feat!: advance lifecycle deprecation from soft to warn

R/adjacency.R

@@ -405,17 +405,17 @@ graph_from_adjacency_matrix <- function(adjmatrix,
   mode <- igraph.match.arg(mode)
 
   if (!is.matrix(adjmatrix) && !inherits(adjmatrix, "Matrix")) {
-    lifecycle::deprecate_soft(
-      "1.6.0",
+    lifecycle::deprecate_warn(
+      "2.0.0",
       "graph_from_adjacency_matrix(adjmatrix = 'must be a matrix')"
     )
     adjmatrix <- as.matrix(1)
   }
 
   if (mode == "undirected") {
     if (!is_symmetric(adjmatrix)) {
-      lifecycle::deprecate_soft(
-        "1.6.0",
+      lifecycle::deprecate_warn(
+        "2.0.0",
         "graph_from_adjacency_matrix(adjmatrix = 'must be symmetric with mode = \"undirected\"')",
         details = 'Use mode = "max" to achieve the original behavior.'
       )

R/as_phylo.R

@@ -10,8 +10,8 @@
 #' @inheritParams ape::as.phylo
 #' @keywords internal
 as_phylo <- function(x, ...) {
-  lifecycle::deprecate_soft(
-    "1.5.0",
+  lifecycle::deprecate_warn(
+    "2.0.0",
     "ape::as.phylo()"
   )
   check_installed("ape", "for using `as.phylo()`")

R/assortativity.R

@@ -148,8 +148,8 @@ assortativity <- function(graph,
                           types1 = NULL,
                           types2 = NULL) {
   if (...length() > 0) {
-    lifecycle::deprecate_soft(
-      "1.6.0",
+    lifecycle::deprecate_warn(
+      "2.0.0",
       "assortativity(... =)",
       details = "Arguments `values` and `values.in` must be named."
     )
@@ -170,17 +170,17 @@ assortativity <- function(graph,
   }
 
   if (missing(values)) {
-    lifecycle::deprecate_soft(
-      "1.6.0",
+    lifecycle::deprecate_warn(
+      "2.0.0",
       "assortativity(types1 =)",
       "assortativity(values =)"
     )
     values <- types1
   }
 
   if (!is.null(types2)) {
-    lifecycle::deprecate_soft(
-      "1.6.0",
+    lifecycle::deprecate_warn(
+      "2.0.0",
       "assortativity(types2 =)",
       "assortativity(values.in =)"
     )

R/centrality.R

@@ -196,8 +196,8 @@ alpha.centrality <- function(graph, nodes = V(graph), alpha = 1, loops = FALSE,
 #' @keywords internal
 #' @export
 estimate_betweenness <- function(graph, vids = V(graph), directed = TRUE, cutoff, weights = NULL) {
-  lifecycle::deprecate_soft(
-    "1.6.0",
+  lifecycle::deprecate_warn(
+    "2.0.0",
     "estimate_betweenness()",
     "betweenness()",
     details = "with the cutoff argument."
@@ -352,8 +352,8 @@ edge_betweenness <- function(graph, e = E(graph),
 #' @export
 estimate_edge_betweenness <- function(graph, e = E(graph),
                                       directed = TRUE, cutoff, weights = NULL) {
-    lifecycle::deprecate_soft(
-    "1.6.0",
+    lifecycle::deprecate_warn(
+    "2.0.0",
     "estimate_edge_betweenness()",
     "edge_betweenness()",
     details = "with the cutoff argument."
@@ -468,8 +468,8 @@ closeness <- function(graph, vids = V(graph),
 #' @export
 estimate_closeness <- function(graph, vids = V(graph), mode = c("out", "in", "all", "total"), cutoff, weights = NULL, normalized = FALSE) {
 
