remove messages in documentation mode

R/api_apply.R

@@ -47,11 +47,14 @@
  # # Callback final tile classification
  # .callback(process = "Apply", event = "recovery",
  # context = environment())
- message("Recovery: band ",
- paste0("'", out_band, "'", collapse = ", "),
- " already exists.")
- message("(If you want to produce a new image, please ",
- "change 'output_dir' or 'version' parameters)")
+ if (.check_messages()) {
+ message("Recovery: band ",
+ paste0("'", out_band, "'", collapse = ", "),
+ " already exists.")
+ message("(If you want to produce a new image, please ",
+ "change 'output_dir' or 'version' parameters)")
+ }
+
  # Create tile based on template
  feature <- .tile_eo_from_files(
  files = out_file, fid = .fi_fid(.fi(feature)),

R/api_check.R

@@ -2247,6 +2247,20 @@
 
  return(progress)
 }
+#' @title Checks if messages should be displayed
+#' @name .check_messages
+#' @return TRUE/FALSE
+#' @keywords internal
+#' @noRd
+.check_messages <- function() {
+ # if working on sits documentation mode, no progress bar
+ if (Sys.getenv("SITS_DOCUMENTATION_MODE") == "true" ||
+ Sys.getenv("SITS_DOCUMENTATION_MODE") == "TRUE") {
+ return(FALSE)
+ }
+ else
+ return(TRUE)
+}
 
 .check_stac_items <- function(items) {
  .check_that(

R/api_combine_predictions.R

@@ -76,12 +76,11 @@
  )
  # Resume feature
  if (file.exists(out_file)) {
- # # Callback final tile classification
- # .callback(process = "tile_classification", event = "recovery",
- # context = environment())
- message("Recovery: tile '", base_tile[["tile"]], "' already exists.")
- message("(If you want to produce a new probability image, please ",
- "change 'output_dir' or 'version' parameters)")
+ if (.check_messages()) {
+ message("Recovery: tile '", base_tile[["tile"]], "' already exists.")
+ message("(If you want to produce a new probability image, please ",
+ "change 'output_dir' or 'version' parameters)")
+ }
  probs_tile <- .tile_probs_from_file(
  file = out_file,
  band = band,

R/api_label_class.R

@@ -8,12 +8,11 @@
  )
  # Resume feature
  if (file.exists(out_file)) {
- # # Callback final tile classification
- # .callback(process = "tile_classification", event = "recovery",
- # context = environment())
- message("Recovery: tile '", tile[["tile"]], "' already exists.")
- message("(If you want to produce a new image, please ",
- "change 'output_dir' or 'version' parameters)")
+ if (.check_messages()) {
+ message("Recovery: tile '", tile[["tile"]], "' already exists.")
+ message("(If you want to produce a new image, please ",
+ "change 'output_dir' or 'version' parameters)")
+ }
  class_tile <- .tile_class_from_file(
  file = out_file, band = band, base_tile = tile
  )

R/api_reclassify.R

@@ -9,12 +9,11 @@
  )
  # Resume feature
  if (file.exists(out_file)) {
- # # Callback final tile classification
- # .callback(process = "tile_classification", event = "recovery",
- # context = environment())
- message("Recovery: tile '", tile[["tile"]], "' already exists.")
- message("(If you want to produce a new image, please ",
- "change 'output_dir' or 'version' parameters)")
+ if (.check_messages()) {
+ message("Recovery: tile '", tile[["tile"]], "' already exists.")
+ message("(If you want to produce a new image, please ",
+ "change 'output_dir' or 'version' parameters)")
+ }
  class_tile <- .tile_class_from_file(
  file = out_file, band = band, base_tile = tile
  )

