diff --git a/DESCRIPTION b/DESCRIPTION
index 6237b7cb..89686a8a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -11,6 +11,7 @@ Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Imports:
+ doFuture,
dplyr,
exactextractr,
future,
@@ -22,7 +23,6 @@ Imports:
terra
Suggests:
covr,
- doFuture,
future.batchtools,
igraph,
knitr,
@@ -38,4 +38,4 @@ Depends:
LazyData: true
Config/testthat/edition: 3
LitrVersionUsed: 0.9.0
-LitrId: 083c5cfaf3173c779a48c55c33eea32b
+LitrId: 87c0f1aa2e25cf3e6bab83b0f987b5f8
diff --git a/NAMESPACE b/NAMESPACE
index cf6edd27..372a9c59 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -28,6 +28,7 @@ export(set_clip_extent)
export(sp_index_grid)
export(switch_packbound)
export(validate_and_repair_vectors)
+import(doFuture)
import(future)
import(future.apply)
importFrom(dplyr,across)
diff --git a/R/preprocessing.R b/R/preprocessing.R
index 4ebb9daa..8b015fdb 100644
--- a/R/preprocessing.R
+++ b/R/preprocessing.R
@@ -40,7 +40,12 @@ rast_short <- function(rasterpath, win) {
is(win, "SpatExtent"))) {
stop("Argument win should be one of named numeric vector or SpatExtent object.\n")
}
- if (is.numeric(win) && !all(grepl("(xmax|xmin|ymax|ymin)", names(win)))) {
+ if (
+ all(
+ is.numeric(win),
+ !all(grepl("(xmax|xmin|ymax|ymin)", names(win))) || is.null(names(win))
+ )
+ ) {
stop("Numeric win without names is detected. Set valid names for all win elements.\n")
}
invisible(terra::rast(rasterpath, win = win))
diff --git a/R/scale_process.R b/R/scale_process.R
index cb657114..6e1a2cd9 100644
--- a/R/scale_process.R
+++ b/R/scale_process.R
@@ -293,6 +293,7 @@ distribute_process_hierarchy <-
#' # distribute_process_multirasters()
#' @import future
#' @import future.apply
+#' @import doFuture
#' @export
distribute_process_multirasters <- function(
filenames,
diff --git a/scomps_rmarkdown_litr.html b/scomps_rmarkdown_litr.html
index 765a79a9..24348e6b 100644
--- a/scomps_rmarkdown_litr.html
+++ b/scomps_rmarkdown_litr.html
@@ -400,7 +400,7 @@ Package setup
usethis::use_package("testthat", "Suggests")
usethis::use_package("units", "Suggests")
usethis::use_package("tigris", "Suggests")
-usethis::use_package("doFuture", "Suggests")
+usethis::use_package("doFuture")
usethis::use_package("future.batchtools", "Suggests")
usethis::use_package("igraph", "Suggests")
usethis::use_package("withr", "Suggests")
@@ -430,6 +430,7 @@ Package setup
## URL:
## https://Spatiotemporal-Exposures-and-Toxicology.github.io/Scalable_GIS
## Imports:
+## doFuture,
## dplyr,
## exactextractr,
## future,
@@ -441,7 +442,6 @@ Package setup
## terra
## Suggests:
## covr,
-## doFuture,
## future.batchtools,
## igraph,
## testthat,
@@ -971,7 +971,12 @@ Create functions
is(win, "SpatExtent"))) {
stop("Argument win should be one of named numeric vector or SpatExtent object.\n")
}
- if (is.numeric(win) && !all(grepl("(xmax|xmin|ymax|ymin)", names(win)))) {
+ if (
+ all(
+ is.numeric(win),
+ !all(grepl("(xmax|xmin|ymax|ymin)", names(win))) || is.null(names(win))
+ )
+ ) {
stop("Numeric win without names is detected. Set valid names for all win elements.\n")
}
invisible(terra::rast(rasterpath, win = win))
@@ -1802,6 +1807,33 @@ Create functions
1,
