From 3326719a272aeb5fd3d2513ba425f19b0e18fc5d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:09:53 +0200 Subject: [PATCH 001/261] feat!: bump graph_from_adjacency_matrix(adjmatrix = 'must be symmetric with mode = \"undirected\"') from deprecate_soft to deprecate_warn --- R/adjacency.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/adjacency.R b/R/adjacency.R index 65b4eb21411..e339d4a16df 100644 --- a/R/adjacency.R +++ b/R/adjacency.R @@ -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.' From 54ab00919ffb3d3f3ce15b5ec42706d81dca346a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:09:57 +0200 Subject: [PATCH 002/261] feat!: bump graph_from_adjacency_matrix(adjmatrix = 'must be a matrix') from deprecate_soft to deprecate_warn --- R/adjacency.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/adjacency.R b/R/adjacency.R index e339d4a16df..49b0517b845 100644 --- a/R/adjacency.R +++ b/R/adjacency.R @@ -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')" ) From 452e90a5594def9c92353ec1e538c12ae3449631 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:10:01 +0200 Subject: [PATCH 003/261] feat!: bump graph.adjacency() from deprecate_soft to deprecate_warn --- R/adjacency.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/adjacency.R b/R/adjacency.R index 49b0517b845..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()" From f36e4cc99b047bb9da2f790074560b89575a66ea Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:10:01 +0200 Subject: [PATCH 004/261] feat!: bump ape::as.phylo() from deprecate_soft to deprecate_warn --- 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 8c3649ba7ae03be72909b410d06cbc0d1364c1c9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:10:04 +0200 Subject: [PATCH 005/261] feat!: bump assortativity(types2 =) from deprecate_soft to deprecate_warn --- R/assortativity.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/assortativity.R b/R/assortativity.R index 5a1b7d2055a..e19f408020f 100644 --- a/R/assortativity.R +++ b/R/assortativity.R @@ -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 dfbcbb08e8b703052d0ff82a7de034b82406c56e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:10:06 +0200 Subject: [PATCH 006/261] feat!: bump assortativity(types1 =) from deprecate_soft to deprecate_warn --- R/assortativity.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/assortativity.R b/R/assortativity.R index e19f408020f..0d2ca7659c8 100644 --- a/R/assortativity.R +++ b/R/assortativity.R @@ -193,7 +193,7 @@ assortativity <- function( } if (missing(values)) { - lifecycle::deprecate_soft( + lifecycle::deprecate_warn( "1.6.0", "assortativity(types1 =)", "assortativity(values =)" From 57e79c2e3dcc1be72edef9469fcd8fb95335d010 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:10:09 +0200 Subject: [PATCH 007/261] feat!: bump assortativity(... =) from deprecate_soft to deprecate_warn --- R/assortativity.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/assortativity.R b/R/assortativity.R index 0d2ca7659c8..de483c65a5c 100644 --- a/R/assortativity.R +++ b/R/assortativity.R @@ -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." From ba35bd58251d6872f94a72cb70041fd3ce878d00 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:10:11 +0200 Subject: [PATCH 008/261] feat!: bump assortativity.degree() from deprecate_soft to deprecate_warn --- R/assortativity.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/assortativity.R b/R/assortativity.R index de483c65a5c..2373fee5152 100644 --- a/R/assortativity.R +++ b/R/assortativity.R @@ -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()" From eab6745786c1110204600705f569059e0721d8b8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:10:14 +0200 Subject: [PATCH 009/261] feat!: bump assortativity.nominal() from deprecate_soft to deprecate_warn --- R/assortativity.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/assortativity.R b/R/assortativity.R index 2373fee5152..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()" From 9e668200b73fbea563f1fd5b7985375d0533e91d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:10:18 +0200 Subject: [PATCH 010/261] feat!: bump get.edge.attribute() from deprecate_soft to deprecate_warn --- R/attributes.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/attributes.R b/R/attributes.R index 87af8d6b304..cb02373107e 100644 --- a/R/attributes.R +++ b/R/attributes.R @@ -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 2aea2c28a7c694b29b42eb1df8f855c42c432761 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:10:22 +0200 Subject: [PATCH 011/261] feat!: bump get.graph.attribute() from deprecate_soft to deprecate_warn --- R/attributes.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/attributes.R b/R/attributes.R index cb02373107e..e284dacb6de 100644 --- a/R/attributes.R +++ b/R/attributes.R @@ -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 From a19b228a259309da9b4b43410cb5b71135647b8a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:10:25 +0200 Subject: [PATCH 012/261] feat!: bump get.vertex.attribute() from deprecate_soft to deprecate_warn --- R/attributes.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/attributes.R b/R/attributes.R index e284dacb6de..efc5de5b9cc 100644 --- a/R/attributes.R +++ b/R/attributes.R @@ -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 From 72a02e36960afe8ece7c1542c6a2aba42f37c9a5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:10:29 +0200 Subject: [PATCH 013/261] feat!: bump is.bipartite() from deprecate_soft to deprecate_warn --- R/attributes.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/attributes.R b/R/attributes.R index efc5de5b9cc..5a6bbb1dc6b 100644 --- a/R/attributes.R +++ b/R/attributes.R @@ -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 From 5898a98916ae81f49f23d1446edf79b1b6c874ea Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:10:33 +0200 Subject: [PATCH 014/261] feat!: bump is.named() from deprecate_soft to deprecate_warn --- R/attributes.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/attributes.R b/R/attributes.R index 5a6bbb1dc6b..35f18897e79 100644 --- a/R/attributes.R +++ b/R/attributes.R @@ -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 From a760e1b2d6d947c4342fb0d164db2f584f4d2fa5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:10:36 +0200 Subject: [PATCH 015/261] feat!: bump is.weighted() from deprecate_soft to deprecate_warn --- R/attributes.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/attributes.R b/R/attributes.R index 35f18897e79..dca32654e92 100644 --- a/R/attributes.R +++ b/R/attributes.R @@ -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 From c4089e686f607db933ee8c7363b0351dd5a07fae Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:10:40 +0200 Subject: [PATCH 016/261] feat!: bump list.edge.attributes() from deprecate_soft to deprecate_warn --- R/attributes.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/attributes.R b/R/attributes.R index dca32654e92..c8a1c832b7c 100644 --- a/R/attributes.R +++ b/R/attributes.R @@ -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()" From 5083fbf2e9e3282c0268a704b77ab63ef9d140c9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:10:43 +0200 Subject: [PATCH 017/261] feat!: bump list.graph.attributes() from deprecate_soft to deprecate_warn --- R/attributes.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/attributes.R b/R/attributes.R index c8a1c832b7c..e74ff5361f8 100644 --- a/R/attributes.R +++ b/R/attributes.R @@ -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()" From 867b14a9512aefdc4d0e5bf1385c647f5dd15324 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:10:47 +0200 Subject: [PATCH 018/261] feat!: bump list.vertex.attributes() from deprecate_soft to deprecate_warn --- R/attributes.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/attributes.R b/R/attributes.R index e74ff5361f8..a06d3c2c559 100644 --- a/R/attributes.R +++ b/R/attributes.R @@ -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()" From 342a1d755065ead329d0188e6a203c1e51ce1d73 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:10:51 +0200 Subject: [PATCH 019/261] feat!: bump remove.edge.attribute() from deprecate_soft to deprecate_warn --- R/attributes.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/attributes.R b/R/attributes.R index a06d3c2c559..8bd27b632a6 100644 --- a/R/attributes.R +++ b/R/attributes.R @@ -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()" From df66b66620af17faaba0d3a5b7b922deb251f259 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:10:55 +0200 Subject: [PATCH 020/261] feat!: bump remove.graph.attribute() from deprecate_soft to deprecate_warn --- R/attributes.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/attributes.R b/R/attributes.R index 8bd27b632a6..b4ad790acb1 100644 --- a/R/attributes.R +++ b/R/attributes.R @@ -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()" From 69dc29d4e02fadee3a1cbc3301fb96f650702215 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:10:59 +0200 Subject: [PATCH 021/261] feat!: bump remove.vertex.attribute() from deprecate_soft to deprecate_warn --- R/attributes.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/attributes.R b/R/attributes.R index b4ad790acb1..6deb5f40f23 100644 --- a/R/attributes.R +++ b/R/attributes.R @@ -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()" From b65dde5a92519f6e73a8b3dffe4b846d555d44d3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:11:02 +0200 Subject: [PATCH 022/261] feat!: bump set.edge.attribute() from deprecate_soft to deprecate_warn --- R/attributes.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/attributes.R b/R/attributes.R index 6deb5f40f23..cbb89fface9 100644 --- a/R/attributes.R +++ b/R/attributes.R @@ -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 From 1d736fc71dbcd4772c85e3a5be1a5691cc3ede6a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:11:07 +0200 Subject: [PATCH 023/261] feat!: bump set.graph.attribute() from deprecate_soft to deprecate_warn --- R/attributes.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/attributes.R b/R/attributes.R index cbb89fface9..510dc75768b 100644 --- a/R/attributes.R +++ b/R/attributes.R @@ -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()" From b227705fd3d7d1f78b0533a9cfb1ad0fa4491fc9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:11:11 +0200 Subject: [PATCH 024/261] feat!: bump set.vertex.attribute() from deprecate_soft to deprecate_warn --- R/attributes.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/attributes.R b/R/attributes.R index 510dc75768b..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()" From e94ceb86072ccd581fae2bb83ccc993c7f960ead Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:11:11 +0200 Subject: [PATCH 025/261] feat!: bump is.igraph() from deprecate_soft to deprecate_warn --- R/basic.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/basic.R b/R/basic.R index 47b00f7e071..ce59edd5f9a 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 From 68980ceb27b37bd5e50037cda245fc2b793841cc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:11:11 +0200 Subject: [PATCH 026/261] feat!: remove deprecated get.edge() (lifecycle::deprecate_stop) --- R/basic.R | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/R/basic.R b/R/basic.R index ce59edd5f9a..4769854df36 100644 --- a/R/basic.R +++ b/R/basic.R @@ -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 374bf8fe2848450b8ffea5130d205e935def5fcb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:11:15 +0200 Subject: [PATCH 027/261] feat!: bump bipartite.mapping() from deprecate_soft to deprecate_warn --- R/bipartite.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/bipartite.R b/R/bipartite.R index 5e640313588..ed0b32f67a4 100644 --- a/R/bipartite.R +++ b/R/bipartite.R @@ -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 ebf30d184548511941ac72280d3045cbd7a1ede4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:11:18 +0200 Subject: [PATCH 028/261] feat!: bump bipartite.projection() from deprecate_soft to deprecate_warn --- R/bipartite.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/bipartite.R b/R/bipartite.R index ed0b32f67a4..a0a73762941 100644 --- a/R/bipartite.R +++ b/R/bipartite.R @@ -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()" From a177fd019d5b28fd292520d8db792a2aa15caf9b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:11:21 +0200 Subject: [PATCH 029/261] feat!: bump bipartite.projection.size() from deprecate_soft to deprecate_warn --- R/bipartite.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/bipartite.R b/R/bipartite.R index a0a73762941..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()" From 6989cc6b7ecc17d595736c320a04475ee81e61a0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:11:31 +0200 Subject: [PATCH 030/261] feat!: bump arpack_defaults() from deprecate_soft to deprecate_warn --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index f239487876f..fb1660e9a10 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -1569,7 +1569,7 @@ hub_score <- function( ) { lifecycle::deprecate_soft("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()", From dab0b8d498b84e5e1cecaf29476e2ef9150849ff Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:11:41 +0200 Subject: [PATCH 031/261] feat!: bump hub_score() from deprecate_soft to deprecate_warn --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index fb1660e9a10..faf04e45348 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -1567,7 +1567,7 @@ 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_warn( "1.6.0", From b9b68258f940b131ce0c30f5c7d8e2c2f386051b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:11:49 +0200 Subject: [PATCH 032/261] feat!: bump arpack_defaults() from deprecate_soft to deprecate_warn --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index faf04e45348..57dcad53ab6 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -1524,7 +1524,7 @@ authority_score <- function( ) { lifecycle::deprecate_soft("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()", From 3dcd6241e27ff33e5f19cdd90c3727d61b3ec478 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:11:58 +0200 Subject: [PATCH 033/261] feat!: bump authority_score() from deprecate_soft to deprecate_warn --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index 57dcad53ab6..a90ea6c6692 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -1522,7 +1522,7 @@ 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_warn( "1.6.0", From 72177d2f7b2955b43e7e7155ae4ffbf3f3d51180 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:12:17 +0200 Subject: [PATCH 034/261] feat!: bump eigen_centrality(scale = 'always as if TRUE') from deprecate_warn to deprecate_stop --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index a90ea6c6692..8917d5d715b 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -1317,7 +1317,7 @@ eigen_centrality <- function( 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" From 63c8dc23b37c12510c0de7a3871aa0d3b21ac1da Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:12:36 +0200 Subject: [PATCH 035/261] feat!: bump eigen_centrality(scale) from deprecate_soft to deprecate_warn --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index 8917d5d715b..7be4a2f89f2 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -1311,7 +1311,7 @@ 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." From 52f998d2a3448fd10845ae9770e7536b5056488f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:12:56 +0200 Subject: [PATCH 036/261] feat!: bump eigen_centrality(options = 'must be a list') from deprecate_soft to deprecate_warn --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index 7be4a2f89f2..928e0ea707e 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -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( From be77e05db531559e620319450ef6c1e40a03397f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:13:16 +0200 Subject: [PATCH 037/261] feat!: bump spectrum(options = 'must be a list') from deprecate_soft to deprecate_warn --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index 928e0ea707e..15f8bbcffd4 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -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( From 5773565819a66bb74147f99b169e2341b0e59948 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:13:36 +0200 Subject: [PATCH 038/261] feat!: bump arpack(options = 'must be a list') from deprecate_soft to deprecate_warn --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index 15f8bbcffd4..7bbb2c64a4a 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -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( From a75bdc5fdee51c2c335f5fbdae5df348b9cec931 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:13:56 +0200 Subject: [PATCH 039/261] feat!: bump estimate_closeness() from deprecate_soft to deprecate_warn --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index 7bbb2c64a4a..8f53eed7bea 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -611,7 +611,7 @@ estimate_closeness <- function( weights = NULL, normalized = FALSE ) { - lifecycle::deprecate_soft( + lifecycle::deprecate_warn( "1.6.0", "estimate_closeness()", "closeness()", From 71681aaae1c912f37355d0b4d28e2440e7c33bb8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:14:15 +0200 Subject: [PATCH 040/261] feat!: bump estimate_edge_betweenness() from deprecate_soft to deprecate_warn --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index 8f53eed7bea..f59ceef9bc8 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -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()", From 7c871cbab82d9a65808f572fdd86b8030737482b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:14:34 +0200 Subject: [PATCH 041/261] feat!: bump estimate_betweenness() from deprecate_soft to deprecate_warn --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index f59ceef9bc8..9f524c1002a 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -336,7 +336,7 @@ estimate_betweenness <- function( cutoff, weights = NULL ) { - lifecycle::deprecate_soft( + lifecycle::deprecate_warn( "1.6.0", "estimate_betweenness()", "betweenness()", From e960bc59def8ddb8cabed943b5847aa8c6ae2225 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:14:53 +0200 Subject: [PATCH 042/261] feat!: bump alpha.centrality() from deprecate_soft to deprecate_warn --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index 9f524c1002a..15965a7add1 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -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, From b83d2d3976dfd535feb0c1eb9a14bf3f691ba30d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:15:12 +0200 Subject: [PATCH 043/261] feat!: bump bonpow() from deprecate_soft to deprecate_warn --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index 15965a7add1..28ccec095cd 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -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, From 29898b06cd973251e08728c6827ef095a9ba0b0b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:15:31 +0200 Subject: [PATCH 044/261] feat!: bump edge.betweenness() from deprecate_soft to deprecate_warn --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index 28ccec095cd..3b954892cd7 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -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, From 3936514a2186978df6bad1f31c729ebeccaf2dcc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:15:49 +0200 Subject: [PATCH 045/261] feat!: bump evcent() from deprecate_soft to deprecate_warn --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index 3b954892cd7..ebd02cb0d92 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -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, From 935f11b6616110a77aa7d481da750baa897c3c83 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:16:09 +0200 Subject: [PATCH 046/261] feat!: bump graph.diversity() from deprecate_soft to deprecate_warn --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index ebd02cb0d92..8a8489453c1 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -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 From 16366b5a8f5e68610058a2008c2f2b5ee9b3fd43 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:16:29 +0200 Subject: [PATCH 047/261] feat!: bump graph.eigen() from deprecate_soft to deprecate_warn --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index 8a8489453c1..5f09c484d2c 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -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, From a55e5247331a1ef435e37e2be73d32246a236150 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:16:48 +0200 Subject: [PATCH 048/261] feat!: bump graph.strength() from deprecate_soft to deprecate_warn --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index 5f09c484d2c..98f91c31eb5 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -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, From 77271e128cdc15d4baeb47bec0d6a3077ee8024b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:17:07 +0200 Subject: [PATCH 049/261] feat!: bump authority.score() from deprecate_warn to deprecate_stop --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index 98f91c31eb5..6e8d776125f 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -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, From e4d7cb3f5bcc5e05d555b3be33cf01749ae0476b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:17:25 +0200 Subject: [PATCH 050/261] feat!: bump hub.score() from deprecate_warn to deprecate_stop --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index 6e8d776125f..b4e14b9b5a2 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -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 From 905d6ed97347a31219d74fa5119105b7cf72910d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:17:44 +0200 Subject: [PATCH 051/261] feat!: bump page.rank() from deprecate_soft to deprecate_warn --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index b4e14b9b5a2..e117af53935 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -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, From 25035cdeabf525a492d2db2e2bc94de3234a32b8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:18:03 +0200 Subject: [PATCH 052/261] feat!: bump subgraph.centrality() from deprecate_soft to deprecate_warn --- R/centrality.