0.8.0 development roadmap: addressing ROpenSci review

[sigmafelix]

Main functions

• [x] Two parallel backends: future and mirai
• [x] Rename par_group_grid
• [x] extract_at as the only function for extract raster values at generic polygons
• [x] Recheck examples of wrapper functions
• [x] Toy examples or make the current examples smaller
• [x] par_cut_coords: add sf::st_zm(drop = TRUE)
• [x] extract_at_poly: st_crs(polys) == st_crs(surf) -> extract_at preprocesses CRS. Still having issues with nonexisting CRS.
• [x] CRS handling for all input classes (i.e., character inputs)
• [x] Elegant way of argument injection in par_grid, par_hierarchy, and par_multiraters, i.e., avoiding positional arguments
  • [x] Use generic argument names x and y in favor of sf/terra conventions
• [ ] ➡️ seamless tar_target integration: return WKT/WKB list to branch out
  • [x] Test branching WKT vs sf objects ... the other argument in extract_at or parallelizable piece of chopin and others' functions?
  • [ ] Hierarchy case: truly nested vs different hierarchy across branch -- spin off a hierarchy definition function from par_hierarchy where takes a simple hierarchy object like the output of par_make_gridset

Auxiliary/internal functions

• [x] Do not export aux functions
• [x] dep_switch: add potential use cases, narrow the scope
  • [x] documentation: supported object types in sf and terra
• [x] Verbosity control for debugging and being explicit about intermediate spatial data manipulation steps (i.e., reprojection, extent setting, etc.)

Documentation

• [x] Clear distinction between summarize_aw (vector-vector) and extract_at_buffer_kernel (vector-raster)
• [x] Move 2D geometries caveats to the later part of README
• [x] Multiple point of entry: add quick start code snippets in README, introductory vignettes, and package documentation
• [x] Remove acronym from DESCRIPTION and consider more generalized package title
• [x] Flowchart
  • [x] Split into clearly separate plots
  • [x] Add explicit elaboration of the plots in README
• [ ] Reorganize vignettes
  • [ ] Benchmark cases into a separate vignette
  • [x] Extend HPC vignettes
• [x] Change default future::plan to future::multisession
  • [x] Internally convert terra input to sf if multisession is detected (#82)
• [x] Precomputing: fix broken figure paths
• [x] Clarify inexhaustive grid in par_group_balanced documentation
• [ ] Add justification to all default argument values
• [x] Fix URLs (to internal and external functions as well as internet links)
• [x] Add CITATION file
  • [x] CITATION.cff to .Rbuildignore
  • [ ] #93
• [x] Remove To run this example
• [x] Clarification of the concept of SEDC in summarize_sedc

Programming practices

• [x] Standard S3 practices for switching functions
• [x] Add expected values in expect_message
• [x] Reduce the number of expect_no_error
• [x] Avoid single long tests
• [x] Legibility of package loading codes: use library
• [x] Community guidelines (i.e., CONTRIBUTING.md)
• [x] Codemetar synchronization (cf. link)
• [x] Standard messaging functions instead of cat or print
• [x] inherits() rather than using grepl() at class() outputs
• [x] Add tests for different operating systems

Exploration

• [ ] wk dependency for lightweight branching
  • [ ] Performance comparison

[sigmafelix]

https://github.com/NIEHS/chopin/commit/9d89ead6032eced4a57bcb1438d206f5f278133a

[sigmafelix]

For dep_switch task, dep_switch is set internal now. Developer's guide on this function might be useful, but I think it is very obvious what it does and its utility in other chopin functions.

[sigmafelix]

Tests for different OSes: skip_on_os() is added when plan::multicore() is applied (i.e., terra-terra inputs). I recall that CI on Windows workers failed with strange mirai related behaviors that were not reproduced in my Windows laptop (on bare R 4.4.1). I will keep track on this issue.

[sigmafelix]

chopin is approved. Before transferring the repository to ropensci, pre-transfer task list is here: https://github.com/ropensci/software-review/issues/638#issuecomment-2371130935

[sigmafelix]

• [ ] Transfer the repo to rOpenSci's "ropensci" GitHub organization under "Settings" in your repo. I have invited you to a team that should allow you to do so. You will need to enable two-factor authentication for your GitHub account.

• [x] This invitation will expire after one week. If it happens write a comment @ropensci-review-bot invite me to ropensci/ which will re-send an invitation. After transfer write a comment @ropensci-review-bot finalize transfer of where is the repo/package name. This will give you admin access back.

• [ ] Fix all links to the GitHub repo to point to the repo under the ropensci organization.

• [x] Delete your current code of conduct file if you had one since rOpenSci's default one will apply, see https://devguide.ropensci.org/collaboration.html#coc-file

• [ ] If you already had a pkgdown website and are ok relying only on rOpenSci central docs building and branding, deactivate the automatic deployment you might have set up

• [ ] remove styling tweaks from your pkgdown config but keep that config file replace the whole current pkgdown website with a redirecting page replace your package docs URL with https://docs.ropensci.org/package_name

• [ ] In addition, in your DESCRIPTION file, include the docs link in the URL field alongside the link to the GitHub repository, e.g.: URL: https://docs.ropensci.org/foobar, https://github.com/ropensci/foobar

• [ ] Skim the docs of the pkgdown automatic deployment, in particular if your website needs MathJax.

• [ ] Fix any links in badges for CI and coverage to point to the new repository URL.

• [x] Increment the package version to reflect the changes you made during review. In NEWS.md, add a heading for the new version and one bullet for each user-facing change, and each developer-facing change that you think is relevant. We're starting to roll out software metadata files to all rOpenSci packages via the Codemeta initiative, see https://docs.ropensci.org/codemetar/ for how to include it in your package, after installing the package - should be easy as running codemetar::write_codemeta() in the root of your package.

• [x] You can add this installation method to your package README install.packages("", repos = "https://ropensci.r-universe.dev") thanks to R-universe.