Merge pull request #502 from olivroy/message-follow

Use `cli::cli_abort()` everywhere.
rich-iannone · Nov 8, 2023 · cd0427b · cd0427b
2 parents 3820ba2 + 2dbcfc1
commit cd0427b
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,9 +2,11 @@ Type: Package
 Package: DiagrammeR
 Title: Graph/Network Visualization
 Version: 1.0.10.9000
-Authors@R:
+Authors@R: c(
     person("Richard", "Iannone", , "riannone@me.com", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0003-3925-190X"))
+           comment = c(ORCID = "0000-0003-3925-190X")),
+    person("Olivier", "Roy", , "olivierroy71@hotmail.com", role = "aut")
+  )
 Description: Build graph/network structures using functions for stepwise
     addition and deletion of nodes and edges. Work with data available in
     tables for bulk addition of nodes, edges, and associated metadata. Use

diff --git a/DiagrammeR.Rproj b/DiagrammeR.Rproj
@@ -22,3 +22,5 @@ PackageCheckArgs: --as-cran --no-manual
 PackageRoxygenize: rd,collate,namespace
 
 UseNativePipeOperator: No
+
+SpellingDictionary: en_US
diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,13 @@
 # DiagrammeR (development version)
 
+* DiagrammeR nows uses testthat 3rd edition (@olivroy, #498)
+
+* No longer use deprecated features from igraph and tidyselect (>= 1.2.0) (@olivroy, #497)
+
+* Error messages have been reviewed and now use cli (@olivroy, #499, #502)
+
+* It is now easier to install suggested packages on the fly. DiagrammeR now uses `rlang::check_installed()` internally. (@olivroy, #499)
+
 # DiagrammeR 1.0.10
 
 * Remove dependency on the **influenceR** package, which also means removing the `get_constraint()` and `get_bridging()` graph inspection functions.
@@ -138,7 +146,7 @@
 
 * Degree data for plots can now be easily obtained using the `get_degree_distribution()` and `get_degree_histogram()` functions
 
-* Global graph attributes are now more easily modifiable using a set of functions for this purpose: `add_global_graph_attrs()`, `clear_global_graph_attrs()`, `delete_global_graph_attrs()`, `get_global_graph_attrs()`, `set_global_graph_attrs()`
+* Global graph attributes are now more easily modifiable using a set of functions for this purpose: `add_global_graph_attrs()`, `delete_global_graph_attrs()`, `get_global_graph_attr_info()`.
 
 * Added option to display different text labels on nodes via the `display` node attribute; this is easily set with the `set_node_attr_to_display()` function
 

diff --git a/R/DiagrammeR.R b/R/DiagrammeR.R
@@ -2,7 +2,7 @@
 #'
 #' @description
 #'
-#' Make diagrams in R using \href{https://github.com/mdaines/viz.js}{viz.js} or
+#' Make diagrams in R using \href{https://github.com/mdaines/viz-js}{viz.js} or
 #' \href{https://github.com/mermaid-js/mermaid}{mermaid.js} with infrastructure
 #' provided by \href{http://www.htmlwidgets.org/}{htmlwidgets}.
 #'

diff --git a/R/add_balanced_tree.R b/R/add_balanced_tree.R
@@ -290,7 +290,7 @@ add_balanced_tree <- function(
   graph_log <-
     add_action_to_log(
       graph_log = graph_log,
-      version_id = nrow(graph_log) + 1,
+      version_id = nrow(graph_log) + 1L,
       function_used = fcn_name,
       time_modified = time_function_start,
       duration = graph_function_duration(time_function_start),

diff --git a/R/add_cycle.R b/R/add_cycle.R
@@ -264,7 +264,7 @@ add_cycle <- function(
   graph_log <-
     add_action_to_log(
       graph_log = graph_log,
-      version_id = nrow(graph_log) + 1,
+      version_id = nrow(graph_log) + 1L,
       function_used = fcn_name,
       time_modified = time_function_start,
       duration = graph_function_duration(time_function_start),

diff --git a/R/add_edge.R b/R/add_edge.R
@@ -260,7 +260,7 @@ add_edge <- function(
 