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centrality.R b/R/centrality.R index e117af53935..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()" From f5a250b9572eaa26f3b12600fea1348024d28da9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:18:05 +0200 Subject: [PATCH 053/261] feat!: bump centr_eigen_tmax(scale = ) from deprecate_soft to deprecate_warn --- R/centralization.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centralization.R b/R/centralization.R index bd6dfb570ef..5f75d4e4d08 100644 --- a/R/centralization.R +++ b/R/centralization.R @@ -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 d0de8786a66e75d9436100bb67a4f12b991470c9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:18:08 +0200 Subject: [PATCH 054/261] feat!: bump centr_eigen(scale = ) from deprecate_soft to deprecate_warn --- R/centralization.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centralization.R b/R/centralization.R index 5f75d4e4d08..15b612fb25e 100644 --- a/R/centralization.R +++ b/R/centralization.R @@ -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`. From 7b8fd587757675e66a1976cc27b9685867dbab39 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:18:10 +0200 Subject: [PATCH 055/261] feat!: bump centr_degree_tmax(loops = 'must be explicit') from deprecate_warn to deprecate_stop --- R/centralization.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centralization.R b/R/centralization.R index 15b612fb25e..dea31724a9c 100644 --- a/R/centralization.R +++ b/R/centralization.R @@ -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." From 23e72d2b62a2806525986cb0192ed05ccee82b24 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:18:13 +0200 Subject: [PATCH 056/261] feat!: bump centralization.betweenness() from deprecate_soft to deprecate_warn --- R/centralization.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centralization.R b/R/centralization.R index dea31724a9c..1f4bcd4f822 100644 --- a/R/centralization.R +++ b/R/centralization.R @@ -219,7 +219,7 @@ centralization.betweenness <- function( normalized = TRUE ) { # nocov start - lifecycle::deprecate_soft( + lifecycle::deprecate_warn( "2.0.0", "centralization.betweenness()", "centr_betw()" From 87641fae49bc05287e7a90a24e7e92028f57f058 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:18:15 +0200 Subject: [PATCH 057/261] feat!: bump centralization.betweenness.tmax() from deprecate_soft to deprecate_warn --- R/centralization.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centralization.R b/R/centralization.R index 1f4bcd4f822..2171ffd54db 100644 --- a/R/centralization.R +++ b/R/centralization.R @@ -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()" From aa96424a988c62b7c8f5e2ce2ad53a30fa51e781 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:18:18 +0200 Subject: [PATCH 058/261] feat!: bump centralization.closeness() from deprecate_soft to deprecate_warn --- R/centralization.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centralization.R b/R/centralization.R index 2171ffd54db..cecc349c837 100644 --- a/R/centralization.R +++ b/R/centralization.R @@ -171,7 +171,7 @@ centralization.closeness <- function( normalized = TRUE ) { # nocov start - lifecycle::deprecate_soft( + lifecycle::deprecate_warn( "2.0.0", "centralization.closeness()", "centr_clo()" From b6a37a4c7c41ee6bca1eec55f6e785a3041fd0a8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:18:20 +0200 Subject: [PATCH 059/261] feat!: bump centralization.closeness.tmax() from deprecate_soft to deprecate_warn --- R/centralization.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centralization.R b/R/centralization.R index cecc349c837..45a570ec78b 100644 --- a/R/centralization.R +++ b/R/centralization.R @@ -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()" From 3e7f50ad0245d4e932ccec36c1ee541bc92bed67 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:18:23 +0200 Subject: [PATCH 060/261] feat!: bump centralization.degree() from deprecate_soft to deprecate_warn --- R/centralization.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centralization.R b/R/centralization.R index 45a570ec78b..d3a7bc8b145 100644 --- a/R/centralization.R +++ b/R/centralization.R @@ -118,7 +118,7 @@ centralization.degree <- function( normalized = TRUE ) { # nocov start - lifecycle::deprecate_soft( + lifecycle::deprecate_warn( "2.0.0", "centralization.degree()", "centr_degree()" From f703d0d0f65d26618459d0c5b7d351f87c868b64 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:18:25 +0200 Subject: [PATCH 061/261] feat!: bump centralization.degree.tmax() from deprecate_soft to deprecate_warn --- R/centralization.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centralization.R b/R/centralization.R index d3a7bc8b145..a60945e80c0 100644 --- a/R/centralization.R +++ b/R/centralization.R @@ -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()" From 11db22529d45892c507ac0407f3598b977b82a16 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:18:28 +0200 Subject: [PATCH 062/261] feat!: bump centralization.evcent() from deprecate_soft to deprecate_warn --- R/centralization.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centralization.R b/R/centralization.R index a60945e80c0..756dbab0e0e 100644 --- a/R/centralization.R +++ b/R/centralization.R @@ -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, From 4d11d8d44e62e2e4b802a88f9a019d2dcad19bcd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:18:30 +0200 Subject: [PATCH 063/261] feat!: bump centralization.evcent.tmax() from deprecate_soft to deprecate_warn --- R/centralization.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centralization.R b/R/centralization.R index 756dbab0e0e..21d5947c4f9 100644 --- a/R/centralization.R +++ b/R/centralization.R @@ -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()" From 5210989d0490a64c05c6c0e1554b9c83c11f52f6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:18:32 +0200 Subject: [PATCH 064/261] feat!: bump centralize.scores() from deprecate_soft to deprecate_warn --- R/centralization.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/centralization.R b/R/centralization.R index 21d5947c4f9..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, From cf82f975b084dff734ddd33e94712df453d941eb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:18:39 +0200 Subject: [PATCH 065/261] feat!: bump maximal_ivs() from deprecate_soft to deprecate_warn --- R/cliques.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/cliques.R b/R/cliques.R index 4bd6018334c..3f78f134e7d 100644 --- a/R/cliques.R +++ b/R/cliques.R @@ -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 60e4b69d9e5f643a4e439cbc310a8fe793970609 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:18:47 +0200 Subject: [PATCH 066/261] feat!: bump clique.number() from deprecate_soft to deprecate_warn --- R/cliques.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/cliques.R b/R/cliques.R index 3f78f134e7d..614c18bff4b 100644 --- a/R/cliques.R +++ b/R/cliques.R @@ -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 From da7dbaab8a5a4442944feefb1df49374320f58af Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:18:54 +0200 Subject: [PATCH 067/261] feat!: bump independence.number() from deprecate_soft to deprecate_warn --- R/cliques.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/cliques.R b/R/cliques.R index 614c18bff4b..d08b58cf6d8 100644 --- a/R/cliques.R +++ b/R/cliques.R @@ -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 From 3437cc574bfc35e4c97b72ce34183a438a92ac6a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:19:02 +0200 Subject: [PATCH 068/261] feat!: bump independent.vertex.sets() from deprecate_soft to deprecate_warn --- R/cliques.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/cliques.R b/R/cliques.R index d08b58cf6d8..b558e6e75d3 100644 --- a/R/cliques.R +++ b/R/cliques.R @@ -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 From 5a308a7ba23b65f7a058cc0c68c39773a0c2aaf3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:19:09 +0200 Subject: [PATCH 069/261] feat!: bump largest.cliques() from deprecate_soft to deprecate_warn --- R/cliques.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/cliques.R b/R/cliques.R index b558e6e75d3..e529a0f0fd0 100644 --- a/R/cliques.R +++ b/R/cliques.R @@ -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 From 165c3274dff78e147ac62c7e3a34427e544d75a0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:19:16 +0200 Subject: [PATCH 070/261] feat!: bump largest.independent.vertex.sets() from deprecate_soft to deprecate_warn --- R/cliques.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/cliques.R b/R/cliques.R index e529a0f0fd0..24bc61de9f4 100644 --- a/R/cliques.R +++ b/R/cliques.R @@ -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()" From 99992c1bd2b65a879825302ee7d43907fcd7df08 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:19:23 +0200 Subject: [PATCH 071/261] feat!: bump maximal.cliques() from deprecate_soft to deprecate_warn --- R/cliques.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/cliques.R b/R/cliques.R index 24bc61de9f4..8850de3a167 100644 --- a/R/cliques.R +++ b/R/cliques.R @@ -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 From 594002064f493725b3bcd639a017e5f1624d2786 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:19:30 +0200 Subject: [PATCH 072/261] feat!: bump maximal.cliques.count() from deprecate_soft to deprecate_warn --- R/cliques.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/cliques.R b/R/cliques.R index 8850de3a167..f6b90e2e7ef 100644 --- a/R/cliques.R +++ b/R/cliques.R @@ -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()" From 3adf45f2d157bc9c0ea74441d74fc458586f65b7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:19:37 +0200 Subject: [PATCH 073/261] feat!: bump maximal.independent.vertex.sets() from deprecate_soft to deprecate_warn --- R/cliques.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/cliques.R b/R/cliques.R index f6b90e2e7ef..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()" From 070b94271f6205a67d8ec8daceb176f586241abf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:19:37 +0200 Subject: [PATCH 074/261] feat!: bump blockGraphs() from deprecate_soft to deprecate_warn --- R/cohesive.blocks.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/cohesive.blocks.R b/R/cohesive.blocks.R index 35844360284..a3924a1d353 100644 --- a/R/cohesive.blocks.R +++ b/R/cohesive.blocks.R @@ -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 2f7fa3c6aa75b949223290ded7ea8557188b1254 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:19:37 +0200 Subject: [PATCH 075/261] feat!: bump cohesive.blocks() from deprecate_soft to deprecate_warn --- R/cohesive.blocks.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/cohesive.blocks.R b/R/cohesive.blocks.R index a3924a1d353..dbcc891628e 100644 --- a/R/cohesive.blocks.R +++ b/R/cohesive.blocks.R @@ -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 From cbd0e9863a4a5674fa6e4a2bf16cc91067556aaf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:19:37 +0200 Subject: [PATCH 076/261] feat!: bump graph.cohesion() from deprecate_soft to deprecate_warn --- R/cohesive.blocks.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/cohesive.blocks.R b/R/cohesive.blocks.R index dbcc891628e..8c5a84fda37 100644 --- a/R/cohesive.blocks.R +++ b/R/cohesive.blocks.R @@ -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 From 505aabaa14b43549411420a9b3b4f97b3ee698f2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:19:37 +0200 Subject: [PATCH 077/261] feat!: bump maxcohesion() from deprecate_soft to deprecate_warn --- R/cohesive.blocks.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/cohesive.blocks.R b/R/cohesive.blocks.R index 8c5a84fda37..e9e161affcc 100644 --- a/R/cohesive.blocks.R +++ b/R/cohesive.blocks.R @@ -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 From a749eb95fcaa4a1211a15c830445e8014c6a8bc4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:19:37 +0200 Subject: [PATCH 078/261] feat!: bump plotHierarchy() from deprecate_soft to deprecate_warn --- R/cohesive.blocks.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/cohesive.blocks.R b/R/cohesive.blocks.R index e9e161affcc..df3588636be 100644 --- a/R/cohesive.blocks.R +++ b/R/cohesive.blocks.R @@ -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 From 1a2680a40fa4eb311e272283f9f7040f52a53b43 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:19:37 +0200 Subject: [PATCH 079/261] feat!: bump exportPajek() from deprecate_soft to deprecate_warn --- R/cohesive.blocks.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/cohesive.blocks.R b/R/cohesive.blocks.R index df3588636be..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, From 97c534084dba7fc254004caf8fb8828bdfa50a7a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:19:42 +0200 Subject: [PATCH 080/261] feat!: bump cluster_label_prop(... = ) from deprecate_soft to deprecate_warn --- R/community.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/community.R b/R/community.R index 352f534ba11..eca6f18ae5d 100644 --- a/R/community.R +++ b/R/community.R @@ -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." From 3dd41a9f90c9953079a9f2dafb48040ae0d4d449 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:19:47 +0200 Subject: [PATCH 081/261] feat!: bump cluster_leading_eigen(options = 'must be a list') from deprecate_soft to deprecate_warn --- R/community.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/community.R b/R/community.R index eca6f18ae5d..de52110225f 100644 --- a/R/community.R +++ b/R/community.R @@ -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( From a39cfa4adbcfc1ad6b6e31a4d3374b60cc79fad2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:19:53 +0200 Subject: [PATCH 082/261] feat!: bump cluster_leiden(resolution_parameter) from deprecate_soft to deprecate_warn --- R/community.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/community.R b/R/community.R index de52110225f..bc6a6325ea7 100644 --- a/R/community.R +++ b/R/community.R @@ -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)" From fc56bf20249012663203d166ec02969a639a68f1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:20:05 +0200 Subject: [PATCH 083/261] feat!: bump modularity_matrix(membership = 'is no longer used') from deprecate_warn to deprecate_stop --- R/community.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/community.R b/R/community.R index bc6a6325ea7..cd276fa3590 100644 --- a/R/community.R +++ b/R/community.R @@ -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')" ) From caa9367a04958872f5b0c38d561c1d76dec39183 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:20:16 +0200 Subject: [PATCH 084/261] feat!: bump code.length() from deprecate_soft to deprecate_warn --- R/community.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/community.R b/R/community.R index cd276fa3590..fc972d53f2f 100644 --- a/R/community.R +++ b/R/community.R @@ -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 From 5013c7eb145681e86822dfdb88ad142dde2f545d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:20:27 +0200 Subject: [PATCH 085/261] feat!: bump contract.vertices() from deprecate_soft to deprecate_warn --- R/community.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/community.R b/R/community.R index fc972d53f2f..5d01007bded 100644 --- a/R/community.R +++ b/R/community.R @@ -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, From 1bb4edf853c6b05fb78d19b098eb0c95dd510378 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:20:39 +0200 Subject: [PATCH 086/261] feat!: bump cutat() from deprecate_soft to deprecate_warn --- R/community.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/community.R b/R/community.R index 5d01007bded..87964c187bf 100644 --- a/R/community.R +++ b/R/community.R @@ -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 From f0c2c5cb22e0069cc578290a4e4a995b092e03cf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:20:49 +0200 Subject: [PATCH 087/261] feat!: bump dendPlot() from deprecate_soft to deprecate_warn --- R/community.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/community.R b/R/community.R index 87964c187bf..3fde31a0f78 100644 --- a/R/community.R +++ b/R/community.R @@ -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 From 18c3bac42d939c105528ee9832b6686082bcc81d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:21:01 +0200 Subject: [PATCH 088/261] feat!: bump edge.betweenness.community() from deprecate_soft to deprecate_warn --- R/community.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/community.R b/R/community.R index 3fde31a0f78..9d6a31c1d15 100644 --- a/R/community.R +++ b/R/community.R @@ -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()" From 9cf30fcbe31f3789c8d6a316d74a513c952c2d2d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:21:12 +0200 Subject: [PATCH 089/261] feat!: bump fastgreedy.community() from deprecate_soft to deprecate_warn --- R/community.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/community.R b/R/community.R index 9d6a31c1d15..e798aa71f27 100644 --- a/R/community.R +++ b/R/community.R @@ -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()" From 89b266bc0a92cdd7758cbdbbfb4f080b7ba986fe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:21:23 +0200 Subject: [PATCH 090/261] feat!: bump infomap.community() from deprecate_soft to deprecate_warn --- R/community.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/community.R b/R/community.R index e798aa71f27..7318aeba24d 100644 --- a/R/community.R +++ b/R/community.R @@ -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, From d0d71533a7849b40ed29e597aee6ef5675860444 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:21:34 +0200 Subject: [PATCH 091/261] feat!: bump is.hierarchical() from deprecate_soft to deprecate_warn --- R/community.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/community.R b/R/community.R index 7318aeba24d..12cd21fea7e 100644 --- a/R/community.R +++ b/R/community.R @@ -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 From 63fed6a76570dde08f05c87d30ce009acde598ea Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:21:46 +0200 Subject: [PATCH 092/261] feat!: bump label.propagation.community() from deprecate_soft to deprecate_warn --- R/community.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/community.R b/R/community.R index 12cd21fea7e..05254240f04 100644 --- a/R/community.R +++ b/R/community.R @@ -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()" From b9dde48d763a804850f392e62e0544769439553c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:21:58 +0200 Subject: [PATCH 093/261] feat!: bump leading.eigenvector.community() from deprecate_soft to deprecate_warn --- R/community.