From e93b89071a43c5ead912d092bc23a1e078b1be88 Mon Sep 17 00:00:00 2001
From: David Blodgett <dblodgett@usgs.gov>
Date: Mon, 19 Aug 2024 07:46:19 -0500
Subject: [PATCH 1/6] example requires nhdplusTools

---
 R/index_points_to_lines.R          | 4 ++++
 man/index_points_to_waterbodies.Rd | 4 ++++
 2 files changed, 8 insertions(+)

diff --git a/R/index_points_to_lines.R b/R/index_points_to_lines.R
index 3e9ae45..564f3e4 100644
--- a/R/index_points_to_lines.R
+++ b/R/index_points_to_lines.R
@@ -392,6 +392,8 @@ index_points_to_lines.hy <- function(x, points,
 #' @export
 #' @examples
 #'
+#' if(require(nhdplusTools)) {
+#'
 #' source(system.file("extdata/sample_data.R", package = "nhdplusTools"))
 #'
 #' waterbodies <- sf::st_transform(
@@ -404,6 +406,8 @@ index_points_to_lines.hy <- function(x, points,
 #' index_points_to_waterbodies(waterbodies, points,
 #'                     search_radius = units::set_units(500, "m"))
 #'
+#' }
+#'
 index_points_to_waterbodies <- function(waterbodies, points, flines = NULL,
                                         search_radius = NULL) {
 
diff --git a/man/index_points_to_waterbodies.Rd b/man/index_points_to_waterbodies.Rd
index d691792..a0ff1a8 100644
--- a/man/index_points_to_waterbodies.Rd
+++ b/man/index_points_to_waterbodies.Rd
@@ -35,6 +35,8 @@ COMID of dominant artificial path
 }
 \examples{
 
+if(require(nhdplusTools)) {
+
 source(system.file("extdata/sample_data.R", package = "nhdplusTools"))
 
 waterbodies <- sf::st_transform(
@@ -48,3 +50,5 @@ index_points_to_waterbodies(waterbodies, points,
                     search_radius = units::set_units(500, "m"))
 
 }
+
+}

From 88dbd90da3d245cd599cedc2ba3f675d503ade85 Mon Sep 17 00:00:00 2001
From: David Blodgett <dblodgett@usgs.gov>
Date: Mon, 19 Aug 2024 11:20:39 -0500
Subject: [PATCH 2/6] bug in logic for suggested packages

---
 R/add_levelpaths.R       | 3 ++-
 vignettes/flow-table.Rmd | 4 ++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/R/add_levelpaths.R b/R/add_levelpaths.R
index c37dc58..e91f814 100644
--- a/R/add_levelpaths.R
+++ b/R/add_levelpaths.R
@@ -146,7 +146,8 @@ add_levelpaths.hy <- function(x, name_attribute, weight_attribute,
     group_split()
 
   cl <- "future"
-  if(inherits(future::plan(), "sequential")) cl = NULL
+  if(!requireNamespace("future", quietly = TRUE) ||
+     inherits(future::plan(), "sequential")) cl = NULL
 
