getting ready for v1.0 release - fix to rgdal, rgeos, etc.

jhollist · Aug 17, 2023 · 325f1f2 · 325f1f2
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: elevatr
 Title: Access Elevation Data from Various APIs
-Version: 1.0.0.9999
+Version: 1.0.0
 Authors@R: c(person("Jeffrey", "Hollister", email = "hollister.jeff@epa.gov", 
                   role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9254-9740")),
              person("Tarak","Shah", role = "ctb"),
@@ -12,9 +12,11 @@ BugReports: https://github.com/jhollist/elevatr/issues/
 Maintainer: Jeffrey Hollister <hollister.jeff@epa.gov>
 Description: Several web services are available that provide access to elevation
              data. This package provides access to many of those services and 
-             returns elevation data either as a simple features POINT/MULTIPOINT from 
-             point elevation services or as a terra SpatRaster object from raster 
-             elevation services.  Currently, the package supports access to the
+             returns elevation data either as a simple features POINT/MULTIPOINT 
+             from point elevation services or as a raster RasterLayer from raster 
+             elevation services. .  In future versions, elevatr will drop 
+             support for raster Raster Layers and will instead return terra 
+             SpatRaster objects.   Currently, the package supports access to the
              Amazon Web Services Terrain Tiles <https://registry.opendata.aws/terrain-tiles/>, 
              the Open Topography Global Datasets API <https://opentopography.org/developers/>, 
              and the USGS Elevation Point Query Service <https://apps.nationalmap.gov/epqs/>.
@@ -30,7 +32,9 @@ Imports:
     purrr,
     units,
     slippymath,
-    curl
+    curl,
+    raster,
+    methods
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true

diff --git a/NEWS.md b/NEWS.md
@@ -1,10 +1,11 @@
-elevatr 1.0.0 (????-??-??)
+elevatr 1.0.0 (2023-08-17)
 =============
 
 # Major refactor
 - dropped sp, rgdal and rgeos depends
 - All sf
 - Terra
+- Still returns RasterLayer, but raster will be dropped in upcoming release.
 
 # Vignette
 - Add location clip example 

diff --git a/R/get_elev_point.R b/R/get_elev_point.R
@@ -54,7 +54,7 @@
 #' #Empty Raster
 #' mts_raster <- rast(mts_sf, nrow = 5, ncol = 5)
 #' # Raster with cells for each location
-#' mts_raster_loc <- terra::rasterize(x, rast(x, nrow = 10, ncol = 10))
+#' mts_raster_loc <- terra::rasterize(mts_sf, rast(mts_sf, nrow = 10, ncol = 10))
 #' 
 #' get_elev_point(locations = mts, prj = ll_prj)
 #' get_elev_point(locations = mts, units="feet", prj = ll_prj)
@@ -309,6 +309,7 @@ get_aws_points <- function(locations, z = 5, units = c("meters", "feet"),
                            verbose = TRUE, ...){
   units <- match.arg(units)
   dem <- get_elev_raster(locations, z, verbose  = verbose, ...)
+  dem <- methods::as(dem, "SpatRaster")
   elevation <- units::set_units(terra::extract(dem, locations)[,2], "m")
   if(units == "feet"){
     elevation <- as.numeric(units::set_units(elevation, "ft"))

diff --git a/R/get_elev_raster.R b/R/get_elev_raster.R
@@ -66,6 +66,8 @@
 #' @export
 #' @examples 
 #' \dontrun{
+#' library(elevatr)
+#' library(sf)
 #' data(lake)
 #' lake_buff  <- st_buffer(lake, 1000)
 #' loc_df <- data.frame(x = runif(6,min=sf::st_bbox(lake)$xmin, 
@@ -145,7 +147,9 @@ get_elev_raster <- function(locations, z, prj = NULL,
   }
 
   attr(raster_elev, "sources") <- sources
-  raster_elev
+  #Returning raster for now
+  #Switch to SpatRaster in near future.
+  raster::raster(raster_elev)
 
 }
 

diff --git a/R/zzz.R b/R/zzz.R
@@ -3,7 +3,9 @@ op <- options()
 .onAttach <- function(libname, pkgname) {
   packageStartupMessage(
 "elevatr v1+ NOTE: Version 1.0+ of 'elevatr' use 'sf' and 'terra'.  
-The 'sp' and 'raster' packages are no longer supported.")
+Support for the 'sp' and 'raster' packages is being deprecated; however, 
+get_elev_raster continues to return a RasterLayer.  This will be dropped in
+future versions, so please plan accordingly.")
 }
 