mode = "buffer",
radius = 1e4L))
+ testthat::expect_error(
+ extract_with(as.list(ncp),
+ ncelev,
+ "GEOID",
+ mode = "buffer",
+ radius = 1e4L))
+ testthat::expect_error(
+ extract_with(sf::st_as_sf(ncp),
+ ncelev,
+ "GEOID",
+ mode = "buffer",
+ radius = 1e4L))
+ testthat::expect_error(
+ extract_with(sf::st_as_sf(ncp),
+ ncelev,
+ 1,
+ mode = "buffer",
+ radius = "Ibidem"))
+ testthat::expect_error(
+ extract_with_buffer(ncp,
+ ncelev,
+ "pid",
+ kernel = "epanechnikov",
+ func = stats::weighted.mean,
+ bandwidth = 1.25e4L,
+ radius = 1e4L,
+ qsegs = 3 + 2i))
})
@@ -2171,19 +2203,27 @@ Create functions
sf::st_crs(pp) <- "EPSG:5070"
ppb <- sf::st_buffer(pp, nQuadSegs = 180, dist = units::set_units(20, "km"))
- system.time({ppb_nc_aw <- aw_covariates(ppb, nc, "id")})
+ testthat::expect_no_error(
+ system.time({ppb_nc_aw <- aw_covariates(ppb, nc, "id")})
+ )
expect_s3_class(ppb_nc_aw, "sf")
# terra
ppb_t <- terra::vect(ppb)
nc_t <- terra::vect(nc)
- system.time({ppb_nc_aw <- aw_covariates(ppb_t, nc_t, "id")})
+ testthat::expect_no_error(
+ system.time({ppb_nc_aw <- aw_covariates(ppb_t, nc_t, "id")})
+ )
expect_s3_class(ppb_nc_aw, "data.frame")
# auto convert formats
- system.time({ppb_nc_aw <- aw_covariates(ppb_t, nc, "id")})
+ testthat::expect_no_error(
+ system.time({ppb_nc_aw <- aw_covariates(ppb_t, nc, "id")})
+ )
expect_s3_class(ppb_nc_aw, "data.frame")
+ # error case
+ testthat::expect_error(aw_covariates(as.list(ppb_t), nc, "id"))
})
@@ -2537,6 +2577,7 @@ Create functions
#' # distribute_process_multirasters()
#' @import future
#' @import future.apply
+#' @import doFuture
#' @export
distribute_process_multirasters <- function(
filenames,
@@ -2893,7 +2934,11 @@ Create functions
withr::local_package("future")
withr::local_package("future.apply")
withr::local_package("dplyr")
- withr::local_options(list(sf_use_s2 = FALSE))
+ withr::local_options(
+ list(
+ sf_use_s2 = FALSE,
+ future.resolve.recursive = 2L
+ ))
ncpath <- testthat::test_path("..", "testdata", "nc_hierarchy.gpkg")
nccnty <- terra::vect(ncpath, layer = "county")
@@ -2938,6 +2983,7 @@ Create functions
testthat::expect_true(anyNA(resnas))
# error case
+ future::plan(future::sequential)
testthat::expect_condition(
resnasx <- distribute_process_multirasters(
filenames = testfiles_corrupted,
@@ -3061,7 +3107,7 @@ Documenting the package and building
## (as 'lib' is unspecified)
##
## The downloaded binary packages are in
-## /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//Rtmpl2Ec4s/downloaded_packages
+## /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpoVqIO2/downloaded_packages
## ── R CMD build ─────────────────────────────────────────────────────────────────
## * checking for file ‘/Users/songi2/Documents/GitHub/Scalable_GIS/scomps/DESCRIPTION’ ... OK
## * preparing ‘scomps’:
@@ -3075,7 +3121,7 @@ Documenting the package and building
## Warning: invalid gid value replaced by that for user 'nobody'
##
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL \
-## /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//Rtmpl2Ec4s/scomps_0.1.2.01122024.tar.gz \
+## /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpoVqIO2/scomps_0.1.2.01122024.tar.gz \