R/api_smooth.R

@@ -14,12 +14,11 @@
  )
  # Resume feature
  if (file.exists(out_file)) {
- # # Callback final tile classification
- # .callback(process = "tile_classification", event = "recovery",
- # context = environment())
- message("Recovery: tile '", tile[["tile"]], "' already exists.")
- message("(If you want to produce a new image, please ",
- "change 'output_dir' or 'version' parameters)")
+ if (.check_messages()) {
+ message("Recovery: tile '", tile[["tile"]], "' already exists.")
+ message("(If you want to produce a new image, please ",
+ "change 'output_dir' or 'version' parameters)")
+ }
  probs_tile <- .tile_probs_from_file(
  file = out_file, band = band, base_tile = tile,
  labels = .tile_labels(tile), update_bbox = FALSE

R/api_uncertainty.R

@@ -15,12 +15,11 @@
  )
  # Resume feature
  if (file.exists(out_file)) {
- # # Callback final tile classification
- # .callback(process = "tile_classification", event = "recovery",
- # context = environment())
- message("Recovery: tile '", tile[["tile"]], "' already exists.")
- message("(If you want to produce a new image, please ",
- "change 'output_dir' or 'version' parameters)")
+ if (.check_messages()) {
+ message("Recovery: tile '", tile[["tile"]], "' already exists.")
+ message("(If you want to produce a new image, please ",
+ "change 'output_dir' or 'version' parameters)")
+ }
  uncert_tile <- .tile_uncertainty_from_file(
  file = out_file,
  band = band,

R/api_variance.R

@@ -12,12 +12,11 @@
  )
  # Resume feature
  if (file.exists(out_file)) {
- # # Callback final tile classification
- # .callback(process = "tile_classification", event = "recovery",
- # context = environment())
- message("Recovery: tile '", tile[["tile"]], "' already exists.")
- message("(If you want to produce a new image, please ",
- "change 'output_dir' or 'version' parameters)")
+ if (.check_messages()) {
+ message("Recovery: tile '", tile[["tile"]], "' already exists.")
+ message("(If you want to produce a new image, please ",
+ "change 'output_dir' or 'version' parameters)")
+ }
  var_tile <- .tile_variance_from_file(
  file = out_file, band = band, base_tile = tile,
  labels = .tile_labels(tile), update_bbox = FALSE

R/sits_classify_cube.R

@@ -46,12 +46,11 @@
  )
  # Resume feature
  if (file.exists(out_file)) {
- # # Callback final tile classification
- # .callback(process = "tile_classification", event = "recovery",
- # context = environment())
- message("Recovery: tile '", tile[["tile"]], "' already exists.")
- message("(If you want to produce a new image, please ",
- "change 'output_dir' or 'version' parameters)")
+ if (.check_messages()) {
+ message("Recovery: tile '", tile[["tile"]], "' already exists.")
+ message("(If you want to produce a new image, please ",
+ "change 'output_dir' or 'version' parameters)")
+ }
  probs_tile <- .tile_probs_from_file(
  file = out_file, band = band, base_tile = tile,
  labels = .ml_labels(ml_model), update_bbox = TRUE

R/sits_cube_copy.R

@@ -102,12 +102,11 @@ sits_cube_copy <- function(cube,
  )
  # Resume feature
  if (.raster_is_valid(out_file, output_dir = output_dir)) {
- # # Callback final tile classification
- # .callback(process = "tile_classification", event = "recovery",
- # context = environment())
- message("Recovery: file '", out_file, "' already exists.")
- message("(If you want to get a new version, please ",
- "change 'output_dir' parameter or delete the existing file)")
+ if (.check_messages()) {
+ message("Recovery: file '", out_file, "' already exists.")
+ message("(If you want to get a new version, please ",
+ "change 'output_dir' parameter or delete the existing file)")
+ }
  asset <- .download_update_asset(
  asset = asset, roi = roi, res = res, out_file = out_file
  )