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/community.R b/R/community.R index 05254240f04..9db05c88a16 100644 --- a/R/community.R +++ b/R/community.R @@ -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()" From 928ba1a172a100cec47835b6ab842126eaf97a4e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:22:09 +0200 Subject: [PATCH 094/261] feat!: bump mod.matrix() from deprecate_soft to deprecate_warn --- R/community.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/community.R b/R/community.R index 9db05c88a16..390e79caa3f 100644 --- a/R/community.R +++ b/R/community.R @@ -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, From 9669bd3ed1cb7118861057fbe81e6c6a42805830 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:22:21 +0200 Subject: [PATCH 095/261] feat!: bump multilevel.community() from deprecate_soft to deprecate_warn --- R/community.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/community.R b/R/community.R index 390e79caa3f..fd01f4898fc 100644 --- a/R/community.R +++ b/R/community.R @@ -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()" From 29e994d7e76a24af8ef516ac7535171a3ea01d79 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:22:33 +0200 Subject: [PATCH 096/261] feat!: bump optimal.community() from deprecate_soft to deprecate_warn --- R/community.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/community.R b/R/community.R index fd01f4898fc..2c431e5914f 100644 --- a/R/community.R +++ b/R/community.R @@ -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 From 03a59aefca5c0601ca8d3dad690ee575ac3a160d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:22:44 +0200 Subject: [PATCH 097/261] feat!: bump showtrace() from deprecate_soft to deprecate_warn --- R/community.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/community.R b/R/community.R index 2c431e5914f..20121e7df9a 100644 --- a/R/community.R +++ b/R/community.R @@ -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 From 0fe2268b2e3e976ab600a68aa8fc2a352d2b264a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:22:55 +0200 Subject: [PATCH 098/261] feat!: bump spinglass.community() from deprecate_soft to deprecate_warn --- R/community.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/community.R b/R/community.R index 20121e7df9a..aca425c44ae 100644 --- a/R/community.R +++ b/R/community.R @@ -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()" From c08d1cd851fe9bc847b252df159a185cdaace1fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:23:06 +0200 Subject: [PATCH 099/261] feat!: bump walktrap.community() from deprecate_soft to deprecate_warn --- R/community.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/community.R b/R/community.R index aca425c44ae..7491e6acedb 100644 --- a/R/community.R +++ b/R/community.R @@ -45,7 +45,7 @@ walktrap.community <- function( membership = TRUE ) { # nocov start - lifecycle::deprecate_soft( + lifecycle::deprecate_warn( "2.0.0", "walktrap.community()", "cluster_walktrap()" From 2b266a7a6d1297df10a5a192f16006c8af289a78 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:23:17 +0200 Subject: [PATCH 100/261] feat!: bump create.communities() from deprecate_soft to deprecate_warn --- R/community.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/community.R b/R/community.R index 7491e6acedb..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, From 97a64707da410d33d6db91425c745a35d8e4fd72 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:23:21 +0200 Subject: [PATCH 101/261] feat!: bump articulation.points() from deprecate_soft to deprecate_warn --- R/components.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/components.R b/R/components.R index fab025773b2..ab9a8e21c50 100644 --- a/R/components.R +++ b/R/components.R @@ -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 5b0e3dde7e7a2efa88e273b8353260b507cb55db Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:23:25 +0200 Subject: [PATCH 102/261] feat!: bump biconnected.components() from deprecate_soft to deprecate_warn --- R/components.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/components.R b/R/components.R index ab9a8e21c50..4add44d966a 100644 --- a/R/components.R +++ b/R/components.R @@ -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()" From 42eccae3c237b35e3ead6847079a172fe253525f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:23:28 +0200 Subject: [PATCH 103/261] feat!: bump cluster.distribution() from deprecate_soft to deprecate_warn --- R/components.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/components.R b/R/components.R index 4add44d966a..41ed83d4256 100644 --- a/R/components.R +++ b/R/components.R @@ -57,7 +57,7 @@ cluster.distribution <- function( ... ) { # nocov start - lifecycle::deprecate_soft( + lifecycle::deprecate_warn( "2.0.0", "cluster.distribution()", "component_distribution()" From 3385bb88f96c6fe314f95285aff19405ad61a70f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:23:32 +0200 Subject: [PATCH 104/261] feat!: bump decompose.graph() from deprecate_soft to deprecate_warn --- R/components.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/components.R b/R/components.R index 41ed83d4256..e52949cecb9 100644 --- a/R/components.R +++ b/R/components.R @@ -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, From f70e080c7fd708f39832181226eb72d54189ba33 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:23:36 +0200 Subject: [PATCH 105/261] feat!: bump no.clusters() from deprecate_soft to deprecate_warn --- R/components.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/components.R b/R/components.R index e52949cecb9..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 From 235ab7bea4b1f631ecded5b56c3d65cae051b5c8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:23:36 +0200 Subject: [PATCH 106/261] feat!: bump igraph.console() from deprecate_soft to deprecate_warn --- 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 22c5001162b0f529b10d0cffe2638fe86f3830b8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:23:43 +0200 Subject: [PATCH 107/261] feat!: bump graph.data.frame() from deprecate_soft to deprecate_warn --- R/conversion.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/conversion.R b/R/conversion.R index 230cd369bd1..1020efd51b9 100644 --- a/R/conversion.R +++ b/R/conversion.R @@ -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 5e35e15db09d01edf4b0d7f2f3a9221d25567341 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:23:50 +0200 Subject: [PATCH 108/261] feat!: bump graph.edgelist() from deprecate_soft to deprecate_warn --- R/conversion.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/conversion.R b/R/conversion.R index 1020efd51b9..42237324d64 100644 --- a/R/conversion.R +++ b/R/conversion.R @@ -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()" From 6e6bfae2ad13f39daf239956bdc586af3fe2c420 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:23:58 +0200 Subject: [PATCH 109/261] feat!: bump as.undirected() from deprecate_soft to deprecate_warn --- R/conversion.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/conversion.R b/R/conversion.R index 42237324d64..dad3f140b7d 100644 --- a/R/conversion.R +++ b/R/conversion.R @@ -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) } From 63ca51552e237db1d7a31260e94355fc5c76dbb9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:24:05 +0200 Subject: [PATCH 110/261] feat!: bump as.directed() from deprecate_soft to deprecate_warn --- R/conversion.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/conversion.R b/R/conversion.R index dad3f140b7d..019b8eb5512 100644 --- a/R/conversion.R +++ b/R/conversion.R @@ -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) } From 37c319ee847adf9fe1fc268eb81cb00d6a97a354 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:24:12 +0200 Subject: [PATCH 111/261] feat!: bump as_incidence_matrix() from deprecate_soft to deprecate_warn --- R/conversion.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/conversion.R b/R/conversion.R index 019b8eb5512..9d131a5b205 100644 --- a/R/conversion.R +++ b/R/conversion.R @@ -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()" From 164e62ff126f566259a9c03bfb2e30f25b9f46b9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:24:19 +0200 Subject: [PATCH 112/261] feat!: bump as_adj() from deprecate_soft to deprecate_warn --- R/conversion.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/conversion.R b/R/conversion.R index 9d131a5b205..9aec75f6557 100644 --- a/R/conversion.R +++ b/R/conversion.R @@ -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, From 3c8b2a8ba4ed3092568b4bcceebb8461502a1c9d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:24:27 +0200 Subject: [PATCH 113/261] feat!: bump get.adjacency.dense(loops = 'must be a character') from deprecate_soft to deprecate_warn --- R/conversion.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/conversion.R b/R/conversion.R index 9aec75f6557..e329fa28cf1 100644 --- a/R/conversion.R +++ b/R/conversion.R @@ -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( From 55788e53a2f4ade587f8a3b6b0efd72477030e0f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:24:34 +0200 Subject: [PATCH 114/261] feat!: bump get.adjedgelist() from deprecate_soft to deprecate_warn --- R/conversion.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/conversion.R b/R/conversion.R index e329fa28cf1..cc4ddc6fe2e 100644 --- a/R/conversion.R +++ b/R/conversion.R @@ -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 From eb1f40c2a1f9a8f953ec5be36edf0dcd4a6aa0ba Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:24:41 +0200 Subject: [PATCH 115/261] feat!: bump get.adjlist() from deprecate_soft to deprecate_warn --- R/conversion.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/conversion.R b/R/conversion.R index cc4ddc6fe2e..69e64a9d633 100644 --- a/R/conversion.R +++ b/R/conversion.R @@ -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 From 4b1b23ed62fdd592c2d7af548bce68f58d8df8c7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:24:49 +0200 Subject: [PATCH 116/261] feat!: bump get.adjacency() from deprecate_soft to deprecate_warn --- R/conversion.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/conversion.R b/R/conversion.R index 69e64a9d633..037e8e9885f 100644 --- a/R/conversion.R +++ b/R/conversion.R @@ -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, From fd0ec96e909b5b4194f77b6b054a60dc8bd602c8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:24:56 +0200 Subject: [PATCH 117/261] feat!: bump get.data.frame() from deprecate_soft to deprecate_warn --- R/conversion.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/conversion.R b/R/conversion.R index 037e8e9885f..840f6062102 100644 --- a/R/conversion.R +++ b/R/conversion.R @@ -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 From 05c0346b45d38ed445b5085bcf2cb8aa3cc7e815 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:25:03 +0200 Subject: [PATCH 118/261] feat!: bump get.edgelist() from deprecate_soft to deprecate_warn --- R/conversion.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/conversion.R b/R/conversion.R index 840f6062102..27b40ca202d 100644 --- a/R/conversion.R +++ b/R/conversion.R @@ -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 From bc8964f2340742cf873a58fadc7feac2a945639e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:25:11 +0200 Subject: [PATCH 119/261] feat!: bump get.incidence() from deprecate_soft to deprecate_warn --- R/conversion.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/conversion.R b/R/conversion.R index 27b40ca202d..1e8ddf37908 100644 --- a/R/conversion.R +++ b/R/conversion.R @@ -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()" From 112e10f2d4e43be0b329015b37a7b9ef96175962 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:25:18 +0200 Subject: [PATCH 120/261] feat!: bump graph.adjlist() from deprecate_soft to deprecate_warn --- R/conversion.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/conversion.R b/R/conversion.R index 1e8ddf37908..d6c2722cae0 100644 --- a/R/conversion.R +++ b/R/conversion.R @@ -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 From abc29ca1a9da428dcb00da54d3ee6252e24dcfe5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:25:24 +0200 Subject: [PATCH 121/261] feat!: bump igraph.from.graphNEL() from deprecate_soft to deprecate_warn --- R/conversion.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/conversion.R b/R/conversion.R index d6c2722cae0..4ad4530bcf1 100644 --- a/R/conversion.R +++ b/R/conversion.R @@ -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()" From 7b2e2a7dfc93b44f0bc7106a024bbd3023149674 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:25:32 +0200 Subject: [PATCH 122/261] feat!: bump igraph.to.graphNEL() from deprecate_soft to deprecate_warn --- R/conversion.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/conversion.R b/R/conversion.R index 4ad4530bcf1..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 From 64ca0469a083665ae3d302fc47a9a44894030140 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:25:34 +0200 Subject: [PATCH 123/261] feat!: bump is.chordal() from deprecate_soft to deprecate_warn --- 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 ed20d1f6d900a8befe9171cdce5b013381dc4648 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:25:37 +0200 Subject: [PATCH 124/261] feat!: bump is.degree.sequence() from deprecate_soft to deprecate_warn --- R/degseq.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/degseq.R b/R/degseq.R index 76a4401822d..7939da114aa 100644 --- a/R/degseq.R +++ b/R/degseq.R @@ -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 b80107de1a4ff0c0d76542336969b910d5958dc3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:25:40 +0200 Subject: [PATCH 125/261] feat!: bump is.graphical.degree.sequence() from deprecate_soft to deprecate_warn --- R/degseq.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/degseq.R b/R/degseq.R index 7939da114aa..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()" From f5071f871e7546ad28d91595dd3b4671cf1135a7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:25:44 +0200 Subject: [PATCH 126/261] feat!: bump power.law.fit() from deprecate_soft to deprecate_warn --- 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 230fcb17f85ffe88cbfe302afd82cfda05d9ed8f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:25:47 +0200 Subject: [PATCH 127/261] feat!: bump dominator.tree() from deprecate_soft to deprecate_warn --- R/flow.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/flow.R b/R/flow.R index 0609fce12c3..e973d6044a1 100644 --- a/R/flow.R +++ b/R/flow.R @@ -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 ad3fef6f90d4829555e4935714684e2947aa0598 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:25:51 +0200 Subject: [PATCH 128/261] feat!: bump edge.connectivity() from deprecate_soft to deprecate_warn --- R/flow.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/flow.R b/R/flow.R index e973d6044a1..a94496eb433 100644 --- a/R/flow.R +++ b/R/flow.R @@ -268,7 +268,7 @@ edge.connectivity <- function( checks = TRUE ) { # nocov start - lifecycle::deprecate_soft( + lifecycle::deprecate_warn( "2.0.0", "edge.connectivity()", "edge_connectivity()" From ddb96af6729f56fbab1cf3adae833659a8acd219 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:25:55 +0200 Subject: [PATCH 129/261] feat!: bump edge.disjoint.paths() from deprecate_soft to deprecate_warn --- R/flow.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/flow.R b/R/flow.R index a94496eb433..64d53da455a 100644 --- a/R/flow.R +++ b/R/flow.R @@ -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()" From b9575f1863198ae3fc5d14d5a6d3e9e55da10020 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:25:58 +0200 Subject: [PATCH 130/261] feat!: bump graph.adhesion() from deprecate_soft to deprecate_warn --- R/flow.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/flow.R b/R/flow.R index 64d53da455a..a4dfec23de3 100644 --- a/R/flow.R +++ b/R/flow.R @@ -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 From 01869afe26354ea01b95ba061d09475b2f4b6a8c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:26:02 +0200 Subject: [PATCH 131/261] feat!: bump graph.maxflow() from deprecate_soft to deprecate_warn --- R/flow.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/flow.R b/R/flow.R index a4dfec23de3..723bd2f1053 100644 --- a/R/flow.R +++ b/R/flow.R @@ -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 From 5685cc14ad4d15050d2bdbd386c1bb1e85e515f5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:26:06 +0200 Subject: [PATCH 132/261] feat!: bump graph.mincut() from deprecate_soft to deprecate_warn --- R/flow.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/flow.R b/R/flow.R index 723bd2f1053..ebe68c976d4 100644 --- a/R/flow.R +++ b/R/flow.R @@ -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, From 97d0e7acebffabd2bf126e2921f742f5cd420e4d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:26:10 +0200 Subject: [PATCH 133/261] feat!: bump is.minimal.separator() from deprecate_soft to deprecate_warn --- R/flow.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/flow.R b/R/flow.R index ebe68c976d4..1c9c7a64939 100644 --- a/R/flow.R +++ b/R/flow.R @@ -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()" From 00c9a31ed94d00f2d0961ef5c44d425bf12554c0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:26:14 +0200 Subject: [PATCH 134/261] feat!: bump is.separator() from deprecate_soft to deprecate_warn --- R/flow.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/flow.R b/R/flow.R index 1c9c7a64939..25b610267d0 100644 --- a/R/flow.R +++ b/R/flow.R @@ -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 From df985fdeb2b006ca2bdd4741e898bd7e09bbfc1c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:26:18 +0200 Subject: [PATCH 135/261] feat!: bump minimal.st.separators() from deprecate_soft to deprecate_warn --- R/flow.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/flow.R b/R/flow.R index 25b610267d0..4d1bd72e2f2 100644 --- a/R/flow.R +++ b/R/flow.R @@ -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()" From 1fa34c4aeca9553c5664503710f957ea9f49f214 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:26:22 +0200 Subject: [PATCH 136/261] feat!: bump minimum.size.separators() from deprecate_soft to deprecate_warn --- R/flow.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/flow.R b/R/flow.R index 4d1bd72e2f2..0484205f85c 100644 --- a/R/flow.R +++ b/R/flow.R @@ -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()" From fc909956b2f58077520cd1977297d472821d3dab Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:26:26 +0200 Subject: [PATCH 137/261] feat!: bump stCuts() from deprecate_soft to deprecate_warn --- R/flow.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/flow.R b/R/flow.R index 0484205f85c..24c8e0005ba 100644 --- a/R/flow.R +++ b/R/flow.R @@ -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 From 06baa1f0d7ea142fa123901f9502ac93dd2456d7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:26:30 +0200 Subject: [PATCH 138/261] feat!: bump stMincuts() from deprecate_soft to deprecate_warn --- R/flow.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/flow.R b/R/flow.R index 24c8e0005ba..c84827f5ec5 100644 --- a/R/flow.R +++ b/R/flow.R @@ -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, From 9531372515f3c4c8ed08a217a28de45fea94422d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:26:33 +0200 Subject: [PATCH 139/261] feat!: bump vertex.connectivity() from deprecate_soft to deprecate_warn --- R/flow.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/flow.R b/R/flow.R index c84827f5ec5..7db03d3abb5 100644 --- a/R/flow.R +++ b/R/flow.R @@ -35,7 +35,7 @@ vertex.connectivity <- function( checks = TRUE ) { # nocov start - lifecycle::deprecate_soft( + lifecycle::deprecate_warn( "2.0.0", "vertex.connectivity()", "vertex_connectivity()" From 8c8cff2191e1ebd9a10b31309fa027eb5c839486 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:26:37 +0200 Subject: [PATCH 140/261] feat!: bump vertex.disjoint.paths() from deprecate_soft to deprecate_warn --- R/flow.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/flow.R b/R/flow.R index 7db03d3abb5..