chore(series): Apply the review nits of the vendoring series

R/centrality.R

@@ -1716,9 +1716,10 @@ diversity <- function(
 #' scores are the same as authority scores.
 #'
 #' @param graph The input graph.
-#' @param scale Logical, whether to scale the result to have a maximum
-#'   score of one. If no scaling is used then the result vector has unit length
-#'   in the Euclidean norm.
+#' @param scale `r lifecycle::badge("superseded")` Logical, whether to scale
+#'   the result to have a maximum score of one, which the C core now always does.
+#'   With `FALSE`, the result vector is rescaled to unit length in the Euclidean norm,
+#'   except for graphs without (nonzero) edges, where all scores stay one.
 #' @param weights Optional positive weight vector for calculating weighted
 #'   scores. If the graph has a `weight` edge attribute, then this is used
 #'   by default. Pass `NA` to ignore the weight attribute. This function

R/community.R

@@ -2283,6 +2283,20 @@ cluster_edge_betweenness <- function(
     as.logical(modularity),
     as.logical(membership)
   )
+  # igraph 0.10 warned about weighted runs in the C core, which no longer does;
+  # only the first of its two warnings reached R.
+  if (!is.null(weights)) {
+    if (isTRUE(as.logical(membership))) {
+      cli::cli_warn(
+        "Membership vector will be selected based on the highest modularity score."
+      )
+    } else if (isTRUE(as.logical(modularity))) {
+      cli::cli_warn(paste(
+        "Modularity calculation with weighted edge betweenness community detection might not make sense --",
+        "modularity treats edge weights as similarities while edge betweenness treats them as distances."
+      ))
+    }
+  }
   if (igraph_opt("add.vertex.names") && is_named(graph)) {
     res$names <- V(graph)$name
   }

R/paths.R

@@ -450,16 +450,6 @@ graph_center <- function(
   )
 }
 
-# Upstream merged the weighted `_dijkstra` variants into the base functions,
-# which take their weights argument (krlmlr/igraph@d8febb1): the
-# `_dijkstra_impl()` names stay, as aliases with the same arguments.
-average_path_length_dijkstra_impl <- average_path_length_impl
-diameter_dijkstra_impl <- diameter_impl
-eccentricity_dijkstra_impl <- eccentricity_impl
-graph_center_dijkstra_impl <- graph_center_impl
-pseudo_diameter_dijkstra_impl <- pseudo_diameter_impl
-radius_dijkstra_impl <- radius_impl
-
 #' @rdname distances
 #' @inheritParams rlang::args_dots_empty
 #' @param directed Whether to consider directed paths in directed graphs,

src/rinterface_extra.c

@@ -6001,20 +6001,10 @@ SEXP Rx_igraph_community_edge_betweenness(SEXP graph, SEXP pweights,
    * weights as path lengths for the betweenness, and to weigh the modularity
    * that picks the membership. So the edges are removed by lengths, and the
    * merges, modularity and membership come from
-   * igraph_community_eb_get_merges() with the weights, as igraph 0.10 did,
-   * with the warnings it gave. */
+   * igraph_community_eb_get_merges() with the weights, as igraph 0.10 did.
+   * The warnings igraph 0.10 gave here are raised by cluster_edge_betweenness(). */
   if (ppweights) {
     IGRAPH_R_CHECK(igraph_community_edge_betweenness(&g, &res, ppeb, 0, 0, 0, 0, directed, /* weights = */ 0, /* lengths = */ ppweights));
-    if (ppmembership) {
-      IGRAPH_WARNING("Membership vector will be selected based on the highest "
-                     "modularity score.");
-    }
-    if (ppmodularity || ppmembership) {
-      IGRAPH_WARNING("Modularity calculation with weighted edge betweenness "
-                     "community detection might not make sense -- modularity treats edge "
-                     "weights as similarities while edge betwenness treats them as "
-                     "distances.");
-    }
     if (ppmerges || ppbridges || ppmodularity || ppmembership) {
       IGRAPH_R_CHECK(igraph_community_eb_get_merges(&g, directed, &res, ppweights, ppmerges, ppbridges, ppmodularity, ppmembership));
     }

tests/testthat/_snaps/aaa-auto.md

@@ -3689,70 +3689,70 @@
       Error in `ensure_igraph()`:
       ! Must provide a graph object (provided `NULL`).
 