R/sits_mixture_model.R

@@ -254,14 +254,13 @@ sits_mixture_model.raster_cube <- function(data, endmembers, ...,
  )
  # Resume feature
  if (.raster_is_valid(out_files, output_dir = output_dir)) {
- # # Callback final tile classification
- # .callback(process = "mixtureModel", event = "recovery",
- # context = environment())
- message("Recovery: fractions ",
- paste0("'", out_fracs, "'", collapse = ", "),
- " already exists.")
- message("(If you want to produce a new image, please ",
- "change 'output_dir' parameters)")
+ if (.check_messages()) {
+ message("Recovery: fractions ",
+ paste0("'", out_fracs, "'", collapse = ", "),
+ " already exists.")
+ message("(If you want to produce a new image, please ",
+ "change 'output_dir' parameters)")
+ }
  # Create tile based on template
  fracs_feature <- .tile_eo_from_files(
  files = out_files,

R/sits_mosaic.R

@@ -223,9 +223,11 @@ sits_mosaic <- function(cube,
  )
  # Resume feature
  if (.raster_is_valid(out_file, output_dir = output_dir)) {
- message("Recovery: file '", out_file, "' already exists.")
- message("(If you want to produce a new cropped image, please ",
- "change 'version' or 'output_dir' parameter)")
+ if (.check_messages()) {
+ message("Recovery: file '", out_file, "' already exists.")
+ message("(If you want to produce a new cropped image, please ",
+ "change 'version' or 'output_dir' parameter)")
+ }
  base_tile <- .tile_from_file(
  file = out_file, base_tile = base_tile,
  band = .tile_bands(base_tile), update_bbox = TRUE,
@@ -278,9 +280,11 @@ sits_mosaic <- function(cube,
  )
  # Resume feature
  if (.raster_is_valid(out_file, output_dir = output_dir)) {
- message("Recovery: file '", out_file, "' already exists.")
- message("(If you want to produce a new cropped image, please ",
- "change 'version' or 'output_dir' parameter)")
+ if (.check_messages()) {
+ message("Recovery: file '", out_file, "' already exists.")
+ message("(If you want to produce a new cropped image, please ",
+ "change 'version' or 'output_dir' parameter)")
+ }
  asset <- .tile_from_file(
  file = out_file, base_tile = asset,
  band = .tile_bands(asset), update_bbox = TRUE,

R/sits_summary.R

@@ -129,8 +129,6 @@ summary.raster_cube <- function(
  # change names
  colnames(sum) <- bands
  # print statistics
- d <- as.character(lubridate::as_date(date))
- cat("Statistics for tile ", tile$tile, " date ", d, "\n")
  sum
 }
 #' @title Summarize data cubes
@@ -209,7 +207,6 @@ summary.probs_cube <- function(
  offset <- .offset(band_conf)
  sum <- summary(values*scale + offset)
  colnames(sum) <- sits_labels(tile)
- cat("Statistics for tile ", tile$tile, "\n")
  sum
 }
 #' @title Summarize data cubes
@@ -288,7 +285,6 @@ summary.variance_cube <- function(
  offset <- .offset(band_conf)
  sum <- summary(values*scale + offset)
  colnames(sum) <- sits_labels(tile)
- cat("Statistics for tile ", tile$tile, "\n")
  sum
 }
 #' @title Summarize data cubes
@@ -364,7 +360,6 @@ summary.class_cube <- function(
  terra::expanse(unit = "km", byValue = TRUE)
  # create a tibble
  areas <- class_areas[,3]
- # get t
- cat("Class Areas for tile ", tile$tile, "\n")
+ # get the result
  data.frame(class = sits_labels(tile), area_km2 = signif(areas, 4))
 }

tests/testthat/test-apply.R

@@ -132,7 +132,11 @@ test_that("Kernel functions", {
  median_2 <- v_obj_md[21,21]
 
