feat!: Allow change of attribute type when setting attribute for all vertices or edges, only attributes of length 1 or the length of the target set allowed

R/attributes.R

@@ -34,6 +34,7 @@
 ##
 
 
+
 #' Graph attributes of a graph
 #'
 #' @param graph Input graph.
@@ -174,11 +175,12 @@ vertex_attr <- function(graph, name, index = V(graph)) {
   } else {
     myattr <-
       .Call(C_R_igraph_mybracket2, graph, igraph_t_idx_attr, igraph_attr_idx_vertex)[[as.character(name)]]
-    if (!missing(index)) {
+    if (is_complete_iterator(index)) {
+      myattr
+    } else {
       index <- as.igraph.vs(graph, index)
-      myattr <- myattr[index]
+      myattr[index]
     }
-    myattr
   }
 }
 
@@ -223,6 +225,7 @@ vertex_attr <- function(graph, name, index = V(graph)) {
 #'   of a subset of vertices.
 #' @param value The new value of the attribute for all (or `index`)
 #'   vertices.
+#'   If `NULL`, the input is returned unchanged.
 #' @return The graph, with the vertex attribute added or set.
 #'
 #' @aliases set.vertex.attribute
@@ -235,31 +238,58 @@ vertex_attr <- function(graph, name, index = V(graph)) {
 #' g
 #' plot(g)
 set_vertex_attr <- function(graph, name, index = V(graph), value) {
-  i_set_vertex_attr(
-    graph = graph, name = name, index = index,
-    value = value
-  )
+  if (is_complete_iterator(index)) {
+    i_set_vertex_attr(graph = graph, name = name, value = value, check = FALSE)
+  } else {
+    i_set_vertex_attr(graph = graph, name = name, index = index, value = value)
+  }
 }
 
-i_set_vertex_attr <- function(graph, name, index = V(graph), value,
-                              check = TRUE) {
+i_set_vertex_attr <- function(graph, name, index = V(graph), value, check = TRUE) {
   if (!is_igraph(graph)) {
     stop("Not a graph object")
   }
+
+  if (is.null(value)) {
+    return(graph)
+  }
+
   single <- is_single_index(index)
+  complete <- is_complete_iterator(index)
   if (!missing(index) && check) {
     index <- as.igraph.vs(graph, index)
   }
   name <- as.character(name)
-  vc <- vcount(graph)
 
   vattrs <- .Call(C_R_igraph_mybracket2, graph, igraph_t_idx_attr, igraph_attr_idx_vertex)
+
+  if (!complete && !(name %in% names(vattrs))) {
+    vattrs[[name]] <- value[rep.int(NA_integer_, vcount(graph))]
+  }
+
   if (single) {
     vattrs[[name]][[index]] <- value
   } else {
-    vattrs[[name]][index] <- value
+    if (length(value) == 1) {
+      value_in <- rep(unname(value), length(index))
+    } else if (length(value) == length(index)) {
+      value_in <- unname(value)
+    } else {
+      stop(
+        "Length of new attribute value must be ",
+        if (length(index) != 1) "1 or ",
+        length(index),
+        ", the number of target vertices, not ",
+        length(value)
+      )
+    }
+
+    if (complete) {
+      vattrs[[name]] <- value_in
+    } else {
+      vattrs[[name]][index] <- value_in
+    }
   }
-  length(vattrs[[name]]) <- vc
 
   .Call(C_R_igraph_mybracket2_set, graph, igraph_t_idx_attr, igraph_attr_idx_vertex, vattrs)
 }
@@ -355,7 +385,7 @@ edge_attr <- function(graph, name, index = E(graph)) {
   } else {
     name <- as.character(name)
     myattr <- .Call(C_R_igraph_mybracket2, graph, igraph_t_idx_attr, igraph_attr_idx_edge)[[name]]
-    if (is.null(index)) {
+    if (is_complete_iterator(index)) {
       myattr
     } else {
       index <- as.igraph.es(graph, index)
@@ -405,6 +435,7 @@ edge_attr <- function(graph, name, index = E(graph)) {
 #'   a subset of edges.
 #' @param value The new value of the attribute for all (or `index`)
 #'   edges.
+#'   If `NULL`, the input is returned unchanged.
 #' @return The graph, with the edge attribute added or set.
 #'
 #' @aliases set.edge.attribute
@@ -417,26 +448,58 @@ edge_attr <- function(graph, name, index = E(graph)) {
 #' g
 #' plot(g)
 set_edge_attr <- function(graph, name, index = E(graph), value) {
-  i_set_edge_attr(graph = graph, name = name, index = index, value = value)
+  if (is_complete_iterator(index)) {
+    i_set_edge_attr(graph = graph, name = name, value = value, check = FALSE)
+  } else {
+    i_set_edge_attr(graph = graph, name = name, index = index, value = value)
+  }
 }
 