       # Iteratively set edge attribute values for
       # the new edge in the graph
-      for (i in 1:ncol(edge_aes_tbl)) {
+      for (i in seq_len(ncol(edge_aes_tbl))) {
         graph <-
           graph %>%
           set_edge_attrs_ws(
@@ -318,7 +318,7 @@ add_edge <- function(
     graph$graph_log <-
       add_action_to_log(
         graph_log = graph$graph_log,
-        version_id = nrow(graph$graph_log) + 1,
+        version_id = nrow(graph$graph_log) + 1L,
         function_used = fcn_name,
         time_modified = time_function_start,
         duration = graph_function_duration(time_function_start),

diff --git a/R/add_edge_clone.R b/R/add_edge_clone.R
@@ -91,7 +91,7 @@ add_edge_clone <- function(
   # to an edge in the graph
   if (!(edge %in% graph$edges_df$id)) {
 
-    abort(
+    cli::cli_abort(
       "The value provided in `edge` does not correspond to an edge in the graph.")
   }
 
@@ -125,12 +125,11 @@ add_edge_clone <- function(
   # Create an edge selection for the
   # new edge in the graph
   graph <-
-    graph %>%
-    select_last_edges_created()
+    select_last_edges_created(graph)
 
   # Iteratively set edge attribute values for
   # the new edges in the graph
-  for (i in 1:ncol(edge_attr_vals)) {
+  for (i in seq_len(ncol(edge_attr_vals))) {
 
     graph$edges_df[
       nrow(graph$edges_df),
@@ -155,7 +154,7 @@ add_edge_clone <- function(
   graph$graph_log <-
     add_action_to_log(
       graph_log = graph$graph_log,
-      version_id = nrow(graph$graph_log) + 1,
+      version_id = nrow(graph$graph_log) + 1L,
       function_used = fcn_name,
       time_modified = time_function_start,
       duration = graph_function_duration(time_function_start),

diff --git a/R/add_edge_df.R b/R/add_edge_df.R
@@ -54,7 +54,7 @@ add_edge_df <- function(
   check_graph_valid(graph)
 
   # Validation: Graph contains nodes
-  check_graph_contains_nodes(graph,extra_msg = " so, edges cannot be added")
+  check_graph_contains_nodes(graph,extra_msg = "So, edges cannot be added.")
 
   # Get the number of edges ever created for
   # this graph
@@ -92,7 +92,7 @@ add_edge_df <- function(
   graph$graph_log <-
     add_action_to_log(
       graph_log = graph$graph_log,
-      version_id = nrow(graph$graph_log) + 1,
+      version_id = nrow(graph$graph_log) + 1L,
       function_used = fcn_name,
       time_modified = time_function_start,
       duration = graph_function_duration(time_function_start),
@@ -103,8 +103,7 @@ add_edge_df <- function(
   # Perform graph actions, if any are available
   if (nrow(graph$graph_actions) > 0) {
     graph <-
-      graph %>%
-      trigger_graph_actions()
+      trigger_graph_actions(graph)
   }
 
   # Write graph backup if the option is set

diff --git a/R/add_edges_from_table.R b/R/add_edges_from_table.R
@@ -298,7 +298,7 @@ add_edges_from_table <- function(
   graph$graph_log <-
     add_action_to_log(
       graph_log = graph$graph_log,
-      version_id = nrow(graph$graph_log) + 1,
+      version_id = nrow(graph$graph_log) + 1L,
       function_used = fcn_name,
       time_modified = time_function_start,
       duration = graph_function_duration(time_function_start),

diff --git a/R/add_edges_w_string.R b/R/add_edges_w_string.R
@@ -179,7 +179,7 @@ add_edges_w_string <- function(
   graph$graph_log <-
     add_action_to_log(
       graph_log = graph$graph_log,
-      version_id = nrow(graph$graph_log) + 1,
+      version_id = nrow(graph$graph_log) + 1L,
       function_used = fcn_name,
       time_modified = time_function_start,
       duration = graph_function_duration(time_function_start),

diff --git a/R/add_forward_edges_ws.R b/R/add_forward_edges_ws.R
@@ -66,9 +66,6 @@ add_forward_edges_ws <- function(
   # Get the time of function start
   time_function_start <- Sys.time()
 