   # reweight sets up ranked upstream paths
   x <- pblapply(x, reweight, override_factor = override_factor,
diff --git a/vignettes/flow-table.Rmd b/vignettes/flow-table.Rmd
index de4f2c3..4380e03 100644
--- a/vignettes/flow-table.Rmd
+++ b/vignettes/flow-table.Rmd
@@ -11,9 +11,9 @@ vignette: >
 ```{r setup, include = FALSE}
 local <- (Sys.getenv("BUILD_VIGNETTES") == "TRUE")
 
-if(!require(nhdplusTools)) local <- FALSE
+if(!requireNamespace("nhdplusTools", quietly = TRUE)) local <- FALSE
 
-if(!local) {
+if(local) {
   nhdplusTools::nhdplusTools_data_dir(tempdir())
 }
 

From b376ef084785b7786da8be008e7e76e2d4bd8d63 Mon Sep 17 00:00:00 2001
From: David Blodgett <dblodgett@usgs.gov>
Date: Tue, 20 Aug 2024 15:44:51 -0500
Subject: [PATCH 3/6] update documentation of UT navigation as not following
 diversions

---
 R/navigation_network.R        | 7 +++++++
 man/navigate_hydro_network.Rd | 6 ++++++
 2 files changed, 13 insertions(+)

diff --git a/R/navigation_network.R b/R/navigation_network.R
index 3598124..6dd9499 100644
--- a/R/navigation_network.R
+++ b/R/navigation_network.R
@@ -41,6 +41,13 @@ get_start_row <- function(x, id) {
 #' @param distance numeric distance in km to limit navigation. The first
 #' catchment that exceeds the provided distance is included.
 #' @details if only `mode` is supplied, require network attributes are displayed.
+#'
+#' NOTE: for "Upstream with tributaries" navigation, if a tributary emanates from
+#' a diversion and is the minor path downstream of that diversion, it is not
+#' followed. This can have a very large impact when a diversion between two
+#' large river systems. For non-dendritic upstream with tributaries
+#' network navigation, use \link{navigate_network_dfs}.
+#'
 #' @returns vector of identifiers found along navigation
 #' @name navigate_hydro_network
 #' @export
diff --git a/man/navigate_hydro_network.Rd b/man/navigate_hydro_network.Rd
index 242bd3a..95ab983 100644
--- a/man/navigate_hydro_network.Rd
+++ b/man/navigate_hydro_network.Rd
@@ -39,6 +39,12 @@ network attributes.
 }
 \details{
 if only \code{mode} is supplied, require network attributes are displayed.
+
+NOTE: for "Upstream with tributaries" navigation, if a tributary emanates from
+a diversion and is the minor path downstream of that diversion, it is not
+followed. This can have a very large impact when a diversion between two
+large river systems. For non-dendritic upstream with tributaries
+network navigation, use \link{navigate_network_dfs}.
 }
 \examples{
 

From b93834748ec3c577366467916fb3e230e3623ad3 Mon Sep 17 00:00:00 2001
From: David Blodgett <dblodgett@usgs.gov>
Date: Wed, 21 Aug 2024 08:58:55 -0500
Subject: [PATCH 4/6] better handling for future not installed

---
 R/add_divergence.R             | 2 +-
 R/add_levelpaths.R             | 4 +---
 R/make_attribute_topology.R    | 2 +-
 R/navigate_connected_paths.R   | 3 ++-
 R/utils.R                      | 5 +++++
 vignettes/advanced_network.Rmd | 3 ++-
 6 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/R/add_divergence.R b/R/add_divergence.R
index de4f559..cbfd9fe 100644
--- a/R/add_divergence.R
+++ b/R/add_divergence.R
@@ -128,7 +128,7 @@ add_divergence.hy <- function(x, coastal_outlet_ids, inland_outlet_ids,
     try(navigate_network_dfs(x = net, starts = i,
                              direction = "up",
                              reset = FALSE))
-  }, net = x, cl = "future")
+  }, net = x, cl = future_available())
 
   paths_df <- data.frame(id = unlist(term),
                          paths = I(unlist(paths,
diff --git a/R/add_levelpaths.R b/R/add_levelpaths.R
index e91f814..77e6d2f 100644
--- a/R/add_levelpaths.R
+++ b/R/add_levelpaths.R
@@ -145,9 +145,7 @@ add_levelpaths.hy <- function(x, name_attribute, weight_attribute,
     group_by(.data$toid) |>
     group_split()
 
-  cl <- "future"
-  if(!requireNamespace("future", quietly = TRUE) ||
-     inherits(future::plan(), "sequential")) cl = NULL
+  cl <- future_available()
 
   # reweight sets up ranked upstream paths
   x <- pblapply(x, reweight, override_factor = override_factor,
diff --git a/R/make_attribute_topology.R b/R/make_attribute_topology.R
index 43fd890..2daae7b 100644
--- a/R/make_attribute_topology.R
+++ b/R/make_attribute_topology.R
@@ -77,7 +77,7 @@ make_attribute_topology.hy <- function(x, min_distance) {
       which(d == min(d, na.rm = TRUE))
     }
 
-  }, nodes = nodes, cl = "future")
+  }, nodes = nodes, cl = future_available())
 
   # Add resulting list as a list column
   nodes$torow <- closest
diff --git a/R/navigate_connected_paths.R b/R/navigate_connected_paths.R
index f53aa44..aa12fc0 100644
--- a/R/navigate_connected_paths.R
+++ b/R/navigate_connected_paths.R
@@ -78,7 +78,8 @@ navigate_connected_paths <- function(x, outlets, status = FALSE) {
   }
 
   pairs <- t(combn(length(id_match), 2))
-  paths <- pbapply(pairs, 1, get_path, all_dn = all_dn, cl = "future")
+
+  paths <- pbapply(pairs, 1, get_path, all_dn = all_dn, cl = future_available())
 
   connected_paths <- paths[lengths(paths) > 0]
 
diff --git a/R/utils.R b/R/utils.R
index 6a98993..fae6c78 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -1,3 +1,8 @@
+future_available <- function() {
+  if(!requireNamespace("future", quietly = TRUE) ||
+     inherits(future::plan(), "sequential")) NULL else "future"
+}
+
 get_outlet_value <- function(x) {
   if(inherits(x$id, "character")) {
     ""
diff --git a/vignettes/advanced_network.Rmd b/vignettes/advanced_network.Rmd
index cd92636..195da7a 100644
--- a/vignettes/advanced_network.Rmd
+++ b/vignettes/advanced_network.Rmd
@@ -191,7 +191,7 @@ lp <-  unique(lp$levelpath)
 terminal_fpath <- dplyr::filter(fpath, id %in% terminal_id)
 
 gif_file <- "levelpath.gif"
-
+try({
 gifski::save_gif({
   for(i in 1:length(lp)) {
     lp_plot <- dplyr::filter(fpath, levelpath == lp[i])
@@ -207,6 +207,7 @@ gifski::save_gif({
 }, gif_file, delay = 0.5)
 
 knitr::include_graphics(gif_file)
+})
 ```
 
