Merge pull request #145 from njtierney/use-lintr-i144

use linter, based off of targets linter. Resolves #144
njtierney · Jan 17, 2025 · 22dd055 · 22dd055
2 parents 56c84fe + dc3ba95
commit 22dd055
Show file tree

Hide file tree

Showing 22 changed files with 340 additions and 268 deletions.
diff --git a/.lintr b/.lintr
@@ -0,0 +1,8 @@
+linters: linters_with_defaults(
+  infix_spaces_linter = NULL,
+  object_length_linter = NULL,
+  object_name_linter = NULL,
+  object_usage_linter = NULL,
+  indentation_linter = NULL)
+exclusions: list("inst/notes/preserver_metadata_benchmarking.Qmd")
+encoding: "UTF-8"
diff --git a/R/geotargets-option.R b/R/geotargets-option.R
@@ -64,15 +64,16 @@ geotargets_option_set <- function(gdal_raster_driver = NULL,
                                   gdal_vector_driver = NULL,
                                   gdal_vector_creation_options = NULL,
                                   terra_preserve_metadata = NULL) {
-  # TODO do this programmatically with formals() or something?  `options()` also accepts a named list
+    # TODO do this programmatically with formals() or something?
+    # `options()` also accepts a named list
   options(
-    "geotargets.gdal.raster.driver" = gdal_raster_driver %||%
+    "geotargets.gdal.raster.driver" = gdal_raster_driver %||% # nolint
       geotargets_option_get("gdal.raster.driver"),
-    "geotargets.gdal.raster.creation.options" = gdal_raster_creation_options %||%
+    "geotargets.gdal.raster.creation.options" = gdal_raster_creation_options %||% # nolint
       geotargets_option_get("gdal.raster.creation.options"),
     "geotargets.gdal.vector.driver" = gdal_vector_driver %||%
       geotargets_option_get("gdal.vector.driver"),
-    "geotargets.gdal.vector.creation.options" = gdal_vector_creation_options %||%
+    "geotargets.gdal.vector.creation.options" = gdal_vector_creation_options %||% #nolint
       geotargets_option_get("gdal.vector.creation.options"),
     "geotargets.terra.preserve.metadata" = terra_preserve_metadata %||%
       geotargets_option_get("terra.preserve.metadata")

