Merge branch 'main' into length-lint

rich-iannone · Nov 16, 2023 · ad17a9c · ad17a9c
2 parents cefe768 + 5ad71cb
commit ad17a9c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -21,7 +21,6 @@ BugReports: https://github.com/rich-iannone/DiagrammeR/issues
 Depends:
     R (>= 3.2)
 Imports:
-    curl,
     dplyr (>= 1.0.7),
     glue (>= 1.5.0),
     htmltools (>= 0.5.2),
@@ -41,6 +40,7 @@ Imports:
     viridis (>= 0.6.2),
     visNetwork (>= 2.1.0)
 Suggests:
+    curl,
     DiagrammeRsvg,
     knitr,
     rmarkdown,

diff --git a/NEWS.md b/NEWS.md
@@ -2,14 +2,16 @@
 
 * DiagrammeR nows uses testthat 3rd edition (@olivroy, #498)
 
-* No longer use deprecated features from igraph and tidyselect (>= 1.2.0) (@olivroy, #497)
+* No longer use deprecated features from tibble, igraph and tidyselect (>= 1.2.0) (@olivroy, #497, #507)
 
 * 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)
 
 * Some conditions were corrected in `trav_in_until()` and `trav_out_until()` (@olivroy, #504)
 
+* `DiagrammeR()` checks the `type` argument more strictly. (@olivroy, #506)
+
 # DiagrammeR 1.0.10
 
 * Remove dependency on the **influenceR** package, which also means removing the `get_constraint()` and `get_bridging()` graph inspection functions.

diff --git a/R/DiagrammeR.R b/R/DiagrammeR.R
@@ -53,7 +53,7 @@
 #' )
 #'
 #' # Load in the 'mtcars' dataset
-#' data(mtcars)
+#' mtcars
 #' connections <- sapply(
 #'  1:ncol(mtcars)
 #'   ,function(i) {
@@ -102,8 +102,6 @@
 #' #   http://www.cs.uku.fi/research/publications/reports/A-2003-1/page91.pdf
 #' # draw some sequence diagrams with DiagrammeR
 #'
-#' library(DiagrammeR)
-#'
 #' DiagrammeR("
 #' sequenceDiagram;
 #'    customer->>ticket seller: ask for ticket;
@@ -131,10 +129,10 @@ DiagrammeR <- function(
   # DiagrammeR will serve as a wrapper function for mermaid and grVis
   if (grepl(x = type, pattern = "[m,M](erm).*")) {
 
-    mermaid(diagram, ... )
+    mermaid(diagram, ...)
 
-  } else if (grepl(x = type, pattern = "[g,G]?[r,R]?.*[v,V][i].*" )) {
-    grViz(diagram, ... )
+  } else if (grepl(x = type, pattern = "[g,G]?[r,R]?.*[v,V][i].*")) {
+    grViz(diagram, ...)
 
   } else {
     abort("The type should be `mermaid` or `grViz`.")

diff --git a/R/add_balanced_tree.R b/R/add_balanced_tree.R
@@ -150,7 +150,8 @@ add_balanced_tree <- function(
         rep(seq(nodes[1],
                 nodes[length(
                   seq(nodes[2],
-                      nodes[length(nodes)]))/k]), k)),
+                      nodes[length(nodes)])) / k]),
+            k)),
       to = seq(nodes[2], nodes[length(nodes)]),
       rel = rel)
 
@@ -271,10 +272,10 @@ add_balanced_tree <- function(
 
   # If the input graph is not empty, combine graphs
   # using the `combine_graphs()` function
-  if (!is_graph_empty(graph)) {
-    graph <- combine_graphs(graph, tree_graph)
-  } else {
+  if (is_graph_empty(graph)) {
     graph <- tree_graph
+  } else {
+    graph <- combine_graphs(graph, tree_graph)
   }
 
   # Update the `last_node` counter

diff --git a/R/add_cycle.R b/R/add_cycle.R
@@ -245,10 +245,10 @@ add_cycle <- function(
 
   # If the input graph is not empty, combine graphs
   # using the `combine_graphs()` function
-  if (!is_graph_empty(graph)) {
-    graph <- combine_graphs(graph, cycle_graph)
-  } else {
+  if (is_graph_empty(graph)) {
     graph <- cycle_graph
+  } else {
+    graph <- combine_graphs(graph, cycle_graph)
   }
 
   # Update the `last_node` counter

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

diff --git a/R/add_edges_from_table.R b/R/add_edges_from_table.R
@@ -165,12 +165,10 @@ add_edges_from_table <- function(
 
   # Optionally set the `rel` attribute from a
   # specified column in the CSV
-  if (!is.null(rel_col)) {
+  if (!is.null(rel_col) && any(colnames(csv) == rel_col)) {
 
-    if (any(colnames(csv) == rel_col)) {
-      colnames(csv)[which(colnames(csv) == rel_col)] <- "rel"
-      csv$rel <- as.character(csv$rel)
-    }
+    colnames(csv)[which(colnames(csv) == rel_col)] <- "rel"
+    csv$rel <- as.character(csv$rel)
   }
 
