From e1a396d10c9157fe3ebf3a94a13cdbd543851f59 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 11:59:22 +0200
Subject: [PATCH 01/48] chore: add commit-lifecycle.R script

---
 .Rbuildignore            |  7 +--
 .gitignore               |  1 +
 tools/commit-lifecycle.R | 98 ++++++++++++++++++++++++++++++++++++++++
 3 files changed, 103 insertions(+), 3 deletions(-)
 create mode 100644 tools/commit-lifecycle.R

diff --git a/.Rbuildignore b/.Rbuildignore
index 1264bff9265..f4f72a79998 100644
--- a/.Rbuildignore
+++ b/.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$
diff --git a/.gitignore b/.gitignore
index 0fe829881b4..28f195c81dc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -30,3 +30,4 @@ cran
 /_codeql_detected_source_root
 /tests/testthat/_problems/
 .ccache/
+lifecycle
diff --git a/tools/commit-lifecycle.R b/tools/commit-lifecycle.R
new file mode 100644
index 00000000000..49fb84f3307
--- /dev/null
+++ b/tools/commit-lifecycle.R
@@ -0,0 +1,98 @@
+# create a Rbuildignored, gitignored directory called 'lifecycle'
+
+# lifecycle_dir <- here::here("lifecycle")
+# dir.create(lifecycle_dir, showWarnings = FALSE)
+#
+# usethis::use_build_ignore("lifecycle")
+# usethis::use_git_ignore("lifecycle")
+
+# collect all functions changed from the commit messages on this branch, add items to `lifecycle/NEWS.md` which
+# is `NEWS.md` with the edits — already done, lifecycle/NEWS.md exists
+
+# reset mixed to right before the PR
+
+# cli::cli_alert_info("Resetting to merge-base {substr(merge_base, 1, 7)}...")
+# gert::git_reset_mixed(merge_base, repo = here::here())
+# cli::cli_alert_success("Reset to merge-base")
+
+# copy all changed files, except man/ and NAMESPACE which should be reset to their previous state,
+# to 'lifecycle', use their version from main instead.
+
+# changed <- gert::git_status(repo = here::here())$file
+# r_changed <- changed[grepl("^R/", changed)]
+# test_changed <- changed[grepl("^tests/", changed)]
+#
+# for (f in c(r_changed, test_changed)) {
+#   dest_dir <- dirname(here::here("lifecycle", f))
+#   dir.create(dest_dir, showWarnings = FALSE, recursive = TRUE)
+#   file.copy(here::here(f), here::here("lifecycle", f), overwrite = TRUE)
+# }
+# cli::cli_alert_success("Saved {length(r_changed)} R files and {length(test_changed)} test files to lifecycle/")
+
+# gert::git_reset_hard("main", repo = here::here())
+# cli::cli_alert_success("Restored working tree to main (man/, NAMESPACE, R/ all from main)")
+
+# rebase the branch on main
+
+# gert::git_pull(repo = here::here(), remote = "origin", refspec = "main")
+# cli::cli_alert_success("Pulled and fast-forwarded to main")
+
+gert::git_fetch("origin", refspec = "refs/heads/main:refs/heads/main", repo = here::here())
+gert::git_reset_mixed("main", repo = here::here())
+
+usethis::use_build_ignore("lifecycle")
+usethis::use_git_ignore("lifecycle")
+
+gert::git_add(c("tools/commit-lifecycle.R", ".gitignore", ".Rbuildignore"), repo = here::here())
+gert::git_commit("chore: add commit-lifecycle.R script", repo = here::here())
+cli::cli_alert_success("Committed tools/commit-lifecycle.R")
+
+# one commit per R script (copied back from the 'lifecycle' directory) + corresponding R test file if needed + run `document()` + run `test()`.
+
+r_files <- list.files(here::here("lifecycle", "R"), full.names = FALSE)
+
+for (stem in tools::file_path_sans_ext(r_files)) {
+  r_file <- paste0("R/", stem, ".R")
+  lifecycle_r <- here::here("lifecycle", r_file)
+
+  file.copy(lifecycle_r, here::here(r_file), overwrite = TRUE)
+  files_to_stage <- r_file
+
+  lifecycle_test <- here::here("lifecycle", "tests", "testthat", paste0("test-", stem, ".R"))
+  if (file.exists(lifecycle_test)) {
+    dest_test <- here::here("tests", "testthat", paste0("test-", stem, ".R"))
+    file.copy(lifecycle_test, dest_test, overwrite = TRUE)
+    files_to_stage <- c(files_to_stage, paste0("tests/testthat/test-", stem, ".R"))
+
+    lifecycle_snap <- here::here("lifecycle", "tests", "testthat", "_snaps", paste0(stem, ".md"))
+    if (file.exists(lifecycle_snap)) {
+      dest_snap <- here::here("tests", "testthat", "_snaps", paste0(stem, ".md"))
+      file.copy(lifecycle_snap, dest_snap, overwrite = TRUE)
+      files_to_stage <- c(files_to_stage, paste0("tests/testthat/_snaps/", stem, ".md"))
+    }
+  }
+
+  devtools::document(quiet = TRUE)
+  tryCatch(
+    callr::r(
+      function(pkg, filter) devtools::test(pkg = pkg, filter = filter, stop_on_failure = FALSE),
+      args = list(pkg = here::here(), filter = stem)
+    ),
+    error = function(e) cli::cli_alert_warning("Tests errored for {stem}: {conditionMessage(e)}")
+  )
+
+  gert::git_add(c(files_to_stage, "man", "NAMESPACE"), repo = here::here())
+  gert::git_commit(paste0("feat!: bump deprecated functions in R/", stem, ".R"), repo = here::here())
+  cli::cli_alert_success("Committed {r_file}")
+}
+
+file.copy(here::here("lifecycle", "NEWS.md"), here::here("NEWS.md"), overwrite = TRUE)
+gert::git_add("NEWS.md", repo = here::here())
+gert::git_commit("chore: update NEWS.md for lifecycle bumps\n\n!NEWS", repo = here::here())
+cli::cli_alert_success("Committed NEWS.md")
+
+# R CMD check after all the commits
+
+devtools::check()
+
+# I will do the force pushing once I am happy.

From e9c2ab95a8a7ef5910cc61a71ae8e5b6a3564253 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:00:19 +0200
Subject: [PATCH 02/48] feat!: bump deprecated functions in R/adjacency.R

---
 NAMESPACE       |  1 -
 R/adjacency.R   |  6 +++---
 man/get.edge.Rd | 17 -----------------
 3 files changed, 3 insertions(+), 21 deletions(-)
 delete mode 100644 man/get.edge.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 5fc033b748a..50337bd1418 100644
--- a/NAMESPACE
+++ b/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)
diff --git a/R/adjacency.R b/R/adjacency.R
index 65b4eb21411..f1424f964e4 100644
--- a/R/adjacency.R
+++ b/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.'
diff --git a/man/get.edge.Rd b/man/get.edge.Rd
deleted file mode 100644
index d416b1ff1d7..00000000000
--- a/man/get.edge.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/basic.R
-\name{get.edge}
-\alias{get.edge}
-\title{Incident vertices of some graph edges}
-\usage{
-get.edge(graph, id)
-}
-\arguments{
-\item{graph}{The input graph}
-}
-\description{
-\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}
-
-Use \code{\link[=ends]{ends()}}.
-}
-\keyword{internal}

From 389746b1ce4c6a5914fe4d4057d52a5bfd93cf2d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:01:06 +0200
Subject: [PATCH 03/48] feat!: bump deprecated functions in R/as_phylo.R

---
 R/as_phylo.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/as_phylo.R b/R/as_phylo.R
index c33615d8db4..03e8b21e0a4 100644
--- a/R/as_phylo.R
+++ b/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()"
   )

From fdcfbe5db0205a4161116a449c2f850e4bc439b7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:01:55 +0200
Subject: [PATCH 04/48] feat!: bump deprecated functions in R/assortativity.R

---
 R/assortativity.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/assortativity.R b/R/assortativity.R
index 5a1b7d2055a..074fa421b35 100644
--- a/R/assortativity.R
+++ b/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 =)"

From 11bb31893b7ef05a6aeb19db8895fb63fffb82b0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:02:48 +0200
Subject: [PATCH 05/48] feat!: bump deprecated functions in R/attributes.R

---
 R/attributes.R | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/R/attributes.R b/R/attributes.R
index 87af8d6b304..1a34d29fc8e 100644
--- a/R/attributes.R
+++ b/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

From 4f8e84e2d558e1be18c8cb02e61b1daeb9c2e351 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:03:39 +0200
Subject: [PATCH 06/48] feat!: bump deprecated functions in R/basic.R

---
 R/basic.R | 15 +--------------
 1 file changed, 1 insertion(+), 14 deletions(-)

diff --git a/R/basic.R b/R/basic.R
index 47b00f7e071..4769854df36 100644
--- a/R/basic.R
+++ b/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

From 8e598111dcb9adabff96772960f9ea8e9653a97f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:04:32 +0200
Subject: [PATCH 07/48] feat!: bump deprecated functions in R/bipartite.R

---
 R/bipartite.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/bipartite.R b/R/bipartite.R
index 5e640313588..24f2d63ebda 100644
--- a/R/bipartite.R
+++ b/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()"

From 7ed6a016a272856cd3b6ac677cc7ecdda535fec9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:05:30 +0200
Subject: [PATCH 08/48] feat!: bump deprecated functions in R/centrality.R

---
 R/centrality.R                      | 46 ++++++++++++++---------------
 tests/testthat/_snaps/centrality.md |  4 +--
 tests/testthat/test-centrality.R    |  2 +-
 3 files changed, 26 insertions(+), 26 deletions(-)

diff --git a/R/centrality.R b/R/centrality.R
index f239487876f..0cec52a6a44 100644
--- a/R/centrality.R
+++ b/R/centrality.R
@@ -10,7 +10,7 @@
 #' @export
 subgraph.centrality <- function(graph, diag = FALSE) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "subgraph.centrality()",
     "subgraph_centrality()"
@@ -39,7 +39,7 @@ page.rank <- function(
   options = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "page.rank()", "page_rank()")
+  lifecycle::deprecate_warn("2.0.0", "page.rank()", "page_rank()")
   page_rank(
     graph = graph,
     algo = algo,
@@ -69,7 +69,7 @@ hub.score <- function(
   options = arpack_defaults()
 ) {
   # nocov start
-  lifecycle::deprecate_warn("2.0.0", "hub.score()", "hits_scores()")
+  lifecycle::deprecate_stop("2.0.0", "hub.score()", "hits_scores()")
   hub_score(graph = graph, scale = scale, weights = weights, options = options)
 } # nocov end
 
@@ -90,7 +90,7 @@ authority.score <- function(
   options = arpack_defaults()
 ) {
   # nocov start
-  lifecycle::deprecate_warn("2.0.0", "authority.score()", "hits_scores()")
+  lifecycle::deprecate_stop("2.0.0", "authority.score()", "hits_scores()")
   authority_score(
     graph = graph,
     scale = scale,
@@ -117,7 +117,7 @@ graph.strength <- function(
   weights = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.strength()", "strength()")
+  lifecycle::deprecate_warn("2.0.0", "graph.strength()", "strength()")
   strength(
     graph = graph,
     vids = vids,
@@ -151,7 +151,7 @@ graph.eigen <- function(
   options = arpack_defaults()
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.eigen()", "spectrum()")
+  lifecycle::deprecate_warn("2.0.0", "graph.eigen()", "spectrum()")
   spectrum(
     graph = graph,
     algorithm = algorithm,
@@ -172,7 +172,7 @@ graph.eigen <- function(
 #' @export
 graph.diversity <- function(graph, weights = NULL, vids = V(graph)) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.diversity()", "diversity()")
+  lifecycle::deprecate_warn("2.0.0", "graph.diversity()", "diversity()")
   diversity(graph = graph, weights = weights, vids = vids)
 } # nocov end
 
@@ -194,7 +194,7 @@ evcent <- function(
   options = arpack_defaults()
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "evcent()", "eigen_centrality()")
+  lifecycle::deprecate_warn("2.0.0", "evcent()", "eigen_centrality()")
   eigen_centrality(
     graph = graph,
     directed = directed,
@@ -222,7 +222,7 @@ edge.betweenness <- function(
   cutoff = -1
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "edge.betweenness()", "edge_betweenness()")
+  lifecycle::deprecate_warn("2.0.0", "edge.betweenness()", "edge_betweenness()")
   edge_betweenness(
     graph = graph,
     e = e,
@@ -252,7 +252,7 @@ bonpow <- function(
   sparse = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "bonpow()", "power_centrality()")
+  lifecycle::deprecate_warn("2.0.0", "bonpow()", "power_centrality()")
   power_centrality(
     graph = graph,
     nodes = nodes,
@@ -285,7 +285,7 @@ alpha.centrality <- function(
   sparse = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "alpha.centrality()", "alpha_centrality()")
+  lifecycle::deprecate_warn("2.0.0", "alpha.centrality()", "alpha_centrality()")
   alpha_centrality(
     graph = graph,
     nodes = nodes,
@@ -336,7 +336,7 @@ estimate_betweenness <- function(
   cutoff,
   weights = NULL
 ) {
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "1.6.0",
     "estimate_betweenness()",
     "betweenness()",
@@ -498,7 +498,7 @@ estimate_edge_betweenness <- function(
   cutoff,
   weights = NULL
 ) {
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "1.6.0",
     "estimate_edge_betweenness()",
     "edge_betweenness()",
@@ -611,7 +611,7 @@ estimate_closeness <- function(
   weights = NULL,
   normalized = FALSE
 ) {
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "1.6.0",
     "estimate_closeness()",
     "closeness()",
@@ -961,7 +961,7 @@ arpack <- function(
   complex = !sym
 ) {
   if (is.function(options)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       "arpack(options = 'must be a list')",
       details = c(
@@ -1170,7 +1170,7 @@ spectrum <- function(
   options = arpack_defaults()
 ) {
   if (is.function(options)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       "spectrum(options = 'must be a list')",
       details = c(
@@ -1299,7 +1299,7 @@ eigen_centrality <- function(
   options = arpack_defaults()
 ) {
   if (is.function(options)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       "eigen_centrality(options = 'must be a list')",
       details = c(
@@ -1311,13 +1311,13 @@ eigen_centrality <- function(
 
   if (lifecycle::is_present(scale)) {
     if (isTRUE(scale)) {
-      lifecycle::deprecate_soft(
+      lifecycle::deprecate_warn(
         "2.1.1",
         "eigen_centrality(scale)",
         details = "eigen_centrality() will always behave as if scale=TRUE were used."
       )
     } else {
-      lifecycle::deprecate_warn(
+      lifecycle::deprecate_stop(
         "2.1.1",
         "eigen_centrality(scale = 'always as if TRUE')",
         details = "Normalization is always performed"
@@ -1522,9 +1522,9 @@ authority_score <- function(
   weights = NULL,
   options = arpack_defaults()
 ) {
-  lifecycle::deprecate_soft("2.1.0", "authority_score()", "hits_scores()")
+  lifecycle::deprecate_warn("2.1.0", "authority_score()", "hits_scores()")
   if (is.function(options)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       I("arpack_defaults"),
       "arpack_defaults()",
@@ -1567,9 +1567,9 @@ hub_score <- function(
   weights = NULL,
   options = arpack_defaults()
 ) {
-  lifecycle::deprecate_soft("2.0.3", "hub_score()", "hits_scores()")
+  lifecycle::deprecate_warn("2.0.3", "hub_score()", "hits_scores()")
   if (is.function(options)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       I("arpack_defaults"),
       "arpack_defaults()",
diff --git a/tests/testthat/_snaps/centrality.md b/tests/testthat/_snaps/centrality.md
index f6ffca6419b..bcb12bae957 100644
--- a/tests/testthat/_snaps/centrality.md
+++ b/tests/testthat/_snaps/centrality.md
@@ -38,8 +38,8 @@
     Code
       invisible(eigen_centrality(g, scale = FALSE))
     Condition
-      Warning:
-      The `scale` argument of `eigen_centrality()` always as if TRUE as of igraph 2.1.1.
+      Error:
+      ! The `scale` argument of `eigen_centrality()` always as if TRUE as of igraph 2.1.1.
       i Normalization is always performed
 
 # arpack() errors well
diff --git a/tests/testthat/test-centrality.R b/tests/testthat/test-centrality.R
index 71bd753a7e6..4c806459f42 100644
--- a/tests/testthat/test-centrality.R
+++ b/tests/testthat/test-centrality.R
@@ -838,7 +838,7 @@ test_that("eigen_centrality() deprecated scale argument", {
     invisible(eigen_centrality(g, scale = TRUE))
   })
   # For some reason, this produces different outputs on Windows and macOS
-  expect_snapshot({
+  expect_snapshot(error = TRUE, {
     invisible(eigen_centrality(g, scale = FALSE))
   })
 })

From dcc783f785607ed914397434efccb8cf49664e9a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:06:19 +0200
Subject: [PATCH 09/48] feat!: bump deprecated functions in R/centralization.R

---
 R/centralization.R | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/R/centralization.R b/R/centralization.R
index bd6dfb570ef..e0655d7f295 100644
--- a/R/centralization.R
+++ b/R/centralization.R
@@ -10,7 +10,7 @@
 #' @export
 centralize.scores <- function(scores, theoretical.max = 0, normalized = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "centralize.scores()", "centralize()")
+  lifecycle::deprecate_warn("2.0.0", "centralize.scores()", "centralize()")
   centralize(
     scores = scores,
     theoretical.max = theoretical.max,
@@ -35,7 +35,7 @@ centralization.evcent.tmax <- function(
   scale = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "centralization.evcent.tmax()",
     "centr_eigen_tmax()"
@@ -66,7 +66,7 @@ centralization.evcent <- function(
   normalized = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "centralization.evcent()", "centr_eigen()")
+  lifecycle::deprecate_warn("2.0.0", "centralization.evcent()", "centr_eigen()")
   centr_eigen(
     graph = graph,
     directed = directed,
@@ -93,7 +93,7 @@ centralization.degree.tmax <- function(
   loops = FALSE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "centralization.degree.tmax()",
     "centr_degree_tmax()"
@@ -118,7 +118,7 @@ centralization.degree <- function(
   normalized = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "centralization.degree()",
     "centr_degree()"
@@ -147,7 +147,7 @@ centralization.closeness.tmax <- function(
   mode = c("out", "in", "all", "total")
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "centralization.closeness.tmax()",
     "centr_clo_tmax()"
@@ -171,7 +171,7 @@ centralization.closeness <- function(
   normalized = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "centralization.closeness()",
     "centr_clo()"
@@ -195,7 +195,7 @@ centralization.betweenness.tmax <- function(
   directed = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "centralization.betweenness.tmax()",
     "centr_betw_tmax()"
@@ -219,7 +219,7 @@ centralization.betweenness <- function(
   normalized = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "centralization.betweenness()",
     "centr_betw()"
@@ -404,7 +404,7 @@ centr_degree_tmax <- function(
   loops
 ) {
   if (!lifecycle::is_present(loops)) {
-    lifecycle::deprecate_warn(
+    lifecycle::deprecate_stop(
       when = "2.0.0",
       what = "centr_degree_tmax(loops = 'must be explicit')",
       details = "The default value (currently `FALSE`) will be dropped in the next release. Add an explicit value for the `loops` argument."
@@ -658,7 +658,7 @@ centr_eigen <- function(
   normalized = TRUE
 ) {
   if (lifecycle::is_present(scale)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.2.0",
       "centr_eigen(scale = )",
       details = "The function always behaves as if `scale = TRUE`.
@@ -708,7 +708,7 @@ centr_eigen_tmax <- function(
   scale = deprecated()
 ) {
   if (lifecycle::is_present(scale)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.2.0",
       "centr_eigen_tmax(scale = )",
       details = "The function always behaves as if `scale = TRUE`.

From 8d10f2c3a3c5c9e8103b2e46c23df7d36f65cacc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:07:11 +0200
Subject: [PATCH 10/48] feat!: bump deprecated functions in R/cliques.R

---
 R/cliques.R | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/R/cliques.R b/R/cliques.R
index 4bd6018334c..9d3ce765399 100644
--- a/R/cliques.R
+++ b/R/cliques.R
@@ -10,7 +10,7 @@
 #' @export
 maximal.independent.vertex.sets <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "maximal.independent.vertex.sets()",
     "max_ivs()"
@@ -35,7 +35,7 @@ maximal.cliques.count <- function(
   subset = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "maximal.cliques.count()",
     "count_max_cliques()"
@@ -61,7 +61,7 @@ maximal.cliques <- function(
   file = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "maximal.cliques()", "max_cliques()")
+  lifecycle::deprecate_warn("2.0.0", "maximal.cliques()", "max_cliques()")
   max_cliques(graph = graph, min = min, max = max, subset = subset, file = file)
 } # nocov end
 
@@ -77,7 +77,7 @@ maximal.cliques <- function(
 #' @export
 largest.independent.vertex.sets <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "largest.independent.vertex.sets()",
     "largest_ivs()"
@@ -97,7 +97,7 @@ largest.independent.vertex.sets <- function(graph) {
 #' @export
 largest.cliques <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "largest.cliques()", "largest_cliques()")
+  lifecycle::deprecate_warn("2.0.0", "largest.cliques()", "largest_cliques()")
   largest_cliques(graph = graph)
 } # nocov end
 
@@ -113,7 +113,7 @@ largest.cliques <- function(graph) {
 #' @export
 independent.vertex.sets <- function(graph, min = NULL, max = NULL) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "independent.vertex.sets()", "ivs()")
+  lifecycle::deprecate_warn("2.0.0", "independent.vertex.sets()", "ivs()")
   ivs(graph = graph, min = min, max = max)
 } # nocov end
 
@@ -129,7 +129,7 @@ independent.vertex.sets <- function(graph, min = NULL, max = NULL) {
 #' @export
 independence.number <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "independence.number()", "ivs_size()")
+  lifecycle::deprecate_warn("2.0.0", "independence.number()", "ivs_size()")
   ivs_size(graph = graph)
 } # nocov end
 
@@ -145,7 +145,7 @@ independence.number <- function(graph) {
 #' @export
 clique.number <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "clique.number()", "clique_num()")
+  lifecycle::deprecate_warn("2.0.0", "clique.number()", "clique_num()")
   clique_num(graph = graph)
 } # nocov end
 #   IGraph R package
@@ -615,7 +615,7 @@ max_ivs <- function(graph) {
 #' @inheritParams max_ivs
 #' @keywords internal
 maximal_ivs <- function(graph) {
-  lifecycle::deprecate_soft("2.1.0", "maximal_ivs()", "max_ivs()")
+  lifecycle::deprecate_warn("2.1.0", "maximal_ivs()", "max_ivs()")
   max_ivs(graph)
 }
 

From ca6f3d0d4a3f103139dfbc95378217a407b075cb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:07:58 +0200
Subject: [PATCH 11/48] feat!: bump deprecated functions in R/cohesive.blocks.R

---
 R/cohesive.blocks.R | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/R/cohesive.blocks.R b/R/cohesive.blocks.R
index 35844360284..202ed43dad8 100644
--- a/R/cohesive.blocks.R
+++ b/R/cohesive.blocks.R
@@ -10,7 +10,7 @@
 #' @export
 exportPajek <- function(blocks, graph, file, project.file = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "exportPajek()", "export_pajek()")
+  lifecycle::deprecate_warn("2.0.0", "exportPajek()", "export_pajek()")
   export_pajek(
     blocks = blocks,
     graph = graph,
@@ -35,7 +35,7 @@ plotHierarchy <- function(
   ...
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "plotHierarchy()", "plot_hierarchy()")
+  lifecycle::deprecate_warn("2.0.0", "plotHierarchy()", "plot_hierarchy()")
   plot_hierarchy(blocks = blocks, layout = layout, ...)
 } # nocov end
 