-  # Get the name of the function
-  fcn_name <- get_calling_fcn()
-
   # Validation: Graph object is valid
   check_graph_valid(graph)
 
@@ -114,11 +111,14 @@ add_forward_edges_ws <- function(
   # the graph
   edges_added <- edges_graph_2 - edges_graph_1
 
+  # Get the name of the function
+  fcn_name <- get_calling_fcn()
+
   # Update the `graph_log` df with an action
   graph$graph_log <-
     add_action_to_log(
       graph_log = graph$graph_log,
-      version_id = nrow(graph$graph_log) + 1,
+      version_id = nrow(graph$graph_log) + 1L,
       function_used = fcn_name,
       time_modified = time_function_start,
       duration = graph_function_duration(time_function_start),
@@ -129,8 +129,7 @@ add_forward_edges_ws <- function(
   # Perform graph actions, if any are available
   if (nrow(graph$graph_actions) > 0) {
     graph <-
-      graph %>%
-      trigger_graph_actions()
+      trigger_graph_actions(graph)
   }
 
   # Write graph backup if the option is set

diff --git a/R/add_full_graph.R b/R/add_full_graph.R
@@ -410,7 +410,7 @@ add_full_graph <- function(
     graph_log <-
       add_action_to_log(
         graph_log = graph_log,
-        version_id = nrow(graph_log) + 1,
+        version_id = nrow(graph_log) + 1L,
         function_used = fcn_name,
         time_modified = time_function_start,
         duration = graph_function_duration(time_function_start),
@@ -452,7 +452,7 @@ add_full_graph <- function(
     graph_log <-
       add_action_to_log(
         graph_log = graph_log,
-        version_id = nrow(graph_log) + 1,
+        version_id = nrow(graph_log) + 1L,
         function_used = fcn_name,
         time_modified = time_function_start,
         duration = graph_function_duration(time_function_start),

diff --git a/R/add_global_graph_attrs.R b/R/add_global_graph_attrs.R
@@ -116,7 +116,7 @@ add_global_graph_attrs <- function(
   graph$graph_log <-
     add_action_to_log(
       graph_log = graph$graph_log,
-      version_id = nrow(graph$graph_log) + 1,
+      version_id = nrow(graph$graph_log) + 1L,
       function_used = fcn_name,
       time_modified = time_function_start,
       duration = graph_function_duration(time_function_start),

diff --git a/R/add_gnm_graph.R b/R/add_gnm_graph.R
@@ -254,7 +254,7 @@ add_gnm_graph <- function(
   graph_log <-
     add_action_to_log(
       graph_log = graph_log,
-      version_id = nrow(graph_log) + 1,
+      version_id = nrow(graph_log) + 1L,
       function_used = fcn_name,
       time_modified = time_function_start,
       duration = graph_function_duration(time_function_start),

diff --git a/R/add_gnp_graph.R b/R/add_gnp_graph.R
@@ -250,7 +250,7 @@ add_gnp_graph <- function(
   graph_log <-
     add_action_to_log(
       graph_log = graph_log,
-      version_id = nrow(graph_log) + 1,
+      version_id = nrow(graph_log) + 1L,
       function_used = fcn_name,
       time_modified = time_function_start,
       duration = graph_function_duration(time_function_start),

diff --git a/R/add_graph_action.R b/R/add_graph_action.R
@@ -66,7 +66,7 @@ add_graph_action <- function(
   # Create a character expression for the
   # function to evaluate at every graph
   # transformation step
-  if (length(fcn_args) == 0) {
+  if (length(fcn_args) == 0L) {
     char_expr <-
       paste0(
         fcn,
@@ -111,8 +111,8 @@ add_graph_action <- function(
   # Create a data frame row with the new graph action
   new_graph_action <-
     data.frame(
-      action_index = ifelse(nrow(graph$graph_actions) == 0, 1,
-                            max(graph$graph_actions$action_index) + 1),
+      action_index = ifelse(nrow(graph$graph_actions) == 0L, 1L,
+                            max(graph$graph_actions$action_index) + 1L),
       action_name = action_name %||% NA_character_,
       expression = char_expr,
       stringsAsFactors = FALSE)
@@ -128,7 +128,7 @@ add_graph_action <- function(
   graph$graph_log <-
     add_action_to_log(
       graph_log = graph$graph_log,
-      version_id = nrow(graph$graph_log) + 1,
+      version_id = nrow(graph$graph_log) + 1L,
       function_used = fcn_name,
       time_modified = time_function_start,
       duration = graph_function_duration(time_function_start),

