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[REVIEW]: bbsAssistant: An R package for downloading and handling data and information from the North American Breeding Bird Survey. #1768

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whedon opened this issue Sep 26, 2019 · 60 comments
Closed
38 tasks done

[REVIEW]: bbsAssistant: An R package for downloading and handling data and information from the North American Breeding Bird Survey. #1768

whedon opened this issue Sep 26, 2019 · 60 comments
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@ethanwhite @kthyng @jsta
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accepted published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review

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@whedon
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whedon commented Sep 26, 2019 •
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Submitting author: @trashbirdecology (Jessica Burnett)
Repository: https://github.com/TrashBirdEcology/bbsAssistant/
Version: v1.0
Editor: @kthyng
Reviewer: @ethanwhite , @jsta
Archive: 10.5066/P93W0EAW

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/4b445373a7a7806c92e17bdd194a8e69"><img src="https://joss.theoj.org/papers/4b445373a7a7806c92e17bdd194a8e69/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/4b445373a7a7806c92e17bdd194a8e69/status.svg)](https://joss.theoj.org/papers/4b445373a7a7806c92e17bdd194a8e69)

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

@ethanwhite & @jsta , 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 @kthyng know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @ethanwhite

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 (@trashbirdecology) 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?

Review checklist for @jsta

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 (@trashbirdecology) 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?
@whedon whedon added the review label Sep 26, 2019
@whedon whedon mentioned this issue Sep 26, 2019
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@whedon
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whedon commented Sep 26, 2019

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

@whedon
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whedon commented Sep 26, 2019 

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Sep 26, 2019

👉 Check article proof 📄 👈

@jsta jsta mentioned this issue Oct 16, 2019
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@kthyng
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kthyng commented Oct 17, 2019

@ethanwhite Will you be able to work on your review soon?

@ethanwhite
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Apologies for they delay. I have it on my high priority list for this week.

@kthyng
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kthyng commented Nov 1, 2019

@ethanwhite Just a friendly ping here.

@ethanwhite
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Thanks @kthyng and apologies again. Hoping to get this done very soon.

@ethanwhite
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I've completed my checklist level review. Below are sections related to fixes for boxes that I haven't checked yet:

Automated tests

  • Two tests are currently failing in my local build for test-get_regions.R, but they seem to be passing on Travis so maybe I have a missing dependency or something. Ubuntu 18.04, R 3.6.1.

Community Guidelines

  • Contributing and CoC links were broken. Fixed in Re-knit README.md trashbirdecology/bbsAssistant#65
  • No clear description of how to "Report issues or problems with software" or "Seek support". There is some language related to reporting issues in
    CONTRIBUTING.md.

State of the field

There are two additional packages that contain some of the functionality described here:

  1. rBBS - This package is acknowledged as a source of some code, but no comparison is made to it in the paper.
  2. rdataretriever (software by my group) - which downloads BBS and loads it into R. This package works on the entire integrated BBS dataset, does not support data manipulation, and does not work with the BBS analyses, so there are definitely meaningful differences from this package and therefore no conflict with publishing this software paper. However, it does have some meaningful overlap and so may be worth mentioning here. It is potentially a useful alternative for users looking to work with a full integrated version of the BBS data.

References

I have some additional suggestions related to the functionality of the package and the API, but those are out of scope for the JOSS review checklist so I will open them as issues over in the bbsAssistant repository. (I will try to remember to tag this issue in case there is interest in considering them as part of this review).

This was referenced Nov 5, 2019
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@kthyng
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kthyng commented Nov 14, 2019

Hi @trashbirdecology! Just want to make sure you saw that @ethanwhite has some recommendations for you for moving forward.

@trashbirdecology
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trashbirdecology commented Nov 22, 2019 •
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@ethanwhite @jsta - we have addressed the unchecked boxes in your reviews (see below).

We have done some major re-writing of code in /R/, which I hope makes the top-level functioning more intuitive. This is outlined in the quick overview vignette.

We have also addressed the issues you opened in the repository, with the exception of adding mapping features (a feature request by @jsta).

@ethanwhite

  • Community guidelines enhanced by adding a CONTRIBUTING.md and codeofconduct.md. Will be pushed to master upon resubmission.
  • Tests were updated. Happy to receive suggestions for improving testing.

@ethanwhite and @jsta

  • A section, State of the Field, and better reference to the relevant packages have been added to the paper.md, and will be regenerated.

We appreciate the time you have already taken to provide critical feedback on this package -- it has been greatly improved.

@ethanwhite
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@trashbirdecology - apologies for the difficulties with rdataretriever (don't see them in this issue any more, but got a email notification about them). The retriculate package that we rely on for talking to Python has introduced a number of bugs and we're in the midst of trying to mitigate these issues through improved installation instructions until they get them fixed. You current mention of this and other associated packages is all that's needed here.