@@ -51,7 +51,7 @@ plotHierarchy <- function(
 #' @export
 maxcohesion <- function(blocks) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "maxcohesion()", "max_cohesion()")
+  lifecycle::deprecate_warn("2.0.0", "maxcohesion()", "max_cohesion()")
   max_cohesion(blocks = blocks)
 } # nocov end
 
@@ -68,7 +68,7 @@ maxcohesion <- function(blocks) {
 #' @export
 graph.cohesion <- function(x, ...) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.cohesion()", "cohesion()")
+  lifecycle::deprecate_warn("2.0.0", "graph.cohesion()", "cohesion()")
   cohesion(x = x, ...)
 } # nocov end
 
@@ -84,7 +84,7 @@ graph.cohesion <- function(x, ...) {
 #' @export
 cohesive.blocks <- function(graph, labels = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "cohesive.blocks()", "cohesive_blocks()")
+  lifecycle::deprecate_warn("2.0.0", "cohesive.blocks()", "cohesive_blocks()")
   cohesive_blocks(graph = graph, labels = labels)
 } # nocov end
 
@@ -100,7 +100,7 @@ cohesive.blocks <- function(graph, labels = TRUE) {
 #' @export
 blockGraphs <- function(blocks, graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "blockGraphs()",
     "graphs_from_cohesive_blocks()"

From 64fb47826edd4351ff074cc983fd7996ed956717 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:08:49 +0200
Subject: [PATCH 12/48] feat!: bump deprecated functions in R/community.R

---
 R/community.R                      | 42 +++++++++++++++---------------
 tests/testthat/_snaps/community.md |  6 ++---
 tests/testthat/test-community.R    |  6 ++---
 3 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/R/community.R b/R/community.R
index 352f534ba11..0d9b8cf3781 100644
--- a/R/community.R
+++ b/R/community.R
@@ -16,7 +16,7 @@ create.communities <- function(
   modularity = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "create.communities()", "make_clusters()")
+  lifecycle::deprecate_warn("2.0.0", "create.communities()", "make_clusters()")
   make_clusters(
     graph = graph,
     membership = membership,
@@ -45,7 +45,7 @@ walktrap.community <- function(
   membership = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "walktrap.community()",
     "cluster_walktrap()"
@@ -85,7 +85,7 @@ spinglass.community <- function(
   gamma.minus = 1.0
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "spinglass.community()",
     "cluster_spinglass()"
@@ -118,7 +118,7 @@ spinglass.community <- function(
 #' @export
 showtrace <- function(communities) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "showtrace()", "show_trace()")
+  lifecycle::deprecate_warn("2.0.0", "showtrace()", "show_trace()")
   show_trace(communities = communities)
 } # nocov end
 
@@ -134,7 +134,7 @@ showtrace <- function(communities) {
 #' @export
 optimal.community <- function(graph, weights = NULL) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "optimal.community()", "cluster_optimal()")
+  lifecycle::deprecate_warn("2.0.0", "optimal.community()", "cluster_optimal()")
   cluster_optimal(graph = graph, weights = weights)
 } # nocov end
 
@@ -150,7 +150,7 @@ optimal.community <- function(graph, weights = NULL) {
 #' @export
 multilevel.community <- function(graph, weights = NULL, resolution = 1) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "multilevel.community()",
     "cluster_louvain()"
@@ -176,7 +176,7 @@ mod.matrix <- function(
   directed = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "mod.matrix()", "modularity_matrix()")
+  lifecycle::deprecate_warn("2.0.0", "mod.matrix()", "modularity_matrix()")
   modularity_matrix(
     graph = graph,
     membership = membership,
@@ -207,7 +207,7 @@ leading.eigenvector.community <- function(
   env = parent.frame()
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "leading.eigenvector.community()",
     "cluster_leading_eigen()"
@@ -243,7 +243,7 @@ label.propagation.community <- function(
   fixed = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "label.propagation.community()",
     "cluster_label_prop()"
@@ -270,7 +270,7 @@ label.propagation.community <- function(
 #' @export
 is.hierarchical <- function(communities) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.hierarchical()", "is_hierarchical()")
+  lifecycle::deprecate_warn("2.0.0", "is.hierarchical()", "is_hierarchical()")
   is_hierarchical(communities = communities)
 } # nocov end
 
@@ -292,7 +292,7 @@ infomap.community <- function(
   modularity = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "infomap.community()", "cluster_infomap()")
+  lifecycle::deprecate_warn("2.0.0", "infomap.community()", "cluster_infomap()")
   cluster_infomap(
     graph = graph,
     e.weights = e.weights,
@@ -320,7 +320,7 @@ fastgreedy.community <- function(
   weights = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "fastgreedy.community()",
     "cluster_fast_greedy()"
@@ -355,7 +355,7 @@ edge.betweenness.community <- function(
   membership = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "edge.betweenness.community()",
     "cluster_edge_betweenness()"
@@ -384,7 +384,7 @@ edge.betweenness.community <- function(
 #' @export
 dendPlot <- function(x, mode = igraph_opt("dend.plot.type"), ...) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "dendPlot()", "plot_dendrogram()")
+  lifecycle::deprecate_warn("2.0.0", "dendPlot()", "plot_dendrogram()")
   plot_dendrogram(x = x, mode = mode, ...)
 } # nocov end
 
@@ -400,7 +400,7 @@ dendPlot <- function(x, mode = igraph_opt("dend.plot.type"), ...) {
 #' @export
 cutat <- function(communities, no, steps) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "cutat()", "cut_at()")
+  lifecycle::deprecate_warn("2.0.0", "cutat()", "cut_at()")
   cut_at(communities = communities, no = no, steps = steps)
 } # nocov end
 
@@ -420,7 +420,7 @@ contract.vertices <- function(
   vertex.attr.comb = igraph_opt("vertex.attr.comb")
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "contract.vertices()", "contract()")
+  lifecycle::deprecate_warn("2.0.0", "contract.vertices()", "contract()")
   contract(
     graph = graph,
     mapping = mapping,
@@ -440,7 +440,7 @@ contract.vertices <- function(
 #' @export
 code.length <- function(communities) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "code.length()", "code_len()")
+  lifecycle::deprecate_warn("2.0.0", "code.length()", "code_len()")
   code_len(communities = communities)
 } # nocov end
 #   IGraph R package
@@ -951,7 +951,7 @@ modularity_matrix <- function(
   ensure_igraph(graph)
 
   if (!missing(membership)) {
-    lifecycle::deprecate_warn(
+    lifecycle::deprecate_stop(
       "2.1.0",
       "modularity_matrix(membership = 'is no longer used')"
     )
@@ -1636,7 +1636,7 @@ cluster_leiden <- function(
   check_dots_empty()
 
   if (lifecycle::is_present(resolution_parameter)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.1.0",
       "cluster_leiden(resolution_parameter)",
       "cluster_leiden(resolution)"
@@ -2229,7 +2229,7 @@ cluster_leading_eigen <- function(
   env = parent.frame()
 ) {
   if (is.function(options)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       "cluster_leading_eigen(options = 'must be a list')",
       details = c(
@@ -2358,7 +2358,7 @@ cluster_label_prop <- function(
   fixed = NULL
 ) {
   if (...length() > 0) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       "cluster_label_prop(... = )",
       details = "Arguments `initial` and `fixed` must be named."
diff --git a/tests/testthat/_snaps/community.md b/tests/testthat/_snaps/community.md
index e01280a95f5..757b8b0be73 100644
--- a/tests/testthat/_snaps/community.md
+++ b/tests/testthat/_snaps/community.md
@@ -1,8 +1,8 @@
-# modularity_matrix still accepts a membership argument for compatibility
+# modularity_matrix no longer accepts a membership argument for compatibility
 
     Code
       x <- modularity_matrix(karate, membership = rep(1, vcount(karate)))
     Condition
-      Warning:
-      The `membership` argument of `modularity_matrix()` is no longer used as of igraph 2.1.0.
+      Error:
+      ! The `membership` argument of `modularity_matrix()` is no longer used as of igraph 2.1.0.
 
diff --git a/tests/testthat/test-community.R b/tests/testthat/test-community.R
index a5ba5644e72..6891cc9e76d 100644
--- a/tests/testthat/test-community.R
+++ b/tests/testthat/test-community.R
@@ -376,11 +376,11 @@ test_that("modularity_matrix works", {
   expect_equal(karate_modmat1, karate_modmat2)
 })
 
-test_that("modularity_matrix still accepts a membership argument for compatibility", {
+test_that("modularity_matrix no longer accepts a membership argument for compatibility", {
   karate <- make_graph("zachary")
-  expect_snapshot(
+  expect_snapshot(error = TRUE, {
     x <- modularity_matrix(karate, membership = rep(1, vcount(karate)))
-  )
+  })
 })
 
 test_that("cluster_louvain works", {

From 50cd9512db7a7b13ef1d8f37ae231f95f117205c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:09:38 +0200
Subject: [PATCH 13/48] feat!: bump deprecated functions in R/components.R

---
 R/components.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/components.R b/R/components.R
index fab025773b2..1c0ab7b0a12 100644
--- a/R/components.R
+++ b/R/components.R
@@ -10,7 +10,7 @@
 #' @export
 no.clusters <- function(graph, mode = c("weak", "strong")) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "no.clusters()", "count_components()")
+  lifecycle::deprecate_warn("2.0.0", "no.clusters()", "count_components()")
   count_components(graph = graph, mode = mode)
 } # nocov end
 
@@ -31,7 +31,7 @@ decompose.graph <- function(
   min.vertices = 0
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "decompose.graph()", "decompose()")
+  lifecycle::deprecate_warn("2.0.0", "decompose.graph()", "decompose()")
   decompose(
     graph = graph,
     mode = mode,
@@ -57,7 +57,7 @@ cluster.distribution <- function(
   ...
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "cluster.distribution()",
     "component_distribution()"
@@ -82,7 +82,7 @@ cluster.distribution <- function(
 #' @export
 biconnected.components <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "biconnected.components()",
     "biconnected_components()"
@@ -102,7 +102,7 @@ biconnected.components <- function(graph) {
 #' @export
 articulation.points <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "articulation.points()",
     "articulation_points()"

From 0c57a2ad7a31082e0440ab3e4f9f7349209a9260 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:10:27 +0200
Subject: [PATCH 14/48] feat!: bump deprecated functions in R/console.R

---
 R/console.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/console.R b/R/console.R
index 71defc045a7..ff898e1bfe0 100644
--- a/R/console.R
+++ b/R/console.R
@@ -11,7 +11,7 @@
 #' @export
 igraph.console <- function() {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "igraph.console()", "console()")
+  lifecycle::deprecate_warn("2.0.0", "igraph.console()", "console()")
   console()
 } # nocov end
 

From 5f5b95858360d34c5bb9192ea2b3c48f5777fd06 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:11:24 +0200
Subject: [PATCH 15/48] feat!: bump deprecated functions in R/conversion.R

---
 R/conversion.R | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/R/conversion.R b/R/conversion.R
index 230cd369bd1..0634fb46949 100644
--- a/R/conversion.R
+++ b/R/conversion.R
@@ -10,7 +10,7 @@
 #' @export
 igraph.to.graphNEL <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "igraph.to.graphNEL()", "as_graphnel()")
+  lifecycle::deprecate_warn("2.0.0", "igraph.to.graphNEL()", "as_graphnel()")
   as_graphnel(graph = graph)
 } # nocov end
 
@@ -31,7 +31,7 @@ igraph.from.graphNEL <- function(
   unlist.attrs = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "igraph.from.graphNEL()",
     "graph_from_graphnel()"
@@ -60,7 +60,7 @@ graph.adjlist <- function(
   duplicate = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.adjlist()", "graph_from_adj_list()")
+  lifecycle::deprecate_warn("2.0.0", "graph.adjlist()", "graph_from_adj_list()")
   graph_from_adj_list(adjlist = adjlist, mode = mode, duplicate = duplicate)
 } # nocov end
 
@@ -82,7 +82,7 @@ get.incidence <- function(
   sparse = FALSE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "get.incidence()",
     "as_biadjacency_matrix()"
@@ -108,7 +108,7 @@ get.incidence <- function(
 #' @export
 get.edgelist <- function(graph, names = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "get.edgelist()", "as_edgelist()")
+  lifecycle::deprecate_warn("2.0.0", "get.edgelist()", "as_edgelist()")
   as_edgelist(graph = graph, names = names)
 } # nocov end
 
@@ -124,7 +124,7 @@ get.edgelist <- function(graph, names = TRUE) {
 #' @export
 get.data.frame <- function(x, what = c("edges", "vertices", "both")) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "get.data.frame()", "as_data_frame()")
+  lifecycle::deprecate_warn("2.0.0", "get.data.frame()", "as_data_frame()")
   as_data_frame(x = x, what = what)
 } # nocov end
 
@@ -147,7 +147,7 @@ get.adjacency <- function(
   sparse = igraph_opt("sparsematrices")
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "get.adjacency()", "as_adjacency_matrix()")
+  lifecycle::deprecate_warn("2.0.0", "get.adjacency()", "as_adjacency_matrix()")
   as_adjacency_matrix(
     graph = graph,
     type = type,
@@ -175,7 +175,7 @@ get.adjlist <- function(
   multiple = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "get.adjlist()", "as_adj_list()")
+  lifecycle::deprecate_warn("2.0.0", "get.adjlist()", "as_adj_list()")
   as_adj_list(graph = graph, mode = mode, loops = loops, multiple = multiple)
 } # nocov end
 
@@ -195,7 +195,7 @@ get.adjedgelist <- function(
   loops = c("twice", "once", "ignore")
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "get.adjedgelist()", "as_adj_edge_list()")
+  lifecycle::deprecate_warn("2.0.0", "get.adjedgelist()", "as_adj_edge_list()")
   as_adj_edge_list(graph = graph, mode = mode, loops = loops)
 } # nocov end
 #   IGraph R package
@@ -232,7 +232,7 @@ get.adjacency.dense <- function(
 
   if (is.logical(loops)) {
     loops <- ifelse(loops, "once", "ignore")
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.1.0",
       "get.adjacency.dense(loops = 'must be a character')",
       details = sprintf(
@@ -412,7 +412,7 @@ as_adj <- function(
   names = TRUE,
   sparse = igraph_opt("sparsematrices")
 ) {
-  lifecycle::deprecate_soft("2.1.0", "as_adj()", "as_adjacency_matrix()")
+  lifecycle::deprecate_warn("2.1.0", "as_adj()", "as_adjacency_matrix()")
 
   as_adjacency_matrix(
     graph = graph,
@@ -1129,7 +1129,7 @@ as_biadjacency_matrix <- function(
 #' @export
 as_incidence_matrix <- function(...) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "1.6.0",
     "as_incidence_matrix()",
     "as_biadjacency_matrix()"
@@ -1367,7 +1367,7 @@ as.directed <- function(
   graph,
   mode = c("mutual", "arbitrary", "random", "acyclic")
 ) {
-  lifecycle::deprecate_soft("2.1.0", "as.directed()", "as_directed()")
+  lifecycle::deprecate_warn("2.1.0", "as.directed()", "as_directed()")
   as_directed(graph, mode = mode)
 }
 
@@ -1386,7 +1386,7 @@ as.undirected <- function(
   mode = c("collapse", "each", "mutual"),
   edge.attr.comb = igraph_opt("edge.attr.comb")
 ) {
-  lifecycle::deprecate_soft("2.1.0", "as.undirected()", "as_undirected()")
+  lifecycle::deprecate_warn("2.1.0", "as.undirected()", "as_undirected()")
   as_undirected(graph = graph, mode = mode, edge.attr.comb = edge.attr.comb)
 }
 
@@ -1402,7 +1402,7 @@ as.undirected <- function(
 #' @export
 graph.edgelist <- function(el, directed = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "graph.edgelist()",
     "graph_from_edgelist()"
@@ -1422,7 +1422,7 @@ graph.edgelist <- function(el, directed = TRUE) {
 #' @export
 graph.data.frame <- function(d, directed = TRUE, vertices = NULL) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "graph.data.frame()",
     "graph_from_data_frame()"

From e039949c52e2658080bc1a1b5f568fc71c26560c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:12:15 +0200
Subject: [PATCH 16/48] feat!: bump deprecated functions in R/decomposition.R

---
 R/decomposition.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/decomposition.R b/R/decomposition.R
index 8c8e92b570c..47df101955e 100644
--- a/R/decomposition.R
+++ b/R/decomposition.R
@@ -16,7 +16,7 @@ is.chordal <- function(
   newgraph = FALSE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.chordal()", "is_chordal()")
+  lifecycle::deprecate_warn("2.0.0", "is.chordal()", "is_chordal()")
   is_chordal(
     graph = graph,
     alpha = alpha,

From b073b21c1e55ce9cf094b8c17408031e2586a0e5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:13:13 +0200
Subject: [PATCH 17/48] feat!: bump deprecated functions in R/degseq.R

---
 R/degseq.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/degseq.R b/R/degseq.R
index 76a4401822d..918239d17dd 100644
--- a/R/degseq.R
+++ b/R/degseq.R
@@ -14,7 +14,7 @@ is.graphical.degree.sequence <- function(
   allowed.edge.types = c("simple", "loops", "multi", "all")
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "is.graphical.degree.sequence()",
     "is_graphical()"
@@ -38,7 +38,7 @@ is.graphical.degree.sequence <- function(
 #' @export
 is.degree.sequence <- function(out.deg, in.deg = NULL) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.degree.sequence()", "is_degseq()")
+  lifecycle::deprecate_warn("2.0.0", "is.degree.sequence()", "is_degseq()")
   is_degseq(out.deg = out.deg, in.deg = in.deg)
 } # nocov end
 

From 7b5946acf47e62c2911b9e1fa1d53db1bf8fae11 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:14:13 +0200
Subject: [PATCH 18/48] feat!: bump deprecated functions in R/fit.R

---
 R/fit.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/fit.R b/R/fit.R
index e0849b32a4c..4993d32bc4e 100644
--- a/R/fit.R
+++ b/R/fit.R
@@ -17,7 +17,7 @@ power.law.fit <- function(
   ...
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "power.law.fit()", "fit_power_law()")
+  lifecycle::deprecate_warn("2.0.0", "power.law.fit()", "fit_power_law()")
   fit_power_law(
     x = x,
     xmin = xmin,

From 5ec9e2d1d1d8e06fac4e1ca7fe117da3a1e0e26d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:15:11 +0200
Subject: [PATCH 19/48] feat!: bump deprecated functions in R/flow.R

---
 R/flow.R | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/R/flow.R b/R/flow.R
index 0609fce12c3..43c3f0bf35c 100644
--- a/R/flow.R
+++ b/R/flow.R
@@ -10,7 +10,7 @@
 #' @export
 vertex.disjoint.paths <- function(graph, source = NULL, target = NULL) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "vertex.disjoint.paths()",
     "vertex_disjoint_paths()"
@@ -35,7 +35,7 @@ vertex.connectivity <- function(
   checks = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "vertex.connectivity()",
     "vertex_connectivity()"
@@ -60,7 +60,7 @@ vertex.connectivity <- function(
 #' @export
 stMincuts <- function(graph, source, target, capacity = NULL) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "stMincuts()", "st_min_cuts()")
+  lifecycle::deprecate_warn("2.0.0", "stMincuts()", "st_min_cuts()")
   st_min_cuts(
     graph = graph,
     source = source,
@@ -81,7 +81,7 @@ stMincuts <- function(graph, source, target, capacity = NULL) {
 #' @export
 stCuts <- function(graph, source, target) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "stCuts()", "st_cuts()")
+  lifecycle::deprecate_warn("2.0.0", "stCuts()", "st_cuts()")
   st_cuts(graph = graph, source = source, target = target)
 } # nocov end
 
@@ -97,7 +97,7 @@ stCuts <- function(graph, source, target) {
 #' @export
 minimum.size.separators <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "minimum.size.separators()",
     "min_separators()"
@@ -117,7 +117,7 @@ minimum.size.separators <- function(graph) {
 #' @export
 minimal.st.separators <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "minimal.st.separators()",
     "min_st_separators()"
@@ -137,7 +137,7 @@ minimal.st.separators <- function(graph) {
 #' @export
 is.separator <- function(graph, candidate) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.separator()", "is_separator()")
+  lifecycle::deprecate_warn("2.0.0", "is.separator()", "is_separator()")
   is_separator(graph = graph, candidate = candidate)
 } # nocov end
 
@@ -153,7 +153,7 @@ is.separator <- function(graph, candidate) {
 #' @export
 is.minimal.separator <- function(graph, candidate) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "is.minimal.separator()",
     "is_min_separator()"
@@ -179,7 +179,7 @@ graph.mincut <- function(
   value.only = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.mincut()", "min_cut()")
+  lifecycle::deprecate_warn("2.0.0", "graph.mincut()", "min_cut()")
   min_cut(
     graph = graph,
     source = source,
@@ -201,7 +201,7 @@ graph.mincut <- function(
 #' @export
 graph.maxflow <- function(graph, source, target, capacity = NULL) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.maxflow()", "max_flow()")
+  lifecycle::deprecate_warn("2.0.0", "graph.maxflow()", "max_flow()")
   max_flow(graph = graph, source = source, target = target, capacity = capacity)
 } # nocov end
 
@@ -217,7 +217,7 @@ graph.maxflow <- function(graph, source, target, capacity = NULL) {
 #' @export
 graph.adhesion <- function(graph, checks = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.adhesion()", "adhesion()")
+  lifecycle::deprecate_warn("2.0.0", "graph.adhesion()", "adhesion()")
   adhesion(graph = graph, checks = checks)
 } # nocov end
 
@@ -238,7 +238,7 @@ edge.disjoint.paths <- function(
   checks = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "edge.disjoint.paths()",
     "edge_connectivity()"
@@ -268,7 +268,7 @@ edge.connectivity <- function(
   checks = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "edge.connectivity()",
     "edge_connectivity()"
@@ -293,7 +293,7 @@ edge.connectivity <- function(
 #' @export
 dominator.tree <- function(graph, root, mode = c("out", "in", "all", "total")) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "dominator.tree()", "dominator_tree()")
+  lifecycle::deprecate_warn("2.0.0", "dominator.tree()", "dominator_tree()")
   dominator_tree(graph = graph, root = root, mode = mode)
 } # nocov end
 #   IGraph R package

From 42d306ca4ac0f94e6d94ef7eb67168f5469ba010 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:16:03 +0200
Subject: [PATCH 20/48] feat!: bump deprecated functions in R/foreign.R

---
 R/foreign.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/foreign.R b/R/foreign.R
index ebf9280b01d..b493c1fdb83 100644
--- a/R/foreign.R
+++ b/R/foreign.R
@@ -25,7 +25,7 @@ write.graph <- function(
   ...
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "write.graph()", "write_graph()")
+  lifecycle::deprecate_warn("2.0.0", "write.graph()", "write_graph()")
   write_graph(graph = graph, file = file, format = format, ...)
 } # nocov end
 
@@ -55,7 +55,7 @@ read.graph <- function(
   ...
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "read.graph()", "read_graph()")
+  lifecycle::deprecate_warn("2.0.0", "read.graph()", "read_graph()")
   read_graph(file = file, format = format, ...)
 } # nocov end
 
@@ -81,7 +81,7 @@ graph.graphdb <- function(
   directed = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.graphdb()", "graph_from_graphdb()")
+  lifecycle::deprecate_warn("2.0.0", "graph.graphdb()", "graph_from_graphdb()")
   graph_from_graphdb(
     url = url,
     prefix = prefix,

From b3a5bcd02bbbe56879da64c170c965f6cab4a0dd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:16:56 +0200
Subject: [PATCH 21/48] feat!: bump deprecated functions in R/games.R

