Merge pull request #11 from r-spatial/2022-11-16_use-testthat-codecov

Author: elipousson

.Rbuildignore

@@ -1,3 +1,5 @@
 ^rgeopackage\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
+^codecov\.yml$
+^README\.Rmd$

DESCRIPTION

@@ -2,29 +2,30 @@ Package: rgeopackage
 Title: Helper Tools in Creating or Handling GeoPackage Files
 Version: 0.0.0.900
 Authors@R: c(
-    person(given = "Floris",
-           family = "Vanderhaeghe",
-           role = c("aut", "cre"),
-           email = "[email protected]",
+    person("Floris", "Vanderhaeghe", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-6378-6229")),
-    person("Research Institute for Nature and Forest", 
-           email = "[email protected]", 
-           role = "cph"))
-Description: The aim of this R package is to provide helper tools in 
-    creating or handling GeoPackage files, in order to complement
-    other R spatial packages or GDAL. The package has no dependencies 
-    on other spatial packages and is not tied to any particular package 
-    by design.
+    person("Research Institute for Nature and Forest", , , "[email protected]", role = "cph"),
+    person("Eli", "Pousson", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0000-0001-8280-1706"))
+  )
+Description: The aim of this R package is to provide helper tools in
+    creating or handling GeoPackage files, in order to complement other R
+    spatial packages or GDAL. The package has no dependencies on other
+    spatial packages and is not tied to any particular package by design.
 License: GPL (>= 3)
 Depends: 
     R (>= 3.1.0)
 Suggests:
+    covr,
     dplyr,
     openssl,
     RSQLite,
     sf,
-    stars
+    stars,
+    testthat (>= 3.0.0),
+    withr
+Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.1

R/rgeopackage-package.R

@@ -0,0 +1,6 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
+NULL

R/timestamp.R

@@ -50,38 +50,38 @@
 #'
 #' # A rewrite changes the checksum:
 #' filepath_notimeset <- file.path(tempdir(), "b_pump_notimeset.gpkg")
-#'   # write 1:
+#' # write 1:
 #' st_write(sf_layer, dsn = filepath_notimeset, delete_dsn = TRUE)
 #' (md5_notimeset1 <- md5sum(filepath_notimeset))
-#'   # write 2:
+#' # write 2:
 #' st_write(sf_layer, dsn = filepath_notimeset, delete_dsn = TRUE)
 #' (md5_notimeset2 <- md5sum(filepath_notimeset))
-#'   # compare:
+#' # compare:
 #' md5_notimeset1 == md5_notimeset2
 #'
 #' # Setting a fixed date
 #' filepath_timeset <- file.path(tempdir(), "b_pump_timeset.gpkg")
 #' (fixed_date <- as.Date("2020-12-25"))
 #' preset_timestamp(fixed_date)
-#'   # write 1 (date):
+#' # write 1 (date):
 #' st_write(sf_layer, dsn = filepath_timeset, delete_dsn = TRUE)
 #' md5_timeset1 <- md5sum(filepath_timeset)
-#'   # write 2 (date):
+#' # write 2 (date):
 #' st_write(sf_layer, dsn = filepath_timeset, delete_dsn = TRUE)
 #' md5_timeset2 <- md5sum(filepath_timeset)
-#'   # compare:
+#' # compare:
 #' all.equal(md5_timeset1, md5_timeset2)
 #'
 #' # Setting a fixed time
 #' (fixed_time <- as.POSIXct("2020-12-25 12:00:00", tz = "CET"))
 #' preset_timestamp(fixed_time)
-#'   # write 3 (time):
+#' # write 3 (time):
 #' st_write(sf_layer, dsn = filepath_timeset, delete_dsn = TRUE)
 #' md5_timeset3 <- md5sum(filepath_timeset)
-#'   # write 4 (time):
+#' # write 4 (time):
 #' st_write(sf_layer, dsn = filepath_timeset, delete_dsn = TRUE)
 #' md5_timeset4 <- md5sum(filepath_timeset)
-#'   # compare:
+#' # compare:
 #' all.equal(md5_timeset3, md5_timeset4)
 #'
 #' # Also works for GPKG 2D gridded coverage (with stars):
@@ -93,36 +93,37 @@
 #' preset_timestamp(fixed_time)
 #'
 #' stars_2d <-
-#' 	system.file("tif/L7_ETMs.tif", package = "stars") %>%
-#' 	read_stars() %>%
-#' 	slice(band, 1)
-#'   # write 1:
+#'   system.file("tif/L7_ETMs.tif", package = "stars") %>%
+#'   read_stars() %>%
+#'   slice(band, 1)
+#' # write 1:
 #' stars_2d %>%
-#' 	write_stars(filepath_stars, driver = "GPKG")
+#'   write_stars(filepath_stars, driver = "GPKG")
 #' md5_stars1 <- md5sum(filepath_stars)
-#'   # write 2:
+#' # write 2:
 #' stars_2d %>%
-#' 	write_stars(filepath_stars, driver = "GPKG")
+#'   write_stars(filepath_stars, driver = "GPKG")
 #' md5_stars2 <- md5sum(filepath_stars)
-#'   # compare:
+#' # compare:
 #' all.equal(md5_stars1, md5_stars2)
 #'
 #' @author Floris Vanderhaeghe, \url{https://github.com/florisvdh}
 #'
 #' @export
 preset_timestamp <- function(timestamp) {
-	if (!inherits(timestamp, c("Date", "POSIXct"))) {
-		stop("timestamp must be a Date or POSIXct object")
-	}
+  if (!inherits(timestamp, c("Date", "POSIXct"))) {
+    stop("timestamp must be a Date or POSIXct object")
+  }
 
