osmapiR: an implementation of OpenStreetMap API v0.6 for R about software-review HOT 89 OPEN

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Package Review

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Documentation

The package includes all the following forms of documentation:

• A statement of need: clearly stating problems the software is designed to solve and its target audience in README
• Installation instructions: for the development version of package and any non-standard dependencies in README
• Vignette(s): demonstrating major functionality that runs successfully locally
• Function Documentation: for all exported functions
• Examples: (that run successfully locally) for all exported functions
• Community guidelines: including contribution guidelines in the README or CONTRIBUTING, and DESCRIPTION with URL, BugReports and Maintainer (which may be autogenerated via Authors@R).

Functionality

• Installation: Installation succeeds as documented.
• Functionality: Any functional claims of the software have been confirmed.
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• Automated tests: Unit tests cover essential functions of the package and a reasonable range of inputs and conditions. All tests pass on the local machine.
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Estimated hours spent reviewing: 1 hr (so far)

• Should the author(s) deem it appropriate, I agree to be acknowledged as a package reviewer ("rev" role) in the package DESCRIPTION file.

Review Comments

This package looks great!
There's a lot of functionality here to dig into!

A few things to clean up:

These functions are still missing @examples in their roxygen blocks: osm_create_gpx, osm_delete_gpx, osm_redaction_object, osm_update_gpx.
I know that was discussed previously, but you need to remove the @examples roxygen tag if it is empty.
If at all possible, I recommend checking the Examples section of R Packages (2e) for ideas about how to show something for these functions.
Users often scroll down to the examples before reading documentation, so having something there to show how the code is intended to work can be helpful, even if it's somewhat contrived (and/or can't actually run).

When I run the tests, there is a lot of "unexpected" output that makes it difficult to see what is happening.
It looks like everything is working in the end, but it would be helpful if you could capture or suppress any expected output, and eliminate anything that shouldn't happen.
For example, test-user_data.R is interrupted by Error in httr2::req_perform(req) : HTTP 404 Not Found.
You deal with that error in osm_get_user_details.R with a try() on lines 67-70.
If you use tryCatch(), you could replace those lines and suppress the confusing error message, with something like this:

out <- tryCatch(
  osm_details_user(user_id = user_id, format = format),
  error = function(e) empty_user()
)

If, on the other hand, you intend for the user to see an error in that case, instead I'd wrap the call in expect_error(), so it doesn't trigger confusing prints when the test runs, similar to this:

  with_mock_dir("mock_details_user_empty", {
    expect_error({empty_usr <- osm_get_user_details(user_id = 2)})
  })

I haven't tracked down the source of the data.frames that print in the test output, but they make it even harder to follow the tests.
I would definitely prefer for those to be suppressed as well!

If you can clean up those pieces, it will make it much easier to see what is supposed to happen as I work through the review!

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I'm happy to submit my review. Full disclaimer: this is my first package review ever, so I hope this is within the scope of what was expected.

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

• Briefly describe any working relationship you have (had) with the package authors.
• As the reviewer I confirm that there are no conflicts of interest for me to review this work (if you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

• A statement of need: clearly stating problems the software is designed to solve and its target audience in README
• Installation instructions: for the development version of package and any non-standard dependencies in README
• Vignette(s): demonstrating major functionality that runs successfully locally
• Function Documentation: for all exported functions
• Examples: (that run successfully locally) for all exported functions
• Community guidelines: including contribution guidelines in the README or CONTRIBUTING, and DESCRIPTION with URL, BugReports and Maintainer (which may be autogenerated via Authors@R).

Functionality

• Installation: Installation succeeds as documented.
• Functionality: Any functional claims of the software have been confirmed.
• Performance: Any performance claims of the software have been confirmed.
• Automated tests: Unit tests cover essential functions of the package and a reasonable range of inputs and conditions. All tests pass on the local machine.
• Packaging guidelines: The package conforms to the rOpenSci packaging guidelines.