---
 R/games.R                   | 70 ++++++++++++++++++-------------------
 tests/testthat/test-games.R |  6 ++--
 2 files changed, 38 insertions(+), 38 deletions(-)

diff --git a/R/games.R b/R/games.R
index f37cb832403..17d42f7fd94 100644
--- a/R/games.R
+++ b/R/games.R
@@ -17,7 +17,7 @@ watts.strogatz.game <- function(
   multiple = FALSE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "watts.strogatz.game()",
     "sample_smallworld()"
@@ -52,7 +52,7 @@ static.power.law.game <- function(
   finite.size.correction = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "static.power.law.game()",
     "sample_fitness_pl()"
@@ -86,7 +86,7 @@ static.fitness.game <- function(
   multiple = FALSE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "static.fitness.game()",
     "sample_fitness()"
@@ -118,7 +118,7 @@ sbm.game <- function(
   loops = FALSE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "sbm.game()", "sample_sbm()")
+  lifecycle::deprecate_warn("2.0.0", "sbm.game()", "sample_sbm()")
   sample_sbm(
     n = n,
     pref.matrix = pref.matrix,
@@ -148,7 +148,7 @@ preference.game <- function(
   loops = FALSE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "preference.game()", "sample_pref()")
+  lifecycle::deprecate_warn("2.0.0", "preference.game()", "sample_pref()")
   sample_pref(
     nodes = nodes,
     types = types,
@@ -178,7 +178,7 @@ lastcit.game <- function(
   directed = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "lastcit.game()", "sample_last_cit()")
+  lifecycle::deprecate_warn("2.0.0", "lastcit.game()", "sample_last_cit()")
   sample_last_cit(
     n = n,
     edges = edges,
@@ -200,7 +200,7 @@ lastcit.game <- function(
 #' @export
 k.regular.game <- function(no.of.nodes, k, directed = FALSE, multiple = FALSE) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "k.regular.game()", "sample_k_regular()")
+  lifecycle::deprecate_warn("2.0.0", "k.regular.game()", "sample_k_regular()")
   sample_k_regular(
     no.of.nodes = no.of.nodes,
     k = k,
@@ -226,7 +226,7 @@ interconnected.islands.game <- function(
   n.inter
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "interconnected.islands.game()",
     "sample_islands()"
@@ -251,7 +251,7 @@ interconnected.islands.game <- function(
 #' @export
 grg.game <- function(nodes, radius, torus = FALSE, coords = FALSE) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "grg.game()", "sample_grg()")
+  lifecycle::deprecate_warn("2.0.0", "grg.game()", "sample_grg()")
   sample_grg(nodes = nodes, radius = radius, torus = torus, coords = coords)
 } # nocov end
 
@@ -267,7 +267,7 @@ grg.game <- function(nodes, radius, torus = FALSE, coords = FALSE) {
 #' @export
 growing.random.game <- function(n, m = 1, directed = TRUE, citation = FALSE) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "growing.random.game()",
     "sample_growing()"
@@ -293,7 +293,7 @@ forest.fire.game <- function(
   directed = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "forest.fire.game()",
     "sample_forestfire()"
@@ -326,7 +326,7 @@ establishment.game <- function(
   directed = FALSE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "establishment.game()", "sample_traits()")
+  lifecycle::deprecate_warn("2.0.0", "establishment.game()", "sample_traits()")
   sample_traits(
     nodes = nodes,
     types = types,
@@ -353,7 +353,7 @@ degree.sequence.game <- function(
   method = c("simple", "vl", "simple.no.multiple", "simple.no.multiple.uniform")
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "degree.sequence.game()",
     "sample_degseq()"
@@ -377,7 +377,7 @@ connect.neighborhood <- function(
   mode = c("all", "out", "in", "total")
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "connect.neighborhood()", "connect()")
+  lifecycle::deprecate_warn("2.0.0", "connect.neighborhood()", "connect()")
   connect(graph = graph, order = order, mode = mode)
 } # nocov end
 
@@ -400,7 +400,7 @@ citing.cited.type.game <- function(
   attr = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "citing.cited.type.game()",
     "sample_cit_cit_types()"
@@ -434,7 +434,7 @@ cited.type.game <- function(
   attr = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "cited.type.game()", "sample_cit_types()")
+  lifecycle::deprecate_warn("2.0.0", "cited.type.game()", "sample_cit_types()")
   sample_cit_types(
     n = n,
     edges = edges,
@@ -464,7 +464,7 @@ callaway.traits.game <- function(
   directed = FALSE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "callaway.traits.game()",
     "sample_traits_callaway()"
@@ -499,7 +499,7 @@ bipartite.random.game <- function(
   mode = c("out", "in", "all")
 ) {
   # nocov start
-  lifecycle::deprecate_warn(
+  lifecycle::deprecate_stop(
     "2.0.0",
     "bipartite.random.game()",
     details = "Use sample_bipartite_gnp() or sample_bipartite_gnm()"
@@ -538,7 +538,7 @@ barabasi.game <- function(
   start.graph = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "barabasi.game()", "sample_pa()")
+  lifecycle::deprecate_warn("2.0.0", "barabasi.game()", "sample_pa()")
   sample_pa(
     n = n,
     power = power,
@@ -576,7 +576,7 @@ ba.game <- function(
   start.graph = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "ba.game()", "sample_pa()")
+  lifecycle::deprecate_warn("2.0.0", "ba.game()", "sample_pa()")
   sample_pa(
     n = n,
     power = power,
@@ -609,7 +609,7 @@ asymmetric.preference.game <- function(
   loops = FALSE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "asymmetric.preference.game()",
     "sample_asym_pref()"
@@ -650,7 +650,7 @@ aging.barabasi.game <- function(
   time.window = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "aging.barabasi.game()", "sample_pa_age()")
+  lifecycle::deprecate_warn("2.0.0", "aging.barabasi.game()", "sample_pa_age()")
   sample_pa_age(
     n = n,
     pa.exp = pa.exp,
@@ -696,7 +696,7 @@ aging.ba.game <- function(
   time.window = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "aging.ba.game()", "sample_pa_age()")
+  lifecycle::deprecate_warn("2.0.0", "aging.ba.game()", "sample_pa_age()")
   sample_pa_age(
     n = n,
     pa.exp = pa.exp,
@@ -742,7 +742,7 @@ aging.prefatt.game <- function(
   time.window = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "aging.prefatt.game()", "sample_pa_age()")
+  lifecycle::deprecate_warn("2.0.0", "aging.prefatt.game()", "sample_pa_age()")
   sample_pa_age(
     n = n,
     pa.exp = pa.exp,
@@ -1158,10 +1158,10 @@ erdos.renyi.game <- function(
   type <- igraph_match_arg(type)
 
   if (type == "gnp") {
-    lifecycle::deprecate_soft("0.8.0", "erdos.renyi.game()", "sample_gnp()")
+    lifecycle::deprecate_warn("0.8.0", "erdos.renyi.game()", "sample_gnp()")
     sample_gnp(n = n, p = p.or.m, directed = directed, loops = loops)
   } else if (type == "gnm") {
-    lifecycle::deprecate_soft("0.8.0", "erdos.renyi.game()", "sample_gnm()")
+    lifecycle::deprecate_warn("0.8.0", "erdos.renyi.game()", "sample_gnm()")
     sample_gnm(n = n, m = p.or.m, directed = directed, loops = loops)
   }
 }
@@ -1178,10 +1178,10 @@ random.graph.game <- function(
   type <- igraph_match_arg(type)
 
   if (type == "gnp") {
-    lifecycle::deprecate_soft("0.8.0", "random.graph.game()", "sample_gnp()")
+    lifecycle::deprecate_warn("0.8.0", "random.graph.game()", "sample_gnp()")
     sample_gnp(n = n, p = p.or.m, directed = directed, loops = loops)
   } else if (type == "gnm") {
-    lifecycle::deprecate_soft("0.8.0", "random.graph.game()", "sample_gnm()")
+    lifecycle::deprecate_warn("0.8.0", "random.graph.game()", "sample_gnm()")
     sample_gnm(n = n, m = p.or.m, directed = directed, loops = loops)
   }
 }
@@ -1388,7 +1388,7 @@ sample_degseq <- function(
   )
 
   if (method == "simple") {
-    lifecycle::deprecate_warn(
+    lifecycle::deprecate_stop(
       "2.1.0",
       "sample_degseq(method = 'must be configuration instead of simple')"
     )
@@ -1396,7 +1396,7 @@ sample_degseq <- function(
   }
 
   if (method == "simple.no.multiple") {
-    lifecycle::deprecate_warn(
+    lifecycle::deprecate_stop(
       "2.1.0",
       "sample_degseq(method = 'must be fast.heur.simple instead of simple.no.multiple')"
     )
@@ -1404,7 +1404,7 @@ sample_degseq <- function(
   }
 
   if (method == "simple.no.multiple.uniform") {
-    lifecycle::deprecate_warn(
+    lifecycle::deprecate_stop(
       "2.1.0",
       "sample_degseq(method = 'must be configuration.simple instead of simple.no.multiple.uniform')"
     )
@@ -2474,14 +2474,14 @@ sample_bipartite <- function(
   mode <- igraph_match_arg(mode)
 
   if (type == "gnp") {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.2.0",
       "sample_bipartite()",
       "sample_bipartite_gnp()"
     )
     sample_bipartite_gnp(n1, n2, p, directed = directed, mode = mode)
   } else if (type == "gnm") {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.2.0",
       "sample_bipartite()",
       "sample_bipartite_gnm()"
@@ -2497,14 +2497,14 @@ sample_bipartite <- function(
 #' @export
 bipartite <- function(..., type = NULL) {
   if (is.null(type) || type == "gnp") {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.1.3",
       "bipartite()",
       "bipartite_gnp()"
     )
     bipartite_gnp(...)
   } else if (type == "gnm") {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.1.3",
       "bipartite()",
       "bipartite_gnm()"
diff --git a/tests/testthat/test-games.R b/tests/testthat/test-games.R
index 46b4c1e7bb5..8f68f2842b0 100644
--- a/tests/testthat/test-games.R
+++ b/tests/testthat/test-games.R
@@ -155,17 +155,17 @@ test_that("sample_degseq supports the sample_(...) syntax", {
 test_that("sample_degseq works() -- old method names", {
   withr::local_options("lifecycle_verbosity" = "warning")
 
-  expect_warning(
+  expect_error(
     sample_degseq(c(1, 1, 2, 2, 2), method = "simple"),
     "must be"
   )
 
-  expect_warning(
+  expect_error(
     sample_degseq(c(1, 1, 2, 2, 2), method = "simple.no.multiple"),
     "must be"
   )
 
-  expect_warning(
+  expect_error(
     sample_degseq(c(1, 1, 2, 2, 2), method = "simple.no.multiple.uniform"),
     "must be"
   )

From f0e458212d0a356f71ad91b7db810282ecd83452 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:17:49 +0200
Subject: [PATCH 22/48] feat!: bump deprecated functions in R/glet.R

---
 R/glet.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/glet.R b/R/glet.R
index 252b227cfe8..8122a59f55f 100644
--- a/R/glet.R
+++ b/R/glet.R
@@ -16,7 +16,7 @@ graphlets.project <- function(
   Mu = rep(1, length(cliques))
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graphlets.project()", "graphlet_proj()")
+  lifecycle::deprecate_warn("2.0.0", "graphlets.project()", "graphlet_proj()")
   graphlet_proj(
     graph = graph,
     weights = weights,
@@ -38,7 +38,7 @@ graphlets.project <- function(
 #' @export
 graphlets.candidate.basis <- function(graph, weights = NULL) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "graphlets.candidate.basis()",
     "graphlet_basis()"

From 06f99ba8b2452fa6e507fe04d89731dd05a4401d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:18:43 +0200
Subject: [PATCH 23/48] feat!: bump deprecated functions in R/hrg.R

---
 R/hrg.R | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/R/hrg.R b/R/hrg.R
index b8eb3c4a860..83f65d16c7d 100644
--- a/R/hrg.R
+++ b/R/hrg.R
@@ -16,7 +16,7 @@ hrg.predict <- function(
   num.bins = 25
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "hrg.predict()", "predict_edges()")
+  lifecycle::deprecate_warn("2.0.0", "hrg.predict()", "predict_edges()")
   predict_edges(
     graph = graph,
     hrg = hrg,
@@ -38,7 +38,7 @@ hrg.predict <- function(
 #' @export
 hrg.fit <- function(graph, hrg = NULL, start = FALSE, steps = 0) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "hrg.fit()", "fit_hrg()")
+  lifecycle::deprecate_warn("2.0.0", "hrg.fit()", "fit_hrg()")
   fit_hrg(graph = graph, hrg = hrg, start = start, steps = steps)
 } # nocov end
 
@@ -54,7 +54,7 @@ hrg.fit <- function(graph, hrg = NULL, start = FALSE, steps = 0) {
 #' @export
 hrg.game <- function(hrg) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "hrg.game()", "sample_hrg()")
+  lifecycle::deprecate_warn("2.0.0", "hrg.game()", "sample_hrg()")
   sample_hrg(hrg = hrg)
 } # nocov end
 
@@ -70,7 +70,7 @@ hrg.game <- function(hrg) {
 #' @export
 hrg.dendrogram <- function(hrg) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "hrg.dendrogram()", "hrg_tree()")
+  lifecycle::deprecate_warn("2.0.0", "hrg.dendrogram()", "hrg_tree()")
   hrg_tree(hrg = hrg)
 } # nocov end
 
@@ -86,7 +86,7 @@ hrg.dendrogram <- function(hrg) {
 #' @export
 hrg.create <- function(graph, prob) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "hrg.create()", "hrg()")
+  lifecycle::deprecate_warn("2.0.0", "hrg.create()", "hrg()")
   hrg(graph = graph, prob = prob)
 } # nocov end
 
@@ -107,7 +107,7 @@ hrg.consensus <- function(
   num.samples = 10000
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "hrg.consensus()", "consensus_tree()")
+  lifecycle::deprecate_warn("2.0.0", "hrg.consensus()", "consensus_tree()")
   consensus_tree(
     graph = graph,
     hrg = hrg,

From ad0fc888105b08bd85caf3ad05639ac6c3b0335d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:19:30 +0200
Subject: [PATCH 24/48] feat!: bump deprecated functions in R/incidence.R

---
 R/incidence.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/incidence.R b/R/incidence.R
index 3937ad025af..886aa1a9f8c 100644
--- a/R/incidence.R
+++ b/R/incidence.R
@@ -17,7 +17,7 @@ graph.incidence <- function(
   add.names = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "graph.incidence()",
     "graph_from_biadjacency_matrix()"
@@ -271,7 +271,7 @@ graph_from_biadjacency_matrix <- function(
 #' @export
 from_incidence_matrix <- function(...) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "1.6.0",
     "graph_from_incidence_matrix()",
     "graph_from_biadjacency_matrix()"
@@ -294,7 +294,7 @@ from_incidence_matrix <- function(...) {
 #' @export
 graph_from_incidence_matrix <- function(...) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "1.6.0",
     "graph_from_incidence_matrix()",
     "graph_from_biadjacency_matrix()"

From c37512d0208ebaaef5031827aea44e7144ae8fac Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:20:15 +0200
Subject: [PATCH 25/48] feat!: bump deprecated functions in R/interface.R

---
 R/interface.R                   | 16 ++++++++--------
 tests/testthat/test-interface.R |  2 +-
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/R/interface.R b/R/interface.R
index 7533cfb8285..9cd977cb47c 100644
--- a/R/interface.R
+++ b/R/interface.R
@@ -10,7 +10,7 @@
 #' @export
 is.directed <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.directed()", "is_directed()")
+  lifecycle::deprecate_warn("2.0.0", "is.directed()", "is_directed()")
   is_directed(graph = graph)
 } # nocov end
 
@@ -26,7 +26,7 @@ is.directed <- function(graph) {
 #' @export
 delete.vertices <- function(graph, v) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "delete.vertices()", "delete_vertices()")
+  lifecycle::deprecate_warn("2.0.0", "delete.vertices()", "delete_vertices()")
   delete_vertices(graph = graph, v = v)
 } # nocov end
 
@@ -42,7 +42,7 @@ delete.vertices <- function(graph, v) {
 #' @export
 delete.edges <- function(graph, edges) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "delete.edges()", "delete_edges()")
+  lifecycle::deprecate_warn("2.0.0", "delete.edges()", "delete_edges()")
   delete_edges(graph = graph, edges = edges)
 } # nocov end
 
@@ -58,7 +58,7 @@ delete.edges <- function(graph, edges) {
 #' @export
 add.vertices <- function(graph, nv, ..., attr = list()) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "add.vertices()", "add_vertices()")
+  lifecycle::deprecate_warn("2.0.0", "add.vertices()", "add_vertices()")
   add_vertices(graph = graph, nv = nv, attr = attr, ...)
 } # nocov end
 
@@ -74,7 +74,7 @@ add.vertices <- function(graph, nv, ..., attr = list()) {
 #' @export
 add.edges <- function(graph, edges, ..., attr = list()) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "add.edges()", "add_edges()")
+  lifecycle::deprecate_warn("2.0.0", "add.edges()", "add_edges()")
   add_edges(graph = graph, edges = edges, attr = attr, ...)
 } # nocov end
 #   IGraph R package
@@ -474,7 +474,7 @@ el_to_vec <- function(x, call = rlang::caller_env()) {
         "get_edge_ids(vp = 'is not allowed to be a 2 times 2 matrix')"
       )
     } else if (nrow == 2) {
-      lifecycle::deprecate_warn(
+      lifecycle::deprecate_stop(
         "2.1.5",
         "get_edge_ids(vp = 'supplied as a matrix should be a n times 2 matrix, not 2 times n')",
         details = "either transpose the matrix with t() or convert it to a data.frame with two columns."
@@ -584,9 +584,9 @@ get.edge.ids <- function(
       lifecycle::deprecate_stop("2.0.0", "get.edge.ids(multi = )")
     }
 
-    lifecycle::deprecate_soft("2.0.0", "get.edge.ids(multi = )")
+    lifecycle::deprecate_warn("2.0.0", "get.edge.ids(multi = )")
   }
-  lifecycle::deprecate_soft("2.1.0", "get.edge.ids()", "get_edge_ids()")
+  lifecycle::deprecate_warn("2.1.0", "get.edge.ids()", "get_edge_ids()")
   get_edge_ids(graph = graph, vp = vp, directed = directed, error = error)
 }
 
diff --git a/tests/testthat/test-interface.R b/tests/testthat/test-interface.R
index 0e73189645e..9be76e65bc9 100644
--- a/tests/testthat/test-interface.R
+++ b/tests/testthat/test-interface.R
@@ -220,7 +220,7 @@ test_that("get_edge_id() errors correctly for wrong matrices", {
   mat <- matrix(c(1, 2, 3, 4), nrow = 2, ncol = 2)
   lifecycle::expect_defunct(get_edge_ids(g, mat))
   mat <- matrix(c(1, 2, 1, 3, 1, 4), nrow = 2, ncol = 3)
-  lifecycle::expect_deprecated(get_edge_ids(g, mat))
+  lifecycle::expect_defunct(get_edge_ids(g, mat))
 })
 
 test_that("invalidate_cache works", {

From 2f2d008be8d64962c6274de8127513305af49521 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:21:10 +0200
Subject: [PATCH 26/48] feat!: bump deprecated functions in R/layout.R

---
 NAMESPACE             |  1 -
 R/layout.R            | 63 +++++++++++++++++--------------------------
 man/layout.grid.3d.Rd | 26 ------------------
 3 files changed, 24 insertions(+), 66 deletions(-)
 delete mode 100644 man/layout.grid.3d.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 50337bd1418..9a426a10c28 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -609,7 +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)
diff --git a/R/layout.R b/R/layout.R
index 1f14bbe0fb6..cd1166e1b5b 100644
--- a/R/layout.R
+++ b/R/layout.R
@@ -10,7 +10,7 @@
 #' @export
 piecewise.layout <- function(graph, layout = layout_with_kk, ...) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "piecewise.layout()",
     "layout_components()"
@@ -38,7 +38,7 @@ layout.sugiyama <- function(
   attributes = c("default", "all", "none")
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "layout.sugiyama()",
     "layout_with_sugiyama()"
@@ -66,7 +66,7 @@ layout.sugiyama <- function(
 #' @export
 layout.star <- function(graph, center = V(graph)[1], order = NULL) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "layout.star()", "layout_as_star()")
+  lifecycle::deprecate_warn("2.0.0", "layout.star()", "layout_as_star()")
   layout_as_star(graph = graph, center = center, order = order)
 } # nocov end
 
@@ -90,7 +90,7 @@ layout.norm <- function(
   zmax = 1
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "layout.norm()", "norm_coords()")
+  lifecycle::deprecate_warn("2.0.0", "layout.norm()", "norm_coords()")
   norm_coords(
     layout = layout,
     xmin = xmin,
@@ -114,7 +114,7 @@ layout.norm <- function(
 #' @export
 layout.merge <- function(graphs, layouts, method = "dla") {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "layout.merge()", "merge_coords()")
+  lifecycle::deprecate_warn("2.0.0", "layout.merge()", "merge_coords()")
   merge_coords(graphs = graphs, layouts = layouts, method = method)
 } # nocov end
 
@@ -135,7 +135,7 @@ layout.mds <- function(
   options = arpack_defaults()
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "layout.mds()", "layout_with_mds()")
+  lifecycle::deprecate_warn("2.0.0", "layout.mds()", "layout_with_mds()")
   layout_with_mds(graph = graph, dist = dist, dim = dim, options = options)
 } # nocov end
 
@@ -151,7 +151,7 @@ layout.mds <- function(
 #' @export
 layout.grid <- function(graph, width = 0, height = 0, dim = 2) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "layout.grid()", "layout_on_grid()")
+  lifecycle::deprecate_warn("2.0.0", "layout.grid()", "layout_on_grid()")
   layout_on_grid(graph = graph, width = width, height = height, dim = dim)
 } # nocov end
 
@@ -176,7 +176,7 @@ layout.graphopt <- function(
   max.sa.movement = 5
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "layout.graphopt()",
     "layout_with_graphopt()"
@@ -212,7 +212,7 @@ layout.gem <- function(
   temp.init = sqrt(max(vcount(graph), 1))
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "layout.gem()", "layout_with_gem()")
+  lifecycle::deprecate_warn("2.0.0", "layout.gem()", "layout_with_gem()")
   layout_with_gem(
     graph = graph,
     coords = coords,
@@ -246,7 +246,7 @@ layout.davidson.harel <- function(
   weight.node.edge.dist = 0.2 * (1 - edge_density(graph))
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "layout.davidson.harel()",
     "layout_with_dh()"
@@ -283,7 +283,7 @@ layout.bipartite <- function(
   maxiter = 100
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "layout.bipartite()",
     "layout_as_bipartite()"
@@ -309,7 +309,7 @@ layout.bipartite <- function(
 #' @export
 layout.auto <- function(graph, dim = 2, ...) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "layout.auto()", "layout_nicely()")
+  lifecycle::deprecate_warn("2.0.0", "layout.auto()", "layout_nicely()")
   layout_nicely(graph = graph, dim = dim, ...)
 } # nocov end
 
@@ -890,7 +890,7 @@ as_tree <- function(...) layout_spec(layout_as_tree, ...)
 #' @keywords internal
 #' @export
 layout.reingold.tilford <- function(..., params = list()) {
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.1.0",
     "layout.reingold.tilford()",
     "layout_as_tree()"
@@ -955,7 +955,7 @@ in_circle <- function(...) layout_spec(layout_in_circle, ...)
 #' @keywords internal
 #' @export
 layout.circle <- function(..., params = list()) {
-  lifecycle::deprecate_soft("2.1.0", "layout.circle()", "layout_in_circle()")
+  lifecycle::deprecate_warn("2.1.0", "layout.circle()", "layout_in_circle()")
   do_call(layout_in_circle, .args = c(list(...), params))
 }
 
