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[REVIEW]: bcdata: An R package for searching & retrieving data from the B.C. Data Catalogue #2927

Closed whedon closed 3 years ago

whedon commented 3 years ago

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

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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

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @MilesMcBain

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 3 years ago

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 :tada:.

:warning: JOSS reduced service mode :warning:

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.

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whedon commented 3 years ago

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

Can't find any papers to compile :-(

arfon commented 3 years ago

@whedon generate pdf from branch joss

whedon commented 3 years ago 
Attempting PDF compilation from custom branch joss. Reticulating splines etc...
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

arfon commented 3 years ago

@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 https://github.com/openjournals/joss-reviews/issues/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 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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

arfon commented 3 years ago

@whedon re-invite @MilesMcBain as reviewer

whedon commented 3 years ago

OK, the reviewer has been re-invited.

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

arfon commented 3 years ago

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 commented 3 years ago

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

whedon commented 3 years ago

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

MilesMcBain commented 3 years ago

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. :+1:

twedl commented 3 years ago

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

whedon commented 3 years ago

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

@whedon commands
MilesMcBain commented 3 years ago

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:

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

boshek commented 3 years ago

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.

boshek commented 3 years ago

@tweed1e - should we consider your review finished now? We are looking to triage and plan how we are going to address the review.

twedl commented 3 years ago

Yes, sorry for the delay, consider it finished. I still have final (positive) thoughts to write down but they shouldn’t make extra work for you or conflict with the other reviewer’s comments.

On Mon, Feb 22, 2021 at 7:24 PM Sam Albers notifications@github.com wrote:

@tweed1e https://github.com/tweed1e - should we consider your review finished now? We are looking to triage and plan how we are going to address the review.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2927#issuecomment-783776153, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZ3LCFW2XN3OP2CRSZACULTALYSVANCNFSM4VH74FHA .

ateucher commented 3 years ago

@whedon generate pdf from branch joss

whedon commented 3 years ago 
Attempting PDF compilation from custom branch joss. Reticulating splines etc...
whedon commented 3 years ago

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

 /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/net/protocol.rb:44:in `connect_nonblock': SSL_connect returned=1 errno=0 state=error: tlsv1 alert internal error (OpenSSL::SSL::SSLError)
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/net/protocol.rb:44:in `ssl_socket_connect'
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/net/http.rb:996:in `connect'
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/net/http.rb:930:in `do_start'
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/net/http.rb:919:in `start'
    from /app/vendor/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/request.rb:727:in `transmit'
    from /app/vendor/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/request.rb:163:in `execute'
    from /app/vendor/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/request.rb:63:in `execute'
    from /app/vendor/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient.rb:66:in `get'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/compilers.rb:106:in `pdf_from_markdown'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/compilers.rb:13:in `generate_pdf'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:59:in `prepare'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:131:in `<top (required)>'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'
ateucher commented 3 years ago

@whedon commands

whedon commented 3 years ago

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository
ateucher commented 3 years ago

@whedon @arfon we have now finished addressing the reviewer's comments:

@MilesMcBain's review identified several blockers to acceptance:

He also had one issue which he strongly recommended we address in terms of user-experience:

@MilesMcBain also had several other excellent suggestions that would make the package better and more consistent for users, and we did address all of those that were possible:

@tweed1e had one blocker to acceptance, which was addressed by bcgov/bcdata#263

Overall the review process was excellent and has made the package, and the paper, much better. Thank you very much to both reviewers!

whedon commented 3 years ago

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

@whedon commands
arfon commented 3 years ago

@ateucher - many thanks for the detailed response.

@tweed1e, @MilesMcBain - please could you come and take another look at this submission and see if these updates address your feedback? If they do, please update your checklists accordingly, if not, please let us know why.

MilesMcBain commented 3 years ago

Hi @afron, all boxes now checked from my perspective. :+1:

arfon commented 3 years ago

@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:

I can then move forward with accepting the submission.

boshek commented 3 years ago

Thanks @arfon

Here is the Zenodo badge: DOI

arfon commented 3 years ago

@whedon set 10.5281/zenodo.4737824 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4737824 is the archive.

arfon commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

 Can't find any papers to compile :-(
arfon commented 3 years ago

@whedon generate pdf from branch joss

whedon commented 3 years ago 
Attempting PDF compilation from custom branch joss. Reticulating splines etc...
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

ateucher commented 3 years ago

@whedon generate pdf from branch joss

whedon commented 3 years ago 
Attempting PDF compilation from custom branch joss. Reticulating splines etc...
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

boshek commented 3 years ago

@whedon generate pdf from branch joss

whedon commented 3 years ago 
Attempting PDF compilation from custom branch joss. Reticulating splines etc...
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

arfon commented 3 years ago

@whedon accept from branch joss

whedon commented 3 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 3 years ago 
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 commented 3 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2288

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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 commented 3 years ago

@whedon accept deposit=true from branch joss