fix(pkgdown,docs): unbreak site build; harden as_ogr; doc/debug fixes

* _pkgdown.yml: add exported get_streamorder and hf_check_merge_invariants
  to the reference index. They were exported in 0.3.4 but never indexed, so
  pkgdown::build_site_github_pages() aborted ("topics missing from index")
  and the Website workflow was failing on every push.
* as_ogr.OGRSQLConnection(): on an ambiguous layer, cli_abort with the
  candidate list (matching read_hydrofabric) instead of print()ing and
  returning the bare connection; also abort on zero readable layers.
* OGRSQLConnection dbSendQuery(): fix the ogr.query.debug message -- the
  sprintf had two placeholders but one arg and nrow() was passed to message()
  rather than sprintf(), so enabling debug errored.
* Docstring fixes: complete the truncated lynker_spatial_auth `token` param;
  add_lengthkm "areas" -> "lengths"; get_hydroseq param referenced a
  nonexistent `topology` arg (-> x); OGRSQLResult \pkg{lazsf} -> \pkg{hfutils};
  arrow_to_sf "metatdata" typo.
* Regenerate favicons from the newer logo (resolves pkgdown sitrep).

Author: Mike Johnson

R/OGRSQLConnection.R

@@ -53,9 +53,9 @@ setMethod("dbSendQuery", "OGRSQLConnection", function(conn, statement, ...) {
     message(
       sprintf(
         "-------------\nOGR debug ....\nSQL:\n%s\nnrows read:\n%i",
-        statement
-      ),
-      nrow(layer_data)
+        statement,
+        nrow(layer_data)
+      )
     )
   }
   if (inherits(layer_data, "try-error")) {

R/OGRSQLResult.R

@@ -3,7 +3,7 @@
 #' OGRSQLResult objects are created by [dbSendQuery()] or [dbSendStatement()],
 #' and encapsulate the result of an SQL statement.
 #' They are a superclass of the [DBIResult-class] class.
-#' The "Usage" section lists the class methods overridden by \pkg{lazsf}.
+#' The "Usage" section lists the class methods overridden by \pkg{hfutils}.
 #' @seealso
 #' The corresponding generic functions
 #' [DBI::dbFetch()], [DBI::dbClearResult()], and

R/auth.R

@@ -1,6 +1,7 @@
 #' Authenticate with Lynker Spatial
-#' @param token An existing OAuth2 token. If NULL, then a new token is provisioned and returned.
-#'              If the token is expired, then
+#' @param token An existing OAuth2 token. If `NULL`, a new token is provisioned
+#'   and returned. If the supplied token is expired, it is refreshed via
+#'   [lynker_spatial_refresh()] before use.
 #' @param ... Unused
 #' @param libs Libraries to configure auth for; any of `"gdal"`, `"duckdb"`,
 #'   `"arrow"`. Default `c("gdal", "duckdb")`. `"arrow"` authenticates via the

R/network_properties.R

@@ -99,9 +99,9 @@ accumulate_downstream <- function(x, id   = "flowpath_id", toid = "flowpath_toid
 #'
 #' @param x A data frame (or tibble) containing at least the identifier column
 #'   given by `id` and the downstream pointer column given by `toid`.
-#' @param id Character scalar. Column name in `topology` with unique node identifiers.
+#' @param id Character scalar. Column name in `x` with unique node identifiers.
 #'   Defaults to `"flowpath_id"`.
-#' @param toid Character scalar. Column name in `topology` with the *downstream* node
+#' @param toid Character scalar. Column name in `x` with the *downstream* node
 #'   identifier for each row. Use `NA` or `0` for outlets/terminals.
 #'   Defaults to `"flowpath_toid"`.
 #'

R/sf_arrow.R

@@ -132,7 +132,7 @@ arrow_to_sf <- function(tbl, metadata) {
   primary_geom <- metadata$primary_column
 
   if (length(geom_cols) < 1) {
-    stop("Malformed file and geo metatdata.")
+    stop("Malformed file and geo metadata.")
   }
   if (!primary_geom %in% geom_cols) {
     primary_geom <- geom_cols[1]

R/sf_ogr.R

@@ -89,20 +89,22 @@ as_ogr.OGRSQLConnection <- function(x, layer, ..., query = NA, ignore_lyrs = "gp
     tbls <- dbListTables(x)
     tbls <- tbls[!grepl(ignore_lyrs, tbls)]
 
-    if (length(tbls) == 1) {
+    if (length(tbls) == 0L) {
+      cli::cli_abort("No readable layers found in the data source.")
+    } else if (length(tbls) == 1L) {
       layer <- tbls
     } else {
-      layer <- NULL
-      print(tbls)
+      cli::cli_abort(c(
+        "Multiple layers found; please specify {.arg layer} explicitly:",
+        ">" = paste(tbls, collapse = ", ")
+      ))
     }
   }
 
-  if (!is.null(layer)) {
-    if (layer %in% dbListTables(x)) {
-      x <- tbl(x, layer)
-    } else {
-      cli::cli_abort("{.val {layer}} not in gpkg.")
-    }
+  if (layer %in% dbListTables(x)) {
+    x <- tbl(x, layer)
+  } else {
+    cli::cli_abort("{.val {layer}} not in gpkg.")
   }
 
   x

R/utils.R

@@ -158,7 +158,7 @@ add_areasqkm <- function(x) {
 #' Safely compute linestring length in km and return a plain numeric vector.
 #'
 #' @param x An `sf` object with LINE* geometry. If `x` is not in a projected
-#'   CRS, `sf::st_length()` will compute ellipsoidal areas when possible.
+#'   CRS, `sf::st_length()` will compute ellipsoidal lengths when possible.
 #'
 #' @return A numeric vector of lengths in kilometers.
 #'

_pkgdown.yml

@@ -111,6 +111,7 @@ reference:
   contents:
   - accumulate_downstream
   - get_hydroseq
+  - get_streamorder
   - add_measures
   - add_areasqkm
   - add_lengthkm
@@ -126,6 +127,7 @@ reference:
   - gpkg_set_version
   - gpkg_get_version
   - hf_check_invariants
+  - hf_check_merge_invariants
   - hf_check_attr_bounds
   - hf_attr_bounds