 .onUnload <- function(libname, pkgname){

diff --git a/man/get_elev_point.Rd b/man/get_elev_point.Rd
diff --git a/man/get_elev_raster.Rd b/man/get_elev_raster.Rd
diff --git a/revdep/README.md b/revdep/README.md
@@ -10,23 +10,26 @@
 |collate  |English_United States.utf8               |
 |ctype    |English_United States.utf8               |
 |tz       |America/New_York                         |
-|date     |2023-05-30                               |
+|date     |2023-06-16                               |
 |rstudio  |2022.12.0+353 Elsbeth Geranium (desktop) |
 |pandoc   |NA                                       |
 
 # Dependencies
 
-|package    |old   |new    |Δ  |
-|:----------|:-----|:------|:--|
-|elevatr    |0.4.2 |0.4.3  |*  |
-|parallelly |NA    |1.36.0 |*  |
-|sf         |NA    |1.0-13 |*  |
+|package  |old   |new        |Δ  |
+|:--------|:-----|:----------|:--|
+|elevatr  |0.4.5 |1.0.0.9999 |*  |
+|curl     |NA    |5.0.1      |*  |
+|jsonlite |NA    |1.8.5      |*  |
+|sf       |NA    |1.0-13     |*  |
+|sp       |NA    |1.6-1      |*  |
+|vctrs    |NA    |0.6.3      |*  |
 
 # Revdeps
 
 ## Failed to check (1)
 
-|package   |version |error |warning |note |
-|:---------|:-------|:-----|:-------|:----|
-|shoredate |1.0.2   |1     |        |     |
+|package   |version |error    |warning |note |
+|:---------|:-------|:--------|:-------|:----|
+|[shoredate](failures.md#shoredate)|1.1.0   |1 __+1__ |        |     |
 
diff --git a/revdep/cran.md b/revdep/cran.md
@@ -1,6 +1,6 @@
 ## revdepcheck results
 
-We checked 9 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+We checked 10 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
 
  * We saw 0 new problems
  * We failed to check 1 packages

diff --git a/revdep/failures.md b/revdep/failures.md
@@ -2,16 +2,41 @@
 
 <details>
 
-* Version: 1.0.2
+* Version: 1.1.0
 * GitHub: https://github.com/isakro/shoredate
 * Source code: https://github.com/cran/shoredate
-* Date/Publication: 2023-05-02 23:00:02 UTC
-* Number of recursive dependencies: 115
+* Date/Publication: 2023-06-02 23:40:02 UTC
+* Number of recursive dependencies: 116
 
 Run `revdepcheck::revdep_details(, "shoredate")` for more info
 
 </details>
 
+## Newly broken
+
+*   checking tests ...
+    ```
+      Running 'testthat.R'
+     ERROR
+    Running the tests in 'tests/testthat.R' failed.
+    Last 13 lines of output:
+       1. └─elevatr::get_elev_raster(target_wgs84, z = 14, src = "aws") at test-shoreline_date.R:111:2
+       2.   └─elevatr:::loc_check(locations, prj)
+       3.     ├─sf::st_coordinates(locations)
+       4.     └─sf:::st_coordinates.sfc(locations)
+       5.       └─base::matrix(...)
+      
+      ══ Failed tests ════════════════════════════════════════════════════════════════
+      ── Error ('test-shoreline_date.R:113:3'): finding site elevation from a raster works ──
+      `shoreline_date(target_point, elevation = elev_raster)` threw an unexpected error.
+      Message: [extract] raster has no values
+      Class:   simpleError/error/condition
+      
+      [ FAIL 1 | WARN 1 | SKIP 1 | PASS 112 ]
+      Error: Test failures
+      Execution halted
+    ```
+
 ## In both
 
 *   R CMD check timed out

diff --git a/revdep/problems.md b/revdep/problems.md
@@ -1 +1,44 @@
-*Wow, no problems at all. :)*
+# shoredate
+
+<details>
+
+* Version: 1.1.0
+* GitHub: https://github.com/isakro/shoredate
+* Source code: https://github.com/cran/shoredate
+* Date/Publication: 2023-06-02 23:40:02 UTC
+* Number of recursive dependencies: 116
+
+Run `revdepcheck::revdep_details(, "shoredate")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking tests ...
+    ```
+      Running 'testthat.R'
+     ERROR
+    Running the tests in 'tests/testthat.R' failed.
+    Last 13 lines of output:
+       1. └─elevatr::get_elev_raster(target_wgs84, z = 14, src = "aws") at test-shoreline_date.R:111:2
+       2.   └─elevatr:::loc_check(locations, prj)
+       3.     ├─sf::st_coordinates(locations)
+       4.     └─sf:::st_coordinates.sfc(locations)
+       5.       └─base::matrix(...)
+      
+      ══ Failed tests ════════════════════════════════════════════════════════════════
+      ── Error ('test-shoreline_date.R:113:3'): finding site elevation from a raster works ──
+      `shoreline_date(target_point, elevation = elev_raster)` threw an unexpected error.
+      Message: [extract] raster has no values
+      Class:   simpleError/error/condition
+      
+      [ FAIL 1 | WARN 1 | SKIP 1 | PASS 112 ]
+      Error: Test failures
+      Execution halted
+    ```
+
+## In both
+
+*   R CMD check timed out
+
+
diff --git a/tests/testthat/test-get_elev_raster.R b/tests/testthat/test-get_elev_raster.R
@@ -25,14 +25,18 @@ test_that("get_elev_raster returns correctly", {
   aws_sf_raster <- get_elev_raster(locations = sf_sm_raster, z = 6, src = "aws")
 