 # Summary

From d8ec44cac6e1f89c489e22e1e27096cd923d1ed6 Mon Sep 17 00:00:00 2001
From: David Blodgett <dblodgett@usgs.gov>
Date: Wed, 21 Aug 2024 11:07:15 -0500
Subject: [PATCH 5/6] more suggested package cleanup

---
 tests/testthat/test_add_pfafstetter.R    |  2 +-
 tests/testthat/test_get_hydro_location.R |  2 +-
 tests/testthat/test_index.R              | 15 ++++++++-------
 vignettes/flow-table.Rmd                 |  1 +
 4 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/tests/testthat/test_add_pfafstetter.R b/tests/testthat/test_add_pfafstetter.R
index f444f1a..5692338 100644
--- a/tests/testthat/test_add_pfafstetter.R
+++ b/tests/testthat/test_add_pfafstetter.R
@@ -1,6 +1,6 @@
 test_that("get_pfaf", {
 
-  if(!require(nhdplusTools)) skip("Missing nhdplusTools")
+  if(!requireNamespace("nhdplusTools", quietly = TRUE)) skip("Missing nhdplusTools")
 
   work_dir <- nhdplusTools::nhdplusTools_data_dir()
 
diff --git a/tests/testthat/test_get_hydro_location.R b/tests/testthat/test_get_hydro_location.R
index 7171093..6300de2 100644
--- a/tests/testthat/test_get_hydro_location.R
+++ b/tests/testthat/test_get_hydro_location.R
@@ -1,5 +1,5 @@
 test_that("get location", {
-  if(!require(nhdplusTools)) skip("Missing nhdplusTools")
+  if(!requireNamespace("nhdplusTools", quietly = TRUE)) skip("Missing nhdplusTools")
 
   source(system.file("extdata", "sample_flines.R", package = "nhdplusTools"))
 
diff --git a/tests/testthat/test_index.R b/tests/testthat/test_index.R
index 5b80776..c7951ef 100644
--- a/tests/testthat/test_index.R
+++ b/tests/testthat/test_index.R
@@ -1,5 +1,5 @@
 test_that("index to waterbodies", {
-  if(!require(nhdplusTools)) skip("Missing nhdplusTools")
+  if(!requireNamespace("nhdplusTools", quietly = TRUE)) skip("Missing nhdplusTools")
 
   source(system.file("extdata/sample_data.R", package = "nhdplusTools"))
 
@@ -52,7 +52,7 @@ test_that("index to waterbodies", {
 
 sr <- units::set_units(0.1, "degrees")
 
-if(require(nhdplusTools)) {
+if(requireNamespace("nhdplusTools", quietly = TRUE)) {
   source(system.file("extdata", "sample_flines.R", package = "nhdplusTools"))
 
   sample_flines <- sf::st_cast(sample_flines, "LINESTRING", warn = FALSE)
@@ -60,7 +60,8 @@ if(require(nhdplusTools)) {
 
 test_that("point indexing to nearest existing node works as expected", {
 
-  if(!require(nhdplusTools)) skip("Missing nhdplusTools")
+  if(!requireNamespace("nhdplusTools", quietly = TRUE)) skip("Missing nhdplusTools")
+  if(!requireNamespace("lwgeom", quietly = TRUE)) skip("Missing lwgeom")
 
   flines_in <- sample_flines
 
@@ -113,7 +114,7 @@ test_that("point indexing to nearest existing node works as expected", {
 
 test_that("point indexing works without measures", {
 
-  if(!require(nhdplusTools)) skip("Missing nhdplusTools")
+  if(!requireNamespace("nhdplusTools", quietly = TRUE)) skip("Missing nhdplusTools")
 
     flines_in <- sample_flines
 
@@ -133,8 +134,8 @@ test_that("point indexing works without measures", {
 
 test_that("point indexing to for multiple points works", {
 
-  if(!require(nhdplusTools)) skip("Missing nhdplusTools")
-
+  if(!requireNamespace("nhdplusTools", quietly = TRUE)) skip("Missing nhdplusTools")
+  if(!requireNamespace("lwgeom", quietly = TRUE)) skip("Missing lwgeom")
   flines_in <- sample_flines
 