-  lifecycle::deprecate_soft(
-    "1.6.0",
+  lifecycle::deprecate_warn(
+    "2.0.0",
     "estimate_closeness()",
     "closeness()",
     details = "with the cutoff argument."
@@ -683,8 +683,8 @@ arpack <- function(func, extra = NULL, sym = FALSE, options = arpack_defaults(),
                    env = parent.frame(), complex = !sym) {
 
   if (is.function(options)) {
-    lifecycle::deprecate_soft(
-      "1.6.0",
+    lifecycle::deprecate_warn(
+      "2.0.0",
       "arpack(options = 'must be a list')",
       details = c("`arpack_defaults()` is now a function, use `options = arpack_defaults()` instead of `options = arpack_defaults`.")
     )
@@ -870,8 +870,8 @@ subgraph_centrality <- function(graph, diag = FALSE) {
 #' @export
 spectrum <- function(graph, algorithm=c("arpack", "auto", "lapack", "comp_auto", "comp_lapack", "comp_arpack"), which=list(), options=arpack_defaults()) {
   if (is.function(options)) {
-    lifecycle::deprecate_soft(
-      "1.6.0",
+    lifecycle::deprecate_warn(
+      "2.0.0",
       "spectrum(options = 'must be a list')",
       details = c("`arpack_defaults()` is now a function, use `options = arpack_defaults()` instead of `options = arpack_defaults`.")
     )
@@ -983,8 +983,8 @@ eigen_centrality <- function(graph,
                              options = arpack_defaults()) {
 
   if (is.function(options)) {
-    lifecycle::deprecate_soft(
-      "1.6.0",
+    lifecycle::deprecate_warn(
+      "2.0.0",
       "eigen_centrality(options = 'must be a list')",
       details = c("`arpack_defaults()` is now a function, use `options = arpack_defaults()` instead of `options = arpack_defaults`.")
     )
@@ -1135,8 +1135,8 @@ diversity <- diversity_impl
 hub_score <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults()) {
 
   if (is.function(options)) {
-    lifecycle::deprecate_soft(
-      "1.6.0",
+    lifecycle::deprecate_warn(
+      "2.0.0",
       "hub_score(options = 'must be a list')",
       details = c("`arpack_defaults()` is now a function, use `options = arpack_defaults()` instead of `options = arpack_defaults`.")
     )
@@ -1155,8 +1155,8 @@ hub_score <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults()
 #' @export
 authority_score <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults()) {
   if (is.function(options)) {
-    lifecycle::deprecate_soft(
-      "1.6.0",
+    lifecycle::deprecate_warn(
+      "2.0.0",
       I("arpack_defaults"),
       "arpack_defaults()",
       details = c("So the function arpack_defaults(), not an object called arpack_defaults.")

R/community.R

@@ -1868,8 +1868,8 @@ cluster_leading_eigen <- function(graph, steps = -1, weights = NULL,
                                   env = parent.frame()) {
 
   if (is.function(options)) {
-    lifecycle::deprecate_soft(
-      "1.6.0",
+    lifecycle::deprecate_warn(
+      "2.0.0",
       "cluster_leading_eigen(options = 'must be a list')",
       details = c("`arpack_defaults()` is now a function, use `options = arpack_defaults()` instead of `options = arpack_defaults`.")
     )
@@ -1986,8 +1986,8 @@ cluster_label_prop <- function(
     initial = NULL,
     fixed = NULL) {
   if (...length() > 0) {
-    lifecycle::deprecate_soft(
-      "1.6.0",
+    lifecycle::deprecate_warn(
+      "2.0.0",
       "cluster_label_prop(... = )",
       details = "Arguments `initial` and `fixed` must be named."
     )

R/conversion.R

@@ -1002,7 +1002,7 @@ as_biadjacency_matrix <- function(graph, types = NULL, attr = NULL,
 #' this naming to avoid confusion with the edge-vertex incidence matrix.
 #' @export
 as_incidence_matrix <- function(...) { # nocov start
-   lifecycle::deprecate_soft("1.6.0", "as_incidence_matrix()", "as_biadjacency_matrix()")
+   lifecycle::deprecate_warn("2.0.0", "as_incidence_matrix()", "as_biadjacency_matrix()")
    as_biadjacency_matrix(...)
 } # nocov end
 #' @rdname graph_from_data_frame

