Merge pull request #104 from ropensci/0.8.3

0.8.3

.github/workflows/check-standard.yaml

@@ -19,7 +19,7 @@ jobs:
       matrix:
         config:
           - {os: macos-latest,   r: 'release'}
-          - {os: macos-13-xlarge,   r: 'release'}
+          # - {os: macos-13-xlarge,   r: 'release'}
           # - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}

.github/workflows/pkgdown.yaml

@@ -39,10 +39,10 @@ jobs:
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
-      - name: Deploy to GitHub pages 🚀
-        if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
-        with:
-          clean: false
-          branch: gh-pages
-          folder: docs
+      # - name: Deploy to GitHub pages 🚀
+      #   if: github.event_name != 'pull_request'
+      #   uses: JamesIves/github-pages-deploy-action@v4.4.1
+      #   with:
+      #     clean: false
+      #     branch: gh-pages
+      #     folder: docs

CITATION.cff

@@ -8,14 +8,14 @@ authors:
   - given-names: Insang
     family-names: Song
     email: geoissong@gmail.com
-    affiliation: NIEHS
+    affiliation: 'Seoul National University'
     orcid: 'https://orcid.org/0000-0001-8732-3256'
   - given-names: Kyle P.
     family-names: Messier
     email: kyle.messier@nih.gov
     affiliation: NIEHS
     orcid: 'https://orcid.org/0000-0001-9508-9623'
-repository-code: 'https://github.com/NIEHS/chopin'
+repository-code: 'https://github.com/ropensci/chopin'
 keywords:
   - spatial data
   - parallel processing

DESCRIPTION

@@ -1,11 +1,15 @@
 Package: chopin
 Title: Computation of Spatial Data by Hierarchical and Objective Partitioning of Inputs for Parallel Processing
-Version: 0.8.2
+Version: 0.8.3
 Authors@R: c(
     person("Insang", "Song", , "geoissong@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8732-3256")),
     person("Kyle", "Messier", role = c("aut", "ctb"),
-           comment = c(ORCID = "0000-0001-9508-9623"))
+           comment = c(ORCID = "0000-0001-9508-9623")),
+    person("Alec L.", "Robitaille", role = c("rev"),
+           comment = "Alec reviewed the package version 0.6.3 for rOpenSci, see <https://github.com/ropensci/software-review/issues/638>"),
+    person("Eric R.", "Scott", role = c("rev"),
+           comment = "Eric reviewed the package version 0.6.3 for rOpenSci, see <https://github.com/ropensci/software-review/issues/638>")
   )
 Description: Geospatial data computation is parallelized by grid, hierarchy,
     or raster files. Based on future and mirai parallel backends, terra and sf
@@ -21,8 +25,8 @@ Description: Geospatial data computation is parallelized by grid, hierarchy,
     simple areal interpolation (`summarize_aw`) and summation of
     exponentially decaying weights (`summarize_sedc`) are also provided.
 License: MIT + file LICENSE
-URL: https://github.com/NIEHS/chopin
-BugReports: https://github.com/NIEHS/chopin/issues
+URL: https://docs.ropensci.org/chopin, https://github.com/ropensci/chopin
+BugReports: https://github.com/ropensci/chopin/issues
 Depends: 
     R (>= 4.1)
 SystemRequirements: netcdf

NEWS.md

@@ -3,7 +3,7 @@
 - README.md: two mermaid plots are pre-generated as png files
 - Internal `clip_*()` functions and `vect_validate()` are removed
 - `par_map_args()` is renamed to `par_convert_f()`
-
+- init.R: one-line initialization for `bbox` class detection (cf. https://github.com/r-spatial/sf/issues/2448)
 
 # 0.7
 - `.check_package` refactoring: no `library()` call is required

R/chopin-package.R

@@ -185,14 +185,12 @@
 #' **Notes on data restrictions**
 #'
 #' `chopin` works best with **two-dimensional** (**planar**) geometries.
-#' Users should disable `s2` spherical geometry mode in `sf` by setting.
+#' Users should disable `s2` spherical geometry mode in `sf` by setting
+#' `sf::sf_use_s2(FALSE)`.
 #' Running any `chopin` functions at spherical or three-dimensional
 #' (e.g., including M/Z dimensions) geometries
 #' may produce incorrect or unexpected results.
 #'
-#' ```r
-#' sf::sf_use_s2(FALSE)
-#' ```
 ## usethis namespace: end
 "_PACKAGE"
 #nolint end