   flines_in <- sf::st_transform(flines_in, 4269)
@@ -227,7 +228,7 @@ test_that("no duplicates when using precision", {
 
 test_that("disambiguate", {
 
-  if(!require(nhdplusTools)) skip("Missing nhdplusTools")
+  if(!requireNamespace("nhdplusTools", quietly = TRUE)) skip("Missing nhdplusTools")
 
   source(system.file("extdata", "sample_flines.R", package = "nhdplusTools"))
 
diff --git a/vignettes/flow-table.Rmd b/vignettes/flow-table.Rmd
index 4380e03..c5ec82e 100644
--- a/vignettes/flow-table.Rmd
+++ b/vignettes/flow-table.Rmd
@@ -12,6 +12,7 @@ vignette: >
 local <- (Sys.getenv("BUILD_VIGNETTES") == "TRUE")
 
 if(!requireNamespace("nhdplusTools", quietly = TRUE)) local <- FALSE
+if(!requireNamespace("mapview", quietly = TRUE)) local <- FALSE
 
 if(local) {
   nhdplusTools::nhdplusTools_data_dir(tempdir())

From f54769716a5ba6050b7a49295971244fa3f3af08 Mon Sep 17 00:00:00 2001
From: David Blodgett <dblodgett@usgs.gov>
Date: Wed, 21 Aug 2024 11:32:42 -0500
Subject: [PATCH 6/6] UT navigation follow divergences now

---
 R/navigation_network.R        | 24 ++++++++++++++++--------
 man/navigate_hydro_network.Rd |  8 ++++----
 2 files changed, 20 insertions(+), 12 deletions(-)

diff --git a/R/navigation_network.R b/R/navigation_network.R
index 6dd9499..eda2110 100644
--- a/R/navigation_network.R
+++ b/R/navigation_network.R
@@ -3,7 +3,7 @@ required_atts_navigate <- function(mode, distance) {
                         DM = c(id, levelpath, dn_levelpath,
                                topo_sort, dn_topo_sort),
                         UT = c(id, levelpath,
-                               topo_sort, dn_topo_sort),
+                               topo_sort, dn_topo_sort, dn_minor_topo_sort),
                         DD = c(id, levelpath, dn_levelpath,
                                topo_sort, dn_topo_sort, dn_minor_topo_sort))
 
@@ -43,10 +43,10 @@ get_start_row <- function(x, id) {
 #' @details if only `mode` is supplied, require network attributes are displayed.
 #'
 #' NOTE: for "Upstream with tributaries" navigation, if a tributary emanates from
-#' a diversion and is the minor path downstream of that diversion, it is not
-#' followed. This can have a very large impact when a diversion between two
-#' large river systems. For non-dendritic upstream with tributaries
-#' network navigation, use \link{navigate_network_dfs}.
+#' a diversion and is the minor path downstream of that diversion, it will be
+#' included. This can have a very large impact when a diversion between two
+#' large river systems. To strictly follow the dendritic network, set the
+#' "dn_minor_topo_sort" attribute to all 0 in x.
 #'
 #' @returns vector of identifiers found along navigation
 #' @name navigate_hydro_network
@@ -138,10 +138,18 @@ get_UT <- function(x, id, distance) {
 
     x <- filter(x, .data$id %in% all)
 
-    filter(x, .data$pathlength_km <= stop_pathlength_km)$id
-  } else {
-    all
+    all <- filter(x, .data$pathlength_km <= stop_pathlength_km)$id
   }
+
+  incoming_div <- filter(x, !id %in% all &
+                           dn_minor_topo_sort %in% x$topo_sort[x$id %in% all])
+
+  extra <- lapply(incoming_div$id, \(i) get_UT(x, i, distance))
+
+  all <- c(all, unique(unlist(extra)))
+
+  return(all)
+
 }
 
 private_get_UT <- function(x, id) {
diff --git a/man/navigate_hydro_network.Rd b/man/navigate_hydro_network.Rd
index 95ab983..ce3fc68 100644
--- a/man/navigate_hydro_network.Rd
+++ b/man/navigate_hydro_network.Rd
@@ -41,10 +41,10 @@ network attributes.
 if only \code{mode} is supplied, require network attributes are displayed.
 
 NOTE: for "Upstream with tributaries" navigation, if a tributary emanates from
-a diversion and is the minor path downstream of that diversion, it is not
-followed. This can have a very large impact when a diversion between two
-large river systems. For non-dendritic upstream with tributaries
-network navigation, use \link{navigate_network_dfs}.
+a diversion and is the minor path downstream of that diversion, it will be
+included. This can have a very large impact when a diversion between two
+large river systems. To strictly follow the dendritic network, set the
+"dn_minor_topo_sort" attribute to all 0 in x.
 }
 \examples{