fix conflicts

DESCRIPTION

@@ -142,6 +142,7 @@ Collate:
  'api_mixture_model.R'
  'api_ml_model.R'
  'api_mosaic.R'
+ 'api_opensearch.R'
  'api_parallel.R'
  'api_period.R'
  'api_plot_time_series.R'
@@ -159,6 +160,7 @@ Collate:
  'api_s2tile.R'
  'api_samples.R'
  'api_segments.R'
+ 'api_select.R'
  'api_sf.R'
  'api_shp.R'
  'api_signal.R'

NAMESPACE

@@ -132,6 +132,7 @@ S3method(.source_collection_access_test,stac_cube)
 S3method(.source_collection_access_test,usgs_cube)
 S3method(.source_cube,stac_cube)
 S3method(.source_filter_tiles,"cdse_cube_sentinel-1-rtc")
+S3method(.source_filter_tiles,"deafrica_cube_sentinel-1-rtc")
 S3method(.source_filter_tiles,"mpc_cube_sentinel-1-grd")
 S3method(.source_filter_tiles,stac_cube)
 S3method(.source_item_get_bands,stac_cube)
@@ -150,6 +151,8 @@ S3method(.source_items_bands_select,stac_cube)
 S3method(.source_items_cube,stac_cube)
 S3method(.source_items_fid,stac_cube)
 S3method(.source_items_new,"aws_cube_landsat-c2-l2")
+S3method(.source_items_new,"deafrica_cube_sentinel-1-rtc")
+S3method(.source_items_new,"deafrica_cube_sentinel-2-l2a")
 S3method(.source_items_new,"mpc_cube_landsat-c2-l2")
 S3method(.source_items_new,"mpc_cube_sentinel-1-grd")
 S3method(.source_items_new,"mpc_cube_sentinel-1-rtc")
@@ -158,12 +161,13 @@ S3method(.source_items_new,aws_cube)
 S3method(.source_items_new,bdc_cube)
 S3method(.source_items_new,cdse_cube)
 S3method(.source_items_new,deafrica_cube)
-S3method(.source_items_new,deafrica_cube_s2_l2a)
 S3method(.source_items_new,hls_cube)
 S3method(.source_items_new,sdc_cube)
 S3method(.source_items_new,usgs_cube)
 S3method(.source_items_tile,"aws_cube_landsat-c2-l2")
 S3method(.source_items_tile,"cdse_cube_sentinel-1-rtc")
+S3method(.source_items_tile,"deafrica_cube_rainfall-chirps-daily")
+S3method(.source_items_tile,"deafrica_cube_rainfall-chirps-monthly")
 S3method(.source_items_tile,"mpc_cube_landsat-c2-l2")
 S3method(.source_items_tile,"mpc_cube_sentinel-1-grd")
 S3method(.source_items_tile,"mpc_cube_sentinel-1-rtc")
@@ -172,8 +176,6 @@ S3method(.source_items_tile,aws_cube)
 S3method(.source_items_tile,bdc_cube)
 S3method(.source_items_tile,cdse_cube)
 S3method(.source_items_tile,deafrica_cube)
-S3method(.source_items_tile,deafrica_cube_rainfall_chirps_daily)
-S3method(.source_items_tile,deafrica_cube_rainfall_chirps_monthly)
 S3method(.source_items_tile,hls_cube)
 S3method(.source_items_tile,sdc_cube)
 S3method(.source_items_tile,usgs_cube)

R/api_accessors.R

@@ -125,7 +125,7 @@
  paste0("EPSG:", .compact(x))
  }
  } else {
-  stop("invalid crs value")
+ stop(.conf("messages", ".as_crs"))
  }
 }
 #' @title Return CRS from a spatial data structure

R/api_accuracy.R

@@ -11,9 +11,9 @@
 #' @return A tibble with predicted and reference values.
 .accuracy_pred_ref <- function(class) {
  # retrieve the predicted values
- pred <- unlist(purrr::map(class$predicted, function(r) r$class))
+ pred <- unlist(purrr::map(class[["predicted"]], function(r) r[["class"]]))
  # retrieve the reference labels
- ref <- class$label
+ ref <- class[["label"]]
  # does the input data contains valid reference labels?
  .check_labels(ref)
  # build the tibble
@@ -52,11 +52,9 @@
  # are in the validation file
  diff_classes <- setdiff(rownames(error_matrix), names(area))
  if (length(diff_classes) > 0 &&
- length(diff_classes) < length(rownames(error_matrix))) {
- warning(
- paste("The classified cube does not have all the classes in the",
- "validation file."),
- call. = FALSE
+ length(diff_classes) < length(rownames(error_matrix))) {
+ warning(.conf("messages", ".accuracy_area_assess"),
+ call. = FALSE
  )
  # Create a numeric vector with zeros
  vec_areas <- rep(0, length(diff_classes))