-	timestamp <- format(timestamp,
-						format = "%Y-%m-%dT%H:%M:%S.000Z",
-						tz = "UTC")
+  timestamp <- format(timestamp,
+    format = "%Y-%m-%dT%H:%M:%S.000Z",
+    tz = "UTC"
+  )
 
-	old <- Sys.getenv("OGR_CURRENT_DATE")
-	Sys.setenv(OGR_CURRENT_DATE = timestamp)
+  old <- Sys.getenv("OGR_CURRENT_DATE")
+  Sys.setenv(OGR_CURRENT_DATE = timestamp)
 
-	return(invisible(old))
+  return(invisible(old))
 }
 
 
@@ -133,19 +134,6 @@ unset_timestamp <- function() Sys.unsetenv("OGR_CURRENT_DATE")
 
 
 
-
-
-
-
-
-
-
-
-
-
-
-
-
 #' Amend the timestamp(s) in a GeoPackage file
 #'
 #' Overwrites all timestamps (column \code{last_change}) of the
@@ -198,40 +186,40 @@ unset_timestamp <- function() Sys.unsetenv("OGR_CURRENT_DATE")
 #'
 #' # A rewrite changes the checksum:
 #' filepath_notimeset <- file.path(tempdir(), "b_pump_notimeset.gpkg")
-#'   # write 1:
+#' # write 1:
 #' st_write(sf_layer, dsn = filepath_notimeset, delete_dsn = TRUE)
 #' (md5_notimeset1 <- md5sum(filepath_notimeset))
-#'   # write 2:
+#' # write 2:
 #' st_write(sf_layer, dsn = filepath_notimeset, delete_dsn = TRUE)
 #' (md5_notimeset2 <- md5sum(filepath_notimeset))
-#'   # compare:
+#' # compare:
 #' md5_notimeset1 == md5_notimeset2
 #'
 #' # Setting a fixed date
 #' filepath_timeset <- file.path(tempdir(), "b_pump_timeset.gpkg")
 #' (fixed_date <- as.Date("2020-12-25"))
-#'   # write 1 (date):
+#' # write 1 (date):
 #' st_write(sf_layer, dsn = filepath_timeset, delete_dsn = TRUE)
 #' amend_timestamp(filepath_timeset, fixed_date)
 #' md5_timeset1 <- md5sum(filepath_timeset)
-#'   # write 2 (date):
+#' # write 2 (date):
 #' st_write(sf_layer, dsn = filepath_timeset, delete_dsn = TRUE)
 #' amend_timestamp(filepath_timeset, fixed_date)
 #' md5_timeset2 <- md5sum(filepath_timeset)
-#'   # compare:
+#' # compare:
 #' all.equal(md5_timeset1, md5_timeset2)
 #'
 #' # Setting a fixed time
 #' (fixed_time <- as.POSIXct("2020-12-25 12:00:00", tz = "CET"))
-#'   # write 3 (time):
+#' # write 3 (time):
 #' st_write(sf_layer, dsn = filepath_timeset, delete_dsn = TRUE)
 #' amend_timestamp(filepath_timeset, fixed_time)
 #' md5_timeset3 <- md5sum(filepath_timeset)
-#'   # write 4 (time):
+#' # write 4 (time):
 #' st_write(sf_layer, dsn = filepath_timeset, delete_dsn = TRUE)
 #' amend_timestamp(filepath_timeset, fixed_time)
 #' md5_timeset4 <- md5sum(filepath_timeset)
-#'   # compare:
+#' # compare:
 #' all.equal(md5_timeset3, md5_timeset4)
 #'
 #' # Also works for GPKG 2D gridded coverage (with stars):
@@ -241,20 +229,20 @@ unset_timestamp <- function() Sys.unsetenv("OGR_CURRENT_DATE")
 #' filepath_stars <- file.path(tempdir(), "stars_2d.gpkg")
 #'
 #' stars_2d <-
-#' 	system.file("tif/L7_ETMs.tif", package = "stars") %>%
-#' 	read_stars() %>%
-#' 	slice(band, 1)
-#'   # write 1:
+#'   system.file("tif/L7_ETMs.tif", package = "stars") %>%
+#'   read_stars() %>%
+#'   slice(band, 1)
+#' # write 1:
 #' stars_2d %>%
-#' 	write_stars(filepath_stars, driver = "GPKG")
+#'   write_stars(filepath_stars, driver = "GPKG")
 #' amend_timestamp(filepath_stars, fixed_time)
 #' md5_stars1 <- md5sum(filepath_stars)
-#'   # write 2:
+#' # write 2:
 #' stars_2d %>%
-#' 	write_stars(filepath_stars, driver = "GPKG")
+#'   write_stars(filepath_stars, driver = "GPKG")
 #' amend_timestamp(filepath_stars, fixed_time)
 #' md5_stars2 <- md5sum(filepath_stars)
-#'   # compare:
+#' # compare:
 #' all.equal(md5_stars1, md5_stars2)
 #'
 #' @author Floris Vanderhaeghe, \url{https://github.com/florisvdh}
@@ -263,54 +251,62 @@ unset_timestamp <- function() Sys.unsetenv("OGR_CURRENT_DATE")
 amend_timestamp <- function(dsn,
                             timestamp = Sys.time(),
                             verbose = TRUE) {
-    stopifnot(file.exists(dsn))
-    stopifnot(is.logical(verbose), !is.na(verbose))
-    # soft checking file format:
-    if (!grepl("\\.gpkg$", dsn)) {
-        stop("Expecting a file with extension '.gpkg'")
-    }
-    if (!inherits(timestamp, c("Date", "POSIXct"))) {
-        stop("timestamp must be a Date or POSIXct object")
-    }
+  stopifnot(file.exists(dsn))
+  stopifnot(is.logical(verbose), !is.na(verbose))
+  # soft checking file format:
+  if (!grepl("\\.gpkg$", dsn)) {
+    stop("Expecting a file with extension '.gpkg'")
+  }
+  if (!inherits(timestamp, c("Date", "POSIXct"))) {
+    stop("timestamp must be a Date or POSIXct object")
+  }
 