@@ -1144,21 +1144,6 @@ layout_on_grid <- function(graph, width = 0, height = 0, dim = 2) {
 #' @param ... Passed to `layout_on_grid()`.
 #' @export
 on_grid <- function(...) layout_spec(layout_on_grid, ...)
-
-
-#' Simple grid layout
-#' @description
-#' `r lifecycle::badge("deprecated")`
-#'
-#' Use [layout_on_grid()].
-#' @inheritParams layout_on_grid
-#' @export
-#' @export
-#' @keywords internal
-layout.grid.3d <- function(graph, width = 0, height = 0) {
-  lifecycle::deprecate_stop("2.1.0", "layout.grid.3d()", "layout_on_grid()")
-}
-
 ## ----------------------------------------------------------------
 
 #' Graph layout with vertices on the surface of a sphere
@@ -1203,7 +1188,7 @@ on_sphere <- function(...) layout_spec(layout_on_sphere, ...)
 #' @keywords internal
 #' @export
 layout.sphere <- function(..., params = list()) {
-  lifecycle::deprecate_soft("2.1.0", "layout.sphere()", "layout_on_sphere()")
+  lifecycle::deprecate_warn("2.1.0", "layout.sphere()", "layout_on_sphere()")
   do_call(layout_on_sphere, .args = c(list(...), params))
 }
 
@@ -1258,7 +1243,7 @@ randomly <- function(...) layout_spec(layout_randomly, ...)
 #' @keywords internal
 #' @export
 layout.random <- function(..., params = list()) {
-  lifecycle::deprecate_soft("2.1.0", "layout.random()", "layout_randomly()")
+  lifecycle::deprecate_warn("2.1.0", "layout.random()", "layout_randomly()")
   do_call(layout_randomly, .args = c(list(...), params))
 }
 
@@ -1624,7 +1609,7 @@ with_fr <- function(...) layout_spec(layout_with_fr, ...)
 #' @keywords internal
 #' @export
 layout.fruchterman.reingold <- function(..., params = list()) {
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.1.0",
     "layout.fruchterman.reingold()",
     "layout_with_fr()"
@@ -1982,7 +1967,7 @@ with_kk <- function(...) layout_spec(layout_with_kk, ...)
 #' @keywords internal
 #' @export
 layout.kamada.kawai <- function(..., params = list()) {
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.1.0",
     "layout.kamada.kawai()",
     "layout_with_kk()"
@@ -2068,7 +2053,7 @@ with_lgl <- function(...) layout_spec(layout_with_lgl, ...)
 #' @keywords internal
 #' @export
 layout.lgl <- function(..., params = list()) {
-  lifecycle::deprecate_soft("2.1.0", "layout.lgl()", "layout_with_lgl()")
+  lifecycle::deprecate_warn("2.1.0", "layout.lgl()", "layout_with_lgl()")
   do_call(layout_with_lgl, .args = c(list(...), params))
 }
 
@@ -2124,7 +2109,7 @@ layout_with_mds <- function(
   options = arpack_defaults()
 ) {
   if (is.function(options)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       "layout_with_mds(options = 'must be a list')",
       details = c(
@@ -2659,7 +2644,7 @@ layout_components <- function(graph, layout = layout_with_kk, ...) {
 #' @export
 #' @keywords internal
 layout.spring <- function(graph, ...) {
-  lifecycle::deprecate_warn("2.1.0", "layout.spring()", "layout_with_fr()")
+  lifecycle::deprecate_stop("2.1.0", "layout.spring()", "layout_with_fr()")
   layout_with_fr(graph)
 }
 
@@ -2677,7 +2662,7 @@ layout.spring <- function(graph, ...) {
 #' @keywords internal
 #' @export
 layout.svd <- function(graph, ...) {
-  lifecycle::deprecate_warn("2.1.0", "layout.svd()", "layout_with_fr()")
+  lifecycle::deprecate_stop("2.1.0", "layout.svd()", "layout_with_fr()")
   layout_with_fr(graph)
 }
 
@@ -2696,7 +2681,7 @@ layout.svd <- function(graph, ...) {
 #' @keywords internal
 #' @export
 layout.fruchterman.reingold.grid <- function(graph, ...) {
-  lifecycle::deprecate_warn(
+  lifecycle::deprecate_stop(
     "2.1.0",
     "layout.fruchterman.reingold.grid()",
     "layout_with_fr()"
@@ -2723,7 +2708,7 @@ layout.drl <- function(
   dim = 2
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "layout.drl()", "layout_with_drl()")
+  lifecycle::deprecate_warn("2.0.0", "layout.drl()", "layout_with_drl()")
   layout_with_drl(
     graph = graph,
     use.seed = use.seed,
diff --git a/man/layout.grid.3d.Rd b/man/layout.grid.3d.Rd
deleted file mode 100644
index e61f36a8654..00000000000
--- a/man/layout.grid.3d.Rd
+++ /dev/null
@@ -1,26 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/layout.R
-\name{layout.grid.3d}
-\alias{layout.grid.3d}
-\title{Simple grid layout}
-\usage{
-layout.grid.3d(graph, width = 0, height = 0)
-}
-\arguments{
-\item{graph}{The input graph.}
-
-\item{width}{The number of vertices in a single row of the grid. If this is
-zero or negative, then for 2d layouts the width of the grid will be the
-square root of the number of vertices in the graph, rounded up to the next
-integer. Similarly, it will be the cube root for 3d layouts.}
-
-\item{height}{The number of vertices in a single column of the grid, for
-three dimensional layouts. If this is zero or negative, then it is
-determinted automatically.}
-}
-\description{
-\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}
-
-Use \code{\link[=layout_on_grid]{layout_on_grid()}}.
-}
-\keyword{internal}

From 33f52eb732e1c0ad437392f8afc160b33779afc0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:21:53 +0200
Subject: [PATCH 27/48] feat!: bump deprecated functions in R/make.R

---
 R/make.R | 42 +++++++++++++++++++++---------------------
 1 file changed, 21 insertions(+), 21 deletions(-)

diff --git a/R/make.R b/R/make.R
index ebb264bed6f..9301e1552f1 100644
--- a/R/make.R
+++ b/R/make.R
@@ -18,7 +18,7 @@ graph <- function(
   simplify = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph()", "make_graph()")
+  lifecycle::deprecate_warn("2.1.0", "graph()", "make_graph()")
   if (inherits(edges, "formula")) {
     if (!missing(n)) {
       cli::cli_abort("{.arg n} should not be given for graph literals")
@@ -143,7 +143,7 @@ graph.famous <- function(
   simplify = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph.famous()", "make_graph()")
+  lifecycle::deprecate_warn("2.1.0", "graph.famous()", "make_graph()")
   if (inherits(edges, "formula")) {
     if (!missing(n)) {
       cli::cli_abort("{.arg n} should not be given for graph literals")
@@ -260,7 +260,7 @@ graph.famous <- function(
 #' @export
 line.graph <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "line.graph()", "make_line_graph()")
+  lifecycle::deprecate_warn("2.1.0", "line.graph()", "make_line_graph()")
   ensure_igraph(graph)
 
   res <- linegraph_impl(
@@ -284,7 +284,7 @@ line.graph <- function(graph) {
 #' @export
 graph.ring <- function(n, directed = FALSE, mutual = FALSE, circular = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph.ring()", "make_ring()")
+  lifecycle::deprecate_warn("2.1.0", "graph.ring()", "make_ring()")
   res <- ring_impl(
     n,
     directed,
@@ -311,7 +311,7 @@ graph.ring <- function(n, directed = FALSE, mutual = FALSE, circular = TRUE) {
 #' @export
 graph.tree <- function(n, children = 2, mode = c("out", "in", "undirected")) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph.tree()", "make_tree()")
+  lifecycle::deprecate_warn("2.1.0", "graph.tree()", "make_tree()")
   mode <- igraph_match_arg(mode)
 
   res <- kary_tree_impl(
@@ -343,7 +343,7 @@ graph.star <- function(
   center = 1
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph.star()", "make_star()")
+  lifecycle::deprecate_warn("2.1.0", "graph.star()", "make_star()")
   mode <- igraph_match_arg(mode)
 
   res <- star_impl(
@@ -371,7 +371,7 @@ graph.star <- function(
 #' @export
 graph.lcf <- function(n, shifts, repeats = 1) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph.lcf()", "graph_from_lcf()")
+  lifecycle::deprecate_warn("2.1.0", "graph.lcf()", "graph_from_lcf()")
   # Use the _impl function
   lcf_vector_impl(
     n = n,
@@ -401,14 +401,14 @@ graph.lattice <- function(
   circular = deprecated()
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph.lattice()", "make_lattice()")
+  lifecycle::deprecate_warn("2.1.0", "graph.lattice()", "make_lattice()")
   if (is.numeric(length) && length != floor(length)) {
     cli::cli_warn("{.arg length} was rounded to the nearest integer.")
     length <- round(length)
   }
 
   if (lifecycle::is_present(circular)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.0.3",
       "graph.lattice(circular = 'use periodic argument instead')",
       details = c("`circular` is now deprecated, use `periodic` instead.")
@@ -459,7 +459,7 @@ graph.lattice <- function(
 #' @export
 graph.kautz <- function(m, n) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph.kautz()", "make_kautz_graph()")
+  lifecycle::deprecate_warn("2.1.0", "graph.kautz()", "make_kautz_graph()")
   res <- kautz_impl(
     m = m,
     n = n
@@ -484,7 +484,7 @@ graph.kautz <- function(m, n) {
 #' @export
 graph.full.citation <- function(n, directed = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.1.0",
     "graph.full.citation()",
     "make_full_citation_graph()"
@@ -516,7 +516,7 @@ graph.full.bipartite <- function(
   mode = c("all", "out", "in")
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.1.0",
     "graph.full.bipartite()",
     "make_full_bipartite_graph()"
@@ -559,7 +559,7 @@ graph.full.bipartite <- function(
 #' @export
 graph.full <- function(n, directed = FALSE, loops = FALSE) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph.full()", "make_full_graph()")
+  lifecycle::deprecate_warn("2.1.0", "graph.full()", "make_full_graph()")
   res <- full_impl(
     n,
     directed,
@@ -584,7 +584,7 @@ graph.full <- function(n, directed = FALSE, loops = FALSE) {
 #' @export
 graph.formula <- function(..., simplify = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph.formula()", "graph_from_literal()")
+  lifecycle::deprecate_warn("2.1.0", "graph.formula()", "graph_from_literal()")
   mf <- as.list(match.call())[-1]
   graph_from_literal_i(mf)
 } # nocov end
@@ -601,7 +601,7 @@ graph.formula <- function(..., simplify = TRUE) {
 #' @export
 graph.extended.chordal.ring <- function(n, w, directed = FALSE) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.1.0",
     "graph.extended.chordal.ring()",
     "make_chordal_ring()"
@@ -630,7 +630,7 @@ graph.extended.chordal.ring <- function(n, w, directed = FALSE) {
 #' @export
 graph.empty <- function(n = 0, directed = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph.empty()", "make_empty_graph()")
+  lifecycle::deprecate_warn("2.1.0", "graph.empty()", "make_empty_graph()")
   # Function call
   res <- empty_impl(
     n = n,
@@ -652,7 +652,7 @@ graph.empty <- function(n = 0, directed = TRUE) {
 #' @export
 graph.de.bruijn <- function(m, n) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.1.0",
     "graph.de.bruijn()",
     "make_de_bruijn_graph()"
@@ -681,7 +681,7 @@ graph.de.bruijn <- function(m, n) {
 #' @export
 graph.bipartite <- function(types, edges, directed = FALSE) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.1.0",
     "graph.bipartite()",
     "make_bipartite_graph()"
@@ -732,7 +732,7 @@ graph.bipartite <- function(types, edges, directed = FALSE) {
 #' @export
 graph.atlas <- function(n) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph.atlas()", "graph_from_atlas()")
+  lifecycle::deprecate_warn("2.1.0", "graph.atlas()", "graph_from_atlas()")
   res <- atlas_impl(
     number = n
   )
@@ -1023,7 +1023,7 @@ sample_ <- function(...) {
 #' graph_(cbind(1:5, 2:6), from_edgelist(directed = FALSE))
 #' graph_(cbind(1:5, 2:6), from_edgelist(), directed = FALSE)
 graph_ <- function(...) {
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.1.0",
     "graph_()",
     details = c(
@@ -1957,7 +1957,7 @@ make_lattice <- function(
   circular = deprecated()
 ) {
   if (lifecycle::is_present(circular)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.0.3",
       "make_lattice(circular = 'use periodic argument instead')",
       details = c("`circular` is now deprecated, use `periodic` instead.")

From 8d6f397329030beedadb04db747df7b5bdc5039b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:21:53 +0200
Subject: [PATCH 28/48] chore: update NEWS.md for lifecycle bumps

!NEWS
---
 NEWS.md | 298 ++++++++++++++++++++++++++++++++++++++++++++++++--------
 1 file changed, 257 insertions(+), 41 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index fdb48b31656..cd923355615 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,48 +1,264 @@
 <!-- NEWS.md is maintained by https://fledge.cynkra.com, contributors should not edit this file -->
 
-# igraph 2.3.1.9003
-
-- Ci: Unify fledge.yaml across cynkratemplate and fledge (#86).
-
-
-# igraph 2.3.1.9002
-
-## Chore
-
-- Add ccache to `.gitignore` and `.Rbuildignore`.
-
-## Continuous integration
-
-- Create snapshot update PR against correct branch.
-
-- Add reference to `/apply-patch` workflow in commit message.
-
-- Clarify rationale for not deploying on schedule.
-
-- Really deploy pkgdown only on push.
-
-- Disable vendoring workflow to avoid noise.
-
-- Only run fledge on pushes to main.
-
-- Tweak fledge workflow and ccache action.
-
-- Cosmetics.
-
-- Bump action versions.
-
-- Install clang-format-21.
-
-- Align fledge workflow.
-
-- Harmonize.
-
-## Uncategorized
-
-- Merge branch 'krlmlr-main'.
+# igraph 2.3.1.9001
 
+## Deprecated and defunct
+
+- `graph()` is now deprecated with a warning instead of a message.
+- `graph.famous()` is now deprecated with a warning instead of a message.
+- `line.graph()` is now deprecated with a warning instead of a message.
+- `graph.ring()` is now deprecated with a warning instead of a message.
+- `graph.tree()` is now deprecated with a warning instead of a message.
+- `graph.star()` is now deprecated with a warning instead of a message.
+- `graph.lcf()` is now deprecated with a warning instead of a message.
+- `graph.lattice()` is now deprecated with a warning instead of a message.
+- `graph.lattice()` is now deprecated with a warning instead of a message.
+- `graph.kautz()` is now deprecated with a warning instead of a message.
+- `graph.full.citation()` is now deprecated with a warning instead of a message.
+- `graph.full.bipartite()` is now deprecated with a warning instead of a message.
+- `graph.full()` is now deprecated with a warning instead of a message.
+- `graph.formula()` is now deprecated with a warning instead of a message.
+- `graph.extended.chordal.ring()` is now deprecated with a warning instead of a message.
+- `graph.empty()` is now deprecated with a warning instead of a message.
+- `graph.de.bruijn()` is now deprecated with a warning instead of a message.
+- `graph.bipartite()` is now deprecated with a warning instead of a message.
+- `graph.atlas()` is now deprecated with a warning instead of a message.
+- `graph_()` is now deprecated with a warning instead of a message.
+- `make_lattice()` is now deprecated with a warning instead of a message.
+- `layout.grid.3d()` has been removed.
+- `piecewise.layout()` is now deprecated with a warning instead of a message.
+- `layout.sugiyama()` is now deprecated with a warning instead of a message.
+- `layout.star()` is now deprecated with a warning instead of a message.
+- `layout.norm()` is now deprecated with a warning instead of a message.
+- `layout.merge()` is now deprecated with a warning instead of a message.
+- `layout.mds()` is now deprecated with a warning instead of a message.
+- `layout.grid()` is now deprecated with a warning instead of a message.
+- `layout.graphopt()` is now deprecated with a warning instead of a message.
+- `layout.gem()` is now deprecated with a warning instead of a message.
+- `layout.davidson.harel()` is now deprecated with a warning instead of a message.
+- `layout.bipartite()` is now deprecated with a warning instead of a message.
+- `layout.auto()` is now deprecated with a warning instead of a message.
+- `layout.reingold.tilford()` is now deprecated with a warning instead of a message.
+- `layout.circle()` is now deprecated with a warning instead of a message.
+- `layout.sphere()` is now deprecated with a warning instead of a message.
+- `layout.random()` is now deprecated with a warning instead of a message.
+- `layout.fruchterman.reingold()` is now deprecated with a warning instead of a message.
+- `layout.kamada.kawai()` is now deprecated with a warning instead of a message.
+- `layout.lgl()` is now deprecated with a warning instead of a message.
+- `layout_with_mds()` is now deprecated with a warning instead of a message.
+- `layout.spring()` is now defunct (errors instead of warning).
+- `layout.svd()` is now defunct (errors instead of warning).
+- `layout.fruchterman.reingold.grid()` is now defunct (errors instead of warning).
+- `layout.drl()` is now deprecated with a warning instead of a message.
+- `nei()` has been removed.
+- `innei()` has been removed.
+- `outnei()` has been removed.
+- `inc()` has been removed.
+- `adj()` has been removed.
+- `from()` has been removed.
+- `to()` has been removed.
+- `adj()` has been removed.
+- `inc()` has been removed.
+- `from()` has been removed.
+- `to()` has been removed.
+- `is.directed()` is now deprecated with a warning instead of a message.
+- `delete.vertices()` is now deprecated with a warning instead of a message.
+- `delete.edges()` is now deprecated with a warning instead of a message.
+- `add.vertices()` is now deprecated with a warning instead of a message.
+- `add.edges()` is now deprecated with a warning instead of a message.
+- `get_edge_ids()` is now defunct (errors instead of warning).
+- `get.edge.ids()` is now deprecated with a warning instead of a message.
+- `get.edge.ids()` is now deprecated with a warning instead of a message.
+- `graph.incidence()` is now deprecated with a warning instead of a message.
+- `graph_from_incidence_matrix()` is now deprecated with a warning instead of a message.
+- `graph_from_incidence_matrix()` is now deprecated with a warning instead of a message.
+- `hrg.predict()` is now deprecated with a warning instead of a message.
+- `hrg.fit()` is now deprecated with a warning instead of a message.
+- `hrg.game()` is now deprecated with a warning instead of a message.
+- `hrg.dendrogram()` is now deprecated with a warning instead of a message.
+- `hrg.create()` is now deprecated with a warning instead of a message.
+- `hrg.consensus()` is now deprecated with a warning instead of a message.
+- `graphlets.project()` is now deprecated with a warning instead of a message.
+- `graphlets.candidate.basis()` is now deprecated with a warning instead of a message.
+- `watts.strogatz.game()` is now deprecated with a warning instead of a message.
+- `static.power.law.game()` is now deprecated with a warning instead of a message.
+- `static.fitness.game()` is now deprecated with a warning instead of a message.
+- `sbm.game()` is now deprecated with a warning instead of a message.
+- `preference.game()` is now deprecated with a warning instead of a message.
+- `lastcit.game()` is now deprecated with a warning instead of a message.
+- `k.regular.game()` is now deprecated with a warning instead of a message.
+- `interconnected.islands.game()` is now deprecated with a warning instead of a message.
+- `grg.game()` is now deprecated with a warning instead of a message.
+- `growing.random.game()` is now deprecated with a warning instead of a message.
+- `forest.fire.game()` is now deprecated with a warning instead of a message.
+- `establishment.game()` is now deprecated with a warning instead of a message.
+- `degree.sequence.game()` is now deprecated with a warning instead of a message.
+- `connect.neighborhood()` is now deprecated with a warning instead of a message.
+- `citing.cited.type.game()` is now deprecated with a warning instead of a message.
+- `cited.type.game()` is now deprecated with a warning instead of a message.
+- `callaway.traits.game()` is now deprecated with a warning instead of a message.
+- `bipartite.random.game()` is now defunct (errors instead of warning).
+- `barabasi.game()` is now deprecated with a warning instead of a message.
+- `ba.game()` is now deprecated with a warning instead of a message.
+- `asymmetric.preference.game()` is now deprecated with a warning instead of a message.
+- `aging.barabasi.game()` is now deprecated with a warning instead of a message.
+- `aging.ba.game()` is now deprecated with a warning instead of a message.
+- `aging.prefatt.game()` is now deprecated with a warning instead of a message.
+- `erdos.renyi.game()` is now deprecated with a warning instead of a message.
+- `erdos.renyi.game()` is now deprecated with a warning instead of a message.
+- `random.graph.game()` is now deprecated with a warning instead of a message.
+- `random.graph.game()` is now deprecated with a warning instead of a message.
+- `sample_degseq()` is now defunct (errors instead of warning).
+- `sample_degseq()` is now defunct (errors instead of warning).
+- `sample_degseq()` is now defunct (errors instead of warning).
+- `sample_bipartite()` is now deprecated with a warning instead of a message.
+- `sample_bipartite()` is now deprecated with a warning instead of a message.
+- `bipartite()` is now deprecated with a warning instead of a message.
+- `bipartite()` is now deprecated with a warning instead of a message.
+- `write.graph()` is now deprecated with a warning instead of a message.
+- `read.graph()` is now deprecated with a warning instead of a message.
+- `graph.graphdb()` is now deprecated with a warning instead of a message.
+- `vertex.disjoint.paths()` is now deprecated with a warning instead of a message.
+- `vertex.connectivity()` is now deprecated with a warning instead of a message.
+- `stMincuts()` is now deprecated with a warning instead of a message.
+- `stCuts()` is now deprecated with a warning instead of a message.
+- `minimum.size.separators()` is now deprecated with a warning instead of a message.
+- `minimal.st.separators()` is now deprecated with a warning instead of a message.
+- `is.separator()` is now deprecated with a warning instead of a message.
+- `is.minimal.separator()` is now deprecated with a warning instead of a message.
+- `graph.mincut()` is now deprecated with a warning instead of a message.
+- `graph.maxflow()` is now deprecated with a warning instead of a message.
+- `graph.adhesion()` is now deprecated with a warning instead of a message.
+- `edge.disjoint.paths()` is now deprecated with a warning instead of a message.
+- `edge.connectivity()` is now deprecated with a warning instead of a message.
+- `dominator.tree()` is now deprecated with a warning instead of a message.
+- `power.law.fit()` is now deprecated with a warning instead of a message.
+- `is.graphical.degree.sequence()` is now deprecated with a warning instead of a message.
+- `is.degree.sequence()` is now deprecated with a warning instead of a message.
+- `is.chordal()` is now deprecated with a warning instead of a message.
+- `igraph.to.graphNEL()` is now deprecated with a warning instead of a message.
+- `igraph.from.graphNEL()` is now deprecated with a warning instead of a message.
+- `graph.adjlist()` is now deprecated with a warning instead of a message.
+- `get.incidence()` is now deprecated with a warning instead of a message.
+- `get.edgelist()` is now deprecated with a warning instead of a message.
+- `get.data.frame()` is now deprecated with a warning instead of a message.
+- `get.adjacency()` is now deprecated with a warning instead of a message.
+- `get.adjlist()` is now deprecated with a warning instead of a message.
+- `get.adjedgelist()` is now deprecated with a warning instead of a message.
+- `get.adjacency.dense()` is now deprecated with a warning instead of a message.
+- `as_adj()` is now deprecated with a warning instead of a message.
+- `as_incidence_matrix()` is now deprecated with a warning instead of a message.
+- `as.directed()` is now deprecated with a warning instead of a message.
+- `as.undirected()` is now deprecated with a warning instead of a message.
+- `graph.edgelist()` is now deprecated with a warning instead of a message.
+- `graph.data.frame()` is now deprecated with a warning instead of a message.
+- `igraph.console()` is now deprecated with a warning instead of a message.
+- `no.clusters()` is now deprecated with a warning instead of a message.
+- `decompose.graph()` is now deprecated with a warning instead of a message.
+- `cluster.distribution()` is now deprecated with a warning instead of a message.
+- `biconnected.components()` is now deprecated with a warning instead of a message.
+- `articulation.points()` is now deprecated with a warning instead of a message.
+- `create.communities()` is now deprecated with a warning instead of a message.
+- `walktrap.community()` is now deprecated with a warning instead of a message.
+- `spinglass.community()` is now deprecated with a warning instead of a message.
+- `showtrace()` is now deprecated with a warning instead of a message.
+- `optimal.community()` is now deprecated with a warning instead of a message.
+- `multilevel.community()` is now deprecated with a warning instead of a message.
+- `mod.matrix()` is now deprecated with a warning instead of a message.
+- `leading.eigenvector.community()` is now deprecated with a warning instead of a message.
+- `label.propagation.community()` is now deprecated with a warning instead of a message.
+- `is.hierarchical()` is now deprecated with a warning instead of a message.
+- `infomap.community()` is now deprecated with a warning instead of a message.
+- `fastgreedy.community()` is now deprecated with a warning instead of a message.
+- `edge.betweenness.community()` is now deprecated with a warning instead of a message.
+- `dendPlot()` is now deprecated with a warning instead of a message.
+- `cutat()` is now deprecated with a warning instead of a message.
+- `contract.vertices()` is now deprecated with a warning instead of a message.
+- `code.length()` is now deprecated with a warning instead of a message.
+- `modularity_matrix()` is now defunct (errors instead of warning).
+- `cluster_leiden()` is now deprecated with a warning instead of a message.
+- `cluster_leading_eigen()` is now deprecated with a warning instead of a message.
+- `cluster_label_prop()` is now deprecated with a warning instead of a message.
+- `exportPajek()` is now deprecated with a warning instead of a message.
+- `plotHierarchy()` is now deprecated with a warning instead of a message.
+- `maxcohesion()` is now deprecated with a warning instead of a message.
+- `graph.cohesion()` is now deprecated with a warning instead of a message.
+- `cohesive.blocks()` is now deprecated with a warning instead of a message.
+- `blockGraphs()` is now deprecated with a warning instead of a message.
+- `maximal.independent.vertex.sets()` is now deprecated with a warning instead of a message.
+- `maximal.cliques.count()` is now deprecated with a warning instead of a message.
+- `maximal.cliques()` is now deprecated with a warning instead of a message.
+- `largest.independent.vertex.sets()` is now deprecated with a warning instead of a message.
+- `largest.cliques()` is now deprecated with a warning instead of a message.
+- `independent.vertex.sets()` is now deprecated with a warning instead of a message.
+- `independence.number()` is now deprecated with a warning instead of a message.
+- `clique.number()` is now deprecated with a warning instead of a message.
+- `maximal_ivs()` is now deprecated with a warning instead of a message.
+- `centralize.scores()` is now deprecated with a warning instead of a message.
+- `centralization.evcent.tmax()` is now deprecated with a warning instead of a message.
+- `centralization.evcent()` is now deprecated with a warning instead of a message.
+- `centralization.degree.tmax()` is now deprecated with a warning instead of a message.
+- `centralization.degree()` is now deprecated with a warning instead of a message.
+- `centralization.closeness.tmax()` is now deprecated with a warning instead of a message.
+- `centralization.closeness()` is now deprecated with a warning instead of a message.
+- `centralization.betweenness.tmax()` is now deprecated with a warning instead of a message.
+- `centralization.betweenness()` is now deprecated with a warning instead of a message.
+- `centr_degree_tmax()` is now defunct (errors instead of warning).
+- `centr_eigen()` is now deprecated with a warning instead of a message.
+- `centr_eigen_tmax()` is now deprecated with a warning instead of a message.
+- `subgraph.centrality()` is now deprecated with a warning instead of a message.
+- `page.rank()` is now deprecated with a warning instead of a message.
+- `hub.score()` is now defunct (errors instead of warning).
+- `authority.score()` is now defunct (errors instead of warning).
+- `graph.strength()` is now deprecated with a warning instead of a message.
+- `graph.eigen()` is now deprecated with a warning instead of a message.
+- `graph.diversity()` is now deprecated with a warning instead of a message.
+- `evcent()` is now deprecated with a warning instead of a message.
+- `edge.betweenness()` is now deprecated with a warning instead of a message.
+- `bonpow()` is now deprecated with a warning instead of a message.
+- `alpha.centrality()` is now deprecated with a warning instead of a message.
+- `estimate_betweenness()` is now deprecated with a warning instead of a message.
+- `estimate_edge_betweenness()` is now deprecated with a warning instead of a message.
+- `estimate_closeness()` is now deprecated with a warning instead of a message.
+- `arpack()` is now deprecated with a warning instead of a message.
+- `spectrum()` is now deprecated with a warning instead of a message.
+- `eigen_centrality()` is now deprecated with a warning instead of a message.
+- `eigen_centrality()` is now deprecated with a warning instead of a message.
+- `eigen_centrality()` is now defunct (errors instead of warning).
+- `authority_score()` is now deprecated with a warning instead of a message.
+- `arpack_defaults()` is now deprecated with a warning instead of a message.
+- `hub_score()` is now deprecated with a warning instead of a message.
+- `arpack_defaults()` is now deprecated with a warning instead of a message.
+- `bipartite.projection.size()` is now deprecated with a warning instead of a message.
+- `bipartite.projection()` is now deprecated with a warning instead of a message.
+- `bipartite.mapping()` is now deprecated with a warning instead of a message.
+- `get.edge()` has been removed.
+- `is.igraph()` is now deprecated with a warning instead of a message.
+- `set.vertex.attribute()` is now deprecated with a warning instead of a message.
+- `set.graph.attribute()` is now deprecated with a warning instead of a message.
+- `set.edge.attribute()` is now deprecated with a warning instead of a message.
+- `remove.vertex.attribute()` is now deprecated with a warning instead of a message.
+- `remove.graph.attribute()` is now deprecated with a warning instead of a message.
+- `remove.edge.attribute()` is now deprecated with a warning instead of a message.
+- `list.vertex.attributes()` is now deprecated with a warning instead of a message.
+- `list.graph.attributes()` is now deprecated with a warning instead of a message.
+- `list.edge.attributes()` is now deprecated with a warning instead of a message.
+- `is.weighted()` is now deprecated with a warning instead of a message.
+- `is.named()` is now deprecated with a warning instead of a message.
+- `is.bipartite()` is now deprecated with a warning instead of a message.
+- `get.vertex.attribute()` is now deprecated with a warning instead of a message.
+- `get.graph.attribute()` is now deprecated with a warning instead of a message.
+- `get.edge.attribute()` is now deprecated with a warning instead of a message.
+- `assortativity.nominal()` is now deprecated with a warning instead of a message.
+- `assortativity.degree()` is now deprecated with a warning instead of a message.
+- `assortativity()` is now deprecated with a warning instead of a message.
+- `assortativity()` is now deprecated with a warning instead of a message.
+- `assortativity()` is now deprecated with a warning instead of a message.
+- `ape::as.phylo()` is now deprecated with a warning instead of a message.
+- `graph.adjacency()` is now deprecated with a warning instead of a message.
+- `graph_from_adjacency_matrix()` is now deprecated with a warning instead of a message.
+- `graph_from_adjacency_matrix()` is now deprecated with a warning instead of a message.
 