## --install-tests --no-docs --no-multiarch --no-demo
## * installing to library ‘/Users/songi2/Library/R/arm64/4.3/library’
## * installing *source* package ‘scomps’ ...
diff --git a/scomps_rmarkdown_litr.rmd b/scomps_rmarkdown_litr.rmd
index 14ce17df..45d2ef0e 100644
--- a/scomps_rmarkdown_litr.rmd
+++ b/scomps_rmarkdown_litr.rmd
@@ -53,7 +53,7 @@ usethis::use_package("covr", "Suggests")
usethis::use_package("testthat", "Suggests")
usethis::use_package("units", "Suggests")
usethis::use_package("tigris", "Suggests")
-usethis::use_package("doFuture", "Suggests")
+usethis::use_package("doFuture")
usethis::use_package("future.batchtools", "Suggests")
usethis::use_package("igraph", "Suggests")
usethis::use_package("withr", "Suggests")
@@ -708,7 +708,12 @@ rast_short <- function(rasterpath, win) {
is(win, "SpatExtent"))) {
stop("Argument win should be one of named numeric vector or SpatExtent object.\n")
}
- if (is.numeric(win) && !all(grepl("(xmax|xmin|ymax|ymin)", names(win)))) {
+ if (
+ all(
+ is.numeric(win),
+ !all(grepl("(xmax|xmin|ymax|ymin)", names(win))) || is.null(names(win))
+ )
+ ) {
stop("Numeric win without names is detected. Set valid names for all win elements.\n")
}
invisible(terra::rast(rasterpath, win = win))
@@ -1601,6 +1606,33 @@ testthat::test_that("extract_with runs well", {
1,
mode = "buffer",
radius = 1e4L))
+ testthat::expect_error(
+ extract_with(as.list(ncp),
+ ncelev,
+ "GEOID",
+ mode = "buffer",
+ radius = 1e4L))
+ testthat::expect_error(
+ extract_with(sf::st_as_sf(ncp),
+ ncelev,
+ "GEOID",
+ mode = "buffer",
+ radius = 1e4L))
+ testthat::expect_error(
+ extract_with(sf::st_as_sf(ncp),
+ ncelev,
+ 1,
+ mode = "buffer",
+ radius = "Ibidem"))
+ testthat::expect_error(
+ extract_with_buffer(ncp,
+ ncelev,
+ "pid",
+ kernel = "epanechnikov",
+ func = stats::weighted.mean,
+ bandwidth = 1.25e4L,
+ radius = 1e4L,
+ qsegs = 3 + 2i))
})
@@ -1999,19 +2031,27 @@ testthat::test_that("aw_covariates works as expected.", {
sf::st_crs(pp) <- "EPSG:5070"
ppb <- sf::st_buffer(pp, nQuadSegs = 180, dist = units::set_units(20, "km"))
- system.time({ppb_nc_aw <- aw_covariates(ppb, nc, "id")})
+ testthat::expect_no_error(
+ system.time({ppb_nc_aw <- aw_covariates(ppb, nc, "id")})
+ )
expect_s3_class(ppb_nc_aw, "sf")
# terra
ppb_t <- terra::vect(ppb)
nc_t <- terra::vect(nc)
- system.time({ppb_nc_aw <- aw_covariates(ppb_t, nc_t, "id")})
+ testthat::expect_no_error(
+ system.time({ppb_nc_aw <- aw_covariates(ppb_t, nc_t, "id")})
+ )
expect_s3_class(ppb_nc_aw, "data.frame")
# auto convert formats
- system.time({ppb_nc_aw <- aw_covariates(ppb_t, nc, "id")})
+ testthat::expect_no_error(
+ system.time({ppb_nc_aw <- aw_covariates(ppb_t, nc, "id")})
+ )
expect_s3_class(ppb_nc_aw, "data.frame")
+ # error case
+ testthat::expect_error(aw_covariates(as.list(ppb_t), nc, "id"))
})
@@ -2377,6 +2417,7 @@ distribute_process_hierarchy <-
#' # distribute_process_multirasters()
#' @import future
#' @import future.apply
+#' @import doFuture
#' @export
distribute_process_multirasters <- function(
filenames,
@@ -2747,7 +2788,11 @@ testthat::test_that("Processes are properly spawned and compute over multiraster
withr::local_package("future")
withr::local_package("future.apply")
withr::local_package("dplyr")
- withr::local_options(list(sf_use_s2 = FALSE))
+ withr::local_options(
+ list(
+ sf_use_s2 = FALSE,
+ future.resolve.recursive = 2L
+ ))
ncpath <- testthat::test_path("..", "testdata", "nc_hierarchy.gpkg")
nccnty <- terra::vect(ncpath, layer = "county")
@@ -2792,6 +2837,7 @@ testthat::test_that("Processes are properly spawned and compute over multiraster
testthat::expect_true(anyNA(resnas))
# error case
+ future::plan(future::sequential)
testthat::expect_condition(
resnasx <- distribute_process_multirasters(
filenames = testfiles_corrupted,
@@ -2987,9 +3033,6 @@ if (dir.exists("../figure")) {
pkgbuild::build(path = ".")