R/init.R

@@ -0,0 +1,2 @@
+# Initialize bbox class detection for sf backward compatibility
+setOldClass("bbox")

README.Rmd

@@ -17,11 +17,11 @@ knitr::opts_chunk$set(
 # Computation of Spatial Data by Hierarchical and Objective Partitioning of Inputs for Parallel Processing <img src="man/figures/logo.svg" align="right" height="210" alt="overlapping irregular grid polygons filled with orange, green, and teal" /></a>
 
 <!-- badges: start -->
-[![cov](https://NIEHS.github.io/chopin/badges/coverage.svg)](https://github.com/NIEHS/chopin/actions)
-[![R-CMD-check](https://github.com/NIEHS/chopin/actions/workflows/check-standard.yaml/badge.svg)](https://github.com/NIEHS/chopin/actions/workflows/check-standard.yaml)
+[![cov](https://docs.ropensci.org/chopin/badges/coverage.svg)](https://github.com/ropensci/chopin/actions)
+[![R-CMD-check](https://github.com/ropensci/chopin/actions/workflows/check-standard.yaml/badge.svg)](https://github.com/ropensci/chopin/actions/workflows/check-standard.yaml)
 [![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/638_status.svg)](https://github.com/ropensci/software-review/issues/638)
 [![Lifecycle:
-experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+experimental](https://img.shields.io/badge/lifecycle-stable-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 
 <!-- badges: end -->
 
@@ -43,7 +43,9 @@ future::plan(future.mirai::mirai_multisession, workers = 4L)
 __Second,__ users choose the proper data parallelization configuration by creating a grid partition of the processing extent, defining the field name with values that are hierarchically coded, or entering multiple raster file paths into `par_multirasters()`. __Finally,__ users run `par_*()` function with the configurations set above to compute spatial variables from input data in parallel:
 
 - `par_grid`: parallelize over artificial grid polygons that are generated from the maximum extent of inputs. `par_pad_grid` is used to generate the grid polygons before running this function.
+
 - `par_hierarchy`: parallelize over hierarchy coded in identifier fields (for example, census blocks in each county in the US)
+
 - `par_multirasters`: parallelize over multiple raster files
 
 
@@ -53,7 +55,9 @@ For grid partitioning, the entire study area will be divided into partly overlap
 Processing functions accept [terra](https://github.com/rspatial/terra)/[sf](https://github.com/r-spatial/sf) classes for spatial data. Raster-vector overlay is done with `exactextractr`. Three helper functions encapsulate multiple geospatial data calculation steps over multiple CPU threads.
 
 - `extract_at`: extract raster values with point buffers or polygons with or without kernel weights
+
 - `summarize_sedc`: calculate sums of [exponentially decaying contributions](https://mserre.sph.unc.edu/BMElab_web/SEDCtutorial/index.html)
+
 - `summarize_aw`: area-weighted covariates based on target and reference polygons
 
 
@@ -87,9 +91,14 @@ For **vector-oriented selection**, we suggest three factors to consider:
 
 ```r
 rlang::check_installed("remotes")
-remotes::install_github("NIEHS/chopin")
+remotes::install_github("ropensci/chopin")
 ```
 
+or you can also set `repos` in `install.packages()` as ROpenSci repository:
+
+```r
+install.packages("chopin", repos = "https://ropensci.r-universe.dev")
+```
 
 ## Examples
 Examples will navigate `par_grid`, `par_hierarchy`, and `par_multirasters` functions in `chopin` to parallelize geospatial operations.
@@ -433,9 +442,6 @@ Parallelization may underperform when the datasets are too small to take advanta
 
 
 ### Notes on data restrictions
-`chopin` works best with **two-dimensional** (**planar**) geometries. Users should disable `s2` spherical geometry mode in `sf` by setting. Running any `chopin` functions at spherical or three-dimensional (e.g., including M/Z dimensions) geometries may produce incorrect or unexpected results.
+`chopin` works best with **two-dimensional** (**planar**) geometries. Users should disable `s2` spherical geometry mode in `sf` by setting `sf::sf_use_s2(FALSE)`. Running any `chopin` functions at spherical or three-dimensional (e.g., including M/Z dimensions) geometries may produce incorrect or unexpected results.
 
-```r
-sf::sf_use_s2(FALSE)
-```