-i_set_edge_attr <- function(graph, name, index = E(graph), value,
-                            check = TRUE) {
+i_set_edge_attr <- function(graph, name, index = E(graph), value, check = TRUE) {
   if (!is_igraph(graph)) {
     stop("Not a graph object")
   }
+
+  if (is.null(value)) {
+    return(graph)
+  }
+
+  complete <- is_complete_iterator(index)
   single <- is_single_index(index)
   name <- as.character(name)
-  if (!missing(index) && check) index <- as.igraph.es(graph, index)
-  ec <- ecount(graph)
+  if (!missing(index) && check) {
+    index <- as.igraph.es(graph, index)
+  }
 
   eattrs <- .Call(C_R_igraph_mybracket2, graph, igraph_t_idx_attr, igraph_attr_idx_edge)
+
+  if (!complete && !(name %in% names(eattrs))) {
+    eattrs[[name]] <- value[rep.int(NA_integer_, ecount(graph))]
+  }
+
   if (single) {
     eattrs[[name]][[index]] <- value
   } else {
-    eattrs[[name]][index] <- value
+    if (length(value) == 1) {
+      value_in <- rep(unname(value), length(index))
+    } else if (length(value) == length(index)) {
+      value_in <- unname(value)
+    } else {
+      stop(
+        "Length of new attribute value must be ",
+        if (length(index) != 1) "1 or ",
+        length(index),
+        ", the number of target edges, not ",
+        length(value)
+      )
+    }
+
+    if (complete) {
+      eattrs[[name]] <- value_in
+    } else {
+      eattrs[[name]][index] <- value_in
+    }
   }
-  length(eattrs[[name]]) <- ec
 
   .Call(C_R_igraph_mybracket2_set, graph, igraph_t_idx_attr, igraph_attr_idx_edge, eattrs)
 }

R/conversion.R

@@ -1047,7 +1047,7 @@ as_long_data_frame <- function(graph) {
 #' as.matrix(g, "adjacency")
 #' as.matrix(g, "edgelist")
 #' # use edge attribute "weight"
-#' E(g)$weight <- rep(1:10, each = ecount(g))
+#' E(g)$weight <- rep(1:10, length.out = ecount(g))
 #' as.matrix(g, "adjacency", sparse = FALSE, attr = "weight")
 #'
 as.matrix.igraph <- function(x, matrix.type = c("adjacency", "edgelist"), ...) {

R/interface.R

@@ -84,12 +84,14 @@ add_edges <- function(graph, edges, ..., attr = list()) {
     idx <- numeric()
   }
 
-  eattrs <- .Call(C_R_igraph_mybracket2, graph, igraph_t_idx_attr, igraph_attr_idx_edge)
   for (i in seq(attrs)) {
-    eattrs[[nam[i]]][idx] <- attrs[[nam[i]]]
+    attr <- attrs[[nam[i]]]
+    if (!is.null(attr)) {
+      graph <- set_edge_attr(graph, nam[[i]], idx, attr)
+    }
   }
 
-  .Call(C_R_igraph_mybracket2_set, graph, igraph_t_idx_attr, igraph_attr_idx_edge, eattrs)
+  graph
 }
 
 #' Add vertices to a graph
@@ -148,12 +150,14 @@ add_vertices <- function(graph, nv, ..., attr = list()) {
     idx <- numeric()
   }
 
-  vattrs <- .Call(C_R_igraph_mybracket2, graph, igraph_t_idx_attr, igraph_attr_idx_vertex)
   for (i in seq(attrs)) {
-    vattrs[[nam[i]]][idx] <- attrs[[nam[i]]]
+    attr <- attrs[[nam[i]]]
+    if (!is.null(attr)) {
+      graph <- set_vertex_attr(graph, nam[[i]], idx, attr)
+    }
   }
 
-  .Call(C_R_igraph_mybracket2_set, graph, igraph_t_idx_attr, igraph_attr_idx_vertex, vattrs)
+  graph
 }
 
