Merge branch 'main' into merge_name

.Rbuildignore

@@ -15,11 +15,11 @@ rdev
 hub
 tic.R
 NOTES
-^\.github/workflows/R-CMD-check\.yaml$
-^\.github/workflows/R-CMD-check-with-db\.yaml$
 ^\.ccache$
 ^\.github$
 ^tic\.R$
 vignettes.awk
 ^\.gitattributes$
 _pkgdown.yml
+docs
+pkgdown

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/rcmdcheck.yml → .github/workflows/R-CMD-check.yaml

@@ -24,6 +24,8 @@ jobs:
  - {os: windows-latest, r: 'release'}
  - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
  - {os: ubuntu-latest, r: 'release'}
+ - {os: ubuntu-latest, r: 'oldrel-1'}
+ - {os: ubuntu-latest, r: 'oldrel-2'}
 
  env:
  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -36,13 +38,12 @@ jobs:
 
  - uses: r-lib/actions/setup-r@v2
  with:
- rtools-version: '42'
  r-version: ${{ matrix.config.r }}
  http-user-agent: ${{ matrix.config.http-user-agent }}
  use-public-rspm: true
 
  - name: Install macOS system dependencies
- if: runner.os == 'macOS'
+ if: runner.os == 'macos'
  run: brew install gdal proj
 
  - uses: r-lib/actions/setup-r-dependencies@v2

.github/workflows/pkgdown.yml → .github/workflows/pkgdown.yaml

@@ -19,6 +19,8 @@ jobs:
  group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
  env:
  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ permissions:
+ contents: write
  steps:
  - uses: actions/checkout@v4
 
@@ -39,7 +41,7 @@ jobs:
 
  - name: Deploy to GitHub pages 🚀
  if: github.event_name != 'pull_request'
- uses: JamesIves/github-pages-deploy-action@v4.4.1
+ uses: JamesIves/github-pages-deploy-action@v4.5.0
  with:
  clean: false
  branch: gh-pages

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+ workflow_dispatch:
+ inputs:
+ config:
+ description: 'A comma separated list of R-hub platforms to use.'
+ type: string
+ default: 'linux,windows,macos'
+ name:
+ description: 'Run name. You can leave this empty now.'
+ type: string
+ id:
+ description: 'Unique ID. You can leave this empty now.'
+ type: string
+
+jobs:
+
+ setup:
+ runs-on: ubuntu-latest
+ outputs:
+ containers: ${{ steps.rhub-setup.outputs.containers }}
+ platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+ steps:
+ # NO NEED TO CHECKOUT HERE
+ - uses: r-hub/actions/setup@v1
+ with:
+ config: ${{ github.event.inputs.config }}
+ id: rhub-setup
+
+ linux-containers:
+ needs: setup
+ if: ${{ needs.setup.outputs.containers != '[]' }}
+ runs-on: ubuntu-latest
+ name: ${{ matrix.config.label }}
+ strategy:
+ fail-fast: false
+ matrix:
+ config: ${{ fromJson(needs.setup.outputs.containers) }}
+ container:
+ image: ${{ matrix.config.container }}
+
+ steps:
+ - uses: r-hub/actions/checkout@v1
+ - uses: r-hub/actions/platform-info@v1
+ with:
+ token: ${{ secrets.RHUB_TOKEN }}
+ job-config: ${{ matrix.config.job-config }}
+ - uses: r-hub/actions/setup-deps@v1
+ with:
+ token: ${{ secrets.RHUB_TOKEN }}
+ job-config: ${{ matrix.config.job-config }}
+ - uses: r-hub/actions/run-check@v1
+ with:
+ token: ${{ secrets.RHUB_TOKEN }}
+ job-config: ${{ matrix.config.job-config }}
+
+ other-platforms:
+ needs: setup
+ if: ${{ needs.setup.outputs.platforms != '[]' }}
+ runs-on: ${{ matrix.config.os }}
+ name: ${{ matrix.config.label }}
+ strategy:
+ fail-fast: false
+ matrix:
+ config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+ steps:
+ - uses: r-hub/actions/checkout@v1
+ - uses: r-hub/actions/setup-r@v1
+ with:
+ job-config: ${{ matrix.config.job-config }}
+ token: ${{ secrets.RHUB_TOKEN }}
+ - uses: r-hub/actions/platform-info@v1
+ with:
+ token: ${{ secrets.RHUB_TOKEN }}
+ job-config: ${{ matrix.config.job-config }}
+ - uses: r-hub/actions/setup-deps@v1
+ with:
+ job-config: ${{ matrix.config.job-config }}
+ token: ${{ secrets.RHUB_TOKEN }}
+ - uses: r-hub/actions/run-check@v1
+ with:
+ job-config: ${{ matrix.config.job-config }}
+ token: ${{ secrets.RHUB_TOKEN }}