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()" From 60ac4e91db1e46d4125609a135d5ac35c99e4017 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:26:41 +0200 Subject: [PATCH 141/261] feat!: bump graph.graphdb() from deprecate_soft to deprecate_warn --- R/foreign.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/foreign.R b/R/foreign.R index ebf9280b01d..763e8776b56 100644 --- a/R/foreign.R +++ b/R/foreign.R @@ -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 3201d3063e43341c3ccfc99bdb251dc69fcee7d7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:26:45 +0200 Subject: [PATCH 142/261] feat!: bump read.graph() from deprecate_soft to deprecate_warn --- R/foreign.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/foreign.R b/R/foreign.R index 763e8776b56..02c391128a4 100644 --- a/R/foreign.R +++ b/R/foreign.R @@ -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 From 7adfc859f98ccadd28105d5df15869ad46ba9d74 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:26:48 +0200 Subject: [PATCH 143/261] feat!: bump write.graph() from deprecate_soft to deprecate_warn --- R/foreign.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/foreign.R b/R/foreign.R index 02c391128a4..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 From e6c2e7b977d82ad8e6c56022a8247fe006f9bea6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:26:55 +0200 Subject: [PATCH 144/261] feat!: bump bipartite() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index f37cb832403..11f2307fb3b 100644 --- a/R/games.R +++ b/R/games.R @@ -2504,7 +2504,7 @@ bipartite <- function(..., type = NULL) { ) bipartite_gnp(...) } else if (type == "gnm") { - lifecycle::deprecate_soft( + lifecycle::deprecate_warn( "2.1.3", "bipartite()", "bipartite_gnm()" From cd15bd96377879d78bd949bf0c4d9ee3332b9d2f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:27:01 +0200 Subject: [PATCH 145/261] feat!: bump bipartite() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index 11f2307fb3b..e3167192600 100644 --- a/R/games.R +++ b/R/games.R @@ -2497,7 +2497,7 @@ 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()" From e2f0d0bacd9a515d989ae2e9d8c6fef0f702c35b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:27:08 +0200 Subject: [PATCH 146/261] feat!: bump sample_bipartite() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index e3167192600..77c6e76e6ac 100644 --- a/R/games.R +++ b/R/games.R @@ -2481,7 +2481,7 @@ sample_bipartite <- function( ) 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()" From df014d48e236f52419dc37d22a66c53cfb115811 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:27:15 +0200 Subject: [PATCH 147/261] feat!: bump sample_bipartite() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index 77c6e76e6ac..50329e78386 100644 --- a/R/games.R +++ b/R/games.R @@ -2474,7 +2474,7 @@ 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()" From 2a10d4c36cdceda8765427ac3708d40ace965432 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:27:29 +0200 Subject: [PATCH 148/261] feat!: bump sample_degseq(method = 'must be configuration.simple instead of simple.no.multiple.uniform') from deprecate_warn to deprecate_stop --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index 50329e78386..7a003f2c159 100644 --- a/R/games.R +++ b/R/games.R @@ -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')" ) From d0c59940767bd15484ec4231b9737ea7187a7f4e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:27:42 +0200 Subject: [PATCH 149/261] feat!: bump sample_degseq(method = 'must be fast.heur.simple instead of simple.no.multiple') from deprecate_warn to deprecate_stop --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index 7a003f2c159..1b6e5f23fc6 100644 --- a/R/games.R +++ b/R/games.R @@ -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')" ) From fc122d82bab77e4ecf2bc43065c5502e89b6f357 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:27:56 +0200 Subject: [PATCH 150/261] feat!: bump sample_degseq(method = 'must be configuration instead of simple') from deprecate_warn to deprecate_stop --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index 1b6e5f23fc6..d32452fcd1d 100644 --- a/R/games.R +++ b/R/games.R @@ -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')" ) From 33c660a91c7b02ad9a56df104b3082b0bbfdffe3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:28:10 +0200 Subject: [PATCH 151/261] feat!: bump random.graph.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index d32452fcd1d..6289a8cdc0a 100644 --- a/R/games.R +++ b/R/games.R @@ -1181,7 +1181,7 @@ random.graph.game <- function( lifecycle::deprecate_soft("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) } } From 4f14ce8ff9b0c1b94b039592f1749a938bbc6b23 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:28:24 +0200 Subject: [PATCH 152/261] feat!: bump random.graph.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index 6289a8cdc0a..9de340aa0fa 100644 --- a/R/games.R +++ b/R/games.R @@ -1178,7 +1178,7 @@ 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_warn("0.8.0", "random.graph.game()", "sample_gnm()") From 726f02c063071a05fe110526e2720f9ac4b3dce0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:28:38 +0200 Subject: [PATCH 153/261] feat!: bump erdos.renyi.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index 9de340aa0fa..c03ca920014 100644 --- a/R/games.R +++ b/R/games.R @@ -1161,7 +1161,7 @@ erdos.renyi.game <- function( lifecycle::deprecate_soft("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) } } From dbb6ec6abf2d77375e2d4a2bf935c9e858c7def1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:28:52 +0200 Subject: [PATCH 154/261] feat!: bump erdos.renyi.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index c03ca920014..e606cb1f414 100644 --- a/R/games.R +++ b/R/games.R @@ -1158,7 +1158,7 @@ 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_warn("0.8.0", "erdos.renyi.game()", "sample_gnm()") From cf4d93b35bf8f338509f147718a26496fb68d944 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:29:06 +0200 Subject: [PATCH 155/261] feat!: bump aging.prefatt.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index e606cb1f414..2888bed6cc6 100644 --- a/R/games.R +++ b/R/games.R @@ -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, From 681ed368e181e67c2e2675f0623eb016e2a7d19a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:29:19 +0200 Subject: [PATCH 156/261] feat!: bump aging.ba.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index 2888bed6cc6..171de882115 100644 --- a/R/games.R +++ b/R/games.R @@ -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, From ee6c869ebe5f491932b327ac258a94d875e0066d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:29:32 +0200 Subject: [PATCH 157/261] feat!: bump aging.barabasi.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index 171de882115..53e7cb0ae69 100644 --- a/R/games.R +++ b/R/games.R @@ -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, From 72cfafb8feb78fcbd43e270be5742d6449845f93 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:29:46 +0200 Subject: [PATCH 158/261] feat!: bump asymmetric.preference.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index 53e7cb0ae69..417e6e6ddee 100644 --- a/R/games.R +++ b/R/games.R @@ -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()" From 70a827d9e0b1e21170787affe77de840adccfc5a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:30:02 +0200 Subject: [PATCH 159/261] feat!: bump ba.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index 417e6e6ddee..843a30fbbdd 100644 --- a/R/games.R +++ b/R/games.R @@ -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, From dccc06a122357032285efbc4e2c4b444ba9ee8e5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:30:19 +0200 Subject: [PATCH 160/261] feat!: bump barabasi.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index 843a30fbbdd..d3f07d2504e 100644 --- a/R/games.R +++ b/R/games.R @@ -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, From 92ac9941d820ebca5faa333a88804f4e37cea15e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:30:34 +0200 Subject: [PATCH 161/261] feat!: bump bipartite.random.game() from deprecate_warn to deprecate_stop --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index d3f07d2504e..1a0c4617ebf 100644 --- a/R/games.R +++ b/R/games.R @@ -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()" From ca65f900845259f6426453876fdb5e21f539a591 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:30:48 +0200 Subject: [PATCH 162/261] feat!: bump callaway.traits.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index 1a0c4617ebf..b712fcc1cff 100644 --- a/R/games.R +++ b/R/games.R @@ -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()" From 09d48fc5100f4bec063fc213062d51c7b2c76d41 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:31:03 +0200 Subject: [PATCH 163/261] feat!: bump cited.type.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index b712fcc1cff..e9b651317e9 100644 --- a/R/games.R +++ b/R/games.R @@ -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, From e739b5497b5312859f0eb64b8d3d63506a84ab92 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:31:18 +0200 Subject: [PATCH 164/261] feat!: bump citing.cited.type.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index e9b651317e9..759bd880fe7 100644 --- a/R/games.R +++ b/R/games.R @@ -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()" From b51275355150fb440e6db0349e557545744754c8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:31:32 +0200 Subject: [PATCH 165/261] feat!: bump connect.neighborhood() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index 759bd880fe7..c9e8023e503 100644 --- a/R/games.R +++ b/R/games.R @@ -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 From 8a6219beb69463ff7fa4d2b809cac8b7912470d5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:31:46 +0200 Subject: [PATCH 166/261] feat!: bump degree.sequence.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index c9e8023e503..e44d188942c 100644 --- a/R/games.R +++ b/R/games.R @@ -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()" From 548abdce8c3a32bf6f310178a48d115bd6c93438 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:31:59 +0200 Subject: [PATCH 167/261] feat!: bump establishment.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index e44d188942c..edfcd17a055 100644 --- a/R/games.R +++ b/R/games.R @@ -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, From cc9bb09a70169d83007921eb63a574e03a477022 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:32:12 +0200 Subject: [PATCH 168/261] feat!: bump forest.fire.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index edfcd17a055..47231846625 100644 --- a/R/games.R +++ b/R/games.R @@ -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()" From a946db3abc597a3333f515457028900e88897ab6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:32:25 +0200 Subject: [PATCH 169/261] feat!: bump growing.random.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index 47231846625..dbd22788f1a 100644 --- a/R/games.R +++ b/R/games.R @@ -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()" From 6abc9c3d796e294446054d39199adb99efc266fd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:32:38 +0200 Subject: [PATCH 170/261] feat!: bump grg.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index dbd22788f1a..bb2c61fbf79 100644 --- a/R/games.R +++ b/R/games.R @@ -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 From 54a5e08ed96d016a7d59e8b7b561465361cb27ff Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:32:53 +0200 Subject: [PATCH 171/261] feat!: bump interconnected.islands.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index bb2c61fbf79..01958017fc5 100644 --- a/R/games.R +++ b/R/games.R @@ -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()" From 2823b3904165880ca8454c0a997a0d1eb710c8c0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:33:07 +0200 Subject: [PATCH 172/261] feat!: bump k.regular.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index 01958017fc5..ad325dbfd9c 100644 --- a/R/games.R +++ b/R/games.R @@ -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, From 676e02047e59efa9078778fa46b6fead4ad72e3b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:33:21 +0200 Subject: [PATCH 173/261] feat!: bump lastcit.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index ad325dbfd9c..68c8d8eb4b5 100644 --- a/R/games.R +++ b/R/games.R @@ -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, From 23b5fa729a6d4abff10056dce781083b8fe3ba9a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:33:35 +0200 Subject: [PATCH 174/261] feat!: bump preference.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index 68c8d8eb4b5..3c66288bcc2 100644 --- a/R/games.R +++ b/R/games.R @@ -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, From 329774e26ea3beba9b36b2b6bad8a230ea177226 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:33:49 +0200 Subject: [PATCH 175/261] feat!: bump sbm.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index 3c66288bcc2..4bdf677708f 100644 --- a/R/games.R +++ b/R/games.R @@ -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, From 5491b7a1736e5ebeebac5751f4eb9e550f7444c1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:34:04 +0200 Subject: [PATCH 176/261] feat!: bump static.fitness.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index 4bdf677708f..7b7a0ae461f 100644 --- a/R/games.R +++ b/R/games.R @@ -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()" From 4b771ae9c679fd7b89dbdc50b4f1a04695cac034 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:34:18 +0200 Subject: [PATCH 177/261] feat!: bump static.power.law.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index 7b7a0ae461f..9723a099474 100644 --- a/R/games.R +++ b/R/games.R @@ -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()" From c51c0faa8da8a1fb93872175a0f58d22bc3a27a2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:34:34 +0200 Subject: [PATCH 178/261] feat!: bump watts.strogatz.game() from deprecate_soft to deprecate_warn --- R/games.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/games.R b/R/games.R index 9723a099474..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()" From 43d7a53f38d88e88a3c9dbeb401a17a56be4c6bc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:34:37 +0200 Subject: [PATCH 179/261] feat!: bump graphlets.candidate.basis() from deprecate_soft to deprecate_warn --- R/glet.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/glet.R b/R/glet.R index 252b227cfe8..450cc4d7c2e 100644 --- a/R/glet.R +++ b/R/glet.R @@ -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 2de86790afd7e72d4fd9295c1fec30f397feecd3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:34:40 +0200 Subject: [PATCH 180/261] feat!: bump graphlets.project() from deprecate_soft to deprecate_warn --- R/glet.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/glet.R b/R/glet.R index 450cc4d7c2e..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, From 5ed548038e36b1e325ae5e562564b95d7f46fef5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:34:44 +0200 Subject: [PATCH 181/261] feat!: bump hrg.consensus() from deprecate_soft to deprecate_warn --- R/hrg.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/hrg.R b/R/hrg.R index b8eb3c4a860..f7a735089bc 100644 --- a/R/hrg.R +++ b/R/hrg.R @@ -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 422473468a54f40a6ab4e18fc0dcb73952d05489 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:34:48 +0200 Subject: [PATCH 182/261] feat!: bump hrg.create() from deprecate_soft to deprecate_warn --- R/hrg.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/hrg.R b/R/hrg.R index f7a735089bc..6533ec69276 100644 --- a/R/hrg.R +++ b/R/hrg.R @@ -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 From 3fa8c55faef153268e2fea4b76ad545bce628439 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:34:52 +0200 Subject: [PATCH 183/261] feat!: bump hrg.dendrogram() from deprecate_soft to deprecate_warn --- R/hrg.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/hrg.R b/R/hrg.R index 6533ec69276..779d438ea23 100644 --- a/R/hrg.R +++ b/R/hrg.R @@ -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 From ab2efd89d9fede4f5b7e17e650dd0cd15a895603 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:34:56 +0200 Subject: [PATCH 184/261] feat!: bump hrg.game() from deprecate_soft to deprecate_warn --- R/hrg.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/hrg.R b/R/hrg.R index 779d438ea23..cf99abcf0fe 100644 --- a/R/hrg.R +++ b/R/hrg.R @@ -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 From d363ddbcd40655dde346d55b09e8194f5f7d4164 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:35:00 +0200 Subject: [PATCH 185/261] feat!: bump hrg.fit() from deprecate_soft to deprecate_warn --- R/hrg.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/hrg.R b/R/hrg.R index cf99abcf0fe..cb9714a219f 100644 --- a/R/hrg.R +++ b/R/hrg.R @@ -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 From c862ff87aca78d21bf8a26d26589706edf52f962 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:35:04 +0200 Subject: [PATCH 186/261] feat!: bump hrg.predict() from deprecate_soft to deprecate_warn --- R/hrg.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/hrg.R b/R/hrg.R index cb9714a219f..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, From 7d9a04c44a940c105b5e1fdb252b13be51a1f003 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:35:07 +0200 Subject: [PATCH 187/261] feat!: bump graph_from_incidence_matrix() from deprecate_soft to deprecate_warn --- R/incidence.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/incidence.R b/R/incidence.R index 3937ad025af..d40a2aecbab 100644 --- a/R/incidence.R +++ b/R/incidence.R @@ -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 41e6c098e61bfb01af0ad4fa940009ed61fe0d38 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:35:10 +0200 Subject: [PATCH 188/261] feat!: bump graph_from_incidence_matrix() from deprecate_soft to deprecate_warn --- R/incidence.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/incidence.R b/R/incidence.R index d40a2aecbab..2dba0cd4bb8 100644 --- a/R/incidence.R +++ b/R/incidence.R @@ -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()" From 16a27a32cd9ba92a680cea0d993a16b81243a4da Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:35:14 +0200 Subject: [PATCH 189/261] feat!: bump graph.incidence() from deprecate_soft to deprecate_warn --- R/incidence.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/incidence.R b/R/incidence.R index 2dba0cd4bb8..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()" From ffa1ec65420883d70092b8d92dbcc3dd7af4d22f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:35:18 +0200 Subject: [PATCH 190/261] feat!: bump get.edge.ids() from deprecate_soft to deprecate_warn --- R/interface.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/interface.R b/R/interface.R index 7533cfb8285..ac4026c9c4a 100644 --- a/R/interface.R +++ b/R/interface.R @@ -586,7 +586,7 @@ get.edge.ids <- function( lifecycle::deprecate_soft("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) } From c5848312a44d913b551bcf81765f636d894c76af Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:35:22 +0200 Subject: [PATCH 191/261] feat!: bump get.edge.ids(multi = ) from deprecate_soft to deprecate_warn --- R/interface.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/interface.R b/R/interface.R index ac4026c9c4a..e43d313f7f9 100644 --- a/R/interface.R +++ b/R/interface.R @@ -584,7 +584,7 @@ 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_warn("2.1.0", "get.edge.ids()", "get_edge_ids()") get_edge_ids(graph = graph, vp = vp, directed = directed, error = error) From d84bda4398949b05cef6706c46ae3b7cb34fc64d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:35:30 +0200 Subject: [PATCH 192/261] feat!: bump get_edge_ids(vp = 'supplied as a matrix should be a n times 2 matrix, not 2 times n') from deprecate_warn to deprecate_stop --- R/interface.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/interface.R b/R/interface.R index e43d313f7f9..8f15fcf996a 100644 --- a/R/interface.R +++ b/R/interface.R @@ -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." From 87d443dd3ae6c3a05d84b2ed84cb06764f3c1bbb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:35:39 +0200 Subject: [PATCH 193/261] feat!: bump add.edges() from deprecate_soft to deprecate_warn --- R/interface.