diff --git a/R/add_grid_2d.R b/R/add_grid_2d.R
@@ -272,7 +272,7 @@ add_grid_2d <- function(
   graph_log <-
     add_action_to_log(
       graph_log = graph_log,
-      version_id = nrow(graph_log) + 1,
+      version_id = nrow(graph_log) + 1L,
       function_used = fcn_name,
       time_modified = time_function_start,
       duration = graph_function_duration(time_function_start),

diff --git a/R/add_grid_3d.R b/R/add_grid_3d.R
@@ -129,12 +129,8 @@ add_grid_3d <- function(
   # Create an edge data frame for the grid graph
   grid_edges <-
     create_edge_df(
-      from = grid %>%
-        get_edge_df() %>%
-        dplyr::pull(from),
-      to = grid %>%
-        get_edge_df() %>%
-        dplyr::pull(to),
+      from = get_edge_df(grid)$from,
+      to = get_edge_df(grid)$to,
       rel = rel)
 
   # Create the grid graph
@@ -273,7 +269,7 @@ add_grid_3d <- function(
   graph_log <-
     add_action_to_log(
       graph_log = graph_log,
-      version_id = nrow(graph_log) + 1,
+      version_id = nrow(graph_log) + 1L,
       function_used = fcn_name,
       time_modified = time_function_start,
       duration = graph_function_duration(time_function_start),

diff --git a/R/add_growing_graph.R b/R/add_growing_graph.R
@@ -250,7 +250,7 @@ add_growing_graph <- function(
   graph_log <-
     add_action_to_log(
       graph_log = graph_log,
-      version_id = nrow(graph_log) + 1,
+      version_id = nrow(graph_log) + 1L,
       function_used = fcn_name,
       time_modified = time_function_start,
       duration = graph_function_duration(time_function_start),

diff --git a/R/add_islands_graph.R b/R/add_islands_graph.R
@@ -243,7 +243,7 @@ add_islands_graph <- function(
   graph_log <-
     add_action_to_log(
       graph_log = graph_log,
-      version_id = nrow(graph_log) + 1,
+      version_id = nrow(graph_log) + 1L,
       function_used = fcn_name,
       time_modified = time_function_start,
       duration = graph_function_duration(time_function_start),

diff --git a/R/add_n_node_clones.R b/R/add_n_node_clones.R
@@ -171,7 +171,7 @@ add_n_node_clones <- function(
   graph$graph_log <-
     add_action_to_log(
       graph_log = graph$graph_log,
-      version_id = nrow(graph$graph_log) + 1,
+      version_id = nrow(graph$graph_log) + 1L,
       function_used = fcn_name,
       time_modified = time_function_start,
       duration = graph_function_duration(time_function_start),

diff --git a/R/add_n_nodes.R b/R/add_n_nodes.R
@@ -125,7 +125,7 @@ add_n_nodes <- function(
   graph$graph_log <-
     add_action_to_log(
       graph_log = graph$graph_log,
-      version_id = nrow(graph$graph_log) + 1,
+      version_id = nrow(graph$graph_log) + 1L,
       function_used = fcn_name,
       time_modified = time_function_start,
       duration = graph_function_duration(time_function_start),

diff --git a/R/add_n_nodes_ws.R b/R/add_n_nodes_ws.R
@@ -94,9 +94,6 @@ add_n_nodes_ws <- function(
   # Get the time of function start
   time_function_start <- Sys.time()
 
-  # Get the name of the function
-  fcn_name <- get_calling_fcn()
-
   # Validation: Graph object is valid
   check_graph_valid(graph)
 
@@ -393,7 +390,7 @@ add_n_nodes_ws <- function(
   graph$graph_log <-
     add_action_to_log(
       graph_log = graph$graph_log,
-      version_id = nrow(graph$graph_log) + 1,
+      version_id = nrow(graph$graph_log) + 1L,
       function_used = fcn_name,
       time_modified = time_function_start,
       duration = graph_function_duration(time_function_start),