Estimated hours spent reviewing: 3

• Should the author(s) deem it appropriate, I agree to be acknowledged as a package reviewer ("rev" role) in the package DESCRIPTION file.

Review Comments

I want to thank @jmaspons for their excellent job in doing this useful package which (full disclaimer) I am very likely to be using in the future.

The package implements more than 20 functions and has a function matching every OSM API call. All the major functions are well documented, with examples, and have dedicated tests. I couldn't find major issues via automated tools, and I can see that the issues flagged by @jonthegeek's review have been addressed*.

My main concern is on understanding what this package is (and how it differs from other potentially related packages and OSMs APIs, such as osmdata) and what it can do.

While I can see significant efforts in documentation functions and readme, I must say that I've been an active OSM contributor since 2014, I'm familiar with all the concepts (changesets, history, gpx traces...) and other APIs, such as overpass. But even with that, I struggle to get a full picture of what this package can do, and more importantly, when it should be used. IMHO, this is important given that OSM discourages automated edits. It could be argued that the audience of this package should be familiar with OSM API already, and therefore, they know the answers to those questions, and I'd be OK with that. However, my experience is that more often than not, people are not familiar with most of OSM's nuisances and would be looking for a package to "work with OSM" searching on a search engine for "OpenStreetMap R package" or "OSM R package" (or similar queries) and may get here. IMHO, a disclaimer, or note for those people either would be appreciated. This is especially relevant considering the nature of the changes that this tool provides, which may be dangerous if used by non-expert OSM mappers (which may ultimately lead to vandalism).

That links to my next item: I find the example on the readme file is useful, well explained, relevant and reproducible, but I wonder how representative it is, given that osmapiR can do way more than that. Again, I'd suggest having an indication on how to get started, which can be a link to the aforementioned help page.

So, as a wrap up, I would suggest improving the readme file with the following suggestions:

• Improve the package description, making it slightly more clearer by extending the succinct "Implements OpenStreetMap API for R." to something like "An R interface to OpenStreetMap API v0.6 for fetching and saving raw geodata from/to the OpenStreetMap database" (copied from https://wiki.openstreetmap.org/wiki/API) to clarify the scope of the package and to make it even clearer disctinction with other OSM's APIs (i.e. overpass).

• Make a note on the scope (when to use or not to use it), and adding any considerations when using it, i.e. mention about automated edits, when putting together disperse information in other parts of the documentation such as API usage (modifying user agent, using a test

• Outline what the package can do, i.e., by mentioning that it can retrieve and update OSM objects, changesets, changeset's discussions, notes, GPS traces and users.

• Indicate how to get started with the package, beyond the example

That said, I acknowledge that A) most of it has been addressed in the ?osmapiR, so it could either be adapted from there and indicate prominently that this is the place to get started, and B) I do not think this is a stopper and could be done after the package is reviewed and accepted (I would kindly contribute with the documentation).

* I didn't notice any warnings when running the tests, and I can see empty examples being deleted, but I can see osm_create_gpx . osm_update_gpxand osm_delete_gpx do not include an empty example, pointing to a dedicated vignette instead, which I believe is missing.

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Another update for @ccamara @adamhsparks. Carlos, you were unable to start the package checks because Adam's' original call to the bot was assign ccamara as reviewer when it should have been assign @ccamara as reviewer. This logged the reviewer as "ccamara", which of course has no meaning in GitHub terms. I've updated the template above to insert the missing @ symbols, so now you're officially recognised as a reviewer here. Adam, you can add this to your list of ...

Now I know!

... even more 🤣

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Another update for @ccamara @adamhsparks. Carlos, you were unable to start the package checks because Adam's' original call to the bot was assign ccamara as reviewer when it should have been assign @ccamara as reviewer. This logged the reviewer as "ccamara", which of course has no meaning in GitHub terms. I've updated the template above to insert the missing @ symbols, so now you're officially recognised as a reviewer here. Adam, you can add this to your list of ...