R/api_apply.R

@@ -9,10 +9,11 @@
 #' @param fn Function to be applied.
 #' @return Tibble where function has been applied.
 .apply <- function(data, col, fn, ...) {
+ .check_set_caller(".apply")
  # pre-condition
- .check_chr_within(col,
- within = names(data),
- msg = "invalid column name"
+ .check_chr_within(
+ col,
+ within = names(data)
  )
  # select data do unpack
  x <- data[col]
@@ -214,15 +215,15 @@
 .apply_capture_expression <- function(...) {
  # Capture dots as a list of quoted expressions
  list_expr <- lapply(substitute(list(...), env = environment()),
- unlist,
- recursive = FALSE
+  unlist,
+  recursive = FALSE
  )[-1]
 
  # Check bands names from expression
  .check_expression(list_expr)
 
  # Get out band
- out_band <- toupper(gsub("_", "-", names(list_expr)))
+ out_band <- toupper(gsub("_", "-", names(list_expr), fixed = TRUE))
  names(list_expr) <- out_band
 
  return(list_expr)

R/api_band.R

@@ -17,7 +17,8 @@
 .band_rename.sits <- function(x, bands) {
  data_bands <- sits_bands(x)
  # pre-condition
- .check_chr(bands,
+ .check_chr(
+ bands,
  allow_empty = FALSE, len_min = length(data_bands),
  len_max = length(data_bands)
  )
@@ -43,7 +44,8 @@
 .band_rename.raster_cube <- function(x, bands) {
  data_bands <- sits_bands(x)
  # pre-condition
- .check_chr(bands,
+ .check_chr(
+ bands,
  allow_empty = FALSE,
  len_min = length(data_bands),
  len_max = length(data_bands)
@@ -62,12 +64,12 @@
  new_bands[data_bands] <- toupper(bands)
  colnames(x) <- unname(new_bands)
 
- x <- tidyr::pivot_longer(x,
+ x <- tidyr::pivot_longer(
+ x,
  cols = toupper(bands),
  names_to = "band",
  values_to = "path"
  )
-
  return(x)
  })
 }
@@ -84,23 +86,23 @@
 #' @param band band name (may be lower or upper case)
 #' @return band name in upper case
 .band_eo <- function(band) {
- gsub("_", "-", toupper(band))
+ gsub("_", "-", toupper(band), fixed = TRUE)
 }
 #' @title Convert band names for derived cubes
 #' @name .band_derived
 #' @noRd
 #' @param band band name (may be lower or upper case)
 #' @return band name in lower case
 .band_derived <- function(band) {
- gsub("_", "-", tolower(band))
+ gsub("_", "-", tolower(band), fixed = TRUE)
 }
 #' @title Convert band names for time series
 #' @name .band_samples
 #' @noRd
 #' @param band band name (may be lower or upper case)
 #' @return band name in upper case
 .band_samples <- function(band) {
- gsub("_", "-", toupper(band))
+ gsub("_", "-", toupper(band), fixed = TRUE)
 }
 #' @title Convert band names for data cube
 #' @name .band_set_case

R/api_bbox.R

@@ -11,7 +11,7 @@
 #'
 .bbox_equal <- function(bbox1, bbox2, tolerance = 0) {
  .is_eq(unlist(bbox1[.bbox_cols]), unlist(bbox2[.bbox_cols]),
- tolerance = tolerance
+  tolerance = tolerance
  )
 }
 #' @title Bounding box API
@@ -66,15 +66,15 @@ NULL
  } else if (.is_point(x)) {
  "point"
  } else {
- stop("cannot extract bbox from object of class ", class(x))
+ stop(.conf("messages", ".bbox_type"), class(x))
  }
 }
 #' @title Switch bbox type
 #' @noRd
 #' @returns One of the arguments passed in `...` according to a bbox type.
 .bbox_switch <- function(x, ...) {
  switch(.bbox_type(x),
- ...
+  ...
  )
 }
 #' @title Extract a bbox
@@ -233,6 +233,6 @@ NULL
  # Convert WKT to sf CRS object
  crs_sf <- sf::st_crs(wkt_crs)
  # Convert sf CRS object to PROJ4 string
- proj4string <- crs_sf$proj4string
+ proj4string <- crs_sf[["proj4string"]]
  return(proj4string)
 }