[REVIEW]: bcdata: An R package for searching & retrieving data from the B.C. Data Catalogue

[whedon]

Submitting author: @boshek (Samuel Albers)
Repository: https://github.com/bcgov/bcdata
Version: 0.2.1
Editor: @arfon
Reviewer: @tweed1e, @MilesMcBain
Archive: 10.5281/zenodo.4737824

⚠️ JOSS reduced service mode ⚠️

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Markdown: [![status](https://joss.theoj.org/papers/5f72a500b49b303cf497fa6ad434af43/status.svg)](https://joss.theoj.org/papers/5f72a500b49b303cf497fa6ad434af43)

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

@tweed1e & @MilesMcBain, 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 @arfon know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @tweed1e

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

• I confirm that I read and will adhere to the JOSS 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 (@boshek) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 @MilesMcBain

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

• I confirm that I read and will adhere to the JOSS 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 (@boshek) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @tweed1e, @MilesMcBain it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ 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:

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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]

PDF failed to compile for issue #2927 with the following error:

Can't find any papers to compile :-(

[arfon]

@whedon generate pdf from branch joss

[whedon]

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[arfon]

@tweed1e, @MilesMcBain - This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #2927 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

Our bot Whedon will send an automated reminder in a couple of weeks to see how you're getting along.

[twedl]

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.

A potential COI is that I work for the Canadian federal government and this package was developed by the BC provincial government. But I've never worked with the authors of the pkg. @arfon can you waive that COI?

[arfon]

A potential COI is that I work for the Canadian federal government and this package was developed by the BC provincial government. But I've never worked with the authors of the pkg. @arfon can you waive that COI?

Yes, this is fine. Thanks for disclosing this - please proceed.

[MilesMcBain]

Sorry @arfon I can't check boxes in the lists, probably because the collaborator invite expired?

[arfon]

@whedon re-invite @MilesMcBain as reviewer

[whedon]

OK, the reviewer has been re-invited.

@MilesMcBain please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[arfon]

Sorry @arfon I can't check boxes in the lists, probably because the collaborator invite expired?

Yes, I think so. Please try the invite link again as I've now re-invited you.

[whedon]

👋 @tweed1e, please update us on how your review is going.

[whedon]

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

[MilesMcBain]

Hi @whedon and @afron Things are progressing smoothly so far. I'm part-way through verifying the functionality. I don't anticipate this software generating major issues or requiring extra time based on what I have seen so far. 👍

[twedl]

@whedon pretty slow, but I hope to make progress soon.

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[MilesMcBain]

I've finished my first pass review.

This is a really great package, potentially best in class.

The dbplyr backend for the WFS API is a genuinely novel development for these types of packages, and I hope it is copied by other similar packages.

I also appreciate from an end user's perspective the attention to detail in the print methods, messages, errors, and warnings. It's quite chatty in a reassuring way, and I think it lowers the level of R experience required for good results significantly.

The documentation is high quality, especially the three vignettes, which do a good job of unveiling features without overwhelming.

There are a few issues to resolve but all fairly minor. Congratulations to the authors!

Current blockers to acceptance are:

• [JOSS Review]: Statement of Need bcgov/bcdata#244
• [JOSS Review]: Community Guidelines - Seeking Support bcgov/bcdata#246
• [JOSS Review]: State of the field bcgov/bcdata#245
• JOSS Review: Software Citations bcgov/bcdata#242

And I would strongly recommend taking some action to rectify usability feedback item 5 (UF5):

• [JOSS Review] UF5: Improve documentation for conversion to bounding box bcgov/bcdata#243

[boshek]

Thank you @MilesMcBain! Your kind words are very much appreciated and your extensive feedback even more so. You've done us and the package such a service. Looking forward to digging into your feedback.

[MilesMcBain]

Hi @afron, all boxes now checked from my perspective. 👍

[arfon]

@boshek - At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

• The title of the archive is the same as the JOSS paper title
• That the authors of the archive are the same as the JOSS paper authors

I can then move forward with accepting the submission.

[boshek]

Thanks @arfon

Here is the Zenodo badge:

[arfon]

@whedon set 10.5281/zenodo.4737824 as archive

[whedon]

OK. 10.5281/zenodo.4737824 is the archive.

[arfon]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #2927 with the following error:

 Can't find any papers to compile :-(

[arfon]

@whedon generate pdf from branch joss

[whedon]

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[ateucher]

@whedon generate pdf from branch joss

[whedon]

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[boshek]

@whedon generate pdf from branch joss

[whedon]

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[arfon]

@whedon accept from branch joss

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.01686 is OK
- 10.32614/RJ-2018-009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2288

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2288, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch joss 

[arfon]

@whedon accept deposit=true from branch joss

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02927 joss-papers#2289
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.02927
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@tweed1e, @MilesMcBain - many thanks for your reviews here! JOSS relies upon the volunteer efforts of people like you and we simply wouldn't be able to do this without you ✨

@boshek - your paper is now accepted and published in JOSS ⚡🚀💥

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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