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[REVIEW]: cde - R package to retrieve data from the Environment Agency Catchment Data Explorer site #1473

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whedon opened this issue May 23, 2019 · 64 comments

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commented May 23, 2019

Submitting author: @robbriers (Robert Briers)
Repository: https://github.com/ropensci/cde
Version: v0.4.1
Editor: @karthik
Reviewer: @jhollist
Archive: 10.5281/zenodo.2577178

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/0d35f75e861fcf47556d70571e226589"><img src="http://joss.theoj.org/papers/0d35f75e861fcf47556d70571e226589/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/0d35f75e861fcf47556d70571e226589/status.svg)](http://joss.theoj.org/papers/0d35f75e861fcf47556d70571e226589)

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

@jhollist, 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 @karthik know.

Please try and complete your review in the next two weeks

Review checklist for @jhollist

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: v0.4.1

  • Authorship: Has the submitting author (@robbriers) 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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commented May 23, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @jhollist 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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commented May 23, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented May 23, 2019

Jeff: Thank you! Noting here that you'll complete the review by early July.

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commented May 23, 2019

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commented Jun 8, 2019

@whedon remind @@jhollist in 3 weeks

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commented Jun 8, 2019

@@jhollist doesn't seem to be a reviewer or author for this submission.

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commented Jun 8, 2019

@whedon remind @jhollist in 3 weeks

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commented Jun 8, 2019

Reminder set for @jhollist in 3 weeks

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commented Jun 20, 2019

Thanks all for giving me the extra time to get this review done! And kudos to @robbriers for a nicely done package.

I have updated the checklist above. For each of the items I did not check I have a few things that I feel should be addressed prior to signing off on those. I have outlined those in an issue on the package repository. See those at ropensci/cde#23

Any questions, please let me know.

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commented Jun 20, 2019

Thanks Jeff!
@robbriers Please review these comments and post your responses. 🙏

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commented Jun 26, 2019

I added a few more comments in Jeff's issue above.

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commented Jun 29, 2019

@whedon generate pdf

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commented Jun 29, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jun 29, 2019

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commented Jun 29, 2019

Updated pdf above and addressed points raised in ropensci/cde#23.
Let me know if anything else needs attention

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commented Jun 29, 2019

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commented Jun 29, 2019

👋 @jhollist, please update us on how your review is going.

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commented Jun 30, 2019

Thanks for the updates @robbriers. @jhollist When you get a chance, can you check out the statement of need?

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commented Jun 30, 2019

@whedon generate pdf

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commented Jun 30, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jun 30, 2019

@whedon check references

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commented Jun 30, 2019

Attempting to check references...
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commented Jun 30, 2019

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commented Jun 30, 2019


OK DOIs

- 10.1016/J.SCITOTENV.2016.09.228 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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commented Jul 1, 2019

Thanks for the updates @robbriers. @jhollist When you get a chance, can you check out the statement of need?

Just took a look at the new proof and statement of need looks good. Going to check on the other things but anticipate signing off on these momentarily.

@labarba labarba added the accepted label Jul 4, 2019

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commented Jul 4, 2019

@labarba fixed zenodo metadata as requested

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commented Jul 4, 2019

@whedon accept

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commented Jul 4, 2019

Attempting dry run of processing paper acceptance...
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commented Jul 4, 2019

Check final proof 👉 openjournals/joss-papers#815

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#815, 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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commented Jul 4, 2019


OK DOIs

- 10.1016/J.SCITOTENV.2016.09.228 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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commented Jul 4, 2019

Paper paragraph 1: malformed citation: [@WWAPUnitedNationsWorldWaterAssessmentProgramme/UN-Water2018]

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commented Jul 4, 2019

While you are there, add a comma after "e.g." on paragraph 4.

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commented Jul 4, 2019

@whedon generate pdf

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commented Jul 4, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jul 4, 2019

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commented Jul 4, 2019

@whedon generate pdf

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commented Jul 4, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jul 4, 2019

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commented Jul 4, 2019

@labarba think that has fixed the problem

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commented Jul 4, 2019

@whedon accept

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commented Jul 4, 2019

Attempting dry run of processing paper acceptance...
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commented Jul 4, 2019


OK DOIs

- 10.1016/J.SCITOTENV.2016.09.228 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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commented Jul 4, 2019

Check final proof 👉 openjournals/joss-papers#816

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#816, 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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commented Jul 4, 2019

@whedon accept deposit=true

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commented Jul 4, 2019

Doing it live! Attempting automated processing of paper acceptance...
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commented Jul 4, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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commented Jul 4, 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#817
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01473
  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...

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commented Jul 4, 2019

Congrats @robbriers! Your JOSS paper is accepted.

Big thanks to our editor: @karthik and reviewer: @jhollist

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commented Jul 4, 2019

👋 Hey @labarba...

Letting you know, @karthik is currently OOO until Friday, August 30th 2019. ❤️

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commented Jul 4, 2019

(Just published this from my airplane seat before doors close for a long-haul. Cool.)

@labarba labarba closed this Jul 4, 2019

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commented Jul 4, 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](http://joss.theoj.org/papers/10.21105/joss.01473/status.svg)](https://doi.org/10.21105/joss.01473)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01473">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01473/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01473/status.svg
   :target: https://doi.org/10.21105/joss.01473

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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commented Jul 4, 2019

:) great - many thanks @labarba @karthik @jhollist

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commented Jul 4, 2019

👋 Hey @robbriers...

Letting you know, @karthik is currently OOO until Friday, August 30th 2019. ❤️

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