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/interface.R b/R/interface.R index 8f15fcf996a..cda60052e59 100644 --- a/R/interface.R +++ b/R/interface.R @@ -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 From 5709e084cd33fc3b9106a984fb08263ddcddf38a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:35:49 +0200 Subject: [PATCH 194/261] feat!: bump add.vertices() from deprecate_soft to deprecate_warn --- R/interface.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/interface.R b/R/interface.R index cda60052e59..9635fea650d 100644 --- a/R/interface.R +++ b/R/interface.R @@ -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 From ed78b8b18c7fdfb07efa038275f4ebaff1e5e168 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:35:58 +0200 Subject: [PATCH 195/261] feat!: bump delete.edges() from deprecate_soft to deprecate_warn --- R/interface.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/interface.R b/R/interface.R index 9635fea650d..2de7f18d55f 100644 --- a/R/interface.R +++ b/R/interface.R @@ -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 From a84fefb7305ee91363679d9b541727745658ed8e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:36:07 +0200 Subject: [PATCH 196/261] feat!: bump delete.vertices() from deprecate_soft to deprecate_warn --- R/interface.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/interface.R b/R/interface.R index 2de7f18d55f..830013fe11a 100644 --- a/R/interface.R +++ b/R/interface.R @@ -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 From f510ce4f5b4d1b558490b3c7c2bb2186245c83de Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:36:17 +0200 Subject: [PATCH 197/261] feat!: bump is.directed() from deprecate_soft to deprecate_warn --- R/interface.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/interface.R b/R/interface.R index 830013fe11a..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 From 4de2378afbc7a3b77f59d3e925b804451a3caa70 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:36:26 +0200 Subject: [PATCH 198/261] feat!: remove deprecated to() (lifecycle::deprecate_stop) --- R/iterators.R | 4 --- tests/testthat/_snaps/iterators.new.md | 42 ++++++++++++++++++++++++++ 2 files changed, 42 insertions(+), 4 deletions(-) create mode 100644 tests/testthat/_snaps/iterators.new.md diff --git a/R/iterators.R b/R/iterators.R index 2cfd3101348..e409c69d97d 100644 --- a/R/iterators.R +++ b/R/iterators.R @@ -1025,10 +1025,6 @@ simple_es_index <- function(x, i, na_ok = FALSE) { ) tmp[as.numeric(x)] } - to <- function(...) { - lifecycle::deprecate_stop("2.1.0", "to()", ".to()") - } - graph <- get_es_graph(x) if (is.null(graph)) { diff --git a/tests/testthat/_snaps/iterators.new.md b/tests/testthat/_snaps/iterators.new.md new file mode 100644 index 00000000000..ac030fa2e78 --- /dev/null +++ b/tests/testthat/_snaps/iterators.new.md @@ -0,0 +1,42 @@ +# printing unconnected vs/es works + + Code + vs + Output + + 10/? vertices (deleted): + [1] 1 2 3 4 5 6 7 8 9 10 + Code + es + Output + + 10/? edges (deleted): + [1] 1 2 3 4 5 6 7 8 9 10 + +--- + + Code + vs + Output + + 10/? vertices (deleted): + [1] 1 2 3 4 5 6 7 8 9 10 + Code + es + Output + + 10/? edges (deleted) (vertex names): + [1] a|b b|c c|d d|e e|f f|g g|h h|i i|j a|j + +# logical indices are not recycled + + Code + V(g)[c(TRUE, FALSE)] + Condition + Error in `FUN()`: + ! Error: Logical index length does not match the number of vertices. Recycling is not allowed. + +--- + + Code + E(g)[c(TRUE, FALSE)] + Condition + Error in `[.igraph.es`: + ! object 'to' not found + From 14e3d5a6632553125c9e46593e6aa4f2faa73f30 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:36:35 +0200 Subject: [PATCH 199/261] feat!: remove deprecated from() (lifecycle::deprecate_stop) --- R/iterators.R | 3 --- tests/testthat/_snaps/iterators.new.md | 2 +- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/R/iterators.R b/R/iterators.R index e409c69d97d..e8101a61601 100644 --- a/R/iterators.R +++ b/R/iterators.R @@ -1010,9 +1010,6 @@ simple_es_index <- function(x, i, na_ok = FALSE) { ) tmp[as.numeric(x)] } - from <- function(...) { - lifecycle::deprecate_stop("2.1.0", "from()", ".from()") - } .to <- function(v) { ## TRUE iff the edge points to at least one vertex in v on.exit(.Call(Rx_igraph_finalizer)) diff --git a/tests/testthat/_snaps/iterators.new.md b/tests/testthat/_snaps/iterators.new.md index ac030fa2e78..4ed67f5da60 100644 --- a/tests/testthat/_snaps/iterators.new.md +++ b/tests/testthat/_snaps/iterators.new.md @@ -38,5 +38,5 @@ E(g)[c(TRUE, FALSE)] Condition Error in `[.igraph.es`: - ! object 'to' not found + ! object 'from' not found From c1a3675d295256d8c9194dd9370ec385e94a7e48 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:36:43 +0200 Subject: [PATCH 200/261] feat!: remove deprecated inc() (lifecycle::deprecate_stop) --- R/iterators.R | 3 --- tests/testthat/_snaps/iterators.new.md | 2 +- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/R/iterators.R b/R/iterators.R index e8101a61601..f42a45ae63c 100644 --- a/R/iterators.R +++ b/R/iterators.R @@ -995,9 +995,6 @@ simple_es_index <- function(x, i, na_ok = FALSE) { adj <- function(...) { lifecycle::deprecate_stop("2.1.0", "adj()", ".inc()") } - inc <- function(...) { - lifecycle::deprecate_stop("2.1.0", "inc()", ".inc()") - } .from <- function(v) { ## TRUE iff the edge originates from at least one vertex in v on.exit(.Call(Rx_igraph_finalizer)) diff --git a/tests/testthat/_snaps/iterators.new.md b/tests/testthat/_snaps/iterators.new.md index 4ed67f5da60..ca072283988 100644 --- a/tests/testthat/_snaps/iterators.new.md +++ b/tests/testthat/_snaps/iterators.new.md @@ -38,5 +38,5 @@ E(g)[c(TRUE, FALSE)] Condition Error in `[.igraph.es`: - ! object 'from' not found + ! object 'inc' not found From 31cbd8cbbe0e73909e743676c25a24907d5eea91 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:36:52 +0200 Subject: [PATCH 201/261] feat!: remove deprecated adj() (lifecycle::deprecate_stop) --- R/iterators.R | 3 --- 1 file changed, 3 deletions(-) diff --git a/R/iterators.R b/R/iterators.R index f42a45ae63c..8a181ec43a5 100644 --- a/R/iterators.R +++ b/R/iterators.R @@ -992,9 +992,6 @@ simple_es_index <- function(x, i, na_ok = FALSE) { ) tmp[as.numeric(x)] } - adj <- function(...) { - lifecycle::deprecate_stop("2.1.0", "adj()", ".inc()") - } .from <- function(v) { ## TRUE iff the edge originates from at least one vertex in v on.exit(.Call(Rx_igraph_finalizer)) From de2f83e94dafdb4174394ae6b78e11cc76ca12f8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:37:00 +0200 Subject: [PATCH 202/261] feat!: remove deprecated to() (lifecycle::deprecate_stop) --- R/iterators.R | 4 ---- tests/testthat/_snaps/iterators.new.md | 4 ++-- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/R/iterators.R b/R/iterators.R index 8a181ec43a5..2b7893541d3 100644 --- a/R/iterators.R +++ b/R/iterators.R @@ -669,10 +669,6 @@ simple_vs_index <- function(x, i, na_ok = FALSE) { ) tmp[as.numeric(x)] } - to <- function(...) { - lifecycle::deprecate_stop("2.1.0", "to()", ".to()") - } - graph <- get_vs_graph(x) if (is.null(graph)) { diff --git a/tests/testthat/_snaps/iterators.new.md b/tests/testthat/_snaps/iterators.new.md index ca072283988..04dc6a82106 100644 --- a/tests/testthat/_snaps/iterators.new.md +++ b/tests/testthat/_snaps/iterators.new.md @@ -29,8 +29,8 @@ Code V(g)[c(TRUE, FALSE)] Condition - Error in `FUN()`: - ! Error: Logical index length does not match the number of vertices. Recycling is not allowed. + Error in `[.igraph.vs`: + ! object 'to' not found --- From 56db3c1c41de71dc81c1a0d464dafdbcdbae4aad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:37:09 +0200 Subject: [PATCH 203/261] feat!: remove deprecated from() (lifecycle::deprecate_stop) --- R/iterators.R | 3 --- tests/testthat/_snaps/iterators.new.md | 2 +- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/R/iterators.R b/R/iterators.R index 2b7893541d3..44e5aa39006 100644 --- a/R/iterators.R +++ b/R/iterators.R @@ -651,9 +651,6 @@ simple_vs_index <- function(x, i, na_ok = FALSE) { ) tmp[as.numeric(x)] } - from <- function(...) { - lifecycle::deprecate_stop("2.1.0", "from()", ".from()") - } .to <- function(e) { ## TRUE iff the vertex is the target of at least one edge in e if (is.logical(e)) { diff --git a/tests/testthat/_snaps/iterators.new.md b/tests/testthat/_snaps/iterators.new.md index 04dc6a82106..f009fa38806 100644 --- a/tests/testthat/_snaps/iterators.new.md +++ b/tests/testthat/_snaps/iterators.new.md @@ -30,7 +30,7 @@ V(g)[c(TRUE, FALSE)] Condition Error in `[.igraph.vs`: - ! object 'to' not found + ! object 'from' not found --- From e1e39e8527945b276cca8f80a3a87101d365cda0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:37:18 +0200 Subject: [PATCH 204/261] feat!: remove deprecated adj() (lifecycle::deprecate_stop) --- R/iterators.R | 3 --- tests/testthat/_snaps/iterators.new.md | 2 +- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/R/iterators.R b/R/iterators.R index 44e5aa39006..5acb01b0ee4 100644 --- a/R/iterators.R +++ b/R/iterators.R @@ -633,9 +633,6 @@ simple_vs_index <- function(x, i, na_ok = FALSE) { inc <- function(...) { lifecycle::deprecate_stop("2.1.0", "inc()", ".inc()") } - adj <- function(...) { - lifecycle::deprecate_stop("2.1.0", "adj()", ".inc()") - } .from <- function(e) { ## TRUE iff the vertex is the source of at least one edge in e if (is.logical(e)) { diff --git a/tests/testthat/_snaps/iterators.new.md b/tests/testthat/_snaps/iterators.new.md index f009fa38806..bb0b61e7f44 100644 --- a/tests/testthat/_snaps/iterators.new.md +++ b/tests/testthat/_snaps/iterators.new.md @@ -30,7 +30,7 @@ V(g)[c(TRUE, FALSE)] Condition Error in `[.igraph.vs`: - ! object 'from' not found + ! object 'adj' not found --- From 2a33bec562fa930257a4b864c2d9c30981dac43f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:37:26 +0200 Subject: [PATCH 205/261] feat!: remove deprecated inc() (lifecycle::deprecate_stop) --- R/iterators.R | 3 --- tests/testthat/_snaps/iterators.new.md | 2 +- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/R/iterators.R b/R/iterators.R index 5acb01b0ee4..58fec903e58 100644 --- a/R/iterators.R +++ b/R/iterators.R @@ -630,9 +630,6 @@ simple_vs_index <- function(x, i, na_ok = FALSE) { ) tmp[as.numeric(x)] } - inc <- function(...) { - lifecycle::deprecate_stop("2.1.0", "inc()", ".inc()") - } .from <- function(e) { ## TRUE iff the vertex is the source of at least one edge in e if (is.logical(e)) { diff --git a/tests/testthat/_snaps/iterators.new.md b/tests/testthat/_snaps/iterators.new.md index bb0b61e7f44..3ca1f771f4e 100644 --- a/tests/testthat/_snaps/iterators.new.md +++ b/tests/testthat/_snaps/iterators.new.md @@ -30,7 +30,7 @@ V(g)[c(TRUE, FALSE)] Condition Error in `[.igraph.vs`: - ! object 'adj' not found + ! object 'inc' not found --- From 373972c563ddf1b7f206038908a1793028e784dd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:37:35 +0200 Subject: [PATCH 206/261] feat!: remove deprecated outnei() (lifecycle::deprecate_stop) --- R/iterators.R | 3 --- tests/testthat/_snaps/iterators.new.md | 2 +- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/R/iterators.R b/R/iterators.R index 58fec903e58..019c0b250e7 100644 --- a/R/iterators.R +++ b/R/iterators.R @@ -611,9 +611,6 @@ simple_vs_index <- function(x, i, na_ok = FALSE) { .outnei <- function(v, mode = c("out", "all", "in", "total")) { .nei(v, mode = mode[1]) } - outnei <- function(...) { - lifecycle::deprecate_stop("2.1.0", "outnei()", ".outnei()") - } .inc <- function(e) { ## TRUE iff the vertex (in the vs) is incident ## to at least one edge in e diff --git a/tests/testthat/_snaps/iterators.new.md b/tests/testthat/_snaps/iterators.new.md index 3ca1f771f4e..b9ab4c4773d 100644 --- a/tests/testthat/_snaps/iterators.new.md +++ b/tests/testthat/_snaps/iterators.new.md @@ -30,7 +30,7 @@ V(g)[c(TRUE, FALSE)] Condition Error in `[.igraph.vs`: - ! object 'inc' not found + ! object 'outnei' not found --- From 3f1fba04ac8947a2250b7ccfd41f41d05d8c4ee7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:37:44 +0200 Subject: [PATCH 207/261] feat!: remove deprecated innei() (lifecycle::deprecate_stop) --- R/iterators.R | 3 --- tests/testthat/_snaps/iterators.new.md | 2 +- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/R/iterators.R b/R/iterators.R index 019c0b250e7..0e0c7828953 100644 --- a/R/iterators.R +++ b/R/iterators.R @@ -605,9 +605,6 @@ simple_vs_index <- function(x, i, na_ok = FALSE) { .innei <- function(v, mode = c("in", "all", "out", "total")) { .nei(v, mode = mode[1]) } - innei <- function(...) { - lifecycle::deprecate_stop("2.1.0", "innei()", ".innei()") - } .outnei <- function(v, mode = c("out", "all", "in", "total")) { .nei(v, mode = mode[1]) } diff --git a/tests/testthat/_snaps/iterators.new.md b/tests/testthat/_snaps/iterators.new.md index b9ab4c4773d..1f73f17afa3 100644 --- a/tests/testthat/_snaps/iterators.new.md +++ b/tests/testthat/_snaps/iterators.new.md @@ -30,7 +30,7 @@ V(g)[c(TRUE, FALSE)] Condition Error in `[.igraph.vs`: - ! object 'outnei' not found + ! object 'innei' not found --- From 057e08584752372fe537ef97716e08a1bd762108 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:37:54 +0200 Subject: [PATCH 208/261] feat!: remove deprecated nei() (lifecycle::deprecate_stop) --- R/iterators.R | 3 --- tests/testthat/_snaps/iterators.new.md | 2 +- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/R/iterators.R b/R/iterators.R index 0e0c7828953..606417d27a3 100644 --- a/R/iterators.R +++ b/R/iterators.R @@ -599,9 +599,6 @@ simple_vs_index <- function(x, i, na_ok = FALSE) { ) tmp[as.numeric(x)] } - nei <- function(...) { - lifecycle::deprecate_stop("2.1.0", "nei()", ".nei()") - } .innei <- function(v, mode = c("in", "all", "out", "total")) { .nei(v, mode = mode[1]) } diff --git a/tests/testthat/_snaps/iterators.new.md b/tests/testthat/_snaps/iterators.new.md index 1f73f17afa3..b9fd4d22c2d 100644 --- a/tests/testthat/_snaps/iterators.new.md +++ b/tests/testthat/_snaps/iterators.new.md @@ -30,7 +30,7 @@ V(g)[c(TRUE, FALSE)] Condition Error in `[.igraph.vs`: - ! object 'innei' not found + ! object 'nei' not found --- From 84912ea55500d80f9e383fd9e56b5552e1b68ba8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:38:06 +0200 Subject: [PATCH 209/261] feat!: bump layout.drl() from deprecate_soft to deprecate_warn --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index 1f14bbe0fb6..a80f809d5c0 100644 --- a/R/layout.R +++ b/R/layout.R @@ -2723,7 +2723,7 @@ 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, From 3b633ff2b370bf241bb48c0749cdb77281392fa8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:38:18 +0200 Subject: [PATCH 210/261] feat!: bump layout.fruchterman.reingold.grid() from deprecate_warn to deprecate_stop --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index a80f809d5c0..90ebd8191a5 100644 --- a/R/layout.R +++ b/R/layout.R @@ -2696,7 +2696,7 @@ 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()" From e72944939a1c08edeb9d44953668733ad60d8c01 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:38:30 +0200 Subject: [PATCH 211/261] feat!: bump layout.svd() from deprecate_warn to deprecate_stop --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index 90ebd8191a5..afd2c57da05 100644 --- a/R/layout.R +++ b/R/layout.R @@ -2677,7 +2677,7 @@ 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) } From 6eaef69cfa97a4a41c811fac0ec55f678a64e88f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:38:43 +0200 Subject: [PATCH 212/261] feat!: bump layout.spring() from deprecate_warn to deprecate_stop --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index afd2c57da05..665e065d190 100644 --- a/R/layout.R +++ b/R/layout.R @@ -2659,7 +2659,7 @@ 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) } From 4fb464c5727d5c615cc990c66b0277f2fb69d72d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:38:55 +0200 Subject: [PATCH 213/261] feat!: bump layout_with_mds(options = 'must be a list') from deprecate_soft to deprecate_warn --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index 665e065d190..2a6e2ffa1c9 100644 --- a/R/layout.R +++ b/R/layout.R @@ -2124,7 +2124,7 @@ 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( From c35b02036c1af683622f99a8367bb6672c2bf5ca Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:39:07 +0200 Subject: [PATCH 214/261] feat!: bump layout.lgl() from deprecate_soft to deprecate_warn --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index 2a6e2ffa1c9..d0e560d2151 100644 --- a/R/layout.R +++ b/R/layout.R @@ -2068,7 +2068,7 @@ 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)) } From 3583dfc737320d265cbea24a209aeae473b2932d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:39:19 +0200 Subject: [PATCH 215/261] feat!: bump layout.kamada.kawai() from deprecate_soft to deprecate_warn --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index d0e560d2151..d9d38dca848 100644 --- a/R/layout.R +++ b/R/layout.R @@ -1982,7 +1982,7 @@ 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()" From d6ee43d7a222d9ffa946a19711aa6670b32bdad1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:39:31 +0200 Subject: [PATCH 216/261] feat!: bump layout.fruchterman.reingold() from deprecate_soft to deprecate_warn --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index d9d38dca848..6990d64bff3 100644 --- a/R/layout.R +++ b/R/layout.R @@ -1624,7 +1624,7 @@ 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()" From 82615b559a0a9007a36d389382deb0b44ddd9f6d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:39:43 +0200 Subject: [PATCH 217/261] feat!: bump layout.random() from deprecate_soft to deprecate_warn --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index 6990d64bff3..3cb9f5c48aa 100644 --- a/R/layout.R +++ b/R/layout.R @@ -1258,7 +1258,7 @@ 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)) } From 5f708bb19247f3d96ad4114625ba50edf363c938 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:39:55 +0200 Subject: [PATCH 218/261] feat!: bump layout.sphere() from deprecate_soft to deprecate_warn --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index 3cb9f5c48aa..82f16c8f712 100644 --- a/R/layout.R +++ b/R/layout.R @@ -1203,7 +1203,7 @@ 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)) } From 30259dd77980fe31e35576e44108684788940491 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:40:08 +0200 Subject: [PATCH 219/261] feat!: bump layout.circle() from deprecate_soft to deprecate_warn --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index 82f16c8f712..a5a5e131533 100644 --- a/R/layout.R +++ b/R/layout.R @@ -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)) } From b88681c01ff104004bfdc609a629232074388a1d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:40:19 +0200 Subject: [PATCH 220/261] feat!: bump layout.reingold.tilford() from deprecate_soft to deprecate_warn --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index a5a5e131533..17f0960e49f 100644 --- a/R/layout.R +++ b/R/layout.R @@ -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()" From 7f6bdbd9204c7088d1c47b370736e2f49f615995 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:40:31 +0200 Subject: [PATCH 221/261] feat!: bump layout.auto() from deprecate_soft to deprecate_warn --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index 17f0960e49f..07ed0f72f1f 100644 --- a/R/layout.R +++ b/R/layout.R @@ -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 From b6b7f192200362ee8fccf161cdbb7f28d0fe14fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:40:44 +0200 Subject: [PATCH 222/261] feat!: bump layout.bipartite() from deprecate_soft to deprecate_warn --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index 07ed0f72f1f..7bda972566e 100644 --- a/R/layout.R +++ b/R/layout.R @@ -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()" From 59eb6c9ef4a4aa3b49daa352e95e8463b2f45fb6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:40:57 +0200 Subject: [PATCH 223/261] feat!: bump layout.davidson.harel() from deprecate_soft to deprecate_warn --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index 7bda972566e..9e615db985a 100644 --- a/R/layout.R +++ b/R/layout.R @@ -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()" From cf9e41d4c0fc88ede96d39f30803dd9f3fd75f87 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:41:09 +0200 Subject: [PATCH 224/261] feat!: bump layout.gem() from deprecate_soft to deprecate_warn --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index 9e615db985a..0b89d6eca0f 100644 --- a/R/layout.R +++ b/R/layout.R @@ -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, From 3182187013a50a4da017772f446049a587a482e0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:41:21 +0200 Subject: [PATCH 225/261] feat!: bump layout.graphopt() from deprecate_soft to deprecate_warn --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index 0b89d6eca0f..23670493fe5 100644 --- a/R/layout.R +++ b/R/layout.R @@ -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()" From cf10f697b237d9dbdb7097fa6cdc325ca536f3e1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:41:32 +0200 Subject: [PATCH 226/261] feat!: bump layout.grid() from deprecate_soft to deprecate_warn --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index 23670493fe5..f0f0bae19db 100644 --- a/R/layout.R +++ b/R/layout.R @@ -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 From 8a1a25c1bb2442bab0ce5e0f60ac5c6b692a734e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:41:44 +0200 Subject: [PATCH 227/261] feat!: bump layout.mds() from deprecate_soft to deprecate_warn --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index f0f0bae19db..89049b34a6f 100644 --- a/R/layout.R +++ b/R/layout.R @@ -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 From b7b73e7472130f5bf2faf1da296b5dd7941fb12c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:41:56 +0200 Subject: [PATCH 228/261] feat!: bump layout.merge() from deprecate_soft to deprecate_warn --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index 89049b34a6f..f957d8bab2d 100644 --- a/R/layout.R +++ b/R/layout.R @@ -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 From b43b4f123cdeb812eb638b3d2bda5a3432e22d92 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:42:08 +0200 Subject: [PATCH 229/261] feat!: bump layout.norm() from deprecate_soft to deprecate_warn --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index f957d8bab2d..1d2054e4100 100644 --- a/R/layout.R +++ b/R/layout.R @@ -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, From 2ad8488d6e83022f07cc318703706afedba3f589 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:42:20 +0200 Subject: [PATCH 230/261] feat!: bump layout.star() from deprecate_soft to deprecate_warn --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index 1d2054e4100..402af3149d0 100644 --- a/R/layout.R +++ b/R/layout.R @@ -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 From 457254a176c7d1f579bfcf090017c58366deaad9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:42:32 +0200 Subject: [PATCH 231/261] feat!: bump layout.sugiyama() from deprecate_soft to deprecate_warn --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index 402af3149d0..5aee7c62ae6 100644 --- a/R/layout.R +++ b/R/layout.R @@ -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()" From 2e38a0cb76290f822445700aa7b62b45b9f86bfe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:42:44 +0200 Subject: [PATCH 232/261] feat!: bump piecewise.layout() from deprecate_soft to deprecate_warn --- R/layout.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/layout.R b/R/layout.R index 5aee7c62ae6..e96168d7ce3 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()" From 6d90106038355fda07fb78b24484e3246a429248 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:42:56 +0200 Subject: [PATCH 233/261] feat!: remove deprecated layout.grid.3d() (lifecycle::deprecate_stop) --- R/layout.R | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/R/layout.R b/R/layout.R index e96168d7ce3..cd1166e1b5b 100644 --- a/R/layout.R +++ b/R/layout.R @@ -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 From f37f384be0aab30e34ec8b1f850e33f9b87fa35e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:43:06 +0200 Subject: [PATCH 234/261] feat!: bump make_lattice(circular = 'use periodic argument instead') from deprecate_soft to deprecate_warn --- R/make.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/make.R b/R/make.R index ebb264bed6f..216d66fa6e5 100644 --- a/R/make.R +++ b/R/make.R @@ -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 1bce84305cff3ffdfd1e054adcb8dca276a08895 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:43:15 +0200 Subject: [PATCH 235/261] feat!: bump graph_() from deprecate_soft to deprecate_warn --- R/make.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/make.R b/R/make.R index 216d66fa6e5..46838068a57 100644 --- a/R/make.R +++ b/R/make.R @@ -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( From 4c6a58e891f06eb9771b44779f0995b03e3373f6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:43:24 +0200 Subject: [PATCH 236/261] feat!: bump graph.atlas() from deprecate_soft to deprecate_warn --- R/make.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/make.R b/R/make.R index 46838068a57..6864bd5a2ac 100644 --- a/R/make.R +++ b/R/make.R @@ -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 ) From 98b4b45a72a695b448a69dbed5bcbebd0479db55 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:43:35 +0200 Subject: [PATCH 237/261] feat!: bump graph.bipartite() from deprecate_soft to deprecate_warn --- R/make.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/make.R b/R/make.R index 6864bd5a2ac..1552dc40a05 100644 --- a/R/make.R +++ b/R/make.R @@ -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()" From 4b9cf2c5970b548670ff4df54275c5b613709341 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:43:45 +0200 Subject: [PATCH 238/261] feat!: bump graph.de.bruijn() from deprecate_soft to deprecate_warn --- R/make.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/make.R b/R/make.R index 1552dc40a05..88c73339754 100644 --- a/R/make.R +++ b/R/make.R @@ -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()" From 84df20771e1d4fda502f7e0d696e2ca7faf197e3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:43:55 +0200 Subject: [PATCH 239/261] feat!: bump graph.empty() from deprecate_soft to deprecate_warn --- R/make.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/make.R b/R/make.R index 88c73339754..bbdace0cba3 100644 --- a/R/make.R +++ b/R/make.R @@ -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, From 39a61b05d5f408bc306cf754ba1f6624bac241a2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:44:04 +0200 Subject: [PATCH 240/261] feat!: bump graph.extended.chordal.ring() from deprecate_soft to deprecate_warn --- R/make.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/make.R b/R/make.R index bbdace0cba3..7b910da31ef 100644 --- a/R/make.R +++ b/R/make.R @@ -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()" From 6e2dcbffe5e46d1326d0f95a2c214bf8f72a83cb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:44:14 +0200 Subject: [PATCH 241/261] feat!: bump graph.formula() from deprecate_soft to deprecate_warn --- R/make.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/make.R b/R/make.R index 7b910da31ef..d7ccff77eaa 100644 --- a/R/make.R +++ b/R/make.R @@ -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 From 7e69def10885d986bc531cffc9b93165248c32b7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:44:22 +0200 Subject: [PATCH 242/261] feat!: bump graph.full() from deprecate_soft to deprecate_warn --- R/make.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/make.R b/R/make.R index d7ccff77eaa..b24f556be32 100644 --- a/R/make.R +++ b/R/make.R @@ -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, From 9b3b49d7b0e037dcd3b3dbb6409e54fdc2ba608e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:44:31 +0200 Subject: [PATCH 243/261] feat!: bump graph.full.bipartite() from deprecate_soft to deprecate_warn --- R/make.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/make.R b/R/make.R index b24f556be32..9166805a9a1 100644 --- a/R/make.R +++ b/R/make.R @@ -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()" From 7ce999b1bd0b1b4180addd2da6dcd920334ce65b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:44:41 +0200 Subject: [PATCH 244/261] feat!: bump graph.full.citation() from deprecate_soft to deprecate_warn --- R/make.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/make.R b/R/make.R index 9166805a9a1..9f3a769f363 100644 --- a/R/make.R +++ b/R/make.R @@ -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()" From 978891098d88ba5cf0ec5feda9a1186c046bf270 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:44:50 +0200 Subject: [PATCH 245/261] feat!: bump graph.kautz() from deprecate_soft to deprecate_warn --- R/make.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/make.R b/R/make.R index 9f3a769f363..53a189de7d5 100644 --- a/R/make.R +++ b/R/make.R @@ -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 From e424b264930eb54233faaec5f911b67b60f5a0ab Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:45:00 +0200 Subject: [PATCH 246/261] feat!: bump graph.lattice(circular = 'use periodic argument instead') from deprecate_soft to deprecate_warn --- R/make.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/make.R b/R/make.R index 53a189de7d5..79359173d07 100644 --- a/R/make.R +++ b/R/make.R @@ -408,7 +408,7 @@ graph.lattice <- function( } 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.") From 899f35e29dd1e0602cfae17c1e65507d2dc32add Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:45:09 +0200 Subject: [PATCH 247/261] feat!: bump graph.lattice() from deprecate_soft to deprecate_warn --- R/make.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/make.R b/R/make.R index 79359173d07..2f29d648d40 100644 --- a/R/make.R +++ b/R/make.R @@ -401,7 +401,7 @@ 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) From 7dfc7452f8ac9281899794984f6ca64565c91aa2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:45:18 +0200 Subject: [PATCH 248/261] feat!: bump graph.lcf() from deprecate_soft to deprecate_warn --- R/make.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/make.R b/R/make.R index 2f29d648d40..2a7525c32c4 100644 --- a/R/make.R +++ b/R/make.R @@ -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, From 5596b66a87868214429dbad07284b256809b8bd8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:45:27 +0200 Subject: [PATCH 249/261] feat!: bump graph.star() from deprecate_soft to deprecate_warn --- R/make.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/make.R b/R/make.R index 2a7525c32c4..f0177c4b608 100644 --- a/R/make.R +++ b/R/make.R @@ -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( From be5389fda42a3b08a08b8b610731400231f9aa44 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:45:36 +0200 Subject: [PATCH 250/261] feat!: bump graph.tree() from deprecate_soft to deprecate_warn --- R/make.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/make.R b/R/make.R index f0177c4b608..9eec43fe16b 100644 --- a/R/make.R +++ b/R/make.R @@ -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( From f2cc9c8bf549276f5af89fa9dd061cd31b9b4908 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:45:44 +0200 Subject: [PATCH 251/261] feat!: bump graph.ring() from deprecate_soft to deprecate_warn --- R/make.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/make.R b/R/make.R index 9eec43fe16b..97459f15e23 100644 --- a/R/make.R +++ b/R/make.R @@ -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, From 43e4aaa95dc03fae0343765383e45655a7a91f1b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:45:53 +0200 Subject: [PATCH 252/261] feat!: bump line.graph() from deprecate_soft to deprecate_warn --- R/make.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/make.R b/R/make.R index 97459f15e23..88a7372984b 100644 --- a/R/make.R +++ b/R/make.R @@ -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( From e9d729aeeece0fab9c52be43d6b1810fc2d3d022 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:46:02 +0200 Subject: [PATCH 253/261] feat!: bump graph.famous() from deprecate_soft to deprecate_warn --- R/make.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/make.R b/R/make.R index 88a7372984b..479a906aeb0 100644 --- a/R/make.R +++ b/R/make.R @@ -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") From e86581a97568bb7d2d7216ebcd3f5d0f87f5c79d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:46:10 +0200 Subject: [PATCH 254/261] feat!: bump graph() from deprecate_soft to deprecate_warn --- R/make.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/make.R b/R/make.R index 479a906aeb0..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") From 7ba1be78bfbfcdec1b036f0aecfb889c7338b2b5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:54:07 +0200 Subject: [PATCH 255/261] chore: script and results --- .Rbuildignore | 1 + lifecycle-TODO.md | 711 +++++++++++++++++++++++++++++++++++++++++ tools/bump-lifecycle.R | 414 ++++++++++++++++++++++++ 3 files changed, 1126 insertions(+) create mode 100644 lifecycle-TODO.md create mode 100644 tools/bump-lifecycle.R diff --git a/.Rbuildignore b/.Rbuildignore index f6cd805ee96..b79b546771e 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -71,3 +71,4 @@ ^BRANCHES\.md$ ^scripts$ ^\.claude$ +^lifecycle-TODO\.md$ diff --git a/lifecycle-TODO.md b/lifecycle-TODO.md new file mode 100644 index 00000000000..262236bd6fe --- /dev/null +++ b/lifecycle-TODO.md @@ -0,0 +1,711 @@ +# lifecycle bump — unresolved test failures + +These commits were made but left tests failing that need manual fixes (tests call deprecated functions expecting a result, not an error): + +## `feat!: bump eigen_centrality(scale = 'always as if TRUE') from deprecate_warn to deprecate_stop` + +- eigen_centrality() deprecated scale argument + +## `feat!: bump eigen_centrality(scale) from deprecate_soft to deprecate_warn` + +- eigen_centrality() deprecated scale argument + +## `feat!: bump eigen_centrality(options = 'must be a list') from deprecate_soft to deprecate_warn` + +- eigen_centrality() deprecated scale argument + +## `feat!: bump spectrum(options = 'must be a list') from deprecate_soft to deprecate_warn` + +- eigen_centrality() deprecated scale argument + +## `feat!: bump arpack(options = 'must be a list') from deprecate_soft to deprecate_warn` + +- eigen_centrality() deprecated scale argument + +## `feat!: bump estimate_closeness() from deprecate_soft to deprecate_warn` + +- eigen_centrality() deprecated scale argument + +## `feat!: bump estimate_edge_betweenness() from deprecate_soft to deprecate_warn` + +- eigen_centrality() deprecated scale argument + +## `feat!: bump estimate_betweenness() from deprecate_soft to deprecate_warn` + +- eigen_centrality() deprecated scale argument + +## `feat!: bump alpha.centrality() from deprecate_soft to deprecate_warn` + +- eigen_centrality() deprecated scale argument + +## `feat!: bump bonpow() from deprecate_soft to deprecate_warn` + +- eigen_centrality() deprecated scale argument + +## `feat!: bump edge.betweenness() from deprecate_soft to deprecate_warn` + +- eigen_centrality() deprecated scale argument + +## `feat!: bump evcent() from deprecate_soft to deprecate_warn` + +- eigen_centrality() deprecated scale argument + +## `feat!: bump graph.diversity() from deprecate_soft to deprecate_warn` + +- eigen_centrality() deprecated scale argument + +## `feat!: bump graph.eigen() from deprecate_soft to deprecate_warn` + +- eigen_centrality() deprecated scale argument + +## `feat!: bump graph.strength() from deprecate_soft to deprecate_warn` + +- eigen_centrality() deprecated scale argument + +## `feat!: bump authority.score() from deprecate_warn to deprecate_stop` + +- eigen_centrality() deprecated scale argument + +## `feat!: bump hub.score() from deprecate_warn to deprecate_stop` + +- eigen_centrality() deprecated scale argument + +## `feat!: bump page.rank() from deprecate_soft to deprecate_warn` + +- eigen_centrality() deprecated scale argument + +## `feat!: bump subgraph.centrality() from deprecate_soft to deprecate_warn` + +- eigen_centrality() deprecated scale argument + +## `feat!: bump modularity_matrix(membership = 'is no longer used') from deprecate_warn to deprecate_stop` + +- modularity_matrix still accepts a membership argument for compatibility + +## `feat!: bump code.length() from deprecate_soft to deprecate_warn` + +- modularity_matrix still accepts a membership argument for compatibility + +## `feat!: bump contract.vertices() from deprecate_soft to deprecate_warn` + +- modularity_matrix still accepts a membership argument for compatibility + +## `feat!: bump cutat() from deprecate_soft to deprecate_warn` + +- modularity_matrix still accepts a membership argument for compatibility + +## `feat!: bump dendPlot() from deprecate_soft to deprecate_warn` + +- modularity_matrix still accepts a membership argument for compatibility + +## `feat!: bump edge.betweenness.community() from deprecate_soft to deprecate_warn` + +- modularity_matrix still accepts a membership argument for compatibility + +## `feat!: bump fastgreedy.community() from deprecate_soft to deprecate_warn` + +- modularity_matrix still accepts a membership argument for compatibility + +## `feat!: bump infomap.community() from deprecate_soft to deprecate_warn` + +- modularity_matrix still accepts a membership argument for compatibility + +## `feat!: bump is.hierarchical() from deprecate_soft to deprecate_warn` + +- modularity_matrix still accepts a membership argument for compatibility + +## `feat!: bump label.propagation.community() from deprecate_soft to deprecate_warn` + +- modularity_matrix still accepts a membership argument for compatibility + +## `feat!: bump leading.eigenvector.community() from deprecate_soft to deprecate_warn` + +- modularity_matrix still accepts a membership argument for compatibility + +## `feat!: bump mod.matrix() from deprecate_soft to deprecate_warn` + +- modularity_matrix still accepts a membership argument for compatibility + +## `feat!: bump multilevel.community() from deprecate_soft to deprecate_warn` + +- modularity_matrix still accepts a membership argument for compatibility + +## `feat!: bump optimal.community() from deprecate_soft to deprecate_warn` + +- modularity_matrix still accepts a membership argument for compatibility + +## `feat!: bump showtrace() from deprecate_soft to deprecate_warn` + +- modularity_matrix still accepts a membership argument for compatibility + +## `feat!: bump spinglass.community() from deprecate_soft to deprecate_warn` + +- modularity_matrix still accepts a membership argument for compatibility + +## `feat!: bump walktrap.community() from deprecate_soft to deprecate_warn` + +- modularity_matrix still accepts a membership argument for compatibility + +## `feat!: bump create.communities() from deprecate_soft to deprecate_warn` + +- modularity_matrix still accepts a membership argument for compatibility + +## `feat!: bump sample_degseq(method = 'must be configuration.simple instead of simple.no.multiple.uniform') from deprecate_warn to deprecate_stop` + +- sample_degseq works() -- old method names + +## `feat!: bump sample_degseq(method = 'must be fast.heur.simple instead of simple.no.multiple') from deprecate_warn to deprecate_stop` + +- sample_degseq works() -- old method names + +## `feat!: bump sample_degseq(method = 'must be configuration instead of simple') from deprecate_warn to deprecate_stop` + +- sample_degseq works() -- old method names + +## `feat!: bump random.graph.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump random.graph.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump erdos.renyi.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump erdos.renyi.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump aging.prefatt.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump aging.ba.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump aging.barabasi.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump asymmetric.preference.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump ba.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump barabasi.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump bipartite.random.game() from deprecate_warn to deprecate_stop` + +- sample_degseq works() -- old method names + +## `feat!: bump callaway.traits.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump cited.type.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump citing.cited.type.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump connect.neighborhood() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump degree.sequence.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump establishment.