  expect_true(median_1 == median_2)
-
+ documentation <- FALSE
+ if (Sys.getenv("SITS_DOCUMENTATION_MODE") == "true") {
+ documentation <- TRUE
+ Sys.setenv("SITS_DOCUMENTATION_MODE" = "false")
+ }
  # Recovery
  out <- capture_messages({
  expect_message({
@@ -147,6 +151,9 @@ test_that("Kernel functions", {
  regexp = "Recovery"
  )
  })
+ if (documentation) {
+ Sys.setenv("SITS_DOCUMENTATION_MODE" = "true")
+ }
  expect_true(grepl("output_dir", out[1]))
  expect_true(grepl("Recovery", out[2]))
  cube_mean <- sits_apply(

tests/testthat/test-combine_predictions.R

@@ -56,6 +56,11 @@ test_that("Combine predictions", {
 
  # Recovery
  # test Recovery
+ documentation <- FALSE
+ if (Sys.getenv("SITS_DOCUMENTATION_MODE") == "true") {
+ documentation <- TRUE
+ Sys.setenv("SITS_DOCUMENTATION_MODE" = "false")
+ }
  out <- capture_messages({
  expect_message(
  object = { sits_combine_predictions(
@@ -67,6 +72,9 @@ test_that("Combine predictions", {
  regexp = "Recovery"
  )
  })
+ if (documentation) {
+ Sys.setenv("SITS_DOCUMENTATION_MODE" = "true")
+ }
  expect_true(grepl("output_dir", out[1]))
 
  # combine predictions

tests/testthat/test-raster.R

@@ -22,6 +22,11 @@ test_that("Single core classification with rfor", {
  )
 
  # testing resume feature
+ documentation <- FALSE
+ if (Sys.getenv("SITS_DOCUMENTATION_MODE") == "true") {
+ documentation <- TRUE
+ Sys.setenv("SITS_DOCUMENTATION_MODE" = "false")
+ }
  out <- capture_messages({
  expect_message(
  object = { sits_classify(
@@ -34,6 +39,9 @@ test_that("Single core classification with rfor", {
  regexp = "Recovery: "
  )
  })
+ if (documentation) {
+ Sys.setenv("SITS_DOCUMENTATION_MODE" = "true")
+ }
  expect_true(grepl("output_dir", out[1]))
 
  sits_labels(sinop_probs) <- c(
@@ -476,7 +484,11 @@ test_that("Classification with post-processing", {
  sinop_probs,
  output_dir = output_dir,
  )
-
+ documentation <- FALSE
+ if (Sys.getenv("SITS_DOCUMENTATION_MODE") == "true") {
+ documentation <- TRUE
+ Sys.setenv("SITS_DOCUMENTATION_MODE" = "false")
+ }
  # testing resume feature
  out <- capture_messages({
  expect_message(
@@ -487,6 +499,9 @@ test_that("Classification with post-processing", {
  regexp = "Recovery"
  )
  })
+ if (documentation) {
+ Sys.setenv("SITS_DOCUMENTATION_MODE" = "true")
+ }
  expect_true(grepl("output_dir", out[1]))
 
  expect_true(all(file.exists(unlist(sinop_class$file_info[[1]]$path))))
@@ -506,7 +521,11 @@ test_that("Classification with post-processing", {
  memsize = 4,
  multicores = 2
  )
-
+ documentation <- FALSE
+ if (Sys.getenv("SITS_DOCUMENTATION_MODE") == "true") {
+ documentation <- TRUE
+ Sys.setenv("SITS_DOCUMENTATION_MODE" = "false")
+ }
  # testing the recovery feature
  out <- capture_messages({
  expect_message(
@@ -519,6 +538,9 @@ test_that("Classification with post-processing", {
  regexp = "Recovery"
  )
  })
+ if (documentation) {
+ Sys.setenv("SITS_DOCUMENTATION_MODE" = "true")
+ }
  expect_true(grepl("output_dir", out[1]))
 
  expect_true(all(file.exists(unlist(sinop_bayes$file_info[[1]]$path))))