   # Extract the ndf from the graph
@@ -231,7 +229,7 @@ add_edges_from_table <- function(
   # Add in an `id` column
   edf <-
     dplyr::bind_cols(
-      data.frame(id = as.integer(1:nrow(edf)) + graph$last_edge),
+      data.frame(id = seq_len(nrow(edf)) + as.integer(graph$last_edge)),
       edf)
 
   # Optionally set the `rel` attribute with a single

diff --git a/R/add_full_graph.R b/R/add_full_graph.R
@@ -101,7 +101,8 @@
 #'     label = TRUE,
 #'     rel = "related_to",
 #'     edge_wt_matrix = edge_wt_matrix,
-#'     keep_loops = FALSE)
+#'     keep_loops = FALSE
+#'   )
 #'
 #' # Show the graph's node
 #' # data frame (ndf)
@@ -198,7 +199,9 @@ add_full_graph <- function(
           new_graph,
           edge_attr = "weight",
           values = as.numeric(edge_wt_matrix)[
-            which(as.numeric(adj_matrix) == 1)])
+            which(as.numeric(adj_matrix) == 1)
+          ]
+        )
     }
   }
 
@@ -221,8 +224,8 @@ add_full_graph <- function(
           values = edge_wt_matrix[
             lower.tri(
               edge_wt_matrix,
-              diag = ifelse(!keep_loops,
-                            FALSE, TRUE))])
+              diag = keep_loops # TRUE or FALSE
+            )])
     }
   }
 
@@ -236,39 +239,33 @@ add_full_graph <- function(
     }
   }
 
-  if (length(label) > 1) {
-    if (length(label) == n) {
-      new_graph$nodes_df[, 3] <- label
-    }
+  if (n > 1 && length(label) == n) {
+    new_graph$nodes_df[, 3] <- label
   }
 
-  if (length(label) == 1) {
-    if (label) {
-      if (!is.null(edge_wt_matrix)) {
-
-        if (!is.null(colnames(edge_wt_matrix))) {
-          ewm_names <- colnames(edge_wt_matrix)
-        }
-        if (!is.null(rownames(edge_wt_matrix))) {
-          ewm_names <- rownames(edge_wt_matrix)
-        }
-
-        if (length(ewm_names) == n) {
-          new_graph$nodes_df[, 3] <- ewm_names
-        }
-      }
+  if (isTRUE(label) && !is.null(edge_wt_matrix)) {
+
+    if (!is.null(colnames(edge_wt_matrix))) {
+      ewm_names <- colnames(edge_wt_matrix)
+    }
+
+    if (!is.null(rownames(edge_wt_matrix))) {
+      ewm_names <- rownames(edge_wt_matrix)
+    }
+
+    if (length(ewm_names) == n) {
+      new_graph$nodes_df[, 3] <- ewm_names
     }
   }
 
   # Add `type` values to all new nodes
-  if (!is.null(type) &&
-      length(type) == 1) {
+  if (length(type) == 1) {
     new_graph$nodes_df[, 2] <- type
   }
 
   # Add `rel` values to all new edges
-  if (!is.null(rel) &&
-      length(rel) == 1) {
+  # NULL is length 0
+  if (length(rel) == 1) {
     new_graph$edges_df[, 4] <- rel
   }
 
@@ -279,7 +276,7 @@ add_full_graph <- function(
 
     if (nrow(node_aes_tbl) < nrow(new_graph$nodes_df)) {
 
-      node_aes$index__ <- 1:nrow(new_graph$nodes_df)
+      node_aes$index__ <- seq_len(nrow(new_graph$nodes_df))
 
       node_aes_tbl <-
         dplyr::as_tibble(node_aes) %>%
@@ -298,7 +295,7 @@ add_full_graph <- function(
 
     if (nrow(node_data_tbl) < nrow(new_graph$nodes_df)) {
 
-      node_data$index__ <- 1:nrow(new_graph$nodes_df)
+      node_data$index__ <- seq_len(nrow(new_graph$nodes_df))
 
       node_data_tbl <-
         dplyr::as_tibble(node_data) %>%

diff --git a/R/add_global_graph_attrs.R b/R/add_global_graph_attrs.R
@@ -73,20 +73,18 @@ add_global_graph_attrs <- function(
 
   # Coerce any logical value for `value` to a
   # lowercase character value
-  if (length(value) == 1) {
-    if (inherits(value, "logical") &&
-        value %in% c(TRUE, FALSE)) {
-      value <- tolower(as.character(value))
-    }
+  # If value is a single true or false
+  if (rlang::is_bool(value)) {
+    value <- tolower(as.character(value))
   }
 
   # Create a table for the attributes
   global_attrs_to_add <-
-    dplyr::tibble(
+    data.frame(
       attr = as.character(attr),
       value = as.character(value),
-      attr_type = as.character(attr_type)) %>%
-    as.data.frame(stringsAsFactors = FALSE)
+      attr_type = as.character(attr_type),
+      stringsAsFactors = FALSE)
 
