Lifecycle

.Rbuildignore

@@ -63,11 +63,12 @@
 ^src/*\.gcda$
 ^src/*\.gcno$
 ^R/release\.R$
-^BRANCHES\.md$
-^scripts$
-^\.claude$
 ^man/dot-igraph.progress\.Rd$
 ^man/dot-igraph.status\.Rd$
 ^man/dot-extract_constructor_and_modifiers\.Rd$
 ^man/dot-apply_modifiers\.Rd$
 ^man/handle_vertex_type_arg\.Rd$
+^BRANCHES\.md$
+^scripts$
+^\.claude$
+^lifecycle$

.gitignore

@@ -30,3 +30,4 @@ cran
 /_codeql_detected_source_root
 /tests/testthat/_problems/
 .ccache/
+lifecycle

NAMESPACE

@@ -376,7 +376,6 @@ export(get.adjlist)
 export(get.all.shortest.paths)
 export(get.data.frame)
 export(get.diameter)
-export(get.edge)
 export(get.edge.attribute)
 export(get.edge.ids)
 export(get.edgelist)
@@ -610,7 +609,6 @@ export(layout.fruchterman.reingold.grid)
 export(layout.gem)
 export(layout.graphopt)
 export(layout.grid)
-export(layout.grid.3d)
 export(layout.kamada.kawai)
 export(layout.lgl)
 export(layout.mds)

R/adjacency.R

@@ -17,7 +17,7 @@ graph.adjacency <- function(
   add.rownames = NA
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "graph.adjacency()",
     "graph_from_adjacency_matrix()"
@@ -293,7 +293,7 @@ graph_from_adjacency_matrix <- function(
   ensure_no_na(adjmatrix, "adjacency matrix", mode)
 
   if (!is.matrix(adjmatrix) && !inherits(adjmatrix, "Matrix")) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       "graph_from_adjacency_matrix(adjmatrix = 'must be a matrix')"
     )
@@ -302,7 +302,7 @@ graph_from_adjacency_matrix <- function(
 
   if (mode == "undirected") {
     if (!is_symmetric(adjmatrix)) {
-      lifecycle::deprecate_soft(
+      lifecycle::deprecate_warn(
         "1.6.0",
         "graph_from_adjacency_matrix(adjmatrix = 'must be symmetric with mode = \"undirected\"')",
         details = 'Use mode = "max" to achieve the original behavior.'

R/as_phylo.R

@@ -10,7 +10,7 @@
 #' @inheritParams ape::as.phylo
 #' @keywords internal
 as_phylo <- function(x, ...) {
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "1.5.0",
     "ape::as.phylo()"
   )

R/assortativity.R

@@ -15,7 +15,7 @@ assortativity.nominal <- function(
   normalized = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "assortativity.nominal()",
     "assortativity_nominal()"
@@ -40,7 +40,7 @@ assortativity.nominal <- function(
 #' @export
 assortativity.degree <- function(graph, directed = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "assortativity.degree()",
     "assortativity_degree()"
@@ -171,7 +171,7 @@ assortativity <- function(
   types2 = NULL
 ) {
   if (...length() > 0) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       "assortativity(... =)",
       details = "Arguments `values` and `values.in` must be named."
@@ -193,7 +193,7 @@ assortativity <- function(
   }
 
   if (missing(values)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       "assortativity(types1 =)",
       "assortativity(values =)"
@@ -202,7 +202,7 @@ assortativity <- function(
   }
 
   if (!is.null(types2)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       "assortativity(types2 =)",
       "assortativity(values.in =)"

R/attributes.R

@@ -10,7 +10,7 @@
 #' @export
 set.vertex.attribute <- function(graph, name, index = V(graph), value) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "set.vertex.attribute()",
     "set_vertex_attr()"
@@ -30,7 +30,7 @@ set.vertex.attribute <- function(graph, name, index = V(graph), value) {
 #' @export
 set.graph.attribute <- function(graph, name, value) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "set.graph.attribute()",
     "set_graph_attr()"
@@ -50,7 +50,7 @@ set.graph.attribute <- function(graph, name, value) {
 #' @export
 set.edge.attribute <- function(graph, name, index = E(graph), value) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "set.edge.attribute()", "set_edge_attr()")
+  lifecycle::deprecate_warn("2.0.0", "set.edge.attribute()", "set_edge_attr()")
   set_edge_attr(graph = graph, name = name, index = index, value = value)
 } # nocov end
 