diff --git a/R/release_bullets.R b/R/release_bullets.R
@@ -1,6 +1,7 @@
-# see ?usethis::use_release_issue()
+# see ?usethis::use_release_issue() #nolint
 release_bullets <- function() {
   c(
-    "update CITATION.cff with `cffr::cff_write(dependencies = FALSE)` (after incrementing version)"
+    "update CITATION.cff with `cffr::cff_write(dependencies = FALSE)`
+    (after incrementing version)"
   )
 }
diff --git a/R/tar-stars.R b/R/tar-stars.R
@@ -8,9 +8,9 @@
 #' `tar_stars()` has the same limitations as [stars::write_stars()], so use with
 #' caution.
 #'
-#' @param name Symbol, name of the target. A target name must be a valid name for
-#'  a symbol in R, and it must not start with a dot. See [targets::tar_target()]
-#'  for more information.
+#' @param name Symbol, name of the target. A target name must be a valid name
+#'  for a symbol in R, and it must not start with a dot. See
+#'  [targets::tar_target()] for more information.
 #' @param command R code to run the target.
 #' @param pattern Code to define a dynamic branching pattern for a target. See
 #'  [targets::tar_target()] for more information.
@@ -45,37 +45,41 @@
 #'       list(
 #'         geotargets::tar_stars(
 #'           stars_example,
-#'           stars::read_stars(system.file("tif", "olinda_dem_utm25s.tif", package = "stars"))
+#'           stars::read_stars(
+#'           system.file("tif", "olinda_dem_utm25s.tif", package = "stars")
+#'           )
 #'         )
 #'       )
 #'     })
 #'     targets::tar_make()
 #'     x <- targets::tar_read(stars_example)
 #'   })
 #' }
-tar_stars <- function(name,
-                      command,
-                      pattern = NULL,
-                      proxy = FALSE,
-                      mdim = FALSE,
-                      ncdf = FALSE,
-                      driver = geotargets_option_get("gdal.raster.driver"),
-                      options = geotargets_option_get("gdal.raster.creation.options"),
-                      ...,
-                      tidy_eval = targets::tar_option_get("tidy_eval"),
-                      packages = targets::tar_option_get("packages"),
-                      library = targets::tar_option_get("library"),
-                      repository = targets::tar_option_get("repository"),
-                      error = targets::tar_option_get("error"),
-                      memory = targets::tar_option_get("memory"),
-                      garbage_collection = targets::tar_option_get("garbage_collection"),
-                      deployment = targets::tar_option_get("deployment"),
-                      priority = targets::tar_option_get("priority"),
-                      resources = targets::tar_option_get("resources"),
-                      storage = targets::tar_option_get("storage"),
-                      retrieval = targets::tar_option_get("retrieval"),
-                      cue = targets::tar_option_get("cue"),
-                      description = targets::tar_option_get("description")) {
+tar_stars <- function(
+        name,
+        command,
+        pattern = NULL,
+        proxy = FALSE,
+        mdim = FALSE,
+        ncdf = FALSE,
+        driver = geotargets_option_get("gdal.raster.driver"),
+        options = geotargets_option_get("gdal.raster.creation.options"),
+        ...,
+        tidy_eval = targets::tar_option_get("tidy_eval"),
+        packages = targets::tar_option_get("packages"),
+        library = targets::tar_option_get("library"),
+        repository = targets::tar_option_get("repository"),
+        error = targets::tar_option_get("error"),
+        memory = targets::tar_option_get("memory"),
+        garbage_collection = targets::tar_option_get("garbage_collection"),
+        deployment = targets::tar_option_get("deployment"),
+        priority = targets::tar_option_get("priority"),
+        resources = targets::tar_option_get("resources"),
+        storage = targets::tar_option_get("storage"),
+        retrieval = targets::tar_option_get("retrieval"),
+        cue = targets::tar_option_get("cue"),
+        description = targets::tar_option_get("description")
+) {
   check_pkg_installed("stars")
   if (ncdf) {
     check_pkg_installed("ncmeta")
@@ -124,28 +128,30 @@ tar_stars <- function(name,
 
 #' @export
 #' @rdname tar_stars
-tar_stars_proxy <- function(name,
-                            command,
-                            pattern = NULL,
-                            mdim = FALSE,
-                            ncdf = FALSE,
-                            driver = geotargets_option_get("gdal.raster.driver"),
-                            options = geotargets_option_get("gdal.raster.creation.options"),
-                            ...,
-                            tidy_eval = targets::tar_option_get("tidy_eval"),
-                            packages = targets::tar_option_get("packages"),
-                            library = targets::tar_option_get("library"),
-                            repository = targets::tar_option_get("repository"),
-                            error = targets::tar_option_get("error"),
-                            memory = targets::tar_option_get("memory"),
-                            garbage_collection = targets::tar_option_get("garbage_collection"),
-                            deployment = targets::tar_option_get("deployment"),
-                            priority = targets::tar_option_get("priority"),
-                            resources = targets::tar_option_get("resources"),
-                            storage = targets::tar_option_get("storage"),
-                            retrieval = targets::tar_option_get("retrieval"),
-                            cue = targets::tar_option_get("cue"),
-                            description = targets::tar_option_get("description")) {
+tar_stars_proxy <- function(
+        name,
+        command,
+        pattern = NULL,
+        mdim = FALSE,
+        ncdf = FALSE,
+        driver = geotargets_option_get("gdal.raster.driver"),
+        options = geotargets_option_get("gdal.raster.creation.options"),
+        ...,
+        tidy_eval = targets::tar_option_get("tidy_eval"),
+        packages = targets::tar_option_get("packages"),
+        library = targets::tar_option_get("library"),
+        repository = targets::tar_option_get("repository"),
+        error = targets::tar_option_get("error"),
+        memory = targets::tar_option_get("memory"),
+        garbage_collection = targets::tar_option_get("garbage_collection"),
+        deployment = targets::tar_option_get("deployment"),
+        priority = targets::tar_option_get("priority"),
+        resources = targets::tar_option_get("resources"),
+        storage = targets::tar_option_get("storage"),
+        retrieval = targets::tar_option_get("retrieval"),
+        cue = targets::tar_option_get("cue"),
+        description = targets::tar_option_get("description")
+) {
   check_pkg_installed("stars")
   if (ncdf) {
     check_pkg_installed("ncmeta")
@@ -196,29 +202,31 @@ tar_stars_proxy <- function(name,
 