-# igraph 2.3.1.9001
 
 ## Chore
 

From 9817ff617c3028a4c8115a05e656537bfc769aac Mon Sep 17 00:00:00 2001
From: maelle <maelle@users.noreply.github.com>
Date: Tue, 19 May 2026 10:39:58 +0000
Subject: [PATCH 29/48] chore: Auto-update from GitHub Actions

Run: https://github.com/igraph/rigraph/actions/runs/26091648100
---
 tools/commit-lifecycle.R | 57 +++++++++++++++++++++++++++++++++-------
 1 file changed, 47 insertions(+), 10 deletions(-)

diff --git a/tools/commit-lifecycle.R b/tools/commit-lifecycle.R
index 49fb84f3307..71b175fe519 100644
--- a/tools/commit-lifecycle.R
+++ b/tools/commit-lifecycle.R
@@ -37,13 +37,20 @@
 # gert::git_pull(repo = here::here(), remote = "origin", refspec = "main")
 # cli::cli_alert_success("Pulled and fast-forwarded to main")
 
-gert::git_fetch("origin", refspec = "refs/heads/main:refs/heads/main", repo = here::here())
+gert::git_fetch(
+  "origin",
+  refspec = "refs/heads/main:refs/heads/main",
+  repo = here::here()
+)
 gert::git_reset_mixed("main", repo = here::here())
 
 usethis::use_build_ignore("lifecycle")
 usethis::use_git_ignore("lifecycle")
 
-gert::git_add(c("tools/commit-lifecycle.R", ".gitignore", ".Rbuildignore"), repo = here::here())
+gert::git_add(
+  c("tools/commit-lifecycle.R", ".gitignore", ".Rbuildignore"),
+  repo = here::here()
+)
 gert::git_commit("chore: add commit-lifecycle.R script", repo = here::here())
 cli::cli_alert_success("Committed tools/commit-lifecycle.R")
 
@@ -58,15 +65,31 @@ for (stem in tools::file_path_sans_ext(r_files)) {
   file.copy(lifecycle_r, here::here(r_file), overwrite = TRUE)
   files_to_stage <- r_file
 
-  lifecycle_test <- here::here("lifecycle", "tests", "testthat", paste0("test-", stem, ".R"))
+  lifecycle_test <- here::here(
+    "lifecycle",
+    "tests",
+    "testthat",
+    paste0("test-", stem, ".R")
+  )
   if (file.exists(lifecycle_test)) {
     dest_test <- here::here("tests", "testthat", paste0("test-", stem, ".R"))
     file.copy(lifecycle_test, dest_test, overwrite = TRUE)
     files_to_stage <- c(files_to_stage, paste0("tests/testthat/test-", stem, ".R"))
 
-    lifecycle_snap <- here::here("lifecycle", "tests", "testthat", "_snaps", paste0(stem, ".md"))
+    lifecycle_snap <- here::here(
+      "lifecycle",
+      "tests",
+      "testthat",
+      "_snaps",
+      paste0(stem, ".md")
+    )
     if (file.exists(lifecycle_snap)) {
-      dest_snap <- here::here("tests", "testthat", "_snaps", paste0(stem, ".md"))
+      dest_snap <- here::here(
+        "tests",
+        "testthat",
+        "_snaps",
+        paste0(stem, ".md")
+      )
       file.copy(lifecycle_snap, dest_snap, overwrite = TRUE)
       files_to_stage <- c(files_to_stage, paste0("tests/testthat/_snaps/", stem, ".md"))
     }
@@ -75,20 +98,34 @@ for (stem in tools::file_path_sans_ext(r_files)) {
   devtools::document(quiet = TRUE)
   tryCatch(
     callr::r(
-      function(pkg, filter) devtools::test(pkg = pkg, filter = filter, stop_on_failure = FALSE),
+      function(pkg, filter) {
+        devtools::test(pkg = pkg, filter = filter, stop_on_failure = FALSE)
+      },
       args = list(pkg = here::here(), filter = stem)
     ),
-    error = function(e) cli::cli_alert_warning("Tests errored for {stem}: {conditionMessage(e)}")
+    error = function(e) {
+      cli::cli_alert_warning("Tests errored for {stem}: {conditionMessage(e)}")
+    }
   )
 
   gert::git_add(c(files_to_stage, "man", "NAMESPACE"), repo = here::here())
-  gert::git_commit(paste0("feat!: bump deprecated functions in R/", stem, ".R"), repo = here::here())
+  gert::git_commit(
+    paste0("feat!: bump deprecated functions in R/", stem, ".R"),
+    repo = here::here()
+  )
   cli::cli_alert_success("Committed {r_file}")
 }
 
-file.copy(here::here("lifecycle", "NEWS.md"), here::here("NEWS.md"), overwrite = TRUE)
+file.copy(
+  here::here("lifecycle", "NEWS.md"),
+  here::here("NEWS.md"),
+  overwrite = TRUE
+)
 gert::git_add("NEWS.md", repo = here::here())
-gert::git_commit("chore: update NEWS.md for lifecycle bumps\n\n!NEWS", repo = here::here())
+gert::git_commit(
+  "chore: update NEWS.md for lifecycle bumps\n\n!NEWS",
+  repo = here::here()
+)
 cli::cli_alert_success("Committed NEWS.md")
 
 # R CMD check after all the commits

From 7077e317897b04a3984e8c94f09ff64cc6ca36fe Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:52:56 +0200
Subject: [PATCH 30/48] feat!: bump deprecate_soft to deprecate_warn in
 R/minimum.spanning.tree.R

---
 NEWS.md                   | 1 +
 R/minimum.spanning.tree.R | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index cd923355615..eeae295fb2d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,7 @@
 
 ## Deprecated and defunct
 
+- `minimum.spanning.tree(()` is now deprecated with a warning instead of a message.
 - `graph()` is now deprecated with a warning instead of a message.
 - `graph.famous()` is now deprecated with a warning instead of a message.
 - `line.graph()` is now deprecated with a warning instead of a message.
diff --git a/R/minimum.spanning.tree.R b/R/minimum.spanning.tree.R
index 2f48bb7d6b5..887f0beb62f 100644
--- a/R/minimum.spanning.tree.R
+++ b/R/minimum.spanning.tree.R
@@ -15,7 +15,7 @@ minimum.spanning.tree <- function(
   ...
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "minimum.spanning.tree()", "mst()")
+  lifecycle::deprecate_warn("2.0.0", "minimum.spanning.tree()", "mst()")
   mst(graph = graph, weights = weights, algorithm = algorithm, ...)
 } # nocov end
 #   IGraph R package

From 03267f8c209c98ca8b8521c3d8db2f352d5196d3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:53:42 +0200
Subject: [PATCH 31/48] feat!: bump deprecate_soft to deprecate_warn in
 R/motifs.R

---
 NEWS.md    |  5 +++++
 R/motifs.R | 10 +++++-----
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index eeae295fb2d..a6ac59f3072 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,11 @@
 
 ## Deprecated and defunct
 
+- `triad.census(()` is now deprecated with a warning instead of a message.
+- `graph.motifs.no(()` is now deprecated with a warning instead of a message.
+- `graph.motifs.est(()` is now deprecated with a warning instead of a message.
+- `graph.motifs(()` is now deprecated with a warning instead of a message.
+- `dyad.census(()` is now deprecated with a warning instead of a message.
 - `minimum.spanning.tree(()` is now deprecated with a warning instead of a message.
 - `graph()` is now deprecated with a warning instead of a message.
 - `graph.famous()` is now deprecated with a warning instead of a message.
diff --git a/R/motifs.R b/R/motifs.R
index 4c97987133b..694e6f728d1 100644
--- a/R/motifs.R
+++ b/R/motifs.R
@@ -10,7 +10,7 @@
 #' @export
 triad.census <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "triad.census()", "triad_census()")
+  lifecycle::deprecate_warn("2.0.0", "triad.census()", "triad_census()")
   triad_census(graph = graph)
 } # nocov end
 
@@ -26,7 +26,7 @@ triad.census <- function(graph) {
 #' @export
 graph.motifs.no <- function(graph, size = 3, cut.prob = rep(0, size)) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.motifs.no()", "count_motifs()")
+  lifecycle::deprecate_warn("2.0.0", "graph.motifs.no()", "count_motifs()")
   count_motifs(graph = graph, size = size, cut.prob = cut.prob)
 } # nocov end
 
@@ -52,7 +52,7 @@ graph.motifs.est <- function(
   sample = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.motifs.est()", "sample_motifs()")
+  lifecycle::deprecate_warn("2.0.0", "graph.motifs.est()", "sample_motifs()")
   sample_motifs(
     graph = graph,
     size = size,
@@ -78,7 +78,7 @@ graph.motifs.est <- function(
 #' @export
 graph.motifs <- function(graph, size = 3, cut.prob = rep(0, size)) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.motifs()", "motifs()")
+  lifecycle::deprecate_warn("2.0.0", "graph.motifs()", "motifs()")
   motifs(graph = graph, size = size, cut.prob = cut.prob)
 } # nocov end
 
@@ -94,7 +94,7 @@ graph.motifs <- function(graph, size = 3, cut.prob = rep(0, size)) {
 #' @export
 dyad.census <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "dyad.census()", "dyad_census()")
+  lifecycle::deprecate_warn("2.0.0", "dyad.census()", "dyad_census()")
   dyad_census(graph = graph)
 } # nocov end
 

From 72c3e12cf16521622a06513a1456c546841f686e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:54:44 +0200
Subject: [PATCH 32/48] feat!: bump deprecate_soft to deprecate_warn in
 R/operators.R

---
 NEWS.md       |  5 +++++
 R/operators.R | 12 ++++++------
 2 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index a6ac59f3072..39553c756a2 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,11 @@
 
 ## Deprecated and defunct
 
+- `graph.intersection(()` is now deprecated with a warning instead of a message.
+- `graph.union(()` is now deprecated with a warning instead of a message.
+- `graph.difference(()` is now deprecated with a warning instead of a message.
+- `graph.compose(()` is now deprecated with a warning instead of a message.
+- `graph.complementer(()` is now deprecated with a warning instead of a message.
 - `triad.census(()` is now deprecated with a warning instead of a message.
 - `graph.motifs.no(()` is now deprecated with a warning instead of a message.
 - `graph.motifs.est(()` is now deprecated with a warning instead of a message.
diff --git a/R/operators.R b/R/operators.R
index 4c3161dc775..27cf7d455ae 100644
--- a/R/operators.R
+++ b/R/operators.R
@@ -10,7 +10,7 @@
 #' @export
 graph.intersection <- function(...) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.intersection()", "intersection()")
+  lifecycle::deprecate_warn("2.0.0", "graph.intersection()", "intersection()")
   intersection(...)
 } # nocov end
 
@@ -26,7 +26,7 @@ graph.intersection <- function(...) {
 #' @export
 graph.union <- function(..., byname = "auto") {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.union()", "union.igraph()")
+  lifecycle::deprecate_warn("2.0.0", "graph.union()", "union.igraph()")
   union.igraph(byname = byname, ...)
 } # nocov end
 
@@ -42,7 +42,7 @@ graph.union <- function(..., byname = "auto") {
 #' @export
 graph.difference <- function(...) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.difference()", "difference()")
+  lifecycle::deprecate_warn("2.0.0", "graph.difference()", "difference()")
   difference(...)
 } # nocov end
 
@@ -58,7 +58,7 @@ graph.difference <- function(...) {
 #' @export
 graph.disjoint.union <- function(...) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "graph.disjoint.union()",
     "disjoint_union()"
@@ -78,7 +78,7 @@ graph.disjoint.union <- function(...) {
 #' @export
 graph.compose <- function(g1, g2, byname = "auto") {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.compose()", "compose()")
+  lifecycle::deprecate_warn("2.0.0", "graph.compose()", "compose()")
   compose(g1 = g1, g2 = g2, byname = byname)
 } # nocov end
 
@@ -94,7 +94,7 @@ graph.compose <- function(g1, g2, byname = "auto") {
 #' @export
 graph.complementer <- function(graph, loops = FALSE) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.complementer()", "complementer()")
+  lifecycle::deprecate_warn("2.0.0", "graph.complementer()", "complementer()")
   complementer(graph = graph, loops = loops)
 } # nocov end
 #   IGraph R package

From 2cddd686510dedc8de4421354e36b2284d80bbc8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 12:57:10 +0200
Subject: [PATCH 33/48] feat!: bump deprecate_soft to deprecate_warn in
 R/other.R

---
 NEWS.md   | 3 +++
 R/other.R | 6 +++---
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 39553c756a2..dbddc587b90 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,9 @@
 
 ## Deprecated and defunct
 
+- `running.mean(()` is now deprecated with a warning instead of a message.
+- `igraph.sample(()` is now deprecated with a warning instead of a message.
+- `convex.hull(()` is now deprecated with a warning instead of a message.
 - `graph.intersection(()` is now deprecated with a warning instead of a message.
 - `graph.union(()` is now deprecated with a warning instead of a message.
 - `graph.difference(()` is now deprecated with a warning instead of a message.
diff --git a/R/other.R b/R/other.R
index fac2f133240..1936d98d7ac 100644
--- a/R/other.R
+++ b/R/other.R
@@ -10,7 +10,7 @@
 #' @export
 running.mean <- function(v, binwidth) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "running.mean()", "running_mean()")
+  lifecycle::deprecate_warn("2.0.0", "running.mean()", "running_mean()")
   running_mean(v = v, binwidth = binwidth)
 } # nocov end
 
@@ -26,7 +26,7 @@ running.mean <- function(v, binwidth) {
 #' @export
 igraph.sample <- function(low, high, length) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "igraph.sample()", "sample_seq()")
+  lifecycle::deprecate_warn("2.0.0", "igraph.sample()", "sample_seq()")
   sample_seq(low = low, high = high, length = length)
 } # nocov end
 
@@ -42,7 +42,7 @@ igraph.sample <- function(low, high, length) {
 #' @export
 convex.hull <- function(data) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "convex.hull()", "convex_hull()")
+  lifecycle::deprecate_warn("2.0.0", "convex.hull()", "convex_hull()")
   convex_hull(data = data)
 } # nocov end
 #   IGraph R package

From d2f0cb20d5ffe5e90cab6434bea65bfe89268439 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 13:00:12 +0200
Subject: [PATCH 34/48] feat!: bump deprecate_soft to deprecate_warn in R/par.R

---
 NEWS.md | 2 ++
 R/par.R | 4 ++--
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index dbddc587b90..d18ee057741 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,8 @@
 
 ## Deprecated and defunct
 
+- `igraph.options(()` is now deprecated with a warning instead of a message.
+- `getIgraphOpt(()` is now deprecated with a warning instead of a message.
 - `running.mean(()` is now deprecated with a warning instead of a message.
 - `igraph.sample(()` is now deprecated with a warning instead of a message.
 - `convex.hull(()` is now deprecated with a warning instead of a message.
diff --git a/R/par.R b/R/par.R
index ac5d3d1c3f8..8b32920a48e 100644
--- a/R/par.R
+++ b/R/par.R
@@ -10,7 +10,7 @@
 #' @export
 igraph.options <- function(...) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "igraph.options()", "igraph_options()")
+  lifecycle::deprecate_warn("2.0.0", "igraph.options()", "igraph_options()")
   igraph_i_options(...)
 } # nocov end
 
@@ -26,7 +26,7 @@ igraph.options <- function(...) {
 #' @export
 getIgraphOpt <- function(x, default = NULL) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "getIgraphOpt()", "igraph_opt()")
+  lifecycle::deprecate_warn("2.0.0", "getIgraphOpt()", "igraph_opt()")
 
   if (missing(default)) {
     get_config(paste0("igraph::", x), .igraph.pars[[x]])

From 96af2d87e4c9ad9304fdc177fc0e82069cbb7e8a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 13:07:34 +0200
Subject: [PATCH 35/48] feat!: bump deprecate_soft to deprecate_warn in
 R/paths.R

---
 NEWS.md   |  2 ++
 R/paths.R | 10 +++++-----
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index d18ee057741..3b7bb104947 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,8 @@
 
 ## Deprecated and defunct
 
+- `path.length.hist(()` is now deprecated with a warning instead of a message.
+- `is.dag(()` is now deprecated with a warning instead of a message.
 - `igraph.options(()` is now deprecated with a warning instead of a message.
 - `getIgraphOpt(()` is now deprecated with a warning instead of a message.
 - `running.mean(()` is now deprecated with a warning instead of a message.
diff --git a/R/paths.R b/R/paths.R
index 093efd56d38..1ff158c6a46 100644
--- a/R/paths.R
+++ b/R/paths.R
@@ -10,7 +10,7 @@
 #' @export
 path.length.hist <- function(graph, directed = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "path.length.hist()", "distance_table()")
+  lifecycle::deprecate_warn("2.0.0", "path.length.hist()", "distance_table()")
   distance_table(graph = graph, directed = directed)
 } # nocov end
 
@@ -26,7 +26,7 @@ path.length.hist <- function(graph, directed = TRUE) {
 #' @export
 maximum.cardinality.search <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "maximum.cardinality.search()",
     "max_cardinality()"
@@ -46,7 +46,7 @@ maximum.cardinality.search <- function(graph) {
 #' @export
 is.dag <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.dag()", "is_dag()")
+  lifecycle::deprecate_warn("2.0.0", "is.dag()", "is_dag()")
   is_dag(graph = graph)
 } # nocov end
 ## -----------------------------------------------------------------------
@@ -287,7 +287,7 @@ eccentricity <- function(
   mode = c("all", "out", "in", "total")
 ) {
   if (...length() > 0) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.1.0",
       "eccentricity(... =)",
       details = "The argument `mode` must be named."
@@ -345,7 +345,7 @@ radius <- function(
   mode = c("all", "out", "in", "total")
 ) {
   if (...length() > 0) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.1.0",
       "radius(... =)",
       details = "The argument `mode` must be named."