@@ -66,7 +66,7 @@ set.edge.attribute <- function(graph, name, index = E(graph), value) {
 #' @export
 remove.vertex.attribute <- function(graph, name) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "remove.vertex.attribute()",
     "delete_vertex_attr()"
@@ -86,7 +86,7 @@ remove.vertex.attribute <- function(graph, name) {
 #' @export
 remove.graph.attribute <- function(graph, name) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "remove.graph.attribute()",
     "delete_graph_attr()"
@@ -106,7 +106,7 @@ remove.graph.attribute <- function(graph, name) {
 #' @export
 remove.edge.attribute <- function(graph, name) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "remove.edge.attribute()",
     "delete_edge_attr()"
@@ -126,7 +126,7 @@ remove.edge.attribute <- function(graph, name) {
 #' @export
 list.vertex.attributes <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "list.vertex.attributes()",
     "vertex_attr_names()"
@@ -146,7 +146,7 @@ list.vertex.attributes <- function(graph) {
 #' @export
 list.graph.attributes <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "list.graph.attributes()",
     "graph_attr_names()"
@@ -166,7 +166,7 @@ list.graph.attributes <- function(graph) {
 #' @export
 list.edge.attributes <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "list.edge.attributes()",
     "edge_attr_names()"
@@ -186,7 +186,7 @@ list.edge.attributes <- function(graph) {
 #' @export
 is.weighted <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.weighted()", "is_weighted()")
+  lifecycle::deprecate_warn("2.0.0", "is.weighted()", "is_weighted()")
   is_weighted(graph = graph)
 } # nocov end
 
@@ -202,7 +202,7 @@ is.weighted <- function(graph) {
 #' @export
 is.named <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.named()", "is_named()")
+  lifecycle::deprecate_warn("2.0.0", "is.named()", "is_named()")
   is_named(graph = graph)
 } # nocov end
 
@@ -218,7 +218,7 @@ is.named <- function(graph) {
 #' @export
 is.bipartite <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.bipartite()", "is_bipartite()")
+  lifecycle::deprecate_warn("2.0.0", "is.bipartite()", "is_bipartite()")
   is_bipartite(graph = graph)
 } # nocov end
 
@@ -234,7 +234,7 @@ is.bipartite <- function(graph) {
 #' @export
 get.vertex.attribute <- function(graph, name, index = V(graph)) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "get.vertex.attribute()", "vertex_attr()")
+  lifecycle::deprecate_warn("2.0.0", "get.vertex.attribute()", "vertex_attr()")
   vertex_attr(graph = graph, name = name, index = index)
 } # nocov end
 
@@ -250,7 +250,7 @@ get.vertex.attribute <- function(graph, name, index = V(graph)) {
 #' @export
 get.graph.attribute <- function(graph, name) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "get.graph.attribute()", "graph_attr()")
+  lifecycle::deprecate_warn("2.0.0", "get.graph.attribute()", "graph_attr()")
   graph_attr(graph = graph, name = name)
 } # nocov end
 
@@ -266,7 +266,7 @@ get.graph.attribute <- function(graph, name) {
 #' @export
 get.edge.attribute <- function(graph, name, index = E(graph)) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "get.edge.attribute()", "edge_attr()")
+  lifecycle::deprecate_warn("2.0.0", "get.edge.attribute()", "edge_attr()")
   edge_attr(graph = graph, name = name, index = index)
 } # nocov end
 #   IGraph R package

R/basic.R

@@ -10,7 +10,7 @@
 #' @export
 is.igraph <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.igraph()", "is_igraph()")
+  lifecycle::deprecate_warn("2.0.0", "is.igraph()", "is_igraph()")
   is_igraph(graph = graph)
 } # nocov end
 #   IGraph R package
@@ -56,19 +56,6 @@ is_igraph <- function(graph) {
   TRUE
 }
 
-#' Incident vertices of some graph edges
-#' @description
-#' `r lifecycle::badge("deprecated")`
-#'
-#' Use [ends()].
-#' @inheritParams ends
-#' @export
-#' @keywords internal
-get.edge <- function(graph, id) {
-  lifecycle::deprecate_stop("2.1.0", "get.edge()", "ends()")
-}
-
-
 #' Head of the edge(s) in a graph
 #'
 #' For undirected graphs, head and tail is not defined.  In this case

R/bipartite.R

@@ -10,7 +10,7 @@
 #' @export
 bipartite.projection.size <- function(graph, types = NULL) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "bipartite.projection.size()",
     "bipartite_projection_size()"
@@ -37,7 +37,7 @@ bipartite.projection <- function(
   remove.type = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "bipartite.projection()",
     "bipartite_projection()"
@@ -64,7 +64,7 @@ bipartite.projection <- function(
 #' @export
 bipartite.mapping <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "bipartite.mapping()",
     "bipartite_mapping()"