Now I know!

... even more 🤣

This editor position is the hardest job I have. 😂

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Hello, I thought I had done it here: #633 (comment) , but I may be missing something. How/Where should I approve any new/same changes? (sorry for the newbie question).

Anyway, and just to clarify: I'm happy with the changes being made and the current status of the project.

There's a template in the guide. I had totally missed that, too. Thanks for the poke, @adamhsparks !

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Sorry for the delay. I'll begin searching for an editor, thanks for the submission!

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Editor checks:

• Fit: The package meets criteria for fit and overlap
• Automated tests: Package has a testing suite and is tested via GitHub Actions
• License: The package has a CRAN accepted license
• Repository: The repository link resolves correctly

Editor comments

Hi there.

I've found a few issues flagged by the initial editor checks:

Missing @examples

You have a few empty #' @examples tags that need to be provided

✖ osmapi_gps_traces.R:180: @examples requires a value.
✖ osmapi_gps_traces.R:222: @examples requires a value.
✖ osmapi_gps_traces.R:250: @examples requires a value.

goodpractice::gp output

── GP osmapiR ───────────────────────────────────────────────────────────────────────────────────────────────────────

It is good practice to

  ✖ write unit tests for all functions, and all package code in general. 86% of code lines are
    covered by test cases.

    R/osm_get_changesets.R:97:NA
    R/osm_get_changesets.R:98:NA
    R/osm_get_changesets.R:99:NA
    R/osm_get_objects.R:65:NA
    R/osm_get_objects.R:68:NA
    ... and 251 more lines

  ✖ avoid long code lines, it is bad for readability. Also, many people prefer editor windows
    that are about 80 characters wide. Try make your lines shorter than 80 characters

    inst/httptest2/redact.R:19:81
    inst/httptest2/redact.R:20:81
    inst/httptest2/redact.R:31:81
    R/oauth2.R:28:81
    R/oauth2.R:29:81
    ... and 1330 more lines

  ✖ avoid sapply(), it is not type safe. It might return a vector, or a list, depending on the
    input data. Consider using vapply() instead.

    tests/testthat/test-osmapiR_objects.R:60:21

─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

Reviewers note highlighted coverage gaps and please inspect what is not covered to see if you think important areas are missed.

devtools::spell_check()

You might consider adding the 'Language' field to your DESCRIPTION file.

DESCRIPTION does not contain 'Language' field. Defaulting to 'en-US'.
No spelling errors found.

Comments on Documentation

I noted the use of '', I would use dQuote{}, myself, and <code>, here I would use `` to denote code blocks, among other things in the ROxygen headers.
I would suggest reviewing the ROxygen documentation https://roxygen2.r-lib.org/index.html and possibly enabling Markdown support for formatting the Rd output.

The README has a misspelled R Package name, it should be ({osmextract})[https://github.com/ropensci/osmextract].
I'd also suggest linking to the other OSM packages everywhere they are listed, e.g. {osmdata}, referred to in the README rather than just leaving them as plain text.

─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

Happy to start looking for reviewers. I recommend using this time to try and address some of the issues raised so they can be checked during review rather that be reflagged.

Let me know if anything is unclear!

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Thank you, @jonthegeek, for your review and thank you @maurolepore for picking up the slack here. I'd missed the conversation on this somehow in my notifications.

@jonthegeek, we'll wait for @ccamara to submit his review so you'll have time to revise yours or add additional thoughts for a while now.

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Hey all, I (finally) read an email from @adamhsparks about this. Just to say: would be happy to review. Looks really interesting and can provide feedback if that would be useful.

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I'm sorry @ccamara, I'm afraid I can't do that. That's something only editors, author1, author-others and reviewers-list are allowed to do.

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🚀

The following problem was found in your submission template:

• HTML variable [due-dates-list] is missing
  Editors: Please ensure these problems with the submission template are rectified. Package checks have been started regardless.

👋

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@ccamara, this is a lovely review, thank you!