# devtools::test()
-
-devtools::install(build = TRUE, dependencies = FALSE, build_vignettes = TRUE, quick = TRUE)
-
```
```{r, include = FALSE}
@@ -3031,6 +3074,14 @@ system("rm -r ./scomps")
# }
# system("mv _pkgdown.yml ./docs")
+devtools::install(build = TRUE, dependencies = FALSE, build_vignettes = TRUE, quick = TRUE)
+
+
devtools::test()
covr::package_coverage()
+```
+
+```{r slurm-submission-template, eval = FALSE, include = FALSE}
+# slurm submission is here
+
```
\ No newline at end of file
diff --git a/tests/testthat/tests.R b/tests/testthat/tests.R
index 106e14eb..28559061 100644
--- a/tests/testthat/tests.R
+++ b/tests/testthat/tests.R
@@ -429,6 +429,33 @@ testthat::test_that("extract_with runs well", {
1,
mode = "buffer",
radius = 1e4L))
+ testthat::expect_error(
+ extract_with(as.list(ncp),
+ ncelev,
+ "GEOID",
+ mode = "buffer",
+ radius = 1e4L))
+ testthat::expect_error(
+ extract_with(sf::st_as_sf(ncp),
+ ncelev,
+ "GEOID",
+ mode = "buffer",
+ radius = 1e4L))
+ testthat::expect_error(
+ extract_with(sf::st_as_sf(ncp),
+ ncelev,
+ 1,
+ mode = "buffer",
+ radius = "Ibidem"))
+ testthat::expect_error(
+ extract_with_buffer(ncp,
+ ncelev,
+ "pid",
+ kernel = "epanechnikov",
+ func = stats::weighted.mean,
+ bandwidth = 1.25e4L,
+ radius = 1e4L,
+ qsegs = 3 + 2i))
})
@@ -537,19 +564,27 @@ testthat::test_that("aw_covariates works as expected.", {
sf::st_crs(pp) <- "EPSG:5070"
ppb <- sf::st_buffer(pp, nQuadSegs = 180, dist = units::set_units(20, "km"))
- system.time({ppb_nc_aw <- aw_covariates(ppb, nc, "id")})
+ testthat::expect_no_error(
+ system.time({ppb_nc_aw <- aw_covariates(ppb, nc, "id")})
+ )
expect_s3_class(ppb_nc_aw, "sf")
# terra
ppb_t <- terra::vect(ppb)
nc_t <- terra::vect(nc)
- system.time({ppb_nc_aw <- aw_covariates(ppb_t, nc_t, "id")})
+ testthat::expect_no_error(
+ system.time({ppb_nc_aw <- aw_covariates(ppb_t, nc_t, "id")})
+ )
expect_s3_class(ppb_nc_aw, "data.frame")
# auto convert formats
- system.time({ppb_nc_aw <- aw_covariates(ppb_t, nc, "id")})
+ testthat::expect_no_error(
+ system.time({ppb_nc_aw <- aw_covariates(ppb_t, nc, "id")})
+ )
expect_s3_class(ppb_nc_aw, "data.frame")
+ # error case
+ testthat::expect_error(aw_covariates(as.list(ppb_t), nc, "id"))
})
@@ -877,7 +912,11 @@ testthat::test_that("Processes are properly spawned and compute over multiraster
withr::local_package("future")
withr::local_package("future.apply")
withr::local_package("dplyr")
- withr::local_options(list(sf_use_s2 = FALSE))
+ withr::local_options(
+ list(
+ sf_use_s2 = FALSE,
+ future.resolve.recursive = 2L
+ ))
ncpath <- testthat::test_path("..", "testdata", "nc_hierarchy.gpkg")
nccnty <- terra::vect(ncpath, layer = "county")
@@ -922,6 +961,7 @@ testthat::test_that("Processes are properly spawned and compute over multiraster
testthat::expect_true(anyNA(resnas))
# error case
+ future::plan(future::sequential)
testthat::expect_condition(
resnasx <- distribute_process_multirasters(
filenames = testfiles_corrupted,
diff --git a/tools/tarballs/scomps_0.1.2.01122024.tar.gz b/tools/tarballs/scomps_0.1.2.01122024.tar.gz
index db242df7..dfcde861 100644
Binary files a/tools/tarballs/scomps_0.1.2.01122024.tar.gz and b/tools/tarballs/scomps_0.1.2.01122024.tar.gz differ