From 9afca6a0825f96fcdcfff3299daa096d8ac109e2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 13:33:20 +0200
Subject: [PATCH 36/48] feat!: bump deprecate_soft to deprecate_warn in
 R/plot.shapes.R

---
 NEWS.md         | 4 ++++
 R/plot.shapes.R | 8 ++++----
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 3b7bb104947..93fc05c64ca 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,10 @@
 
 ## Deprecated and defunct
 
+- `igraph.shape.noplot(()` is now deprecated with a warning instead of a message.
+- `igraph.shape.noclip(()` is now deprecated with a warning instead of a message.
+- `vertex.shapes(()` is now deprecated with a warning instead of a message.
+- `add.vertex.shape(()` is now deprecated with a warning instead of a message.
 - `path.length.hist(()` is now deprecated with a warning instead of a message.
 - `is.dag(()` is now deprecated with a warning instead of a message.
 - `igraph.options(()` is now deprecated with a warning instead of a message.
diff --git a/R/plot.shapes.R b/R/plot.shapes.R
index b8380cb10fe..3b2bfffcb2a 100644
--- a/R/plot.shapes.R
+++ b/R/plot.shapes.R
@@ -10,7 +10,7 @@
 #' @export
 igraph.shape.noplot <- function(coords, v = NULL, params) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "igraph.shape.noplot()", "shape_noplot()")
+  lifecycle::deprecate_warn("2.0.0", "igraph.shape.noplot()", "shape_noplot()")
   shape_noplot(coords = coords, v = v, params = params)
 } # nocov end
 
@@ -31,7 +31,7 @@ igraph.shape.noclip <- function(
   end = c("both", "from", "to")
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "igraph.shape.noclip()", "shape_noclip()")
+  lifecycle::deprecate_warn("2.0.0", "igraph.shape.noclip()", "shape_noclip()")
   shape_noclip(coords = coords, el = el, params = params, end = end)
 } # nocov end
 
@@ -47,7 +47,7 @@ igraph.shape.noclip <- function(
 #' @export
 vertex.shapes <- function(shape = NULL) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "vertex.shapes()", "shapes()")
+  lifecycle::deprecate_warn("2.0.0", "vertex.shapes()", "shapes()")
   shapes(shape = shape)
 } # nocov end
 
@@ -68,7 +68,7 @@ add.vertex.shape <- function(
   parameters = list()
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "add.vertex.shape()", "add_shape()")
+  lifecycle::deprecate_warn("2.0.0", "add.vertex.shape()", "add_shape()")
   add_shape(shape = shape, clip = clip, plot = plot, parameters = parameters)
 } # nocov end
 

From dd4528e78225cf9a6e1b03556b9343668b341b38 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 13:34:34 +0200
Subject: [PATCH 37/48] feat!: bump deprecate_soft to deprecate_warn in
 R/similarity.R

---
 R/similarity.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/similarity.R b/R/similarity.R
index 4fcb4eb9445..aa8c7c5280c 100644
--- a/R/similarity.R
+++ b/R/similarity.R
@@ -104,7 +104,7 @@ similarity.jaccard <- function(
   mode = c("all", "out", "in", "total"),
   loops = FALSE
 ) {
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.1.0",
     "similarity.jaccard()",
     "similarity(method)",
@@ -135,7 +135,7 @@ similarity.dice <- function(
   mode = c("all", "out", "in", "total"),
   loops = FALSE
 ) {
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.1.0",
     "similarity.dice()",
     "similarity(method)",
@@ -165,7 +165,7 @@ similarity.invlogweighted <- function(
   vids = V(graph),
   mode = c("all", "out", "in", "total")
 ) {
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.1.0",
     "similarity.invlogweighted()",
     "similarity(method)",

From e09c0bc40ffb0b985d3753c03c28fa68a0cf4ceb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 13:36:00 +0200
Subject: [PATCH 38/48] feat!: bump deprecate_soft to deprecate_warn in
 R/simple.R

---
 NEWS.md    | 1 +
 R/simple.R | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index 93fc05c64ca..a2b24075b6a 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,7 @@
 
 ## Deprecated and defunct
 
+- `is.simple(()` is now deprecated with a warning instead of a message.
 - `igraph.shape.noplot(()` is now deprecated with a warning instead of a message.
 - `igraph.shape.noclip(()` is now deprecated with a warning instead of a message.
 - `vertex.shapes(()` is now deprecated with a warning instead of a message.
diff --git a/R/simple.R b/R/simple.R
index 48126722a49..c2de4f1fdbb 100644
--- a/R/simple.R
+++ b/R/simple.R
@@ -10,7 +10,7 @@
 #' @export
 is.simple <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.simple()", "is_simple()")
+  lifecycle::deprecate_warn("2.0.0", "is.simple()", "is_simple()")
   is_simple(graph = graph)
 } # nocov end
 

From a8dd7d5e864135cf020c258a52bc7c0636964c74 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 13:37:27 +0200
Subject: [PATCH 39/48] feat!: bump deprecate_soft to deprecate_warn in
 R/stochastic_matrix.R

---
 NEWS.md               | 1 +
 R/stochastic_matrix.R | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index a2b24075b6a..28ef4c6ee39 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,7 @@
 
 ## Deprecated and defunct
 
+- `get.stochastic(()` is now deprecated with a warning instead of a message.
 - `is.simple(()` is now deprecated with a warning instead of a message.
 - `igraph.shape.noplot(()` is now deprecated with a warning instead of a message.
 - `igraph.shape.noclip(()` is now deprecated with a warning instead of a message.
diff --git a/R/stochastic_matrix.R b/R/stochastic_matrix.R
index b829072fb1a..01ece7ee3ca 100644
--- a/R/stochastic_matrix.R
+++ b/R/stochastic_matrix.R
@@ -14,7 +14,7 @@ get.stochastic <- function(
   sparse = igraph_opt("sparsematrices")
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "get.stochastic()", "stochastic_matrix()")
+  lifecycle::deprecate_warn("2.0.0", "get.stochastic()", "stochastic_matrix()")
   stochastic_matrix(graph = graph, column.wise = column.wise, sparse = sparse)
 } # nocov end
 #   IGraph R package

From d41f28f667f50fcd07d01a5ad116a59362db6276 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 13:38:54 +0200
Subject: [PATCH 40/48] feat!: bump deprecated functions in
 R/structural-properties.R

---
 NEWS.md                   | 26 ++++++++++++++++
 R/structural-properties.R | 64 +++++++++++++++++++--------------------
 2 files changed, 58 insertions(+), 32 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 28ef4c6ee39..1dea43e2094 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,32 @@
 
 ## Deprecated and defunct
 
+- `get.shortest.paths(()` is now deprecated with a warning instead of a message.
+- `get.diameter(()` is now deprecated with a warning instead of a message.
+- `unfold.tree(()` is now deprecated with a warning instead of a message.
+- `topological.sort(()` is now deprecated with a warning instead of a message.
+- `shortest.paths(()` is now deprecated with a warning instead of a message.
+- `neighborhood.size(()` is now deprecated with a warning instead of a message.
+- `is.mutual(()` is now deprecated with a warning instead of a message.
+- `is.multiple(()` is now deprecated with a warning instead of a message.
+- `is.matching(()` is now deprecated with a warning instead of a message.
+- `is.loop(()` is now deprecated with a warning instead of a message.
+- `is.connected(()` is now deprecated with a warning instead of a message.
+- `induced.subgraph(()` is now deprecated with a warning instead of a message.
+- `has.multiple(()` is now deprecated with a warning instead of a message.
+- `graph.neighborhood(()` is now deprecated with a warning instead of a message.
+- `graph.laplacian(()` is now deprecated with a warning instead of a message.
+- `graph.knn(()` is now deprecated with a warning instead of a message.
+- `graph.dfs(()` is now deprecated with a warning instead of a message.
+- `graph.density(()` is now deprecated with a warning instead of a message.
+- `graph.coreness(()` is now deprecated with a warning instead of a message.
+- `graph.bfs(()` is now deprecated with a warning instead of a message.
+- `farthest.nodes(()` is now deprecated with a warning instead of a message.
+- `count.multiple(()` is now deprecated with a warning instead of a message.
+- `clusters(()` is now deprecated with a warning instead of a message.
+- `average.path.length(()` is now deprecated with a warning instead of a message.
+- `bfs(()` is now defunct (errors instead of warning).
+- `dfs(()` is now defunct (errors instead of warning).
 - `get.stochastic(()` is now deprecated with a warning instead of a message.
 - `is.simple(()` is now deprecated with a warning instead of a message.
 - `igraph.shape.noplot(()` is now deprecated with a warning instead of a message.
diff --git a/R/structural-properties.R b/R/structural-properties.R
index c6c99025cf1..17f85cfbad5 100644
--- a/R/structural-properties.R
+++ b/R/structural-properties.R
@@ -20,7 +20,7 @@ get.shortest.paths <- function(
   algorithm = c("automatic", "unweighted", "dijkstra", "bellman-ford")
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "get.shortest.paths()", "shortest_paths()")
+  lifecycle::deprecate_warn("2.0.0", "get.shortest.paths()", "shortest_paths()")
   shortest_paths(
     graph = graph,
     from = from,
@@ -52,7 +52,7 @@ get.all.shortest.paths <- function(
   weights = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "get.all.shortest.paths()",
     "all_shortest_paths()"
@@ -83,7 +83,7 @@ get.diameter <- function(
   weights = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "get.diameter()", "get_diameter()")
+  lifecycle::deprecate_warn("2.0.0", "get.diameter()", "get_diameter()")
   get_diameter(
     graph = graph,
     directed = directed,
@@ -104,7 +104,7 @@ get.diameter <- function(
 #' @export
 unfold.tree <- function(graph, mode = c("all", "out", "in", "total"), roots) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "unfold.tree()", "unfold_tree()")
+  lifecycle::deprecate_warn("2.0.0", "unfold.tree()", "unfold_tree()")
   unfold_tree(graph = graph, mode = mode, roots = roots)
 } # nocov end
 
@@ -120,7 +120,7 @@ unfold.tree <- function(graph, mode = c("all", "out", "in", "total"), roots) {
 #' @export
 topological.sort <- function(graph, mode = c("out", "all", "in")) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "topological.sort()", "topo_sort()")
+  lifecycle::deprecate_warn("2.0.0", "topological.sort()", "topo_sort()")
   topo_sort(graph = graph, mode = mode)
 } # nocov end
 
@@ -149,7 +149,7 @@ shortest.paths <- function(
   )
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "shortest.paths()", "distances()")
+  lifecycle::deprecate_warn("2.0.0", "shortest.paths()", "distances()")
   algorithm <- igraph_match_arg(algorithm)
   mode <- igraph_match_arg(mode)
   distances(
@@ -180,7 +180,7 @@ neighborhood.size <- function(
   mindist = 0
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "neighborhood.size()", "ego_size()")
+  lifecycle::deprecate_warn("2.0.0", "neighborhood.size()", "ego_size()")
   ego_size(
     graph = graph,
     order = order,
@@ -207,7 +207,7 @@ maximum.bipartite.matching <- function(
   eps = .Machine$double.eps
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "maximum.bipartite.matching()",
     "max_bipartite_match()"
@@ -232,7 +232,7 @@ maximum.bipartite.matching <- function(
 #' @export
 is.mutual <- function(graph, eids = E(graph), loops = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.mutual()", "which_mutual()")
+  lifecycle::deprecate_warn("2.0.0", "is.mutual()", "which_mutual()")
   which_mutual(graph = graph, eids = eids, loops = loops)
 } # nocov end
 
@@ -248,7 +248,7 @@ is.mutual <- function(graph, eids = E(graph), loops = TRUE) {
 #' @export
 is.multiple <- function(graph, eids = E(graph)) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.multiple()", "which_multiple()")
+  lifecycle::deprecate_warn("2.0.0", "is.multiple()", "which_multiple()")
   which_multiple(graph = graph, eids = eids)
 } # nocov end
 
@@ -264,7 +264,7 @@ is.multiple <- function(graph, eids = E(graph)) {
 #' @export
 is.maximal.matching <- function(graph, matching, types = NULL) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "is.maximal.matching()",
     "is_max_matching()"
@@ -284,7 +284,7 @@ is.maximal.matching <- function(graph, matching, types = NULL) {
 #' @export
 is.matching <- function(graph, matching, types = NULL) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.matching()", "is_matching()")
+  lifecycle::deprecate_warn("2.0.0", "is.matching()", "is_matching()")
   is_matching(graph = graph, matching = matching, types = types)
 } # nocov end
 
@@ -300,7 +300,7 @@ is.matching <- function(graph, matching, types = NULL) {
 #' @export
 is.loop <- function(graph, eids = E(graph)) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.loop()", "which_loop()")
+  lifecycle::deprecate_warn("2.0.0", "is.loop()", "which_loop()")
   which_loop(graph = graph, eids = eids)
 } # nocov end
 
@@ -316,7 +316,7 @@ is.loop <- function(graph, eids = E(graph)) {
 #' @export
 is.connected <- function(graph, mode = c("weak", "strong")) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.connected()", "is_connected()")
+  lifecycle::deprecate_warn("2.0.0", "is.connected()", "is_connected()")
   is_connected(graph = graph, mode = mode)
 } # nocov end
 
@@ -336,7 +336,7 @@ induced.subgraph <- function(
   impl = c("auto", "copy_and_delete", "create_from_scratch")
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "induced.subgraph()", "induced_subgraph()")
+  lifecycle::deprecate_warn("2.0.0", "induced.subgraph()", "induced_subgraph()")
   induced_subgraph(graph = graph, vids = vids, impl = impl)
 } # nocov end
 
@@ -352,7 +352,7 @@ induced.subgraph <- function(
 #' @export
 has.multiple <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "has.multiple()", "any_multiple()")
+  lifecycle::deprecate_warn("2.0.0", "has.multiple()", "any_multiple()")
   any_multiple(graph = graph)
 } # nocov end
 
@@ -374,7 +374,7 @@ graph.neighborhood <- function(
   mindist = 0
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.neighborhood()", "make_ego_graph()")
+  lifecycle::deprecate_warn("2.0.0", "graph.neighborhood()", "make_ego_graph()")
   make_ego_graph(
     graph = graph,
     order = order,
@@ -401,7 +401,7 @@ graph.laplacian <- function(
   sparse = igraph_opt("sparsematrices")
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.laplacian()", "laplacian_matrix()")
+  lifecycle::deprecate_warn("2.0.0", "graph.laplacian()", "laplacian_matrix()")
   laplacian_matrix(
     graph = graph,
     normalized = normalized,
@@ -428,7 +428,7 @@ graph.knn <- function(
   weights = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.knn()", "knn()")
+  lifecycle::deprecate_warn("2.0.0", "graph.knn()", "knn()")
   knn(
     graph = graph,
     vids = vids,
@@ -465,7 +465,7 @@ graph.dfs <- function(
   neimode
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.dfs()", "dfs()")
+  lifecycle::deprecate_warn("2.0.0", "graph.dfs()", "dfs()")
   dfs(
     graph = graph,
     root = root,
@@ -495,7 +495,7 @@ graph.dfs <- function(
 #' @export
 graph.density <- function(graph, loops = FALSE) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.density()", "edge_density()")
+  lifecycle::deprecate_warn("2.0.0", "graph.density()", "edge_density()")
   edge_density(graph = graph, loops = loops)
 } # nocov end
 
@@ -511,7 +511,7 @@ graph.density <- function(graph, loops = FALSE) {
 #' @export
 graph.coreness <- function(graph, mode = c("all", "out", "in")) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.coreness()", "coreness()")
+  lifecycle::deprecate_warn("2.0.0", "graph.coreness()", "coreness()")
   coreness(graph = graph, mode = mode)
 } # nocov end
 
@@ -544,7 +544,7 @@ graph.bfs <- function(
   neimode
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.bfs()", "bfs()")
+  lifecycle::deprecate_warn("2.0.0", "graph.bfs()", "bfs()")
   bfs(
     graph = graph,
     root = root,
@@ -581,7 +581,7 @@ farthest.nodes <- function(
   weights = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "farthest.nodes()", "farthest_vertices()")
+  lifecycle::deprecate_warn("2.0.0", "farthest.nodes()", "farthest_vertices()")
   farthest_vertices(
     graph = graph,
     directed = directed,
@@ -602,7 +602,7 @@ farthest.nodes <- function(
 #' @export
 degree.distribution <- function(graph, cumulative = FALSE, ...) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "degree.distribution()",
     "degree_distribution()"
@@ -622,7 +622,7 @@ degree.distribution <- function(graph, cumulative = FALSE, ...) {
 #' @export
 count.multiple <- function(graph, eids = E(graph)) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "count.multiple()", "count_multiple()")
+  lifecycle::deprecate_warn("2.0.0", "count.multiple()", "count_multiple()")
   count_multiple(graph = graph, eids = eids)
 } # nocov end
 
@@ -638,7 +638,7 @@ count.multiple <- function(graph, eids = E(graph)) {
 #' @export
 clusters <- function(graph, mode = c("weak", "strong")) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "clusters()", "components()")
+  lifecycle::deprecate_warn("2.0.0", "clusters()", "components()")
   components(graph = graph, mode = mode)
 } # nocov end
 
@@ -660,7 +660,7 @@ average.path.length <- function(
   details = FALSE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "average.path.length()", "mean_distance()")
+  lifecycle::deprecate_warn("2.0.0", "average.path.length()", "mean_distance()")
   mean_distance(
     graph = graph,
     weights = weights,
@@ -1639,7 +1639,7 @@ subgraph_from_edges <- function(graph, eids, delete.vertices = TRUE) {
 #' @export
 subgraph.edges <- function(graph, eids, delete.vertices = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.1.0",
     "subgraph.edges()",
     "subgraph_from_edges()"
@@ -2725,7 +2725,7 @@ bfs <- function(
   }
 
   if (lifecycle::is_present(father)) {
-    lifecycle::deprecate_warn("2.2.0", "bfs(father = )", "bfs(parent = )")
+    lifecycle::deprecate_stop("2.2.0", "bfs(father = )", "bfs(parent = )")
     if (missing(parent)) {
       parent <- father
     }
@@ -2987,7 +2987,7 @@ dfs <- function(
   }
 
   if (lifecycle::is_present(father)) {
-    lifecycle::deprecate_warn("2.2.0", "dfs(father = )", "dfs(parent = )")
+    lifecycle::deprecate_stop("2.2.0", "dfs(father = )", "dfs(parent = )")
     if (missing(parent)) {
       parent <- father
     }
@@ -3336,7 +3336,7 @@ laplacian_matrix <- function(
 ) {
   # Argument checks
   if (lifecycle::is_present(normalized)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.0.3",
       "make_lattice(normalized = 'provide normalization instead')",
       details = c(

From 977c19427603e7c2238e79227b9932d0ef9dcbed Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 13:40:05 +0200
Subject: [PATCH 41/48] feat!: bump deprecate_soft to deprecate_warn in
 R/structure.info.R

---
 NEWS.md            | 1 +
 R/structure.info.R | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index 1dea43e2094..1b497b0ef55 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,7 @@
 
 ## Deprecated and defunct
 
+- `are.connected(()` is now deprecated with a warning instead of a message.
 - `get.shortest.paths(()` is now deprecated with a warning instead of a message.
 - `get.diameter(()` is now deprecated with a warning instead of a message.
 - `unfold.tree(()` is now deprecated with a warning instead of a message.
diff --git a/R/structure.info.R b/R/structure.info.R
index 813a2a9f93a..3f24c0f6b5b 100644
--- a/R/structure.info.R
+++ b/R/structure.info.R
@@ -10,7 +10,7 @@
 #' @export
 are.connected <- function(graph, v1, v2) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "are.connected()", "are_adjacent()")
+  lifecycle::deprecate_warn("2.0.0", "are.connected()", "are_adjacent()")
   are_adjacent(graph = graph, v1 = v1, v2 = v2)
 } # nocov end
 

From 1378cc961cf3b65549a80de7a2defb983e5609a7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 13:41:39 +0200
Subject: [PATCH 42/48] feat!: bump deprecate_soft to deprecate_warn in
 R/tkplot.R

---
 NEWS.md    |  9 +++++++++
 R/tkplot.R | 20 ++++++++++----------
 2 files changed, 19 insertions(+), 10 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 1b497b0ef55..f01f57897ee 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,15 @@
 
 ## Deprecated and defunct
 
+- `tkplot.setcoords(()` is now deprecated with a warning instead of a message.
+- `tkplot.rotate(()` is now deprecated with a warning instead of a message.
+- `tkplot.reshape(()` is now deprecated with a warning instead of a message.
+- `tkplot.off(()` is now deprecated with a warning instead of a message.
+- `tkplot.getcoords(()` is now deprecated with a warning instead of a message.
+- `tkplot.fit.to.screen(()` is now deprecated with a warning instead of a message.
+- `tkplot.close(()` is now deprecated with a warning instead of a message.
+- `tkplot.center(()` is now deprecated with a warning instead of a message.
+- `tkplot.canvas(()` is now deprecated with a warning instead of a message.
 - `are.connected(()` is now deprecated with a warning instead of a message.
 - `get.shortest.paths(()` is now deprecated with a warning instead of a message.
 - `get.diameter(()` is now deprecated with a warning instead of a message.
diff --git a/R/tkplot.R b/R/tkplot.R
index 0e39ec364a8..1092800a955 100644
--- a/R/tkplot.R
+++ b/R/tkplot.R
@@ -10,7 +10,7 @@
 #' @export
 tkplot.setcoords <- function(tkp.id, coords) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "tkplot.setcoords()", "tk_set_coords()")
+  lifecycle::deprecate_warn("2.0.0", "tkplot.setcoords()", "tk_set_coords()")
   tk_set_coords(tkp.id = tkp.id, coords = coords)
 } # nocov end
 
@@ -26,7 +26,7 @@ tkplot.setcoords <- function(tkp.id, coords) {
 #' @export
 tkplot.rotate <- function(tkp.id, degree = NULL, rad = NULL) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "tkplot.rotate()", "tk_rotate()")
+  lifecycle::deprecate_warn("2.0.0", "tkplot.rotate()", "tk_rotate()")
   tk_rotate(tkp.id = tkp.id, degree = degree, rad = rad)
 } # nocov end
 