   # Get the global graph attributes already set
   # in the graph object

diff --git a/R/add_gnm_graph.R b/R/add_gnm_graph.R
@@ -131,7 +131,7 @@ add_gnm_graph <- function(
 
     if (nrow(node_aes_tbl) < nrow(sample_gnm_graph$nodes_df)) {
 
-      node_aes$index__ <- 1:nrow(sample_gnm_graph$nodes_df)
+      node_aes$index__ <- seq_len(nrow(sample_gnm_graph$nodes_df))
 
       node_aes_tbl <-
         dplyr::as_tibble(node_aes) %>%
@@ -150,7 +150,7 @@ add_gnm_graph <- function(
 
     if (nrow(node_data_tbl) < nrow(sample_gnm_graph$nodes_df)) {
 
-      node_data$index__ <- 1:nrow(sample_gnm_graph$nodes_df)
+      node_data$index__ <- seq_len(nrow(sample_gnm_graph$nodes_df))
 
       node_data_tbl <-
         dplyr::as_tibble(node_data) %>%
@@ -169,11 +169,11 @@ add_gnm_graph <- function(
 
     if (nrow(edge_aes_tbl) < nrow(sample_gnm_graph$edges_df)) {
 
-      edge_aes$index__ <- 1:nrow(sample_gnm_graph$edges_df)
+      edge_aes$index__ <- seq_len(nrow(sample_gnm_graph$edges_df))
 
       edge_aes_tbl <-
         dplyr::as_tibble(edge_aes) %>%
-        dplyr::select(-index__)
+        dplyr::select(-"index__")
     }
 
     if ("id" %in% colnames(edge_aes_tbl)) {
@@ -188,7 +188,7 @@ add_gnm_graph <- function(
 
     if (nrow(edge_data_tbl) < nrow(sample_gnm_graph$edges_df)) {
 
-      edge_data$index__ <- 1:nrow(sample_gnm_graph$edges_df)
+      edge_data$index__ <- seq_len(nrow(sample_gnm_graph$edges_df))
 
       edge_data_tbl <-
         dplyr::as_tibble(edge_data) %>%
@@ -234,10 +234,10 @@ add_gnm_graph <- function(
 
   # If the input graph is not empty, combine graphs
   # using the `combine_graphs()` function
-  if (!is_graph_empty(graph)) {
-    graph <- combine_graphs(graph, sample_gnm_graph)
-  } else {
+  if (is_graph_empty(graph)) {
     graph <- sample_gnm_graph
+  } else {
+    graph <- combine_graphs(graph, sample_gnm_graph)
   }
 
   # Update the `last_node` counter

diff --git a/R/add_gnp_graph.R b/R/add_gnp_graph.R
@@ -128,7 +128,7 @@ add_gnp_graph <- function(
 
     if (nrow(node_aes_tbl) < nrow(sample_gnp_graph$nodes_df)) {
 
-      node_aes$index__ <- 1:nrow(sample_gnp_graph$nodes_df)
+      node_aes$index__ <- seq_len(nrow(sample_gnp_graph$nodes_df))
 
       node_aes_tbl <-
         dplyr::as_tibble(node_aes) %>%
@@ -185,7 +185,7 @@ add_gnp_graph <- function(
 
     if (nrow(edge_data_tbl) < nrow(sample_gnp_graph$edges_df)) {
 
-      edge_data$index__ <- 1:nrow(sample_gnp_graph$edges_df)
+      edge_data$index__ <- seq_len(nrow(sample_gnp_graph$edges_df))
 
       edge_data_tbl <-
         dplyr::as_tibble(edge_data) %>%
@@ -231,10 +231,10 @@ add_gnp_graph <- function(
 
   # If the input graph is not empty, combine graphs
   # using the `combine_graphs()` function
-  if (!is_graph_empty(graph)) {
-    graph <- combine_graphs(graph, sample_gnp_graph)
-  } else {
+  if (is_graph_empty(graph)) {
     graph <- sample_gnp_graph
+  } else {
+    graph <- combine_graphs(graph, sample_gnp_graph)
   }
 
   # Update the `last_node` counter

diff --git a/R/add_grid_2d.R b/R/add_grid_2d.R
@@ -253,10 +253,10 @@ add_grid_2d <- function(
 
   # If the input graph is not empty, combine graphs
   # using the `combine_graphs()` function
-  if (!is_graph_empty(graph)) {
-    graph <- combine_graphs(graph, grid_graph)
-  } else {
+  if (is_graph_empty(graph)) {
     graph <- grid_graph
+  } else {
+    graph <- combine_graphs(graph, grid_graph)
   }
 
   # Update the `last_node` counter

diff --git a/R/add_grid_3d.R b/R/add_grid_3d.R
@@ -250,10 +250,10 @@ add_grid_3d <- function(
 
   # If the input graph is not empty, combine graphs
   # using the `combine_graphs()` function
-  if (!is_graph_empty(graph)) {
-    graph <- combine_graphs(graph, grid_graph)
-  } else {
+  if (is_graph_empty(graph)) {
     graph <- grid_graph
+  } else {
+    graph <- combine_graphs(graph, grid_graph)
   }
 
   # Update the `last_node` counter