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump forest.fire.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump growing.random.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump grg.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump interconnected.islands.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump k.regular.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump lastcit.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump preference.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump sbm.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump static.fitness.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump static.power.law.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump watts.strogatz.game() from deprecate_soft to deprecate_warn` + +- sample_degseq works() -- old method names + +## `feat!: bump get_edge_ids(vp = 'supplied as a matrix should be a n times 2 matrix, not 2 times n') from deprecate_warn to deprecate_stop` + +- get_edge_id() errors correctly for wrong matrices + +## `feat!: bump add.edges() from deprecate_soft to deprecate_warn` + +- get_edge_id() errors correctly for wrong matrices + +## `feat!: bump add.vertices() from deprecate_soft to deprecate_warn` + +- get_edge_id() errors correctly for wrong matrices + +## `feat!: bump delete.edges() from deprecate_soft to deprecate_warn` + +- get_edge_id() errors correctly for wrong matrices + +## `feat!: bump delete.vertices() from deprecate_soft to deprecate_warn` + +- get_edge_id() errors correctly for wrong matrices + +## `feat!: bump is.directed() from deprecate_soft to deprecate_warn` + +- get_edge_id() errors correctly for wrong matrices + +## `feat!: remove deprecated to() (lifecycle::deprecate_stop)` + +- iterators work +- indexing by numbers works +- selecting edges using vertex names works +- indexing with characters work as expected +- variable lookup in environment works +- E(g) returns complete iterator, completeness is lost with next subsetting +- ids of vertex and edge sequences are correct +- ids of vertex and edge sequence remain after removing graph +- vs/es keeps names +- both edge and vertex names +- printing connected vs/es works +- printing named connected vs/es works +- unconnected vs/es can be reused with the same graph +- logical indices are not recycled + +## `feat!: remove deprecated from() (lifecycle::deprecate_stop)` + +- iterators work +- indexing by numbers works +- selecting edges using vertex names works +- indexing with characters work as expected +- variable lookup in environment works +- E(g) returns complete iterator, completeness is lost with next subsetting +- ids of vertex and edge sequences are correct +- ids of vertex and edge sequence remain after removing graph +- vs/es keeps names +- both edge and vertex names +- printing connected vs/es works +- printing named connected vs/es works +- unconnected vs/es can be reused with the same graph +- logical indices are not recycled + +## `feat!: remove deprecated inc() (lifecycle::deprecate_stop)` + +- iterators work +- indexing by numbers works +- selecting edges using vertex names works +- indexing with characters work as expected +- variable lookup in environment works +- E(g) returns complete iterator, completeness is lost with next subsetting +- ids of vertex and edge sequences are correct +- ids of vertex and edge sequence remain after removing graph +- vs/es keeps names +- both edge and vertex names +- printing connected vs/es works +- printing named connected vs/es works +- unconnected vs/es can be reused with the same graph +- logical indices are not recycled + +## `feat!: remove deprecated adj() (lifecycle::deprecate_stop)` + +- iterators work +- indexing by numbers works +- selecting edges using vertex names works +- indexing with characters work as expected +- variable lookup in environment works +- E(g) returns complete iterator, completeness is lost with next subsetting +- ids of vertex and edge sequences are correct +- ids of vertex and edge sequence remain after removing graph +- vs/es keeps names +- both edge and vertex names +- printing connected vs/es works +- printing named connected vs/es works +- unconnected vs/es can be reused with the same graph +- logical indices are not recycled + +## `feat!: remove deprecated to() (lifecycle::deprecate_stop)` + +- iterators work +- complex attributes work +- indexing by numbers works +- selecting edges using vertex names works +- indexing with characters work as expected +- variable lookup in environment works +- V(g) returns complete iterator, completeness is lost with next subsetting +- E(g) returns complete iterator, completeness is lost with next subsetting +- ids of vertex and edge sequences are correct +- ids of vertex and edge sequence remain after removing graph +- vs/es keeps names +- both edge and vertex names +- printing connected vs/es works +- printing named connected vs/es works +- unconnected vs/es can be reused with the same graph +- logical indices are not recycled + +## `feat!: remove deprecated from() (lifecycle::deprecate_stop)` + +- iterators work +- complex attributes work +- indexing by numbers works +- selecting edges using vertex names works +- indexing with characters work as expected +- variable lookup in environment works +- V(g) returns complete iterator, completeness is lost with next subsetting +- E(g) returns complete iterator, completeness is lost with next subsetting +- ids of vertex and edge sequences are correct +- ids of vertex and edge sequence remain after removing graph +- vs/es keeps names +- both edge and vertex names +- printing connected vs/es works +- printing named connected vs/es works +- unconnected vs/es can be reused with the same graph +- logical indices are not recycled + +## `feat!: remove deprecated adj() (lifecycle::deprecate_stop)` + +- iterators work +- complex attributes work +- indexing by numbers works +- selecting edges using vertex names works +- indexing with characters work as expected +- variable lookup in environment works +- V(g) returns complete iterator, completeness is lost with next subsetting +- E(g) returns complete iterator, completeness is lost with next subsetting +- ids of vertex and edge sequences are correct +- ids of vertex and edge sequence remain after removing graph +- vs/es keeps names +- both edge and vertex names +- printing connected vs/es works +- printing named connected vs/es works +- unconnected vs/es can be reused with the same graph +- logical indices are not recycled + +## `feat!: remove deprecated inc() (lifecycle::deprecate_stop)` + +- iterators work +- complex attributes work +- indexing by numbers works +- selecting edges using vertex names works +- indexing with characters work as expected +- variable lookup in environment works +- V(g) returns complete iterator, completeness is lost with next subsetting +- E(g) returns complete iterator, completeness is lost with next subsetting +- ids of vertex and edge sequences are correct +- ids of vertex and edge sequence remain after removing graph +- vs/es keeps names +- both edge and vertex names +- printing connected vs/es works +- printing named connected vs/es works +- unconnected vs/es can be reused with the same graph +- logical indices are not recycled + +## `feat!: remove deprecated outnei() (lifecycle::deprecate_stop)` + +- iterators work +- complex attributes work +- indexing by numbers works +- selecting edges using vertex names works +- indexing with characters work as expected +- variable lookup in environment works +- V(g) returns complete iterator, completeness is lost with next subsetting +- E(g) returns complete iterator, completeness is lost with next subsetting +- ids of vertex and edge sequences are correct +- ids of vertex and edge sequence remain after removing graph +- vs/es keeps names +- both edge and vertex names +- printing connected vs/es works +- printing named connected vs/es works +- unconnected vs/es can be reused with the same graph +- logical indices are not recycled + +## `feat!: remove deprecated innei() (lifecycle::deprecate_stop)` + +- iterators work +- complex attributes work +- indexing by numbers works +- selecting edges using vertex names works +- indexing with characters work as expected +- variable lookup in environment works +- V(g) returns complete iterator, completeness is lost with next subsetting +- E(g) returns complete iterator, completeness is lost with next subsetting +- ids of vertex and edge sequences are correct +- ids of vertex and edge sequence remain after removing graph +- vs/es keeps names +- both edge and vertex names +- printing connected vs/es works +- printing named connected vs/es works +- unconnected vs/es can be reused with the same graph +- logical indices are not recycled + +## `feat!: remove deprecated nei() (lifecycle::deprecate_stop)` + +- iterators work +- complex attributes work +- indexing by numbers works +- selecting edges using vertex names works +- indexing with characters work as expected +- variable lookup in environment works +- V(g) returns complete iterator, completeness is lost with next subsetting +- E(g) returns complete iterator, completeness is lost with next subsetting +- ids of vertex and edge sequences are correct +- ids of vertex and edge sequence remain after removing graph +- vs/es keeps names +- both edge and vertex names +- printing connected vs/es works +- printing named connected vs/es works +- unconnected vs/es can be reused with the same graph +- logical indices are not recycled + +## `feat!: bump make_lattice(circular = 'use periodic argument instead') from deprecate_soft to deprecate_warn` + +- graph_from_literal() and simple undirected graphs +- graph_from_literal() and undirected explosion +- graph_from_literal() and simple directed graphs +- graph_from_literal() and directed explosion +- graph_from_literal(simplify = FALSE) +- graph is not updated if not in LHS +- graph is updated if in LHS + +## `feat!: bump graph_() from deprecate_soft to deprecate_warn` + +- graph_from_literal() and simple undirected graphs +- graph_from_literal() and undirected explosion +- graph_from_literal() and simple directed graphs +- graph_from_literal() and directed explosion +- graph_from_literal(simplify = FALSE) +- graph is not updated if not in LHS +- graph is updated if in LHS + +## `feat!: bump graph.atlas() from deprecate_soft to deprecate_warn` + +- graph_from_literal() and simple undirected graphs +- graph_from_literal() and undirected explosion +- graph_from_literal() and simple directed graphs +- graph_from_literal() and directed explosion +- graph_from_literal(simplify = FALSE) +- graph is not updated if not in LHS +- graph is updated if in LHS + +## `feat!: bump graph.bipartite() from deprecate_soft to deprecate_warn` + +- graph_from_literal() and simple undirected graphs +- graph_from_literal() and undirected explosion +- graph_from_literal() and simple directed graphs +- graph_from_literal() and directed explosion +- graph_from_literal(simplify = FALSE) +- graph is not updated if not in LHS +- graph is updated if in LHS + +## `feat!: bump graph.de.bruijn() from deprecate_soft to deprecate_warn` + +- graph_from_literal() and simple undirected graphs +- graph_from_literal() and undirected explosion +- graph_from_literal() and simple directed graphs +- graph_from_literal() and directed explosion +- graph_from_literal(simplify = FALSE) +- graph is not updated if not in LHS +- graph is updated if in LHS + +## `feat!: bump graph.empty() from deprecate_soft to deprecate_warn` + +- graph_from_literal() and simple undirected graphs +- graph_from_literal() and undirected explosion +- graph_from_literal() and simple directed graphs +- graph_from_literal() and directed explosion +- graph_from_literal(simplify = FALSE) +- graph is not updated if not in LHS +- graph is updated if in LHS + +## `feat!: bump graph.extended.chordal.ring() from deprecate_soft to deprecate_warn` + +- graph_from_literal() and simple undirected graphs +- graph_from_literal() and undirected explosion +- graph_from_literal() and simple directed graphs +- graph_from_literal() and directed explosion +- graph_from_literal(simplify = FALSE) +- graph is not updated if not in LHS +- graph is updated if in LHS + +## `feat!: bump graph.formula() from deprecate_soft to deprecate_warn` + +- graph_from_literal() and simple undirected graphs +- graph_from_literal() and undirected explosion +- graph_from_literal() and simple directed graphs +- graph_from_literal() and directed explosion +- graph_from_literal(simplify = FALSE) +- graph is not updated if not in LHS +- graph is updated if in LHS + +## `feat!: bump graph.full() from deprecate_soft to deprecate_warn` + +- graph_from_literal() and simple undirected graphs +- graph_from_literal() and undirected explosion +- graph_from_literal() and simple directed graphs +- graph_from_literal() and directed explosion +- graph_from_literal(simplify = FALSE) +- graph is not updated if not in LHS +- graph is updated if in LHS + +## `feat!: bump graph.full.bipartite() from deprecate_soft to deprecate_warn` + +- graph_from_literal() and simple undirected graphs +- graph_from_literal() and undirected explosion +- graph_from_literal() and simple directed graphs +- graph_from_literal() and directed explosion +- graph_from_literal(simplify = FALSE) +- graph is not updated if not in LHS +- graph is updated if in LHS + +## `feat!: bump graph.full.citation() from deprecate_soft to deprecate_warn` + +- graph_from_literal() and simple undirected graphs +- graph_from_literal() and undirected explosion +- graph_from_literal() and simple directed graphs +- graph_from_literal() and directed explosion +- graph_from_literal(simplify = FALSE) +- graph is not updated if not in LHS +- graph is updated if in LHS + +## `feat!: bump graph.kautz() from deprecate_soft to deprecate_warn` + +- graph_from_literal() and simple undirected graphs +- graph_from_literal() and undirected explosion +- graph_from_literal() and simple directed graphs +- graph_from_literal() and directed explosion +- graph_from_literal(simplify = FALSE) +- graph is not updated if not in LHS +- graph is updated if in LHS + +## `feat!: bump graph.lattice(circular = 'use periodic argument instead') from deprecate_soft to deprecate_warn` + +- graph_from_literal() and simple undirected graphs +- graph_from_literal() and undirected explosion +- graph_from_literal() and simple directed graphs +- graph_from_literal() and directed explosion +- graph_from_literal(simplify = FALSE) +- graph is not updated if not in LHS +- graph is updated if in LHS + +## `feat!: bump graph.lattice() from deprecate_soft to deprecate_warn` + +- graph_from_literal() and simple undirected graphs +- graph_from_literal() and undirected explosion +- graph_from_literal() and simple directed graphs +- graph_from_literal() and directed explosion +- graph_from_literal(simplify = FALSE) +- graph is not updated if not in LHS +- graph is updated if in LHS + +## `feat!: bump graph.lcf() from deprecate_soft to deprecate_warn` + +- graph_from_literal() and simple undirected graphs +- graph_from_literal() and undirected explosion +- graph_from_literal() and simple directed graphs +- graph_from_literal() and directed explosion +- graph_from_literal(simplify = FALSE) +- graph is not updated if not in LHS +- graph is updated if in LHS + +## `feat!: bump graph.star() from deprecate_soft to deprecate_warn` + +- graph_from_literal() and simple undirected graphs +- graph_from_literal() and undirected explosion +- graph_from_literal() and simple directed graphs +- graph_from_literal() and directed explosion +- graph_from_literal(simplify = FALSE) +- graph is not updated if not in LHS +- graph is updated if in LHS + +## `feat!: bump graph.tree() from deprecate_soft to deprecate_warn` + +- graph_from_literal() and simple undirected graphs +- graph_from_literal() and undirected explosion +- graph_from_literal() and simple directed graphs +- graph_from_literal() and directed explosion +- graph_from_literal(simplify = FALSE) +- graph is not updated if not in LHS +- graph is updated if in LHS + +## `feat!: bump graph.ring() from deprecate_soft to deprecate_warn` + +- graph_from_literal() and simple undirected graphs +- graph_from_literal() and undirected explosion +- graph_from_literal() and simple directed graphs +- graph_from_literal() and directed explosion +- graph_from_literal(simplify = FALSE) +- graph is not updated if not in LHS +- graph is updated if in LHS + +## `feat!: bump line.graph() from deprecate_soft to deprecate_warn` + +- graph_from_literal() and simple undirected graphs +- graph_from_literal() and undirected explosion +- graph_from_literal() and simple directed graphs +- graph_from_literal() and directed explosion +- graph_from_literal(simplify = FALSE) +- graph is not updated if not in LHS +- graph is updated if in LHS + +## `feat!: bump graph.famous() from deprecate_soft to deprecate_warn` + +- graph_from_literal() and simple undirected graphs +- graph_from_literal() and undirected explosion +- graph_from_literal() and simple directed graphs +- graph_from_literal() and directed explosion +- graph_from_literal(simplify = FALSE) +- graph is not updated if not in LHS +- graph is updated if in LHS + +## `feat!: bump graph() from deprecate_soft to deprecate_warn` + +- graph_from_literal() and simple undirected graphs +- graph_from_literal() and undirected explosion +- graph_from_literal() and simple directed graphs +- graph_from_literal() and directed explosion +- graph_from_literal(simplify = FALSE) +- graph is not updated if not in LHS +- graph is updated if in LHS + diff --git a/tools/bump-lifecycle.R b/tools/bump-lifecycle.R new file mode 100644 index 00000000000..81c0ce783b5 --- /dev/null +++ b/tools/bump-lifecycle.R @@ -0,0 +1,414 @@ +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)))) +} + +# 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)) { + 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() From 1e764b19ba6b3e805b7f353fdab3b239148760b1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:54:34 +0200 Subject: [PATCH 256/261] test: 1 fix --- lifecycle-TODO.md | 75 ----------------------------- tests/testthat/_snaps/centrality.md | 4 +- tests/testthat/test-centrality.R | 2 +- 3 files changed, 3 insertions(+), 78 deletions(-) diff --git a/lifecycle-TODO.md b/lifecycle-TODO.md index 262236bd6fe..bf05124da89 100644 --- a/lifecycle-TODO.md +++ b/lifecycle-TODO.md @@ -2,81 +2,6 @@ These commits were made but left tests failing that need manual fixes (tests call deprecated functions expecting a result, not an error): -## `feat!: bump eigen_centrality(scale = 'always as if TRUE') from deprecate_warn to deprecate_stop` - -- eigen_centrality() deprecated scale argument - -## `feat!: bump eigen_centrality(scale) from deprecate_soft to deprecate_warn` - -- eigen_centrality() deprecated scale argument - -## `feat!: bump eigen_centrality(options = 'must be a list') from deprecate_soft to deprecate_warn` - -- eigen_centrality() deprecated scale argument - -## `feat!: bump spectrum(options = 'must be a list') from deprecate_soft to deprecate_warn` - -- eigen_centrality() deprecated scale argument - -## `feat!: bump arpack(options = 'must be a list') from deprecate_soft to deprecate_warn` - -- eigen_centrality() deprecated scale argument - -## `feat!: bump estimate_closeness() from deprecate_soft to deprecate_warn` - -- eigen_centrality() deprecated scale argument - -## `feat!: bump estimate_edge_betweenness() from deprecate_soft to deprecate_warn` - -- eigen_centrality() deprecated scale argument - -## `feat!: bump estimate_betweenness() from deprecate_soft to deprecate_warn` - -- eigen_centrality() deprecated scale argument - -## `feat!: bump alpha.centrality() from deprecate_soft to deprecate_warn` - -- eigen_centrality() deprecated scale argument - -## `feat!: bump bonpow() from deprecate_soft to deprecate_warn` - -- eigen_centrality() deprecated scale argument - -## `feat!: bump edge.betweenness() from deprecate_soft to deprecate_warn` - -- eigen_centrality() deprecated scale argument - -## `feat!: bump evcent() from deprecate_soft to deprecate_warn` - -- eigen_centrality() deprecated scale argument - -## `feat!: bump graph.diversity() from deprecate_soft to deprecate_warn` - -- eigen_centrality() deprecated scale argument - -## `feat!: bump graph.eigen() from deprecate_soft to