@@ -42,7 +42,7 @@ tkplot.rotate <- function(tkp.id, degree = NULL, rad = NULL) {
 #' @export
 tkplot.reshape <- function(tkp.id, newlayout, ..., params) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "tkplot.reshape()", "tk_reshape()")
+  lifecycle::deprecate_warn("2.0.0", "tkplot.reshape()", "tk_reshape()")
   tk_reshape(tkp.id = tkp.id, newlayout = newlayout, params = params, ...)
 } # nocov end
 
@@ -58,7 +58,7 @@ tkplot.reshape <- function(tkp.id, newlayout, ..., params) {
 #' @export
 tkplot.off <- function() {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "tkplot.off()", "tk_off()")
+  lifecycle::deprecate_warn("2.0.0", "tkplot.off()", "tk_off()")
   tk_off()
 } # nocov end
 
@@ -74,7 +74,7 @@ tkplot.off <- function() {
 #' @export
 tkplot.getcoords <- function(tkp.id, norm = FALSE) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "tkplot.getcoords()", "tk_coords()")
+  lifecycle::deprecate_warn("2.0.0", "tkplot.getcoords()", "tk_coords()")
   tk_coords(tkp.id = tkp.id, norm = norm)
 } # nocov end
 
@@ -90,7 +90,7 @@ tkplot.getcoords <- function(tkp.id, norm = FALSE) {
 #' @export
 tkplot.fit.to.screen <- function(tkp.id, width = NULL, height = NULL) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "tkplot.fit.to.screen()", "tk_fit()")
+  lifecycle::deprecate_warn("2.0.0", "tkplot.fit.to.screen()", "tk_fit()")
   tk_fit(tkp.id = tkp.id, width = width, height = height)
 } # nocov end
 
@@ -106,7 +106,7 @@ tkplot.fit.to.screen <- function(tkp.id, width = NULL, height = NULL) {
 #' @export
 tkplot.export.postscript <- function(tkp.id) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "tkplot.export.postscript()",
     "tk_postscript()"
@@ -126,7 +126,7 @@ tkplot.export.postscript <- function(tkp.id) {
 #' @export
 tkplot.close <- function(tkp.id, window.close = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "tkplot.close()", "tk_close()")
+  lifecycle::deprecate_warn("2.0.0", "tkplot.close()", "tk_close()")
   tk_close(tkp.id = tkp.id, window.close = window.close)
 } # nocov end
 
@@ -142,7 +142,7 @@ tkplot.close <- function(tkp.id, window.close = TRUE) {
 #' @export
 tkplot.center <- function(tkp.id) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "tkplot.center()", "tk_center()")
+  lifecycle::deprecate_warn("2.0.0", "tkplot.center()", "tk_center()")
   tk_center(tkp.id = tkp.id)
 } # nocov end
 
@@ -158,7 +158,7 @@ tkplot.center <- function(tkp.id) {
 #' @export
 tkplot.canvas <- function(tkp.id) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "tkplot.canvas()", "tk_canvas()")
+  lifecycle::deprecate_warn("2.0.0", "tkplot.canvas()", "tk_canvas()")
   tk_canvas(tkp.id = tkp.id)
 } # nocov end
 #   IGraph R package

From 49c740d1eff8cc36ec249361e149e724ba1f7703 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 13:42:47 +0200
Subject: [PATCH 43/48] feat!: bump deprecate_soft to deprecate_warn in
 R/topology.R

---
 NEWS.md      |  2 ++
 R/topology.R | 10 +++++-----
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index f01f57897ee..41055bcdeba 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,8 @@
 
 ## Deprecated and defunct
 
+- `permute.vertices(()` is now deprecated with a warning instead of a message.
+- `automorphisms(()` is now deprecated with a warning instead of a message.
 - `tkplot.setcoords(()` is now deprecated with a warning instead of a message.
 - `tkplot.rotate(()` is now deprecated with a warning instead of a message.
 - `tkplot.reshape(()` is now deprecated with a warning instead of a message.
diff --git a/R/topology.R b/R/topology.R
index 8386e479087..2d951b778c8 100644
--- a/R/topology.R
+++ b/R/topology.R
@@ -10,7 +10,7 @@
 #' @export
 permute.vertices <- function(graph, permutation) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "permute.vertices()", "permute()")
+  lifecycle::deprecate_warn("2.0.0", "permute.vertices()", "permute()")
   permute(graph = graph, permutation = permutation)
 } # nocov end
 
@@ -26,7 +26,7 @@ permute.vertices <- function(graph, permutation) {
 #' @export
 graph.isocreate <- function(size, number, directed = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "graph.isocreate()",
     "graph_from_isomorphism_class()"
@@ -54,7 +54,7 @@ graph.automorphisms <- function(
   sh = c("fm", "f", "fs", "fl", "flm", "fsm")
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "graph.automorphisms()",
     "count_automorphisms()"
@@ -78,7 +78,7 @@ canonical.permutation <- function(
   sh = c("fm", "f", "fs", "fl", "flm", "fsm")
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "canonical.permutation()",
     "canonical_permutation()"
@@ -102,7 +102,7 @@ automorphisms <- function(
   sh = c("fm", "f", "fs", "fl", "flm", "fsm")
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "automorphisms()", "count_automorphisms()")
+  lifecycle::deprecate_warn("2.0.0", "automorphisms()", "count_automorphisms()")
   count_automorphisms(graph = graph, colors = colors, sh = sh)
 } # nocov end
 

From 12a64ac0ec4e813a92847c09d19bdaf803fae638 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 13:43:48 +0200
Subject: [PATCH 44/48] feat!: bump deprecate_soft to deprecate_warn in
 R/triangles.R

---
 R/triangles.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/triangles.R b/R/triangles.R
index a318bc66c6e..723d1fc08bb 100644
--- a/R/triangles.R
+++ b/R/triangles.R
@@ -10,7 +10,7 @@
 #' @export
 adjacent.triangles <- function(graph, vids = V(graph)) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "adjacent.triangles()",
     "count_triangles()"

From c763bdae1c7e8d54a83581eaf88f0b63c5648ce6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 13:46:02 +0200
Subject: [PATCH 45/48] feat!: bump deprecate_soft to deprecate_warn in
 R/versions.R

---
 NEWS.md      | 1 +
 R/versions.R | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index 41055bcdeba..07f8ebd4528 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,7 @@
 
 ## Deprecated and defunct
 
+- `igraph.version(()` is now deprecated with a warning instead of a message.
 - `permute.vertices(()` is now deprecated with a warning instead of a message.
 - `automorphisms(()` is now deprecated with a warning instead of a message.
 - `tkplot.setcoords(()` is now deprecated with a warning instead of a message.
diff --git a/R/versions.R b/R/versions.R
index 4855aa30ffe..5effcc955f6 100644
--- a/R/versions.R
+++ b/R/versions.R
@@ -202,7 +202,7 @@ clear_native_ptr <- function(g) {
 #' @export
 igraph.version <- function() {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "igraph.version()", "igraph_version()")
+  lifecycle::deprecate_warn("2.0.0", "igraph.version()", "igraph_version()")
   igraph_version()
 } # nocov end
 

From e26db2522e3bf56de1247d3116605b13aaf9c2fc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 13:54:21 +0200
Subject: [PATCH 46/48] chore: tools

---
 tools/bump-lifecycle.R   | 440 +++++++++++++++++++++++++++++++++++++++
 tools/commit-lifecycle.R |  30 ++-
 tools/handle-lifecycle.R |  98 +++++++++
 3 files changed, 550 insertions(+), 18 deletions(-)
 create mode 100644 tools/bump-lifecycle.R
 create mode 100644 tools/handle-lifecycle.R

diff --git a/tools/bump-lifecycle.R b/tools/bump-lifecycle.R
new file mode 100644
index 00000000000..24bccd6e139
--- /dev/null
+++ b/tools/bump-lifecycle.R
@@ -0,0 +1,440 @@
+library(treesitter)
+library(treesitter.r)
+
+# --- Reset to baseline (undo any previous partial run) ---
+# .claude/settings.local.json is untracked, so git reset --hard leaves it alone.
+# This script is tracked, so we save and restore it across the reset.
+local({
+  baseline <- "fb68fc60b2e673a2994885ed454dbbaca709096c"
+  script_path <- here::here("tools", "bump-lifecycle.R")
+  saved <- readLines(script_path, warn = FALSE)
+  cli::cli_alert_info("Resetting to {substr(baseline, 1L, 7L)} ...")
+  system2("git", c("-C", here::here(), "reset", "--hard", baseline))
+  writeLines(saved, script_path)
+  cli::cli_alert_success("Restored tools/bump-lifecycle.R")
+})
+
+lang <- treesitter.r::language()
+
+# deprecate_soft / deprecate_warn / deprecate_stop are all 14 chars — same length,
+# so substr<-() replacement never shifts line/column positions.
+next_level <- c(
+  deprecate_soft = "deprecate_warn",
+  deprecate_warn = "deprecate_stop"
+)
+
+# Uncomment to inspect node types for a sample expression:
+# text <- 'lifecycle::deprecate_soft("1.0.0", "foo()")'
+# node_show_s_expression(tree_root_node(parser_parse(parser(lang), text)))
+
+# --- tree navigation helpers ---
+
+fn_to_call <- function(fn_node) {
+  # "deprecate_X" identifier -> namespace_operator -> call
+  node_parent(node_parent(fn_node))
+}
+
+# A pure shim is a function whose body contains exactly one statement: the deprecate_stop() call.
+is_pure_shim <- function(fn_node) {
+  call_node <- fn_to_call(fn_node)
+  body_node <- node_parent(call_node) # braced_expression (the { } body)
+  fn_def_node <- node_parent(body_node) # function_definition
+  asgn_node <- node_parent(fn_def_node) # binary_operator (<-)
+
+  if (node_type(fn_def_node) != "function_definition") {
+    return(FALSE)
+  }
+  if (node_type(asgn_node) != "binary_operator") {
+    return(FALSE)
+  }
+  length(node_named_children(body_node)) == 1L
+}
+
+get_asgn_node <- function(fn_node) {
+  node_parent(node_parent(node_parent(fn_to_call(fn_node))))
+}
+
+get_fn_name <- function(fn_node) {
+  node_text(node_named_children(get_asgn_node(fn_node))[[1L]])
+}
+
+# Returns TRUE if fn_name appears as an identifier in any R file other than current_path.
+# Used to protect shims that are still referenced internally.
+is_referenced_elsewhere <- function(fn_name, current_path) {
+  escaped <- gsub("([.^$|*+?(){}\\[\\]])", "\\\\\\1", fn_name)
+  pattern <- paste0("(?<![A-Za-z0-9._])", escaped, "(?![A-Za-z0-9._])")
+  other_files <- setdiff(r_files, current_path)
+  any(vapply(other_files, function(f) {
+    any(grepl(pattern, readLines(f, warn = FALSE), perl = TRUE))
+  }, logical(1)))
+}
+
+# Scan backwards from first_fn_line (1-indexed) past blank lines and roxygen #' lines.
+preceding_doc_range <- function(lines, first_fn_line) {
+  i <- first_fn_line - 1L
+  while (i >= 1L && grepl("^\\s*(#'.*)?$", lines[i])) {
+    i <- i - 1L
+  }
+  if (i + 1L > first_fn_line - 1L) {
+    integer(0L)
+  } else {
+    seq(i + 1L, first_fn_line - 1L)
+  }
+}
+
+# --- test helpers ---
+
+# Add `error = TRUE` to the expect_snapshot() call at row_1indexed in test_file.
+add_error_true <- function(test_file, row_1indexed) {
+  if (!file.exists(test_file)) {
+    return(invisible(FALSE))
+  }
+  lines <- readLines(test_file, warn = FALSE)
+  text <- paste(lines, collapse = "\n")
+  root <- tree_root_node(parser_parse(parser(lang), text))
+
+  q <- query(
+    lang,
+    '(call function: (identifier) @fn (#eq? @fn "expect_snapshot"))'
+  )
+  caps <- query_captures(q, root)
+  fn_nodes <- caps$node[caps$name == "fn"]
+
+  for (fn in fn_nodes) {
+    if (point_row(node_start_point(fn)) + 1L != row_1indexed) {
+      next
+    }
+
+    call_node <- node_parent(fn)
+    args_node <- Filter(
+      \(n) node_type(n) == "arguments",
+      node_children(call_node)
+    )
+    if (length(args_node) == 0L) {
+      next
+    }
+    args_node <- args_node[[1L]]
+
+    if (grepl("error\\s*=\\s*TRUE", node_text(args_node))) {
+      return(invisible(FALSE))
+    }
+
+    # Insert `error = TRUE, ` right after the opening `(`
+    open_row <- point_row(node_start_point(args_node)) + 1L
+    open_col <- point_column(node_start_point(args_node)) + 1L
+    line <- lines[open_row]
+    lines[open_row] <- paste0(
+      substr(line, 1L, open_col),
+      "error = TRUE, ",
+      substr(line, open_col + 1L, nchar(line))
+    )
+    writeLines(lines, test_file)
+    return(invisible(TRUE))
+  }
+  invisible(FALSE)
+}
+
+# Patch expect_snapshot() calls for lifecycle errors found by run_one().
+# failures: list of {msg, src_file, line} returned from the callr subprocess.
+fix_lifecycle_snapshot_failures <- function(failures, root) {
+  fixed <- FALSE
+  for (f in failures) {
+    if (!grepl("lifecycle_error_deprecated|defunctError|defunct", f$msg)) next
+    src_file <- f$src_file
+    line     <- f$line
+    if (is.null(src_file) || is.null(line) || is.na(line)) next
+    file_path <- if (file.exists(src_file)) src_file else {
+      file.path(root, "tests", "testthat", basename(src_file))
+    }
+    if (!file.exists(file_path)) next
+    if (add_error_true(file_path, line)) fixed <- TRUE
+  }
+  fixed
+}
+
+# --- test runner ---
+
+# Accumulates {commit, tests} pairs for changes that left tests failing.
+unresolved_failures <- list()
+n_commits <- 0L
+
+# Returns character vector of still-failing test names (empty if all pass).
+run_tests <- function(path) {
+  src_name  <- fs::path_ext_remove(fs::path_file(path))
+  test_file <- here::here("tests", "testthat", paste0("test-", src_name, ".R"))
+  if (!file.exists(test_file)) return(character(0))
+
+  root <- here::here()
+
+  # Each call runs in a fresh subprocess — no memory accumulation in the main session.
+  run_one <- function(update_snapshots = FALSE) {
+    callr::r(
+      function(root, src_name, update_snapshots) {
+        if (update_snapshots) options(testthat.snapshot.update = TRUE)
+        result <- testthat::test_local(
+          root, filter = src_name, stop_on_failure = FALSE, reporter = "minimal"
+        )
+        df <- as.data.frame(result)
+        failures <- list()
+        for (fr in result) {
+          for (exp in fr) {
+            if (!inherits(exp, c("expectation_failure", "expectation_error"))) next
+            msg      <- tryCatch(conditionMessage(exp), error = function(e) "")
+            srcref   <- tryCatch(exp$srcref, error = function(e) NULL)
+            src_file <- tryCatch(attr(srcref, "srcfile")$filename, error = function(e) NULL)
+            line     <- tryCatch(as.integer(srcref)[1L], error = function(e) NA_integer_)
+            failures[[length(failures) + 1L]] <- list(msg = msg, src_file = src_file, line = line)
+          }
+        }
+        list(
+          n_fail    = sum(df$failed, na.rm = TRUE) + sum(df$error, na.rm = TRUE),
+          bad_tests = df$test[df$failed + df$error > 0L],
+          failures  = failures
+        )
+      },
+      args = list(root = root, src_name = src_name, update_snapshots = update_snapshots)
+    )
+  }
+
+  out <- run_one()
+
+  if (out$n_fail > 0L && fix_lifecycle_snapshot_failures(out$failures, root)) {
+    out <- run_one()
+  }
+
+  if (out$n_fail > 0L) {
+    out <- run_one(update_snapshots = TRUE)
+    if (out$n_fail > 0L) {
+      bad <- out$bad_tests
+      cli::cli_alert_warning(
+        "{out$n_fail} test(s) still failing after snapshot update (need manual fixes): {paste(bad, collapse = ', ')}"
+      )
+      return(bad)
+    }
+  }
+
+  character(0)
+}
+
+commit_change <- function(path, msg) {
+  bad <- run_tests(path)
+  if (length(bad) > 0L) {
+    unresolved_failures[[length(unresolved_failures) + 1L]] <<- list(
+      commit = msg,
+      tests  = bad
+    )
+  }
+  gert::git_add(fs::path_rel(path, here::here()))
+  # Stage any modified test or snapshot files produced during the test run
+  status <- gert::git_status()
+  extra <- status$file[startsWith(status$file, "tests/") & !status$staged]
+  if (length(extra) > 0L) {
+    gert::git_add(extra)
+  }
+  gert::git_commit(msg)
+  n_commits <<- n_commits + 1L
+}
+
+write_unresolved_report <- function() {
+  if (length(unresolved_failures) == 0L) return(invisible(NULL))
+  out <- here::here("lifecycle-TODO.md")
+  lines <- c(
+    "# lifecycle bump — unresolved test failures",
+    "",
+    paste0(
+      "These commits were made but left tests failing that need manual fixes ",
+      "(tests call deprecated functions expecting a result, not an error):"
+    ),
+    ""
+  )
+  for (item in unresolved_failures) {
+    lines <- c(
+      lines,
+      paste0("## `", item$commit, "`"),
+      "",
+      paste0("- ", item$tests),
+      ""
+    )
+  }
+  writeLines(lines, out)
+  cli::cli_alert_warning("Wrote {length(unresolved_failures)} unresolved item(s) to lifecycle-TODO.md")
+}
+
+# --- queries ---
+
+bump_query <- query(
+  lang,
+  '
+  (call
+    function: (namespace_operator
+      lhs: (identifier) @ns
+      rhs: (identifier) @fn)
+    arguments: (arguments
+      (argument)
+      (argument value: (string content: (string_content) @what)))
+    (#eq? @ns "lifecycle")
+    (#match? @fn "^deprecate_(soft|warn)$"))
+'
+)
+
+stop_query <- query(
+  lang,
+  '
+  (call
+    function: (namespace_operator
+      lhs: (identifier) @ns
+      rhs: (identifier) @fn)
+    arguments: (arguments
+      (argument)
+      (argument value: (string content: (string_content) @what)))
+    (#eq? @ns "lifecycle")
+    (#eq? @fn "deprecate_stop"))
+'
+)
+
+# --- per-file processing ---
+
+process_file <- function(path) {
+
+  # ---- 1. BUMP: deprecate_soft -> deprecate_warn, deprecate_warn -> deprecate_stop ----
+
+  lines <- readLines(path, warn = FALSE)
+  root <- tree_root_node(parser_parse(
+    parser(lang),
+    paste(lines, collapse = "\n")
+  ))
+  matches <- query_matches(bump_query, root)[[1]]
+
+  if (length(matches) > 0L) {
+    fn_nodes <- lapply(matches, \(m) m$node[m$name == "fn"][[1]])
+    what_nodes <- lapply(matches, \(m) m$node[m$name == "what"][[1]])
+    rows <- vapply(fn_nodes, \(n) point_row(node_start_point(n)), numeric(1))
+    cols <- vapply(fn_nodes, \(n) point_column(node_start_point(n)), numeric(1))
+    old_names <- vapply(fn_nodes, node_text, character(1))
+    whats <- vapply(what_nodes, node_text, character(1))
+
+    # Calls with >2 args produce a duplicate match for the same @fn node.
+    # Keep only the first occurrence (args 1+2 = version+what).
+    dups <- duplicated(paste(rows, cols, sep = ":"))
+    fn_nodes <- fn_nodes[!dups]
+    what_nodes <- what_nodes[!dups]
+    rows <- rows[!dups]
+    cols <- cols[!dups]
+    old_names <- old_names[!dups]
+    whats <- whats[!dups]
+
+    for (i in order(rows, decreasing = TRUE)) {
+      r <- rows[i] + 1L
+      c <- cols[i] + 1L
+      new_name <- next_level[[old_names[i]]]
+      substr(lines[r], c, c + 13L) <- new_name
+      writeLines(lines, path)
+      msg <- sprintf(
+        "feat!: bump %s from %s to %s",
+        whats[i],
+        old_names[i],
+        new_name
+      )
+      commit_change(path, msg)
+    }
+  }
+
+  # ---- 2. REMOVE: pure deprecate_stop shim functions ----
+
+  # Re-parse after bumps (newly-bumped deprecate_stop shims are included here).
+  lines <- readLines(path, warn = FALSE)
+  root <- tree_root_node(parser_parse(
+    parser(lang),
+    paste(lines, collapse = "\n")
+  ))
+  stop_matches <- query_matches(stop_query, root)[[1]]
+  fn_nodes <- lapply(stop_matches, \(m) m$node[m$name == "fn"][[1]])
+  what_nodes <- lapply(stop_matches, \(m) m$node[m$name == "what"][[1]])
+
+  # Same deduplication: calls with a third argument (e.g. `with`) match twice.
+  if (length(fn_nodes) > 0L) {
+    stop_rows <- vapply(
+      fn_nodes,
+      \(n) point_row(node_start_point(n)),
+      numeric(1)
+    )
+    stop_cols <- vapply(
+      fn_nodes,
+      \(n) point_column(node_start_point(n)),
+      numeric(1)
+    )
+    stop_dups <- duplicated(paste(stop_rows, stop_cols, sep = ":"))
+    fn_nodes <- fn_nodes[!stop_dups]
+    what_nodes <- what_nodes[!stop_dups]
+  }
+
+  if (length(fn_nodes) == 0L) {
+    return(invisible(NULL))
+  }
+
+  shim_mask <- vapply(fn_nodes, is_pure_shim, logical(1))
+  fn_shims <- fn_nodes[shim_mask]
+  what_shims <- what_nodes[shim_mask]
+  if (length(fn_shims) == 0L) {
+    return(invisible(NULL))
+  }
+
+  asgn_nodes <- lapply(fn_shims, get_asgn_node)
+  starts <- vapply(
+    asgn_nodes,
+    \(n) point_row(node_start_point(n)) + 1L,
+    numeric(1)
+  )
+  ends <- vapply(asgn_nodes, \(n) point_row(node_end_point(n)) + 1L, numeric(1))
+  whats <- vapply(what_shims, node_text, character(1))
+
+  for (j in order(starts, decreasing = TRUE)) {
+    fn_name <- get_fn_name(fn_shims[[j]])
+    if (is_referenced_elsewhere(fn_name, path)) {
+      cli::cli_alert_warning(
+        "Skipping removal of {fn_name}(): still referenced in other R files (fix iterators manually)"
+      )
+      unresolved_failures[[length(unresolved_failures) + 1L]] <<- list(
+        commit = sprintf("feat!: remove deprecated %s (lifecycle::deprecate_stop)", whats[j]),
+        tests  = paste0(fn_name, "() skipped: still referenced in other R files")
+      )
+      next
+    }
+    lines <- readLines(path, warn = FALSE)
+    doc_range <- preceding_doc_range(lines, starts[j])
+    fn_range <- seq(starts[j], ends[j])
+    after_line <- ends[j] + 1L
+    trail <- if (
+      after_line <= length(lines) && grepl("^\\s*$", lines[after_line])
+    ) {
+      after_line
+    } else {
+      integer(0L)
+    }
+    writeLines(lines[-c(doc_range, fn_range, trail)], path)
+    msg <- sprintf(
+      "feat!: remove deprecated %s (lifecycle::deprecate_stop)",
+      whats[j]
+    )
+    commit_change(path, msg)
+  }
+}
+
+# --- run over all R source files ---
+
+r_files <- fs::dir_ls(here::here("R"), glob = "*.R")
+
+cli::cli_progress_bar(
+  total = length(r_files),
+  format      = "{cli::pb_bar} {cli::pb_current}/{cli::pb_total} | {n_commits} commits | ETA {cli::pb_eta} | {cli::pb_status}",
+  format_done = "{cli::pb_total} files done | {n_commits} commits in {cli::pb_elapsed}",
+  clear = FALSE
+)
+for (path in r_files) {
+  cli::cli_progress_update(status = basename(path))
+  process_file(path)
+  cli::cli_progress_update(inc = 1L)
+}
+cli::cli_progress_done()
+
+write_unresolved_report()
diff --git a/tools/commit-lifecycle.R b/tools/commit-lifecycle.R
index 71b175fe519..30de5ae3083 100644
--- a/tools/commit-lifecycle.R
+++ b/tools/commit-lifecycle.R
@@ -37,20 +37,18 @@
 # gert::git_pull(repo = here::here(), remote = "origin", refspec = "main")
 # cli::cli_alert_success("Pulled and fast-forwarded to main")
 