-# eccentricity_dijkstra_impl basic
+# eccentricity_impl modes
 
     Code
-      eccentricity_dijkstra_impl(graph = g)
+      eccentricity_impl(graph = g)
     Output
       [1] 2 1 2
 
 ---
 
     Code
-      eccentricity_dijkstra_impl(graph = g, mode = "in")
+      eccentricity_impl(graph = g, mode = "in")
     Output
       [1] 2 1 2
 
-# eccentricity_dijkstra_impl errors
+# eccentricity_impl errors
 
     Code
-      eccentricity_dijkstra_impl(graph = NULL)
+      eccentricity_impl(graph = NULL)
     Condition
       Error in `ensure_igraph()`:
       ! Must provide a graph object (provided `NULL`).
 
-# graph_center_dijkstra_impl basic
+# graph_center_impl modes
 
     Code
-      graph_center_dijkstra_impl(graph = g)
+      graph_center_impl(graph = g)
     Output
       + 1/3 vertex:
       [1] 2
 
 ---
 
     Code
-      graph_center_dijkstra_impl(graph = g, mode = "in")
+      graph_center_impl(graph = g, mode = "in")
     Output
       + 1/3 vertex:
       [1] 2
 
-# graph_center_dijkstra_impl errors
+# graph_center_impl errors
 
     Code
-      graph_center_dijkstra_impl(graph = NULL)
+      graph_center_impl(graph = NULL)
     Condition
       Error in `ensure_igraph()`:
       ! Must provide a graph object (provided `NULL`).
 
-# radius_dijkstra_impl basic
+# radius_impl modes
 
     Code
-      radius_dijkstra_impl(graph = g)
+      radius_impl(graph = g)
     Output
       [1] 1
 
 ---
 
     Code
-      radius_dijkstra_impl(graph = g, mode = "in")
+      radius_impl(graph = g, mode = "in")
     Output
       [1] 1
 
-# radius_dijkstra_impl errors
+# radius_impl errors
 
     Code
-      radius_dijkstra_impl(graph = NULL)
+      radius_impl(graph = NULL)
     Condition
       Error in `ensure_igraph()`:
       ! Must provide a graph object (provided `NULL`).
@@ -3795,45 +3795,6 @@
       Error in `ensure_igraph()`:
       ! Must provide a graph object (provided `NULL`).
 
-# pseudo_diameter_dijkstra_impl basic
-
-    Code
-      pseudo_diameter_dijkstra_impl(graph = g, start_vid = 1)
-    Output
-      $diameter
-      [1] 2
-
-      $from
-      [1] 0
-
-      $to
-      [1] 2
-
-
----
-
-    Code
-      pseudo_diameter_dijkstra_impl(graph = g, start_vid = 1, directed = FALSE,
-        unconnected = FALSE)
-    Output
-      $diameter
-      [1] 2
-
-      $from
-      [1] 0
-
-      $to
-      [1] 2
-
-
-# pseudo_diameter_dijkstra_impl errors
-
-    Code
-      pseudo_diameter_dijkstra_impl(graph = NULL, start_vid = 1)
-    Condition
-      Error in `ensure_igraph()`:
-      ! Must provide a graph object (provided `NULL`).
-
 # diversity_impl basic
 
     Code

tests/testthat/test-aaa-auto.R

@@ -3827,92 +3827,92 @@ test_that("contract_vertices_impl errors", {
   ))
 })
 
-# 150. eccentricity_dijkstra_impl
+# 150. eccentricity_impl
 
-test_that("eccentricity_dijkstra_impl basic", {
+test_that("eccentricity_impl modes", {
   igraph_local_seed(20250909)
   g <- path_graph_impl(
     n = 3
   )
 
