[REVIEW]: rgugik: Search and Retrieve Spatial Data from the Polish Head Office of Geodesy and Cartography in R

[whedon]

Submitting author: @kadyb (Krzysztof Dyba)
Repository: https://github.com/kadyb/rgugik
Version: v0.2.1
Editor: @kbarnhart
Reviewer: @adamhsparks, @mikerspencer
Archive: 10.5281/zenodo.4606706

⚠️ JOSS reduced service mode ⚠️

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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.)

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@adamhsparks & @mikerspencer, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ 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 @adamhsparks

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 (@kadyb) 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 @mikerspencer

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 (@kadyb) 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. @adamhsparks, @mikerspencer 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.

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

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[whedon]

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

OK DOIs

- 10.32614/RJ-2018-009 is OK
- 10.2830/63132 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[whedon]

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

[whedon]

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

[kbarnhart]

@mikerspencer and @adamhsparks, we have an automatic reminder two weeks into the review. Feel free to provide an update if you have one. And if you have any issues as you work on your reviews, please let me know. Sometimes reviewers have permissions issues with being able to check the checkboxes, if that comes up for you, just let me know and I should be able to fix it.

[adamhsparks]

I have to admit, I'm a bit slow off the mark here and can't remember what I've actually done. If I check this invitation, https://github.com/openjournals/joss-reviews/invitations GitHub says it's expired. Did I manage to accept before that happened?

[kbarnhart]

@whedon re-invite @adamhsparks as reviewer

[whedon]

OK, the reviewer has been re-invited.

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

[kbarnhart]

This should be a fresh invite link. Let me know if you have issues with check-boxes after using it.

[adamhsparks]

Ok, that's great. Now the tick boxes work for me. 🙏

[kbarnhart]

@mikerspencer and @adamhsparks, a friendly reminder that we are nearing the end of the six week period in which JOSS requests you complete your reviews. If you have any questions, please let me know.

[adamhsparks]

Thanks for the reminder. This is on my to-do list for today.

[adamhsparks]

Overall the package is well written and I'm impressed with the real-world use-case examples in the vignettes. This will be a great benefit to the community by providing an easy to use resource for a reproducible workflow that centralises data fetching for this data resource. Other tools that offer access to this resource are discussed, along with the advantages of this tool over them.

The contribution guidelines are some of the most clear I've seen. Well done!

I've opened a few issues in the repository for the code or documentation issues I've found or other thoughts.

Here are some more specific comments on the paper and package.

1. I think that the paper would benefit from some edits for clarity and flow, so I've not ticked that off yet. I found the writing to be mostly clear, all of the content was covered as required, but in some places the language was awkward and hard to follow.
2. Two functions have zero test coverage, geonames_download() and borders_download(), the reason for this isn't clear to me.
3. I noted that the test coverage in the README badge, ~87% and paper, don't match what I get locally, ~80%. I'm unsure of the reasons for such a discrepancy?
4. There are four vignettes in the pkgdown website, but only three in the package as installed from the master branch?
5. In several places "digital elevation model" is spelled as "Digital Elevation Model", this is not correct, it is not a proper noun.
6. The package passes all the normal R CMD checks and whatnot and has even used CI to run lintr on the code, which really shows effort put into writing good code. 🙏

[kbarnhart]

@adamhsparks thanks for your review. @kadyb if discussion is necessary regarding any of the comments I'd recommend making an issue in the main repository. Otherwise you can respond here.

@mikerspencer a friendly reminder to provide an update on your review.

Thanks again to both of you for contributing to the JOSS review process.

[mikerspencer]

Thanks @kbarnhart. It's amazing 6 weeks have passed so quickly. My son's school started back today, so I've suddenly got a normal amount of time. I'll work through the review and get it back today or tomorrow.

[kbarnhart]

@mikerspencer thanks for letting me know. At JOSS, we aim to be very understanding that the pandemic has changed people's time availability (e.g. , see this blog post from early in the pandemic). Just keep me posted if you need more time beyond this week.

[mikerspencer]

@kbarnhart I've finished my review. There's a lot to commend, especially how clearly the package is structured and documented.

I've raised a couple of minor issues (61, 62 & 63), but unfortunately I was unable to test functionality due to issue 64. Issue 64 is a connection error when downloading datasets, which consistently occurs at ~15 MB through a download. The issue doesn't affect smaller downloads, e.g. the 2.4 MB files in the automated tests. I've tested at two different times of day and am reasonably sure my internet connection is stable. I'm unsure what to recommend, but have suggested adding larger files to the automated download tests.

[kbarnhart]

@whedon set v0.2.1 as version

[whedon]

OK. v0.2.1 is the version.

[kbarnhart]

@whedon set 10.5281/zenodo.4606706 as archive

note 10.5281/zenodo.4606706 is the DOI for this version and 10.5281/zenodo.4606705 is the DOI for all versions.

[whedon]

OK. 10.5281/zenodo.4606706 is the archive.

[kbarnhart]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.32614/RJ-2018-009 is OK
- 10.2830/63132 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#2144

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2144, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kbarnhart]

@kadyb I've now recommended that this submission be accepted and published. One of the JOSS editors in chief @openjournals/joss-eics will handle the submission from here. Congratulations.

Thanks to @adamhsparks and @mikerspencer for contributing thoughtful and thorough reviews.

[arfon]

@kadyb - I've made a few formatting fixes and small language changes in kadyb/rgugik#74 - please let me know what you think.

Also, the footnotes on the first page were overflowing the margin of the paper so I moved them to links. Hopefully this is OK? If not, an alternative would be to make these proper references in the BibTeX.

[kadyb]

@whedon generate pdf

[whedon]

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

[kadyb]

@arfon, all these changes are fine for us. Thanks!

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.32614/RJ-2018-009 is OK
- 10.2830/63132 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#2146

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2146, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[arfon]

@whedon accept deposit=true

[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.02948 joss-papers#2149
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02948
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]

@adamhsparks, @mikerspencer - many thanks for your reviews here and to @kbarnhart for editing this submission! JOSS relies upon the volunteer effort of folks like yourselves and we simply wouldn't be able to do this without you ✨

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

[whedon]

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

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[kadyb]

Thanks again to everyone for participating and helping in this submission!