@whedon accept deposit=true

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@whedon whedon commented Nov 1, 2019

Doing it live! Attempting automated processing of paper acceptance...
@whedon whedon added the accepted label Nov 1, 2019
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@danielskatz danielskatz commented Nov 1, 2019

👋 @vbaliga - thanks for doing the extra work to get this in JOSS!

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@whedon whedon commented Nov 1, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Nov 1, 2019

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#1078
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01856
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

@danielskatz danielskatz closed this Nov 1, 2019
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@whedon whedon commented Nov 1, 2019

🎉🎉🎉 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](https://joss.theoj.org/papers/10.21105/joss.01856/status.svg)](https://doi.org/10.21105/joss.01856)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01856">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01856/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01856/status.svg
   :target: https://doi.org/10.21105/joss.01856

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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@vbaliga vbaliga commented Nov 1, 2019

Hi @danielskatz,
Thank you sincerely for all your help! @shreeramsenthi and I both appreciate your patience in getting us through the extra steps and we are very happy to now be published in JOSS.
Best regards,
Vikram Baliga

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