.github/workflows/test-coverage.yaml

@@ -23,15 +23,15 @@ jobs:
 
  - uses: r-lib/actions/setup-r-dependencies@v2
  with:
- extra-packages: any::covr, any::XML
+ extra-packages: any::covr
  needs: coverage
 
  - name: Test coverage
  run: |
  covr::codecov(
  quiet = FALSE,
  clean = FALSE,
- install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+ install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
  )
  shell: Rscript {0}
 
@@ -44,7 +44,7 @@ jobs:
 
  - name: Upload test results
  if: failure()
- uses: actions/upload-artifact@v3
+ uses: actions/upload-artifact@v4
  with:
  name: coverage-test-failures
  path: ${{ runner.temp }}/package

.github/workflows/tic-db.yml

@@ -50,7 +50,7 @@ jobs:
  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v4
 
  - uses: r-lib/actions/setup-r@v2
  with:
@@ -145,7 +145,7 @@ jobs:
 
  - name: "[Stage] Upload R CMD check artifacts"
  if: failure()
- uses: actions/upload-artifact@v2
+ uses: actions/upload-artifact@v4
  with:
  name: ${{ runner.os }}-r${{ matrix.config.r }}-results
  path: check

.gitignore

@@ -19,3 +19,4 @@ nc.prj
 nc.dbf
 nc.shx
 docs/
+tests/testthat/Rplots.pdf

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: sf
-Version: 1.0-16
+Version: 1.0-17
 Title: Simple Features for R
 Authors@R:
  c(person(given = "Edzer",
@@ -78,7 +78,7 @@ Suggests:
  dplyr (>= 1.0.0),
  ggplot2,
  knitr,
- lwgeom (>= 0.2-1),
+ lwgeom (>= 0.2-14),
  maps,
  mapview,
  Matrix,
@@ -113,14 +113,16 @@ LinkingTo:
 VignetteBuilder: 
  knitr
 Encoding: UTF-8
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
 Config/testthat/edition: 2
+Config/needs/coverage: XML
 SystemRequirements: GDAL (>= 2.0.1), GEOS (>= 3.4.0),
  PROJ (>= 4.8.0), sqlite3
 Collate: 
  'RcppExports.R'
  'init.R'
+ 'import-standalone-s3-register.R'
  'crs.R'
  'bbox.R'
  'read.R'

NAMESPACE

@@ -393,7 +393,6 @@ export(gdal_utils)
 export(gdal_write)
 export(gdal_write_mdim)
 export(get_key_pos)
-export(pivot_wider.sf)
 export(plot_sf)
 export(rawToHex)
 export(read_sf)

NEWS.md

@@ -1,7 +1,23 @@
-# version 1.0-16
+# version 1.0-17
+
+* `st_sf()` no longer strips `tbl` or `tbl_df` class labels; #2378
+
+* `st_layers()` returns an object of class `c("sf_layers", "data.frame")`, with a dedicated `print` method.
+
+* when `dim` is not `XYZM`, `sf_as_sf.data.frame()` interprets a length 4 `coords` argument to specify the corners of a rectangular polygon; #2357
+
+* `st_interpolate_aw()` gains an `na.rm` argument, for removing features with `NA` attributes before interpolating; #830
 