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Apologies @jmaspons @ccamara and @adamhsparks for checks not appearing previously. The call was issued exactly when our system was in rebuild mode, as mentioned in our Dev Guide (4th point in the list). I'll manually trigger the check results now.

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@jmaspons a pleasure! Thanks for fixing the vignettes part so quickly (I detected another problem, though: rmarkdown is now required to build vignettes, so needs to be specified (see PR jmaspons/osmapiR#24) or added as a required dependency.

Yes, to be honest, when I started reviewing your package yesterday, your name sounded familiar, and I realised that it was a happy coincidence that our paths crossed on OSM a the day before! (For the record: that doesn't mean any conflict of interest in my review).

@mpadge thank you very much for the friendly explanation. You're building such a great community here by treating people so well!

@adamhsparks the experience couldn't have been more positive for me and I'm learning a lot here. I'm not sure if there's anything else I need to do as a reviewer.

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@ccamara, we wait for @jmaspons to make the requested changes and then the reviews have the chance to comment further or approve

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Thanks to everybody involved in the review! There is no NEWS file yet as there is no release. I will submit the package after the review as I expect that the planned changes can fit the current API of the package.

Response to @jonthegeek

I implemented all the suggestions with jmaspons/osmapiR#21

• Reduce output in the tests using expect_snapshot() and the suggested changes to catch expected errors.
• Add examples for: osm_create_gpx, osm_delete_gpx & osm_update_gpx in a vignette, and for osm_redaction_object.

Response to @ccamara

I implemented the suggestions with jmaspons/osmapiR#25

• Improve the package description in the README.
• Add option to install vignettes when using remotes::github_install().

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Reviewer Response

Final approval (post-review)

• The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing: 1.5

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Thank you, @jonthegeek. @ccamara, John's correct, there's a template and I'm just making sure that I have final approval from the reviewers clearly stated here.

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Thanks for submitting to rOpenSci, our editors and @ropensci-review-bot will reply soon. Type @ropensci-review-bot help for help.

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Editor check started

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Thanks, about to send the query.

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Editor check started

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Checks for osmapiR (v0.0.0.22)

git hash: 5878c081

• ✔️ Package name is available
• ✔️ has a 'codemeta.json' file.
• ✔️ has a 'contributing' file.
• ✖️ The following functions have no documented return values: [osm_delete_note, osm_hide_comment_changeset_discussion, osm_redaction_object]
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✖️ These functions do not have examples: [osm_create_gpx, osm_delete_gpx, osm_delete_note, osm_hide_comment_changeset_discussion, osm_redaction_object, osm_update_gpx].
• ✔️ Package has continuous integration checks.
• ✔️ Package coverage is 84.7%.
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.

Important: All failing checks above must be addressed prior to proceeding

Package License: GPL (>= 3)

1. Package Dependencies

2. Statistical Properties

This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.

2a. Network visualisation

Click to see the interactive network visualisation of calls between objects in package

3. goodpractice and other checks

Editor-in-Chief Instructions:

Processing may not proceed until the items marked with ✖️ have been resolved.

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Thanks for the submission @jmaspons! Once you've fixed the above "X", you can trigger the review-bot to re-check the package.

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Hi! Some failing checks are difficult to address. The missing return values in the documentation of [osm_delete_note, osm_hide_comment_changeset_discussion, osm_redaction_object] correspond to functions with API calls restricted to moderators of OpenStreetMap. I don't have this perms and the wiki doesn't define the returned values. The same for the missing examples of these functions.

For the missing examples in the documentation of [osm_create_gpx, osm_delete_gpx, osm_update_gpx], I can try to build a vignette similar to the one explaining how to edit OSM objects, but I prefer to do it later. These are functions that result in editions in the OpenStreetMap servers and I think it's better to put and extra step to avoid editions just for testing the functions.

The missing examples correspond to simple enough functions. If I find some moderator wanting to help with the package I will complete the missing parts.