deprecate_warn` - -- eigen_centrality() deprecated scale argument - -## `feat!: bump graph.strength() from deprecate_soft to deprecate_warn` - -- eigen_centrality() deprecated scale argument - -## `feat!: bump authority.score() from deprecate_warn to deprecate_stop` - -- eigen_centrality() deprecated scale argument - -## `feat!: bump hub.score() from deprecate_warn to deprecate_stop` - -- eigen_centrality() deprecated scale argument - -## `feat!: bump page.rank() from deprecate_soft to deprecate_warn` - -- eigen_centrality() deprecated scale argument - -## `feat!: bump subgraph.centrality() from deprecate_soft to deprecate_warn` - -- eigen_centrality() deprecated scale argument ## `feat!: bump modularity_matrix(membership = 'is no longer used') from deprecate_warn to deprecate_stop` 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 d96bb79baa73f1b1ca6f17f0c82196c39279fce9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 15:56:21 +0200 Subject: [PATCH 257/261] test: 1 fix --- lifecycle-TODO.md | 73 ------------------------------ tests/testthat/_snaps/community.md | 6 +-- tests/testthat/test-community.R | 6 +-- 3 files changed, 6 insertions(+), 79 deletions(-) diff --git a/lifecycle-TODO.md b/lifecycle-TODO.md index bf05124da89..c8df2ec064a 100644 --- a/lifecycle-TODO.md +++ b/lifecycle-TODO.md @@ -2,79 +2,6 @@ These commits were made but left tests failing that need manual fixes (tests call deprecated functions expecting a result, not an error): - -## `feat!: bump modularity_matrix(membership = 'is no longer used') from deprecate_warn to deprecate_stop` - -- modularity_matrix still accepts a membership argument for compatibility - -## `feat!: bump code.length() from deprecate_soft to deprecate_warn` - -- modularity_matrix still accepts a membership argument for compatibility - -## `feat!: bump contract.vertices() from deprecate_soft to deprecate_warn` - -- modularity_matrix still accepts a membership argument for compatibility - -## `feat!: bump cutat() from deprecate_soft to deprecate_warn` - -- modularity_matrix still accepts a membership argument for compatibility - -## `feat!: bump dendPlot() from deprecate_soft to deprecate_warn` - -- modularity_matrix still accepts a membership argument for compatibility - -## `feat!: bump edge.betweenness.community() from deprecate_soft to deprecate_warn` - -- modularity_matrix still accepts a membership argument for compatibility - -## `feat!: bump fastgreedy.community() from deprecate_soft to deprecate_warn` - -- modularity_matrix still accepts a membership argument for compatibility - -## `feat!: bump infomap.community() from deprecate_soft to deprecate_warn` - -- modularity_matrix still accepts a membership argument for compatibility - -## `feat!: bump is.hierarchical() from deprecate_soft to deprecate_warn` - -- modularity_matrix still accepts a membership argument for compatibility - -## `feat!: bump label.propagation.community() from deprecate_soft to deprecate_warn` - -- modularity_matrix still accepts a membership argument for compatibility - -## `feat!: bump leading.eigenvector.community() from deprecate_soft to deprecate_warn` - -- modularity_matrix still accepts a membership argument for compatibility - -## `feat!: bump mod.matrix() from deprecate_soft to deprecate_warn` - -- modularity_matrix still accepts a membership argument for compatibility - -## `feat!: bump multilevel.community() from deprecate_soft to deprecate_warn` - -- modularity_matrix still accepts a membership argument for compatibility - -## `feat!: bump optimal.community() from deprecate_soft to deprecate_warn` - -- modularity_matrix still accepts a membership argument for compatibility - -## `feat!: bump showtrace() from deprecate_soft to deprecate_warn` - -- modularity_matrix still accepts a membership argument for compatibility - -## `feat!: bump spinglass.community() from deprecate_soft to deprecate_warn` - -- modularity_matrix still accepts a membership argument for compatibility - -## `feat!: bump walktrap.community() from deprecate_soft to deprecate_warn` - -- modularity_matrix still accepts a membership argument for compatibility - -## `feat!: bump create.communities() from deprecate_soft to deprecate_warn` - -- modularity_matrix still accepts a membership argument for compatibility - ## `feat!: bump sample_degseq(method = 'must be configuration.simple instead of simple.no.multiple.uniform') from deprecate_warn to deprecate_stop` - sample_degseq works() -- old method names 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 e8301d5e0e5f1669b9dd58bb85c195c2fdeecb69 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 16:00:56 +0200 Subject: [PATCH 258/261] test: fix for `feat!: bump sample_degseq(method = 'must be configuration.simple instead of simple.no.multiple.uniform') from deprecate_warn to deprecate_stop` --- lifecycle-TODO.md | 124 ------------------------------------ tests/testthat/test-games.R | 6 +- 2 files changed, 3 insertions(+), 127 deletions(-) diff --git a/lifecycle-TODO.md b/lifecycle-TODO.md index c8df2ec064a..40a51f00fc0 100644 --- a/lifecycle-TODO.md +++ b/lifecycle-TODO.md @@ -2,130 +2,6 @@ These commits were made but left tests failing that need manual fixes (tests call deprecated functions expecting a result, not an error): -## `feat!: bump sample_degseq(method = 'must be configuration.simple instead of simple.no.multiple.uniform') from deprecate_warn to deprecate_stop` - -- sample_degseq works() -- old method names - -## `feat!: bump sample_degseq(method = 'must be fast.heur.simple instead of simple.no.multiple') from deprecate_warn to deprecate_stop` - -- sample_degseq works() -- old method names - -## `feat!: bump sample_degseq(method = 'must be configuration instead of simple') from deprecate_warn to deprecate_stop` - -- sample_degseq works() -- old method names - -## `feat!: bump random.graph.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump random.graph.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump erdos.renyi.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump erdos.renyi.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump aging.prefatt.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump aging.ba.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump aging.barabasi.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump asymmetric.preference.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump ba.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump barabasi.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump bipartite.random.game() from deprecate_warn to deprecate_stop` - -- sample_degseq works() -- old method names - -## `feat!: bump callaway.traits.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump cited.type.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump citing.cited.type.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump connect.neighborhood() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump degree.sequence.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump establishment.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump forest.fire.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump growing.random.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump grg.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump interconnected.islands.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump k.regular.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump lastcit.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump preference.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump sbm.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump static.fitness.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump static.power.law.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - -## `feat!: bump watts.strogatz.game() from deprecate_soft to deprecate_warn` - -- sample_degseq works() -- old method names - ## `feat!: bump get_edge_ids(vp = 'supplied as a matrix should be a n times 2 matrix, not 2 times n') from deprecate_warn to deprecate_stop` - get_edge_id() errors correctly for wrong matrices 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 3e6c9e6e87dfaf6b3dca351e5f182833941f13b9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 16:09:47 +0200 Subject: [PATCH 259/261] fix: iterators --- R/iterators.R | 14 +++++++------- tools/bump-lifecycle.R | 26 ++++++++++++++++++++++++++ 2 files changed, 33 insertions(+), 7 deletions(-) diff --git a/R/iterators.R b/R/iterators.R index 606417d27a3..21d13c472e7 100644 --- a/R/iterators.R +++ b/R/iterators.R @@ -672,11 +672,11 @@ simple_vs_index <- function(x, i, na_ok = FALSE) { # Functions (only visible if called or if no duplicate) top <- rlang::new_environment(list( .nei = .nei, - nei = nei, + nei = .nei, .innei = .innei, - innei = innei, + innei = .innei, .outnei = .outnei, - outnei = outnei, + outnei = .outnei, .inc = .inc, inc = inc, adj = adj, @@ -1010,12 +1010,12 @@ simple_es_index <- function(x, i, na_ok = FALSE) { # Functions (only visible if called or if no duplicate) top <- rlang::new_environment(list( .inc = .inc, - inc = inc, - adj = adj, + inc = .inc, + adj = .inc, .from = .from, - from = from, + from = .from, .to = .to, - to = to, + to = .to, `%--%` = `%--%`, `%->%` = `%->%`, `%<-%` = `%<-%` diff --git a/tools/bump-lifecycle.R b/tools/bump-lifecycle.R index 81c0ce783b5..24bccd6e139 100644 --- a/tools/bump-lifecycle.R +++ b/tools/bump-lifecycle.R @@ -54,6 +54,21 @@ 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("(? Date: Tue, 12 May 2026 16:12:42 +0200 Subject: [PATCH 260/261] fix: iterators again --- R/iterators.R | 8 ++++---- tests/testthat/test-interface.R | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/R/iterators.R b/R/iterators.R index 21d13c472e7..0094a7b2c27 100644 --- a/R/iterators.R +++ b/R/iterators.R @@ -678,12 +678,12 @@ simple_vs_index <- function(x, i, na_ok = FALSE) { .outnei = .outnei, outnei = .outnei, .inc = .inc, - inc = inc, - adj = adj, + inc = .inc, + adj = .inc, .from = .from, - from = from, + from = .from, .to = .to, - to = to, + to = .to, .data = list(attrs) )) 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 5a4cdbd73885621c2f2cfd962f15fd10d932111b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 12 May 2026 16:13:55 +0200 Subject: [PATCH 261/261] fix: ok --- lifecycle-TODO.md | 225 +------------------------ tests/testthat/_snaps/iterators.new.md | 42 ----- 2 files changed, 1 insertion(+), 266 deletions(-) delete mode 100644 tests/testthat/_snaps/iterators.new.md diff --git a/lifecycle-TODO.md b/lifecycle-TODO.md index 40a51f00fc0..e84f9e5ec37 100644 --- a/lifecycle-TODO.md +++ b/lifecycle-TODO.md @@ -2,230 +2,7 @@ These commits were made but left tests failing that need manual fixes (tests call deprecated functions expecting a result, not an error): -## `feat!: bump get_edge_ids(vp = 'supplied as a matrix should be a n times 2 matrix, not 2 times n') from deprecate_warn to deprecate_stop` - -- get_edge_id() errors correctly for wrong matrices - -## `feat!: bump add.edges() from deprecate_soft to deprecate_warn` - -- get_edge_id() errors correctly for wrong matrices - -## `feat!: bump add.vertices() from deprecate_soft to deprecate_warn` - -- get_edge_id() errors correctly for wrong matrices - -## `feat!: bump delete.edges() from deprecate_soft to deprecate_warn` - -- get_edge_id() errors correctly for wrong matrices - -## `feat!: bump delete.vertices() from deprecate_soft to deprecate_warn` - -- get_edge_id() errors correctly for wrong matrices - -## `feat!: bump is.directed() from deprecate_soft to deprecate_warn` - -- get_edge_id() errors correctly for wrong matrices - -## `feat!: remove deprecated to() (lifecycle::deprecate_stop)` - -- iterators work -- indexing by numbers works -- selecting edges using vertex names works -- indexing with characters work as expected -- variable lookup in environment works -- E(g) returns complete iterator, completeness is lost with next subsetting -- ids of vertex and edge sequences are correct -- ids of vertex and edge sequence remain after removing graph -- vs/es keeps names -- both edge and vertex names -- printing connected vs/es works -- printing named connected vs/es works -- unconnected vs/es can be reused with the same graph -- logical indices are not recycled - -## `feat!: remove deprecated from() (lifecycle::deprecate_stop)` - -- iterators work -- indexing by numbers works -- selecting edges using vertex names works -- indexing with characters work as expected -- variable lookup in environment works -- E(g) returns complete iterator, completeness is lost with next subsetting -- ids of vertex and edge sequences are correct -- ids of vertex and edge sequence remain after removing graph -- vs/es keeps names -- both edge and vertex names -- printing connected vs/es works -- printing named connected vs/es works -- unconnected vs/es can be reused with the same graph -- logical indices are not recycled - -## `feat!: remove deprecated inc() (lifecycle::deprecate_stop)` - -- iterators work -- indexing by numbers works -- selecting edges using vertex names works -- indexing with characters work as expected -- variable lookup in environment works -- E(g) returns complete iterator, completeness is lost with next subsetting -- ids of vertex and edge sequences are correct -- ids of vertex and edge sequence remain after removing graph -- vs/es keeps names -- both edge and vertex names -- printing connected vs/es works -- printing named connected vs/es works -- unconnected vs/es can be reused with the same graph -- logical indices are not recycled - -## `feat!: remove deprecated adj() (lifecycle::deprecate_stop)` - -- iterators work -- indexing by numbers works -- selecting edges using vertex names works -- indexing with characters work as expected -- variable lookup in environment works -- E(g) returns complete iterator, completeness is lost with next subsetting -- ids of vertex and edge sequences are correct -- ids of vertex and edge sequence remain after removing graph -- vs/es keeps names -- both edge and vertex names -- printing connected vs/es works -- printing named connected vs/es works -- unconnected vs/es can be reused with the same graph -- logical indices are not recycled - -## `feat!: remove deprecated to() (lifecycle::deprecate_stop)` - -- iterators work -- complex attributes work -- indexing by numbers works -- selecting edges using vertex names works -- indexing with characters work as expected -- variable lookup in environment works -- V(g) returns complete iterator, completeness is lost with next subsetting -- E(g) returns complete iterator, completeness is lost with next subsetting -- ids of vertex and edge sequences are correct -- ids of vertex and edge sequence remain after removing graph -- vs/es keeps names -- both edge and vertex names -- printing connected vs/es works -- printing named connected vs/es works -- unconnected vs/es can be reused with the same graph -- logical indices are not recycled - -## `feat!: remove deprecated from() (lifecycle::deprecate_stop)` - -- iterators work -- complex attributes work -- indexing by numbers works -- selecting edges using vertex names works -- indexing with characters work as expected -- variable lookup in environment works -- V(g) returns complete iterator, completeness is lost with next subsetting -- E(g) returns complete iterator, completeness is lost with next subsetting -- ids of vertex and edge sequences are correct -- ids of vertex and edge sequence remain after removing graph -- vs/es keeps names -- both edge and vertex names -- printing connected vs/es works -- printing named connected vs/es works -- unconnected vs/es can be reused with the same graph -- logical indices are not recycled - -## `feat!: remove deprecated adj() (lifecycle::deprecate_stop)` - -- iterators work -- complex attributes work -- indexing by numbers works -- selecting edges using vertex names works -- indexing with characters work as expected -- variable lookup in environment works -- V(g) returns complete iterator, completeness is lost with next subsetting -- E(g) returns complete iterator, completeness is lost with next subsetting -- ids of vertex and edge sequences are correct -- ids of vertex and edge sequence remain after removing graph -- vs/es keeps names -- both edge and vertex names -- printing connected vs/es works -- printing named connected vs/es works -- unconnected vs/es can be reused with the same graph -- logical indices are not recycled - -## `feat!: remove deprecated inc() (lifecycle::deprecate_stop)` - -- iterators work -- complex attributes work -- indexing by numbers works -- selecting edges using vertex names works -- indexing with characters work as expected -- variable lookup in environment works -- V(g) returns complete iterator, completeness is lost with next subsetting -- E(g) returns complete iterator, completeness is lost with next subsetting -- ids of vertex and edge sequences are correct -- ids of vertex and edge sequence remain after removing graph -- vs/es keeps names -- both edge and vertex names -- printing connected vs/es works -- printing named connected vs/es works -- unconnected vs/es can be reused with the same graph -- logical indices are not recycled - -## `feat!: remove deprecated outnei() (lifecycle::deprecate_stop)` - -- iterators work -- complex attributes work -- indexing by numbers works -- selecting edges using vertex names works -- indexing with characters work as expected -- variable lookup in environment works -- V(g) returns complete iterator, completeness is lost with next subsetting -- E(g) returns complete iterator, completeness is lost with next subsetting -- ids of vertex and edge sequences are correct -- ids of vertex and edge sequence remain after removing graph -- vs/es keeps names -- both edge and vertex names -- printing connected vs/es works -- printing named connected vs/es works -- unconnected vs/es can be reused with the same graph -- logical indices are not recycled - -## `feat!: remove deprecated innei() (lifecycle::deprecate_stop)` - -- iterators work -- complex attributes work -- indexing by numbers works -- selecting edges using vertex names works -- indexing with characters work as expected -- variable lookup in environment works -- V(g) returns complete iterator, completeness is lost with next subsetting -- E(g) returns complete iterator, completeness is lost with next subsetting -- ids of vertex and edge sequences are correct -- ids of vertex and edge sequence remain after removing graph -- vs/es keeps names -- both edge and vertex names -- printing connected vs/es works -- printing named connected vs/es works -- unconnected vs/es can be reused with the same graph -- logical indices are not recycled - -## `feat!: remove deprecated nei() (lifecycle::deprecate_stop)` - -- iterators work -- complex attributes work -- indexing by numbers works -- selecting edges using vertex names works -- indexing with characters work as expected -- variable lookup in environment works -- V(g) returns complete iterator, completeness is lost with next subsetting -- E(g) returns complete iterator, completeness is lost with next subsetting -- ids of vertex and edge sequences are correct -- ids of vertex and edge sequence remain after removing graph -- vs/es keeps names -- both edge and vertex names -- printing connected vs/es works -- printing named connected vs/es works -- unconnected vs/es can be reused with the same graph -- logical indices are not recycled + ## `feat!: bump make_lattice(circular = 'use periodic argument instead') from deprecate_soft to deprecate_warn` diff --git a/tests/testthat/_snaps/iterators.new.md b/tests/testthat/_snaps/iterators.new.md deleted file mode 100644 index b9fd4d22c2d..00000000000 --- a/tests/testthat/_snaps/iterators.new.md +++ /dev/null @@ -1,42 +0,0 @@ -# printing unconnected vs/es works - - Code - vs - Output - + 10/? vertices (deleted): - [1] 1 2 3 4 5 6 7 8 9 10 - Code - es - Output - + 10/? edges (deleted): - [1] 1 2 3 4 5 6 7 8 9 10 - ---- - - Code - vs - Output - + 10/? vertices (deleted): - [1] 1 2 3 4 5 6 7 8 9 10 - Code - es - Output - + 10/? edges (deleted) (vertex names): - [1] a|b b|c c|d d|e e|f f|g g|h h|i i|j a|j - -# logical indices are not recycled - - Code - V(g)[c(TRUE, FALSE)] - Condition - Error in `[.igraph.vs`: - ! object 'nei' not found - ---- - - Code - E(g)[c(TRUE, FALSE)] - Condition - Error in `[.igraph.es`: - ! object 'inc' not found -