 * `merge.sf()` no longer renames geometry column; #2334
 
+# version 1.0-16
+
+* `st_join()` no longer renames the geometry column; #2327
+
+* `st_sample()` works when unprojected polygon geometry crosses the antemeridian; #2331
+
+* clean up and modernization of S3 registration of methods and tests; #2285, #2288, #2316, #2341, #2342, by @olivroy
+
 * `[.sfc` works when setting argument `op`; #2320
 
 * `st_sample()` for polygons is sensitive to setting `oriented = TRUE` to prevent wrongly correcting ring directions; #2308

R/RcppExports.R

@@ -57,6 +57,10 @@ CPL_transform <- function(sfc, crs, AOI, pipeline, reverse = FALSE, desired_accu
  .Call(`_sf_CPL_transform`, sfc, crs, AOI, pipeline, reverse, desired_accuracy, allow_ballpark)
 }
 
+CPL_transform_bounds <- function(bb, crs_dst, densify_pts = 21L) {
+ .Call(`_sf_CPL_transform_bounds`, bb, crs_dst, densify_pts)
+}
+
 CPL_wrap_dateline <- function(sfc, opt, quiet = TRUE) {
  .Call(`_sf_CPL_wrap_dateline`, sfc, opt, quiet)
 }

R/aggregate.R

@@ -50,6 +50,10 @@ aggregate.sf = function(x, by, FUN, ..., do_union = TRUE, simplify = TRUE,
  a = aggregate(x[unlist(i), , drop = FALSE],
  list(rep(seq_len(nrow(by)), lengths(i))), FUN, ...)
  nrow_diff = nrow(by) - nrow(a)
+
+ if (is.matrix(a[[2]])) # https://github.com/r-spatial/sf/issues/2375
+ a = data.frame(a[1], as.data.frame(a[[2]]))
+
  if(nrow_diff > 0) {
  a_na = a[rep(NA, nrow(by)),] # 'top-up' missing rows
  a_na[a$Group.1,] = a
@@ -82,9 +86,7 @@ aggregate.sf = function(x, by, FUN, ..., do_union = TRUE, simplify = TRUE,
  else
  paste0("Group.", seq_along(by))
  agr[n] = "identity"
- st_agr(x) = agr
-
- x
+ st_set_agr(x, agr)
  }
 }
 
@@ -95,8 +97,10 @@ aggregate.sf = function(x, by, FUN, ..., do_union = TRUE, simplify = TRUE,
 #' @param x object of class \code{sf}, for which we want to aggregate attributes
 #' @param to object of class \code{sf} or \code{sfc}, with the target geometries
 #' @param extensive logical; if TRUE, the attribute variables are assumed to be spatially extensive (like population) and the sum is preserved, otherwise, spatially intensive (like population density) and the mean is preserved.
+#' @param na.rm logical; if `TRUE` remove features with `NA` attributes from `x` before interpolating
 #' @param ... ignored
 #' @param keep_NA logical; if \code{TRUE}, return all features in \code{to}, if \code{FALSE} return only those with non-NA values (but with \code{row.names} the index corresponding to the feature in \code{to})
+#' @details if `extensive` is `TRUE` and `na.rm` is set to `TRUE`, geometries with `NA` are effectively treated as having zero attribute values.
 #' @examples
 #' nc = st_read(system.file("shape/nc.shp", package="sf"))
 #' g = st_make_grid(nc, n = c(10, 5))
@@ -113,12 +117,14 @@ st_interpolate_aw = function(x, to, extensive, ...) UseMethod("st_interpolate_aw
 