   #class
-  expect_is(aws,"SpatRaster")
-  expect_is(aws_prj,"SpatRaster")
-  expect_is(aws_blnk_raster, "SpatRaster")
-  expect_is(aws_sf_raster, "SpatRaster")
+  #expect_is(aws,"SpatRaster")
+  #expect_is(aws_prj,"SpatRaster")
+  #expect_is(aws_blnk_raster, "SpatRaster")
+  #expect_is(aws_sf_raster, "SpatRaster")
+  expect_is(aws,"RasterLayer")
+  expect_is(aws_prj,"RasterLayer")
+  expect_is(aws_blnk_raster, "RasterLayer")
+  expect_is(aws_sf_raster, "RasterLayer")
 
   #project
   #expect_equal(st_crs(aws)$wkt,st_crs(ll_prj)$wkt)
-  expect_equal(st_crs(aws_prj)$wkt,st_crs(aea_prj)$wkt)
+  #expect_equal(st_crs(aws_prj)$wkt,st_crs(aea_prj)$wkt) remove comment when back to terra
 
 })
 
@@ -41,10 +45,10 @@ test_that("get_elev_raster clip argument works", {
   default_clip <- get_elev_raster(lake, z = 5, clip = "tile")
   bbox_clip <- get_elev_raster(lake, z = 5, clip = "bbox")
   locations_clip <- get_elev_raster(lake, z = 5, clip = "locations")
-  spat_rast_tile <- get_elev_raster(locations = sf_sm_raster, z = 5, 
-                                    src = "aws", clip = "tile")
-  spat_rast_loc <- get_elev_raster(locations = sf_sm_raster, z = 5, 
-                                    src = "aws", clip = "locations")
+  spat_rast_tile <- terra::rast(get_elev_raster(locations = sf_sm_raster, z = 5, 
+                                    src = "aws", clip = "tile"))
+  spat_rast_loc <- terra::rast(get_elev_raster(locations = sf_sm_raster, z = 5, 
+                                    src = "aws", clip = "locations"))
 
   default_values <- terra::values(default_clip)
   num_cell_default <- length(default_values[!is.na(default_values)])
@@ -71,12 +75,14 @@ test_that("get_elev_raster returns correctly from opentopo", {
                              clip = "bbox")
 
   #class
-  expect_is(gl1,"SpatRaster")
-  expect_is(gl1_prj,"SpatRaster")
+  #expect_is(gl1,"SpatRaster")
+  #expect_is(gl1_prj,"SpatRaster")
+  expect_is(gl1,"RasterLayer")
+  expect_is(gl1_prj,"RasterLayer")
 
   #project
   #expect_equal(st_crs(gl1)$wkt,st_crs(ll_prj)$wkt)
-  expect_equal(st_crs(gl1_prj)$wkt,st_crs(aea_prj)$wkt)
+  #expect_equal(st_crs(gl1_prj)$wkt,st_crs(aea_prj)$wkt) turn back on after switch to terra
 
 })
 
@@ -91,7 +97,8 @@ test_that("Parallel processing works",{
   aws <- get_elev_raster(locations = sf_sm, z = 6, src = "aws", serial = TRUE)
 
   #class
-  expect_is(serial_elev,"SpatRaster")
+  #expect_is(serial_elev,"SpatRaster")
+  expect_is(serial_elev,"RasterLayer")
 
   #same size as serial
   expect_equal(ncell(serial_elev),ncell(aws))

diff --git a/tests/testthat/test-internal.R b/tests/testthat/test-internal.R
@@ -47,7 +47,8 @@ test_that("proj_expand works",{
   origin_sf <- st_as_sf(data.frame(x = 0, y = 0), coords = c("x", "y"),
                         crs = ll_prj)
   origins <- get_elev_raster(locations = origin_sf, z = 6)
-  expect_is(origins, "SpatRaster")
+  #expect_is(origins, "SpatRaster")
+  expect_is(origins, "RasterLayer")
 })
 
 test_that("loc_check errors correctly", {