-gert::git_fetch(
-  "origin",
-  refspec = "refs/heads/main:refs/heads/main",
-  repo = here::here()
-)
-gert::git_reset_mixed("main", repo = here::here())
+if (gert::git_ahead_behind("main", repo = here::here())$ahead == 0) {
+  gert::git_fetch("origin", refspec = "refs/heads/main:refs/heads/main", repo = here::here())
+  gert::git_reset_mixed("main", repo = here::here())
+} else {
+  cli::cli_alert_info("Commits already ahead of main — skipping reset, resuming")
+}
 
-usethis::use_build_ignore("lifecycle")
-usethis::use_git_ignore("lifecycle")
+if (gert::git_ahead_behind("main", repo = here::here())$ahead == 0) {
+  usethis::use_build_ignore("lifecycle")
+  usethis::use_git_ignore("lifecycle")
 
-gert::git_add(
-  c("tools/commit-lifecycle.R", ".gitignore", ".Rbuildignore"),
-  repo = here::here()
-)
+gert::git_add(c("tools/commit-lifecycle.R", ".gitignore", ".Rbuildignore"), repo = here::here())
 gert::git_commit("chore: add commit-lifecycle.R script", repo = here::here())
 cli::cli_alert_success("Committed tools/commit-lifecycle.R")
 
@@ -98,14 +96,10 @@ for (stem in tools::file_path_sans_ext(r_files)) {
   devtools::document(quiet = TRUE)
   tryCatch(
     callr::r(
-      function(pkg, filter) {
-        devtools::test(pkg = pkg, filter = filter, stop_on_failure = FALSE)
-      },
+      function(pkg, filter) devtools::test(pkg = pkg, filter = filter, stop_on_failure = FALSE),
       args = list(pkg = here::here(), filter = stem)
     ),
-    error = function(e) {
-      cli::cli_alert_warning("Tests errored for {stem}: {conditionMessage(e)}")
-    }
+    error = function(e) cli::cli_alert_warning("Tests errored for {stem}: {conditionMessage(e)}")
   )
 
   gert::git_add(c(files_to_stage, "man", "NAMESPACE"), repo = here::here())
diff --git a/tools/handle-lifecycle.R b/tools/handle-lifecycle.R
new file mode 100644
index 00000000000..f0b9a98e417
--- /dev/null
+++ b/tools/handle-lifecycle.R
@@ -0,0 +1,98 @@
+# For each R file still containing lifecycle::deprecate_soft or lifecycle::deprecate_warn:
+# advance the level with regex, document, test (stop on error so you can fix),
+# prompt to continue, add NEWS item, commit.
+
+already_committed <- system2("git", c("diff", "--name-only", "main..HEAD"), stdout = TRUE)
+already_committed <- basename(already_committed[grepl("^R/", already_committed)])
+
+r_files <- sort(setdiff(
+  list.files(here::here("R"), pattern = "\\.R$", full.names = FALSE),
+  already_committed
+))
+
+for (f in r_files) {
+  path <- here::here("R", f)
+  lines <- readLines(path, warn = FALSE)
+
+  has_soft <- any(grepl("lifecycle::deprecate_soft", lines, fixed = TRUE))
+  has_warn <- any(grepl("lifecycle::deprecate_warn", lines, fixed = TRUE))
+
+  if (!has_soft && !has_warn) next
+
+  stem <- tools::file_path_sans_ext(f)
+  cli::cli_alert_info("Processing R/{f}")
+
+  # Extract function names before replacement for NEWS
+  extract_fns <- function(lines, level) {
+    hits <- grep(paste0("lifecycle::", level), lines, fixed = TRUE, value = TRUE)
+    m <- regmatches(hits, regexpr(
+      paste0('lifecycle::', level, '\\([^,]+,\\s*"([^("]+)\\('),
+      hits, perl = TRUE
+    ))
+    sub(paste0('.*"'), "", m[nzchar(m)])
+  }
+  soft_fns <- extract_fns(lines, "deprecate_soft")
+  warn_fns  <- extract_fns(lines, "deprecate_warn")
+
+  # Advance: warn -> stop first to avoid double-replacement
+  lines <- gsub("lifecycle::deprecate_warn", "lifecycle::deprecate_stop", lines, fixed = TRUE)
+  lines <- gsub("lifecycle::deprecate_soft", "lifecycle::deprecate_warn", lines, fixed = TRUE)
+  writeLines(lines, path)
+
+  devtools::document(quiet = TRUE)
+
+  # Tests — stop on failure so the user can fix
+  if (file.exists(here::here("tests", "testthat", paste0("test-", stem, ".R")))) {
+    callr::r(
+      function(pkg, filter) devtools::test(pkg = pkg, filter = filter, stop_on_failure = TRUE),
+      args = list(pkg = here::here(), filter = stem)
+    )
+  }
+
+  answer <- readline(paste0("Tests passed for R/", f, ". Commit? [Enter = yes / n = stop] "))
+  if (trimws(tolower(answer)) == "n") stop("Stopped at R/", f, ". Fix, then commit manually and re-run.")
+
+  # Add NEWS items
+  news_entries <- c(
+    if (length(soft_fns) > 0)
+      paste0("- `", soft_fns, "()` is now deprecated with a warning instead of a message."),
+    if (length(warn_fns) > 0)
+      paste0("- `", warn_fns, "()` is now defunct (errors instead of warning).")
+  )
+
+  news_lines <- readLines(here::here("NEWS.md"), warn = FALSE)
+  depr_idx <- which(news_lines == "## Deprecated and defunct")
+
+  if (length(depr_idx) > 0) {
+    insert_pos <- depr_idx[[1]] + 2L
+    new_news <- c(
+      news_lines[seq_len(insert_pos - 1L)],
+      news_entries,
+      news_lines[seq(insert_pos, length(news_lines))]
+    )
+  } else {
+    first_ver_idx <- which(grepl("^# igraph", news_lines))[[1]]
+    new_news <- c(
+      news_lines[seq_len(first_ver_idx)],
+      "",
+      "## Deprecated and defunct",
+      "",
+      news_entries,
+      "",
+      news_lines[seq(first_ver_idx + 1L, length(news_lines))]
+    )
+  }
+  writeLines(new_news, here::here("NEWS.md"))
+
+  commit_msg <- if (has_soft && has_warn) {
+    paste0("feat!: bump deprecated functions in R/", f)
+  } else if (has_soft) {
+    paste0("feat!: bump deprecate_soft to deprecate_warn in R/", f)
+  } else {
+    paste0("feat!: bump deprecate_warn to deprecate_stop in R/", f)
+  }
+
+  gert::git_add(c(paste0("R/", f), "man", "NAMESPACE", "NEWS.md"), repo = here::here())
+  gert::git_commit(commit_msg, repo = here::here())
+  cli::cli_alert_success("Committed R/{f}")
+}

From 3805f60e5a59053c2b7605531897ea2edfb7008b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 19 May 2026 15:05:00 +0200
Subject: [PATCH 47/48] oops

---
 tools/commit-lifecycle.R | 42 ++++++++++++++++++++++++++++------------
 1 file changed, 30 insertions(+), 12 deletions(-)

diff --git a/tools/commit-lifecycle.R b/tools/commit-lifecycle.R
index 30de5ae3083..36521d3e358 100644
--- a/tools/commit-lifecycle.R
+++ b/tools/commit-lifecycle.R
@@ -38,19 +38,29 @@
 # cli::cli_alert_success("Pulled and fast-forwarded to main")
 
 if (gert::git_ahead_behind("main", repo = here::here())$ahead == 0) {
-  gert::git_fetch("origin", refspec = "refs/heads/main:refs/heads/main", repo = here::here())
+  gert::git_fetch(
+    "origin",
+    refspec = "refs/heads/main:refs/heads/main",
+    repo = here::here()
+  )
   gert::git_reset_mixed("main", repo = here::here())
 } else {
-  cli::cli_alert_info("Commits already ahead of main — skipping reset, resuming")
+  cli::cli_alert_info(
+    "Commits already ahead of main — skipping reset, resuming"
+  )
 }
 
 if (gert::git_ahead_behind("main", repo = here::here())$ahead == 0) {
   usethis::use_build_ignore("lifecycle")
   usethis::use_git_ignore("lifecycle")
 
-gert::git_add(c("tools/commit-lifecycle.R", ".gitignore", ".Rbuildignore"), repo = here::here())
-gert::git_commit("chore: add commit-lifecycle.R script", repo = here::here())
-cli::cli_alert_success("Committed tools/commit-lifecycle.R")
+  gert::git_add(
+    c("tools/commit-lifecycle.R", "tools/handle-lifecycle.R", ".gitignore", ".Rbuildignore"),
+    repo = here::here()
+  )
+  gert::git_commit("chore: add commit-lifecycle.R script", repo = here::here())
+  cli::cli_alert_success("Committed tools/commit-lifecycle.R")
+}
 
 # one commit per R script (copied back from the 'lifecycle' directory) + corresponding R test file if needed + run `document()` + run `test()`.
 
@@ -94,13 +104,21 @@ for (stem in tools::file_path_sans_ext(r_files)) {
   }
 
   devtools::document(quiet = TRUE)
-  tryCatch(
-    callr::r(
-      function(pkg, filter) devtools::test(pkg = pkg, filter = filter, stop_on_failure = FALSE),
-      args = list(pkg = here::here(), filter = stem)
-    ),
-    error = function(e) cli::cli_alert_warning("Tests errored for {stem}: {conditionMessage(e)}")
-  )
+  if (file.exists(lifecycle_test)) {
+    tryCatch(
+      callr::r(
+        function(pkg, filter) {
+          devtools::test(pkg = pkg, filter = filter, stop_on_failure = FALSE)
+        },
+        args = list(pkg = here::here(), filter = stem)
+      ),
+      error = function(e) {
+        cli::cli_alert_warning(
+          "Tests errored for {stem}: {conditionMessage(e)}"
+        )
+      }
+    )
+  }
 
   gert::git_add(c(files_to_stage, "man", "NAMESPACE"), repo = here::here())
   gert::git_commit(

From 4950cf7b366ff283fe675de4c1203ecccae19d00 Mon Sep 17 00:00:00 2001
From: maelle <maelle@users.noreply.github.com>
Date: Tue, 19 May 2026 13:13:04 +0000
Subject: [PATCH 48/48] chore: Auto-update from GitHub Actions

Run: https://github.com/igraph/rigraph/actions/runs/26099065495
---
 tools/bump-lifecycle.R   | 96 ++++++++++++++++++++++++++++------------
 tools/handle-lifecycle.R | 73 +++++++++++++++++++++++-------
 2 files changed, 125 insertions(+), 44 deletions(-)

diff --git a/tools/bump-lifecycle.R b/tools/bump-lifecycle.R
index 24bccd6e139..e940961f15c 100644
--- a/tools/bump-lifecycle.R
+++ b/tools/bump-lifecycle.R
@@ -64,9 +64,13 @@ is_referenced_elsewhere <- function(fn_name, current_path) {
   escaped <- gsub("([.^$|*+?(){}\\[\\]])", "\\\\\\1", fn_name)
   pattern <- paste0("(?<![A-Za-z0-9._])", escaped, "(?![A-Za-z0-9._])")
   other_files <- setdiff(r_files, current_path)
-  any(vapply(other_files, function(f) {
-    any(grepl(pattern, readLines(f, warn = FALSE), perl = TRUE))
-  }, logical(1)))
+  any(vapply(
+    other_files,
+    function(f) {
+      any(grepl(pattern, readLines(f, warn = FALSE), perl = TRUE))
+    },
+    logical(1)
+  ))
 }
 
 # Scan backwards from first_fn_line (1-indexed) past blank lines and roxygen #' lines.
@@ -139,14 +143,22 @@ add_error_true <- function(test_file, row_1indexed) {
 fix_lifecycle_snapshot_failures <- function(failures, root) {
   fixed <- FALSE
   for (f in failures) {
-    if (!grepl("lifecycle_error_deprecated|defunctError|defunct", f$msg)) next
+    if (!grepl("lifecycle_error_deprecated|defunctError|defunct", f$msg)) {
+      next
+    }
     src_file <- f$src_file
-    line     <- f$line
-    if (is.null(src_file) || is.null(line) || is.na(line)) next
-    file_path <- if (file.exists(src_file)) src_file else {
+    line <- f$line
+    if (is.null(src_file) || is.null(line) || is.na(line)) {
+      next
+    }
+    file_path <- if (file.exists(src_file)) {
+      src_file
+    } else {
       file.path(root, "tests", "testthat", basename(src_file))
     }
-    if (!file.exists(file_path)) next
+    if (!file.exists(file_path)) {
+      next
+    }
     if (add_error_true(file_path, line)) fixed <- TRUE
   }
   fixed
@@ -160,9 +172,11 @@ n_commits <- 0L
 
 # Returns character vector of still-failing test names (empty if all pass).
 run_tests <- function(path) {
-  src_name  <- fs::path_ext_remove(fs::path_file(path))
+  src_name <- fs::path_ext_remove(fs::path_file(path))
   test_file <- here::here("tests", "testthat", paste0("test-", src_name, ".R"))
-  if (!file.exists(test_file)) return(character(0))
+  if (!file.exists(test_file)) {
+    return(character(0))
+  }
 
   root <- here::here()
 
@@ -170,29 +184,49 @@ run_tests <- function(path) {
   run_one <- function(update_snapshots = FALSE) {
     callr::r(
       function(root, src_name, update_snapshots) {
-        if (update_snapshots) options(testthat.snapshot.update = TRUE)
+        if (update_snapshots) {
+          options(testthat.snapshot.update = TRUE)
+        }
         result <- testthat::test_local(
-          root, filter = src_name, stop_on_failure = FALSE, reporter = "minimal"
+          root,
+          filter = src_name,
+          stop_on_failure = FALSE,
+          reporter = "minimal"
         )
         df <- as.data.frame(result)
         failures <- list()
         for (fr in result) {
           for (exp in fr) {
-            if (!inherits(exp, c("expectation_failure", "expectation_error"))) next
-            msg      <- tryCatch(conditionMessage(exp), error = function(e) "")
-            srcref   <- tryCatch(exp$srcref, error = function(e) NULL)
-            src_file <- tryCatch(attr(srcref, "srcfile")$filename, error = function(e) NULL)
-            line     <- tryCatch(as.integer(srcref)[1L], error = function(e) NA_integer_)
-            failures[[length(failures) + 1L]] <- list(msg = msg, src_file = src_file, line = line)
+            if (!inherits(exp, c("expectation_failure", "expectation_error"))) {
+              next
+            }
+            msg <- tryCatch(conditionMessage(exp), error = function(e) "")
+            srcref <- tryCatch(exp$srcref, error = function(e) NULL)
+            src_file <- tryCatch(
+              attr(srcref, "srcfile")$filename,
+              error = function(e) NULL
+            )
+            line <- tryCatch(as.integer(srcref)[1L], error = function(e) {
+              NA_integer_
+            })
+            failures[[length(failures) + 1L]] <- list(
+              msg = msg,
+              src_file = src_file,
+              line = line
+            )
           }
         }
         list(
-          n_fail    = sum(df$failed, na.rm = TRUE) + sum(df$error, na.rm = TRUE),
+          n_fail = sum(df$failed, na.rm = TRUE) + sum(df$error, na.rm = TRUE),
           bad_tests = df$test[df$failed + df$error > 0L],
-          failures  = failures
+          failures = failures
         )
       },
-      args = list(root = root, src_name = src_name, update_snapshots = update_snapshots)
+      args = list(
+        root = root,
+        src_name = src_name,
+        update_snapshots = update_snapshots
+      )
     )
   }
 
@@ -221,7 +255,7 @@ commit_change <- function(path, msg) {
   if (length(bad) > 0L) {
     unresolved_failures[[length(unresolved_failures) + 1L]] <<- list(
       commit = msg,
-      tests  = bad
+      tests = bad
     )
   }
   gert::git_add(fs::path_rel(path, here::here()))
@@ -236,7 +270,9 @@ commit_change <- function(path, msg) {
 }
 
 write_unresolved_report <- function() {
-  if (length(unresolved_failures) == 0L) return(invisible(NULL))
+  if (length(unresolved_failures) == 0L) {
+    return(invisible(NULL))
+  }
   out <- here::here("lifecycle-TODO.md")
   lines <- c(
     "# lifecycle bump — unresolved test failures",
@@ -257,7 +293,9 @@ write_unresolved_report <- function() {
     )
   }
   writeLines(lines, out)
-  cli::cli_alert_warning("Wrote {length(unresolved_failures)} unresolved item(s) to lifecycle-TODO.md")
+  cli::cli_alert_warning(
+    "Wrote {length(unresolved_failures)} unresolved item(s) to lifecycle-TODO.md"
+  )
 }
 
 # --- queries ---
@@ -295,7 +333,6 @@ stop_query <- query(
 # --- per-file processing ---
 
 process_file <- function(path) {
-
   # ---- 1. BUMP: deprecate_soft -> deprecate_warn, deprecate_warn -> deprecate_stop ----
 
   lines <- readLines(path, warn = FALSE)
@@ -395,8 +432,11 @@ process_file <- function(path) {
         "Skipping removal of {fn_name}(): still referenced in other R files (fix iterators manually)"
       )
       unresolved_failures[[length(unresolved_failures) + 1L]] <<- list(
-        commit = sprintf("feat!: remove deprecated %s (lifecycle::deprecate_stop)", whats[j]),
-        tests  = paste0(fn_name, "() skipped: still referenced in other R files")
+        commit = sprintf(
+          "feat!: remove deprecated %s (lifecycle::deprecate_stop)",
+          whats[j]
+        ),
+        tests = paste0(fn_name, "() skipped: still referenced in other R files")
       )
       next
     }
@@ -426,7 +466,7 @@ r_files <- fs::dir_ls(here::here("R"), glob = "*.R")
 
 cli::cli_progress_bar(
   total = length(r_files),
-  format      = "{cli::pb_bar} {cli::pb_current}/{cli::pb_total} | {n_commits} commits | ETA {cli::pb_eta} | {cli::pb_status}",
+  format = "{cli::pb_bar} {cli::pb_current}/{cli::pb_total} | {n_commits} commits | ETA {cli::pb_eta} | {cli::pb_status}",
   format_done = "{cli::pb_total} files done | {n_commits} commits in {cli::pb_elapsed}",
   clear = FALSE
 )
diff --git a/tools/handle-lifecycle.R b/tools/handle-lifecycle.R
index f0b9a98e417..5103b1c8e37 100644
--- a/tools/handle-lifecycle.R
+++ b/tools/handle-lifecycle.R
@@ -2,8 +2,15 @@
 # advance the level with regex, document, test (stop on error so you can fix),
 # prompt to continue, add NEWS item, commit.
 
-already_committed <- system2("git", c("diff", "--name-only", "main..HEAD"), stdout = TRUE)
-already_committed <- basename(already_committed[grepl("^R/", already_committed)])
+already_committed <- system2(
+  "git",
+  c("diff", "--name-only", "main..HEAD"),
+  stdout = TRUE
+)
+already_committed <- basename(already_committed[grepl(
+  "^R/",
+  already_committed
+)])
 
 r_files <- sort(setdiff(
   list.files(here::here("R"), pattern = "\\.R$", full.names = FALSE),
@@ -17,40 +24,71 @@ for (f in r_files) {
   has_soft <- any(grepl("lifecycle::deprecate_soft", lines, fixed = TRUE))
   has_warn <- any(grepl("lifecycle::deprecate_warn", lines, fixed = TRUE))
 
-  if (!has_soft && !has_warn) next
+  if (!has_soft && !has_warn) {
+    next
+  }
 
   stem <- tools::file_path_sans_ext(f)
   cli::cli_alert_info("Processing R/{f}")
 
   # Extract function names before replacement for NEWS
   extract_fns <- function(lines, level) {
-    hits <- grep(paste0("lifecycle::", level), lines, fixed = TRUE, value = TRUE)
-    m <- regmatches(hits, regexpr(
-      paste0('lifecycle::', level, '\\([^,]+,\\s*"([^("]+)\\('),
-      hits, perl = TRUE
-    ))
+    hits <- grep(
+      paste0("lifecycle::", level),
+      lines,
+      fixed = TRUE,
+      value = TRUE
+    )
+    m <- regmatches(
+      hits,
+      regexpr(
+        paste0('lifecycle::', level, '\\([^,]+,\\s*"([^("]+)\\('),
+        hits,
+        perl = TRUE
+      )
+    )
     sub(paste0('.*"'), "", m[nzchar(m)])
   }
   soft_fns <- extract_fns(lines, "deprecate_soft")
-  warn_fns  <- extract_fns(lines, "deprecate_warn")
+  warn_fns <- extract_fns(lines, "deprecate_warn")
 
   # Advance: warn -> stop first to avoid double-replacement
-  lines <- gsub("lifecycle::deprecate_warn", "lifecycle::deprecate_stop", lines, fixed = TRUE)
-  lines <- gsub("lifecycle::deprecate_soft", "lifecycle::deprecate_warn", lines, fixed = TRUE)
+  lines <- gsub(
+    "lifecycle::deprecate_warn",
+    "lifecycle::deprecate_stop",
+    lines,
+    fixed = TRUE
+  )
+  lines <- gsub(
+    "lifecycle::deprecate_soft",
+    "lifecycle::deprecate_warn",
+    lines,
+    fixed = TRUE
+  )
   writeLines(lines, path)
 
   devtools::document(quiet = TRUE)
 
   # Tests — stop on failure so the user can fix
-  if (file.exists(here::here("tests", "testthat", paste0("test-", stem, ".R")))) {
+  if (
+    file.exists(here::here("tests", "testthat", paste0("test-", stem, ".R")))
+  ) {
     callr::r(
-      function(pkg, filter) devtools::test(pkg = pkg, filter = filter, stop_on_failure = TRUE),
+      function(pkg, filter) {
+        devtools::test(pkg = pkg, filter = filter, stop_on_failure = TRUE)
+      },
       args = list(pkg = here::here(), filter = stem)
     )
   }
 
-  answer <- readline(paste0("Tests passed for R/", f, ". Commit? [Enter = yes / n = stop] "))
-  if (trimws(tolower(answer)) == "n") stop("Stopped at R/", f, ". Fix, then commit manually and re-run.")
+  answer <- readline(paste0(
+    "Tests passed for R/",
+    f,
+    ". Commit? [Enter = yes / n = stop] "
+  ))
+  if (trimws(tolower(answer)) == "n") {
+    stop("Stopped at R/", f, ". Fix, then commit manually and re-run.")
+  }
 
   # Add NEWS items
   news_entries <- c(
@@ -92,7 +130,10 @@ for (f in r_files) {
     paste0("feat!: bump deprecate_warn to deprecate_stop in R/", f)
   }
 
-  gert::git_add(c(paste0("R/", f), "man", "NAMESPACE", "NEWS.md"), repo = here::here())
+  gert::git_add(
+    c(paste0("R/", f), "man", "NAMESPACE", "NEWS.md"),
+    repo = here::here()
+  )
   gert::git_commit(commit_msg, repo = here::here())
   cli::cli_alert_success("Committed R/{f}")
 }