Can we go ahead with the review despite the remaining "X", @ldecicco-USGS ?

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I've got moderator permissions for the testing server! I will complete the docs in the next days.

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Just to be clear, the "return" documentation in the R package just needs a description of what is coming back. So for example, for the function osm_hide_comment_changeset_discussion , you could add:

#' @return xml output from the osm service

The small functions with no examples are fine.

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All returns are now documented. Some requests return nothing, others an xml that is parsed to a data.frame + package classes

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Thanks, about to send the query.

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Editor check started

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Checks for osmapiR (v0.0.0.23)

git hash: c75f5c03

• ✔️ Package name is available
• ✔️ has a 'codemeta.json' file.
• ✔️ has a 'contributing' file.
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✖️ These functions do not have examples: [osm_create_gpx, osm_delete_gpx, osm_redaction_object, osm_update_gpx].
• ✔️ Package has continuous integration checks.
• ✔️ Package coverage is 85.8%.
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.

Important: All failing checks above must be addressed prior to proceeding

Package License: GPL (>= 3)

1. Package Dependencies

2. Statistical Properties

This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.

2a. Network visualisation

Click to see the interactive network visualisation of calls between objects in package

3. goodpractice and other checks

Editor-in-Chief Instructions:

Processing may not proceed until the items marked with ✖️ have been resolved.

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@ropensci-review-bot assign @adamhsparks as editor

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Assigned! @adamhsparks is now the editor

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@ropensci-review-bot assign jonthegeek as reviewer

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jonthegeek added to the reviewers list. Review due date is 2024-05-20. Thanks jonthegeek for accepting to review! Please refer to our reviewer guide.

rOpenSci’s community is our best asset. We aim for reviews to be open, non-adversarial, and focused on improving software quality. Be respectful and kind! See our reviewers guide and code of conduct for more.

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@jonthegeek: If you haven't done so, please fill this form for us to update our reviewers records.

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📆 jonthegeek you have 2 days left before the due date for your review (2024-05-20).

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I'm so sorry for the delay! I presented at NYR this past week. I'm finally digging into this today!

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I'm sorry @jonthegeek, I'm afraid I can't do that. That's something only editors, author1, author-others and reviewers-list are allowed to do.

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@adamhsparks There have been a bunch of commits since the package was checked, so I wanted to get that processing... and it looks like I'm not able to do so. I'll push forward with my review regardless, but it looks like things might not be fully configured.

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Thanks, about to send the query.

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Editor check started

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Checks for osmapiR (v0.0.0.32)

git hash: 054a021e

• ✔️ Package name is available
• ✔️ has a 'codemeta.json' file.
• ✔️ has a 'contributing' file.
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✖️ These functions do not have examples: [osm_create_gpx, osm_delete_gpx, osm_redaction_object, osm_update_gpx].
• ✔️ Package has continuous integration checks.
• ✔️ Package coverage is 91.1%.
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.

Important: All failing checks above must be addressed prior to proceeding

Package License: GPL (>= 3)

1. Package Dependencies

2. Statistical Properties

This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.

2a. Network visualisation

Click to see the interactive network visualisation of calls between objects in package

3. goodpractice and other checks

Editor-in-Chief Instructions:

Processing may not proceed until the items marked with ✖️ have been resolved.

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@ropensci-review-bot assign ccamara as reviewer

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ccamara added to the reviewers list. Review due date is 2024-06-11. Thanks ccamara for accepting to review! Please refer to our reviewer guide.

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Thanks for the feedback, @jonthegeek ! I fixed your comments in jmaspons/osmapiR#21 and found a new issue jmaspons/osmapiR#22

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📆 ccamara you have 2 days left before the due date for your review (2024-06-11).

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@adamhsparks There have been some changes since last review, so I wanted to check the package, but I can't do that. I'm reviewing it nevertheless, and may submit review soon, but worth checking anyway?