R/incidence.R

@@ -277,7 +277,7 @@ graph_from_biadjacency_matrix <- function(incidence, directed = FALSE,
 #' this naming to avoid confusion with the edge-vertex incidence matrix.
 #' @export
 from_incidence_matrix <- function(...) { # nocov start
-   lifecycle::deprecate_soft("1.6.0", "graph_from_incidence_matrix()", "graph_from_biadjacency_matrix()")
+   lifecycle::deprecate_warn("2.0.0", "graph_from_incidence_matrix()", "graph_from_biadjacency_matrix()")
    graph_from_biadjacency_matrix(...)
 } # nocov end
 #' From incidence matrix
@@ -295,6 +295,6 @@ from_incidence_matrix <- function(...) { # nocov start
 #' this naming to avoid confusion with the edge-vertex incidence matrix.
 #' @export
 graph_from_incidence_matrix <- function(...) { # nocov start
-   lifecycle::deprecate_soft("1.6.0", "graph_from_incidence_matrix()", "graph_from_biadjacency_matrix()")
+   lifecycle::deprecate_warn("2.0.0", "graph_from_incidence_matrix()", "graph_from_biadjacency_matrix()")
    graph_from_biadjacency_matrix(...)
 } # nocov end

R/layout.R

@@ -1687,8 +1687,8 @@ layout_with_mds <- function(graph, dist = NULL, dim = 2,
                             options = arpack_defaults()) {
 
   if (is.function(options)) {
-    lifecycle::deprecate_soft(
-      "1.6.0",
+    lifecycle::deprecate_warn(
+      "2.0.0",
       "layout_with_mds(options = 'must be a list')",
       details = c("`arpack_defaults()` is now a function, use `options = arpack_defaults()` instead of `options = arpack_defaults`.")
     )

tests/testthat/_snaps/graph.adjacency.md

@@ -21,7 +21,7 @@
       graph_from_adjacency_matrix(m, mode = "undirected")
     Condition
       Warning:
-      The `adjmatrix` argument of `graph_from_adjacency_matrix()` must be symmetric with mode = "undirected" as of igraph 1.6.0.
+      The `adjmatrix` argument of `graph_from_adjacency_matrix()` must be symmetric with mode = "undirected" as of igraph 2.0.0.
       i Use mode = "max" to achieve the original behavior.
     Output
       IGRAPH U--- 2 2 -- 
@@ -53,7 +53,7 @@
       graph_from_adjacency_matrix(m2, mode = "undirected")
     Condition
       Warning:
-      The `adjmatrix` argument of `graph_from_adjacency_matrix()` must be symmetric with mode = "undirected" as of igraph 1.6.0.
+      The `adjmatrix` argument of `graph_from_adjacency_matrix()` must be symmetric with mode = "undirected" as of igraph 2.0.0.
       i Use mode = "max" to achieve the original behavior.
     Output
       IGRAPH U--- 2 0 -- 
@@ -62,7 +62,7 @@
       graph_from_adjacency_matrix(1)
     Condition
       Warning:
-      The `adjmatrix` argument of `graph_from_adjacency_matrix()` must be a matrix as of igraph 1.6.0.
+      The `adjmatrix` argument of `graph_from_adjacency_matrix()` must be a matrix as of igraph 2.0.0.
     Output
       IGRAPH D--- 1 1 -- 
       + edge:
@@ -71,7 +71,7 @@
       graph_from_adjacency_matrix(1, mode = "undirected")
     Condition
       Warning:
-      The `adjmatrix` argument of `graph_from_adjacency_matrix()` must be a matrix as of igraph 1.6.0.
+      The `adjmatrix` argument of `graph_from_adjacency_matrix()` must be a matrix as of igraph 2.0.0.
     Output
       IGRAPH U--- 1 1 -- 
       + edge:
@@ -101,7 +101,7 @@
       graph_from_adjacency_matrix(m, mode = "undirected")
     Condition
       Warning:
-      The `adjmatrix` argument of `graph_from_adjacency_matrix()` must be symmetric with mode = "undirected" as of igraph 1.6.0.
+      The `adjmatrix` argument of `graph_from_adjacency_matrix()` must be symmetric with mode = "undirected" as of igraph 2.0.0.
       i Use mode = "max" to achieve the original behavior.
     Output
       IGRAPH U--- 2 2 -- 
@@ -133,7 +133,7 @@
       graph_from_adjacency_matrix(m2, mode = "undirected")
     Condition
       Warning:
-      The `adjmatrix` argument of `graph_from_adjacency_matrix()` must be symmetric with mode = "undirected" as of igraph 1.6.0.
+      The `adjmatrix` argument of `graph_from_adjacency_matrix()` must be symmetric with mode = "undirected" as of igraph 2.0.0.
       i Use mode = "max" to achieve the original behavior.
     Output
       IGRAPH U--- 2 0 --