-    if (!requireNamespace("RSQLite", quietly = TRUE)) {
-        stop("Package \"RSQLite\" is needed when using this function. ",
-             "Please install it.",
-             call. = FALSE)
-    }
+  if (!requireNamespace("RSQLite", quietly = TRUE)) {
+    stop("Package \"RSQLite\" is needed when using this function. ",
+      "Please install it.",
+      call. = FALSE
+    )
+  }
 
-    timestamp <- format(timestamp,
-                        format = "%Y-%m-%dT%H:%M:%S.000Z",
-                        tz = "UTC")
+  timestamp <- format(timestamp,
+    format = "%Y-%m-%dT%H:%M:%S.000Z",
+    tz = "UTC"
+  )
 
-    con <- RSQLite::dbConnect(RSQLite::SQLite(), dsn)
-    updatequery <- sprintf("UPDATE gpkg_contents SET last_change = '%s'",
-                           timestamp)
-    rows <- RSQLite::dbExecute(con, updatequery)
-    if (verbose) {
-        message(
-            rows,
-            " row(s) of the gpkg_contents table have been set with timestamp ",
-            timestamp)
-    }
+  con <- RSQLite::dbConnect(RSQLite::SQLite(), dsn)
+  updatequery <- sprintf(
+    "UPDATE gpkg_contents SET last_change = '%s'",
+    timestamp
+  )
+  rows <- RSQLite::dbExecute(con, updatequery)
+  if (verbose) {
+    message(
+      rows,
+      " row(s) of the gpkg_contents table have been set with timestamp ",
+      timestamp
+    )
+  }
 
-    has_metadata <-
-        nrow(RSQLite::dbGetQuery(con, "SELECT name FROM sqlite_master
+  has_metadata <-
+    nrow(RSQLite::dbGetQuery(con, "SELECT name FROM sqlite_master
 						WHERE name == 'gpkg_metadata_reference'")) > 0
-    if (has_metadata) {
-        updatequery <-
-            sprintf("UPDATE gpkg_metadata_reference SET timestamp = '%s'",
-                    timestamp)
-        rows <- RSQLite::dbExecute(con, updatequery)
-        if (verbose) {
-            message(
-                rows,
-                " row(s) of the gpkg_metadata_reference table have ",
-                "been set with timestamp ",
-                timestamp)
-        }
+  if (has_metadata) {
+    updatequery <-
+      sprintf(
+        "UPDATE gpkg_metadata_reference SET timestamp = '%s'",
+        timestamp
+      )
+    rows <- RSQLite::dbExecute(con, updatequery)
+    if (verbose) {
+      message(
+        rows,
+        " row(s) of the gpkg_metadata_reference table have ",
+        "been set with timestamp ",
+        timestamp
+      )
     }
+  }
 
-    RSQLite::dbDisconnect(con)
-    return(invisible(NULL))
+  RSQLite::dbDisconnect(con)
+  return(invisible(NULL))
 }