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@ropensci-review-bot submit review #633 (comment) time 1

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Logged review for jonthegeek (hours: 1)

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@ropensci-review-bot submit review #633 (comment) time 3

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Logged review for ccamara (hours: 3)

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Checks for osmapiR (v0.0.0.36)

git hash: ed615e82

• ✔️ Package name is available
• ✔️ has a 'codemeta.json' file.
• ✔️ has a 'contributing' file.
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✔️ All functions have examples.
• ✔️ Package has continuous integration checks.
• ✔️ Package coverage is 92.9%.
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.

Package License: GPL (>= 3)

1. Package Dependencies

2. Statistical Properties

This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.

2a. Network visualisation

Click to see the interactive network visualisation of calls between objects in package

3. goodpractice and other checks

Editor-in-Chief Instructions:

This package is in top shape and may be passed on to a handling editor

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Apologies @jmaspons @ccamara and @adamhsparks for checks not appearing previously. The call was issued exactly when our system was in rebuild mode, as mentioned in our Dev Guide (4th point in the list). I'll manually trigger the check results now.

Thanks, @mpadge. I admit, I didn't read that bullet point before. Now I know!

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Thanks for the review, @ccamara! I will try to improve the README with your feedback and, as you would like to contribute with the docs, I will ask you to review the PR.

but I can see osm_create_gpx . osm_update_gpxand osm_delete_gpx do not include an empty example, pointing to a dedicated vignette instead, which I believe is missing.

I will check what's missing to include the vignette in the package, but you can check it at https://jmaspons.github.io/osmapiR/articles/how_to_edit_gps_traces.html

P.S.: now I realize that we just meet in an OSM changelog discussion recently. Perhaps we are neighbours :)

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PR with improvements in the README and docs based on the review of @ccamara at jmaspons/osmapiR#25

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@jmaspons , I reviewed the PR and looks great to me. Excellent job.

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Hey all, I (finally) read an email from @adamhsparks about this. Just to say: would be happy to review. Looks really interesting and can provide feedback if that would be useful.

Should we wait for the review of @Robinlovelace, @adamhsparks ? He offered to review the package but has not been assigned as a reviewer. I'm not in a hurry, and I'm happy with the feedback. As soon as you give me the OK, I will submit the package to CRAN.

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@jmaspons, no, Robin was not a reviewer of this package. We have all the reviews in and are waiting on your changes.

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Ok @adamhsparks. From my side, if there is no new feedback from reviewers, I would call it done with jmaspons/osmapiR#21 and jmaspons/osmapiR#25

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@jmaspons, please submit your response so that the bot updates the issue.

We ask that you respond to reviewers’ comments within 2 weeks of the last-submitted review, but you may make updates to your package or respond at any time. Your response should include a link to the updated NEWS.md of your package. Here is an author response example. We encourage ongoing conversations between authors and reviewers. See the reviewing guide for more details.

See: see https://devguide.ropensci.org/authors-guide.html for more details.

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@ropensci-review-bot submit response #633 (comment)

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I'm sorry @adamhsparks, I'm afraid I can't do that. That's something only author1 and author-others are allowed to do.

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@jmaspons, can you please submit your response?

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@ropensci-review-bot submit response #633 (comment)

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

@ropensci-review-bot help

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@ropensci-review-bot submit response #633 (comment)

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Logged author response!

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@jmaspons, thank you!

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@jonthegeek and @ccamara, when you have time, could you approve the changes that have been made or offer further suggestions? 🙏

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Hello, I thought I had done it here: #633 (comment) , but I may be missing something. How/Where should I approve any new/same changes? (sorry for the newbie question).

Anyway, and just to clarify: I'm happy with the changes being made and the current status of the project.

EDIT: I'm adding the template

Reviewer Response

Final approval (post-review)

• The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing: 4

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@jmaspons: please post your response with @ropensci-review-bot submit response <url to issue comment> if you haven't done so already (this is an automatic reminder).

Here's the author guide for response. https://devguide.ropensci.org/authors-guide.html

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