-  expect_snapshot(eccentricity_dijkstra_impl(
+  expect_snapshot(eccentricity_impl(
     graph = g
   ))
-  expect_snapshot(eccentricity_dijkstra_impl(
+  expect_snapshot(eccentricity_impl(
     graph = g,
     mode = "in"
   ))
 
   # Structured tests
-  result <- eccentricity_dijkstra_impl(
+  result <- eccentricity_impl(
     graph = g
   )
   expect_true(is.numeric(result))
 })
 
-test_that("eccentricity_dijkstra_impl errors", {
+test_that("eccentricity_impl errors", {
   igraph_local_seed(20250909)
-  expect_snapshot_igraph_error(eccentricity_dijkstra_impl(
+  expect_snapshot_igraph_error(eccentricity_impl(
     graph = NULL
   ))
 })
 
-# 151. graph_center_dijkstra_impl
+# 151. graph_center_impl
 
-test_that("graph_center_dijkstra_impl basic", {
+test_that("graph_center_impl modes", {
   igraph_local_seed(20250909)
   g <- path_graph_impl(
     n = 3
   )
 
-  expect_snapshot(graph_center_dijkstra_impl(
+  expect_snapshot(graph_center_impl(
     graph = g
   ))
-  expect_snapshot(graph_center_dijkstra_impl(
+  expect_snapshot(graph_center_impl(
     graph = g,
     mode = "in"
   ))
 
   # Structured tests
-  result <- graph_center_dijkstra_impl(
+  result <- graph_center_impl(
     graph = g
   )
   expect_s3_class(result, "igraph.vs")
 })
 
-test_that("graph_center_dijkstra_impl errors", {
+test_that("graph_center_impl errors", {
   igraph_local_seed(20250909)
-  expect_snapshot_igraph_error(graph_center_dijkstra_impl(
+  expect_snapshot_igraph_error(graph_center_impl(
     graph = NULL
   ))
 })
 
-# 152. radius_dijkstra_impl
+# 152. radius_impl
 
-test_that("radius_dijkstra_impl basic", {
+test_that("radius_impl modes", {
   igraph_local_seed(20250909)
   g <- path_graph_impl(
     n = 3
   )
 
-  expect_snapshot(radius_dijkstra_impl(
+  expect_snapshot(radius_impl(
     graph = g
   ))
-  expect_snapshot(radius_dijkstra_impl(
+  expect_snapshot(radius_impl(
     graph = g,
     mode = "in"
   ))
 
   # Structured tests
-  result <- radius_dijkstra_impl(
+  result <- radius_impl(
     graph = g
   )
   expect_true(is.numeric(result))
 })
 
-test_that("radius_dijkstra_impl errors", {
+test_that("radius_impl errors", {
   igraph_local_seed(20250909)
-  expect_snapshot_igraph_error(radius_dijkstra_impl(
+  expect_snapshot_igraph_error(radius_impl(
     graph = NULL
   ))
 })
@@ -3952,43 +3952,6 @@ test_that("pseudo_diameter_impl errors", {
   ))
 })
 
-# 154. pseudo_diameter_dijkstra_impl
-
-test_that("pseudo_diameter_dijkstra_impl basic", {
-  igraph_local_seed(20250909)
-  g <- path_graph_impl(
-    n = 3
-  )
-
-  expect_snapshot(pseudo_diameter_dijkstra_impl(
-    graph = g,
-    start_vid = 1
-  ))
-  expect_snapshot(pseudo_diameter_dijkstra_impl(
-    graph = g,
-    start_vid = 1,
-    directed = FALSE,
-    unconnected = FALSE
-  ))
-
-  # Structured tests
-  result <- pseudo_diameter_dijkstra_impl(
-    graph = g,
-    start_vid = 1
-  )
-  expect_type(result, "list")
-})
-
-test_that("pseudo_diameter_dijkstra_impl errors", {
-  igraph_local_seed(20250909)
-  expect_snapshot_igraph_error(
-    pseudo_diameter_dijkstra_impl(
-      graph = NULL,
-      start_vid = 1
-    )
-  )
-})
-
 # 155. diversity_impl
 
 test_that("diversity_impl basic", {