 #' tar_stars method with no tidy eval etc.
 #' @noRd
-tar_stars_raw <- function(name,
-                          command,
-                          pattern = NULL,
-                          proxy,
-                          mdim = FALSE,
-                          ncdf = FALSE,
-                          driver = geotargets_option_get("gdal.raster.driver"),
-                          options = geotargets_option_get("gdal.raster.creation.options"),
-                          ...,
-                          tidy_eval = targets::tar_option_get("tidy_eval"),
-                          packages = targets::tar_option_get("packages"),
-                          library = targets::tar_option_get("library"),
-                          repository = targets::tar_option_get("repository"),
-                          error = targets::tar_option_get("error"),
-                          memory = targets::tar_option_get("memory"),
-                          garbage_collection = targets::tar_option_get("garbage_collection"),
-                          deployment = targets::tar_option_get("deployment"),
-                          priority = targets::tar_option_get("priority"),
-                          resources = targets::tar_option_get("resources"),
-                          storage = targets::tar_option_get("storage"),
-                          retrieval = targets::tar_option_get("retrieval"),
-                          cue = targets::tar_option_get("cue"),
-                          description = targets::tar_option_get("description")) {
+tar_stars_raw <- function(
+        name,
+        command,
+        pattern = NULL,
+        proxy,
+        mdim = FALSE,
+        ncdf = FALSE,
+        driver = geotargets_option_get("gdal.raster.driver"),
+        options = geotargets_option_get("gdal.raster.creation.options"),
+        ...,
+        tidy_eval = targets::tar_option_get("tidy_eval"),
+        packages = targets::tar_option_get("packages"),
+        library = targets::tar_option_get("library"),
+        repository = targets::tar_option_get("repository"),
+        error = targets::tar_option_get("error"),
+        memory = targets::tar_option_get("memory"),
+        garbage_collection = targets::tar_option_get("garbage_collection"),
+        deployment = targets::tar_option_get("deployment"),
+        priority = targets::tar_option_get("priority"),
+        resources = targets::tar_option_get("resources"),
+        storage = targets::tar_option_get("storage"),
+        retrieval = targets::tar_option_get("retrieval"),
+        cue = targets::tar_option_get("cue"),
+        description = targets::tar_option_get("description")
+) {
   driver <- driver %||% "GTiff"
   options <- options %||% character(0)
 