 #' @export
 #' @name interpolate_aw
-st_interpolate_aw.sf = function(x, to, extensive, ..., keep_NA = FALSE) {
+st_interpolate_aw.sf = function(x, to, extensive, ..., keep_NA = FALSE, na.rm = FALSE) {
  if (!inherits(to, "sf") && !inherits(to, "sfc")) {
  to <- try(st_as_sf(to))
  if (inherits(to, "try-error"))
  stop("st_interpolate_aw requires geometries in argument to")
  }
+ if (isTRUE(na.rm))
+ x = x[! apply(is.na(x), 1, any),]
 
  if (! all_constant(x))
  warning("st_interpolate_aw assumes attributes are constant or uniform over areas of x")

R/arith.R

@@ -137,7 +137,7 @@ Ops.sfc <- function(e1, e2) {
  if (.Generic == "-")
  e2 <- -e2
  return(opp_sfc(e1, as.numeric(e2), 0L, NA_crs_))
- } else if (.Generic %in% c("*", "/") && is.numeric(e2) && (length(e2) == 1 || is_only_diag(e2))) {
+ } else if (.Generic %in% c("*", "/") && is.numeric(e2) && (length(e2) == 1 || (is_only_pos_diag(e2)))) {
  if (is.matrix(e2)) e2 <- diag(e2)
  if (.Generic == "/")
  e2 <- 1 / e2
@@ -168,10 +168,11 @@ Ops.sfc <- function(e1, e2) {
  st_crs(e1)
  else # geometry got displaced:
  NA_crs_
- st_sfc(ret, crs = crs, precision = attr(e1, "precision"))
+ st_sfc(ret, crs = crs, precision = attr(e1, "precision"), recompute_bbox = TRUE) # also check_ring_dir, if polygons? #2377
  } else
  ret
 }
-is_only_diag <- function(x) {
- is.matrix(x) && all(`diag<-`(x, 0) == 0) # nocov
+
+is_only_pos_diag <- function(x) {
+ is.matrix(x) && all(`diag<-`(x, 0) == 0) && all(diag(x) >= 0) # nocov
 }

R/gdal_utils.R

@@ -33,12 +33,12 @@ resampling_method = function(option = "near") {
 #' @param colorfilename character; name of color file for \code{demprocessing} (mandatory if \code{processing="color-relief"})
 #' @return \code{info} returns a character vector with the raster metadata; all other utils return (invisibly) a logical indicating success (i.e., \code{TRUE}); in case of failure, an error is raised.
 #' @export
-#' @seealso \link{gdal_addo} for adding overlays to a raste file; \link{st_layers} to query geometry type(s) and crs from layers in a (vector) data source
+#' @seealso \link{gdal_addo} for adding overlays to a raster file; \link{st_layers} to query geometry type(s) and crs from layers in a (vector) data source
 #' @examples
 #'
 #' if (sf_extSoftVersion()["GDAL"] > "2.1.0") {
-#' # info utils can be used to list information about about a raster
-#' # dataset. More info: https://gdal.org/programs/ngdalinfo.html
+#' # info utils can be used to list information about a raster
+#' # dataset. More info: https://gdal.org/programs/gdalinfo.html
 #' in_file <- system.file("tif/geomatrix.tif", package = "sf")
 #' gdal_utils("info", in_file, options = c("-mm", "-proj4"))
 #'
@@ -54,7 +54,7 @@ resampling_method = function(option = "near") {
 #' )
 #' # The parameters can be specified as c("name") or c("name", "value"). The
 #' # vectortranslate utils can perform also various operations during the
-#' # conversion process. For example we can reproject the features during the
+#' # conversion process. For example, we can reproject the features during the
 #' # translation.
 #' gdal_utils(
 #' util = "vectortranslate",

R/geom-measures.R

@@ -128,7 +128,7 @@ st_perimeter = function(x, ...) {
  if (!requireNamespace("lwgeom", quietly = TRUE))
  stop("package lwgeom required, please install it first")
  # note that units are handled appropriately by lwgeom
- lwgeom::st_perimeter(x)
+ lwgeom::st_perimeter_lwgeom(x)
  }
 }