 #' Delete edges from a graph

R/iterators.R

@@ -317,6 +317,7 @@ E <- function(graph, P = NULL, path = NULL, directed = TRUE) {
   if (is.null(P) && is.null(path)) {
     ec <- ecount(graph)
     res <- seq_len(ec)
+    res <- set_complete_iterator(res)
   } else if (!is.null(P)) {
     on.exit(.Call(C_R_igraph_finalizer))
     res <- .Call(
@@ -340,7 +341,6 @@ E <- function(graph, P = NULL, path = NULL, directed = TRUE) {
   }
 
   class(res) <- "igraph.es"
-  res <- set_complete_iterator(res)
   add_vses_graph_ref(res, graph)
 }
 

R/structural.properties.R

@@ -2118,7 +2118,7 @@ laplacian_matrix <- function(graph, normalized = FALSE, weights = NULL,
 #' is_max_matching(g, m2)
 #' is_max_matching(g, m3)
 #'
-#' V(g)$type <- c(FALSE, TRUE)
+#' V(g)$type <- rep(c(FALSE, TRUE), 3)
 #' print_all(g, v = TRUE)
 #' max_bipartite_match(g)
 #'

revdep/README.md

@@ -1,24 +1,19 @@
 # Revdeps
 
-## Failed to check (9)
-
-|package   |version |error |warning |note |
-|:---------|:-------|:-----|:-------|:----|
-|DRviaSPCN |?       |      |        |     |
-|genekitr  |?       |      |        |     |
-|immcp     |?       |      |        |     |
-|numbat    |?       |      |        |     |
-|Platypus  |?       |      |        |     |
-|NA        |?       |      |        |     |
-|tidySEM   |?       |      |        |     |
-|vivid     |?       |      |        |     |
-|NA        |?       |      |        |     |
-
-## New problems (3)
+## New problems (12)
 
 |package      |version |error  |warning |note |
 |:------------|:-------|:------|:-------|:----|
-|[causaleffect](problems.md#causaleffect)|1.3.15  |__+1__ |1       |     |
-|[R6causal](problems.md#r6causal)|0.7.0   |       |__+1__  |     |
+|[backbone](problems.md#backbone)|2.1.1   |__+1__ |        |     |
+|[deepdep](problems.md#deepdep)|0.4.1   |__+1__ |        |     |
+|[egor](problems.md#egor)|1.22.12 |__+1__ |        |     |
+|[GREMLINS](problems.md#gremlins)|0.2.0   |__+1__ |__+1__  |1    |
+|[incidentally](problems.md#incidentally)|1.0.1   |       |__+1__  |     |
+|[mstknnclust](problems.md#mstknnclust)|0.3.1   |       |__+1__  |     |
+|[nat](problems.md#nat)|1.8.19  |__+1__ |1       |     |
+|[netmeta](problems.md#netmeta)|2.7-0   |__+1__ |        |1    |
+|[NetOrigin](problems.md#netorigin)|1.1-4   |__+1__ |        |     |
+|[poppr](problems.md#poppr)|2.9.3   |__+1__ |1       |1    |
 |[sfnetworks](problems.md#sfnetworks)|0.6.1   |__+1__ |        |     |
+|[signnet](problems.md#signnet)|1.0.0   |__+1__ |        |1    |
 

revdep/cran.md

@@ -1,30 +1,49 @@
 ## revdepcheck results
 
-We checked 752 reverse dependencies (750 from CRAN + 2 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+We checked 12 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
 
- * We saw 3 new problems
- * We failed to check 7 packages
+ * We saw 12 new problems
+ * We failed to check 0 packages
 
 Issues with CRAN packages are summarised below.
 
 ### New problems
 (This reports the first line of each new failure)
 
-* causaleffect
+* backbone
+  checking tests ... ERROR
+
+* deepdep
+  checking tests ... ERROR
+
+* egor
+  checking tests ... ERROR
+
+* GREMLINS
   checking examples ... ERROR
+  checking re-building of vignette outputs ... WARNING
+
+* incidentally
+  checking re-building of vignette outputs ... WARNING
 
-* R6causal
+* mstknnclust
   checking re-building of vignette outputs ... WARNING
 
+* nat
+  checking tests ... ERROR
+
+* netmeta
+  checking examples ... ERROR
+
+* NetOrigin
+  checking examples ... ERROR
+
+* poppr
+  checking tests ... ERROR
+
 * sfnetworks
   checking tests ... ERROR
 
-### Failed to check
+* signnet
+  checking examples ... ERROR
 
-* DRviaSPCN (NA)
-* genekitr  (NA)
-* immcp     (NA)
-* numbat    (NA)
-* Platypus  (NA)
-* tidySEM   (NA)
-* vivid     (NA)