@trashbirdecology @kthyng - these changes all look great and I very much appreciate the productive engagement both on these issues and suggestions related to design! It's been a pleasure working with you both. I've completed the rest of the check boxes and consider this software paper ready for publication.

@trashbirdecology
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trashbirdecology commented Nov 26, 2019 via email •
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@jsta
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jsta commented Nov 26, 2019

Looks good to me. The issues I raised with the initial review have all been addressed. Only thing I see remaining is that the paper still mentions the feather file format even though this functionality has been removed?

@whedon
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whedon commented Nov 26, 2019 

Attempting PDF compilation. Reticulating splines etc...

@trashbirdecology
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trashbirdecology commented Nov 26, 2019 via email

@whedon
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whedon commented Nov 26, 2019

👉 Check article proof 📄 👈

@kthyng
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kthyng commented Nov 26, 2019

Great! I see the go-ahead from @ethanwhite.

@jsta can you confirm that the recent change has resolved your last concern?

@jsta
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jsta commented Nov 27, 2019

Looks good. 👍

@kthyng
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kthyng commented Dec 2, 2019

Great! We can begin the final acceptance process then.

@kthyng
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kthyng commented Dec 2, 2019

@whedon generate pdf

@whedon
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whedon commented Dec 2, 2019 

Attempting PDF compilation. Reticulating splines etc...

@whedon
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Author

whedon commented Dec 2, 2019 

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Dec 2, 2019

👉 Check article proof 📄 👈

@kthyng
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kthyng commented Dec 2, 2019

@trashbirdecology Looks like the changes to the references haven't made it through?

@trashbirdecology
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@whedon generate pdf

@whedon
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whedon commented Dec 2, 2019 

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Dec 2, 2019

👉 Check article proof 📄 👈

@trashbirdecology
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trashbirdecology commented Dec 2, 2019 •
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@kthyng the changes should be updated.

DOI for V1.0 software: 10.5066/P93W0EAW
Version release: https://github.com/TrashBirdEcology/bbsAssistant/releases/tag/v1.0

@kthyng
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kthyng commented Dec 3, 2019

@whedon set v1.0 as version

@whedon
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whedon commented Dec 3, 2019

OK. v1.0 is the version.

@kthyng
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kthyng commented Dec 3, 2019

@whedon set 10.5066/P93W0EAW as archive

@whedon
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whedon commented Dec 3, 2019

OK. 10.5066/P93W0EAW is the archive.

@kthyng
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kthyng commented Dec 3, 2019

@trashbirdecology I'm not familiar with this archive setup. Normally with Zenodo I would go to the website of your submission there and make sure the title and author list match your paper. Can you do that for your archive?

@trashbirdecology
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@kthyng I apologies for being a difficult customer here, but I am not sure what you mean by this? The DOI archive (https://doi.org/10.5066/P93W0EAW) contains a .zip file of the V1.0 release instance of the package.

@kthyng
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kthyng commented Dec 4, 2019

@trashbirdecology You're not being difficult at all! I see at your archive link now that your title and author list is consistent with your JOSS submission. I wanted to check that since it isn't always true.

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kthyng commented Dec 4, 2019

@whedon accept

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whedon commented Dec 4, 2019 

Attempting dry run of processing paper acceptance...

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whedon commented Dec 4, 2019 


OK DOIs

- 10.1650/CONDOR-17-83.1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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whedon commented Dec 4, 2019

Check final proof 👉 openjournals/joss-papers#1152

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1152, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

@kthyng
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kthyng commented Dec 4, 2019

@whedon accept deposit=true

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whedon commented Dec 4, 2019 

Doing it live! Attempting automated processing of paper acceptance...

@whedon whedon added the accepted label Dec 4, 2019
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whedon commented Dec 4, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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whedon commented Dec 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 👉 Creating pull request for 10.21105.joss.01768 joss-papers#1153
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01768
  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...

@trashbirdecology
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trashbirdecology commented Dec 4, 2019 via email

@kthyng
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kthyng commented Dec 4, 2019

Congratulations on your new paper @trashbirdecology!!! Many thanks to reviewers @ethanwhite and @jsta for your time and expertise.

@kthyng kthyng closed this as completed Dec 4, 2019
@whedon
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whedon commented Dec 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](https://joss.theoj.org/papers/10.21105/joss.01768/status.svg)](https://doi.org/10.21105/joss.01768)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01768">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01768/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01768/status.svg
   :target: https://doi.org/10.21105/joss.01768

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:

@trashbirdecology
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Congratulations on your new paper @trashbirdecology!!! Many thanks to reviewers @ethanwhite and @jsta for your time and expertise.

thank you for handling @kthyng

@whedon whedon added published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. labels Mar 2, 2020
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