diff --git a/R/tar-terra-rast.R b/R/tar-terra-rast.R
@@ -12,9 +12,9 @@
 #' the `SpatRaster` object itself.
 #'
 #'
-#' @param name Symbol, name of the target. A target
-#'   name must be a valid name for a symbol in R, and it
-#'   must not start with a dot. See [targets::tar_target()] for more information.
+#' @param name Symbol, name of the target. A target name must be a valid name
+#'   for a symbol in R, and it must not start with a dot. See
+#'   [targets::tar_target()] for more information.
 #' @param command R code to run the target.
 #' @param pattern Code to define a dynamic branching pattern for a target. See
 #'   [targets::tar_target()] for more information.
@@ -56,27 +56,29 @@
 #'     x <- targets::tar_read(terra_rast_example)
 #'   })
 #' }
-tar_terra_rast <- function(name,
-                           command,
-                           pattern = NULL,
-                           filetype = geotargets_option_get("gdal.raster.driver"),
-                           gdal = geotargets_option_get("gdal.raster.creation.options"),
-                           preserve_metadata = geotargets_option_get("terra.preserve.metadata"),
-                           ...,
-                           tidy_eval = targets::tar_option_get("tidy_eval"),
-                           packages = targets::tar_option_get("packages"),
-                           library = targets::tar_option_get("library"),
-                           repository = targets::tar_option_get("repository"),
-                           error = targets::tar_option_get("error"),
-                           memory = targets::tar_option_get("memory"),
-                           garbage_collection = targets::tar_option_get("garbage_collection"),
-                           deployment = targets::tar_option_get("deployment"),
-                           priority = targets::tar_option_get("priority"),
-                           resources = targets::tar_option_get("resources"),
-                           storage = targets::tar_option_get("storage"),
-                           retrieval = targets::tar_option_get("retrieval"),
-                           cue = targets::tar_option_get("cue"),
-                           description = targets::tar_option_get("description")) {
+tar_terra_rast <- function(
+        name,
+        command,
+        pattern = NULL,
+        filetype = geotargets_option_get("gdal.raster.driver"),
+        gdal = geotargets_option_get("gdal.raster.creation.options"),
+        preserve_metadata = geotargets_option_get("terra.preserve.metadata"),
+        ...,
+        tidy_eval = targets::tar_option_get("tidy_eval"),
+        packages = targets::tar_option_get("packages"),
+        library = targets::tar_option_get("library"),
+        repository = targets::tar_option_get("repository"),
+        error = targets::tar_option_get("error"),
+        memory = targets::tar_option_get("memory"),
+        garbage_collection = targets::tar_option_get("garbage_collection"),
+        deployment = targets::tar_option_get("deployment"),
+        priority = targets::tar_option_get("priority"),
+        resources = targets::tar_option_get("resources"),
+        storage = targets::tar_option_get("storage"),
+        retrieval = targets::tar_option_get("retrieval"),
+        cue = targets::tar_option_get("cue"),
+        description = targets::tar_option_get("description")
+) {
   filetype <- filetype %||% "GTiff"
 
   # check that filetype option is available
@@ -114,10 +116,18 @@ tar_terra_rast <- function(name,
     library = library,
     format = targets::tar_format(
       read = tar_rast_read(preserve_metadata = preserve_metadata),
-      write = tar_rast_write(filetype = filetype, gdal = gdal, preserve_metadata = preserve_metadata),
+      write = tar_rast_write(
+          filetype = filetype,
+          gdal = gdal,
+          preserve_metadata = preserve_metadata
+          ),
       marshal = function(object) terra::wrap(object),
       unmarshal = function(object) terra::unwrap(object),
-      substitute = list(filetype = filetype, gdal = gdal, preserve_metadata = preserve_metadata)
+      substitute = list(
+          filetype = filetype,
+          gdal = gdal,
+          preserve_metadata = preserve_metadata
+          )
     ),
     repository = repository,
     iteration = "list", # only "list" works right now
@@ -151,7 +161,8 @@ tar_rast_read <- function(preserve_metadata) {
 tar_rast_write <- function(filetype, gdal, preserve_metadata) {
   switch(preserve_metadata,
     zip = function(object, path) {
-      # write the raster in a fresh local tempdir() that disappears when function is done
+      # write the raster in a fresh local tempdir() that disappears when
+      # function is done
       tmp <- withr::local_tempdir()
       raster_tmp_file <- file.path(tmp, basename(path))
       zip_tmp_file <- file.path(tmp, "object.zip")