refactor: move optional arguments of misc functions behind the ellipsis

R/coloring.R

@@ -12,6 +12,7 @@
 #' linear time.
 #'
 #' @param graph The graph object to color.
+#' @inheritParams rlang::args_dots_empty
 #' @param heuristic The selection heuristic for the next vertex to consider.
 #'   Possible values are: \dQuote{colored_neighbors} selects the vertex with the
 #'   largest number of already colored neighbors. \dQuote{dsatur} selects the
@@ -32,8 +33,31 @@
 #'
 greedy_vertex_coloring <- function(
   graph,
+  ...,
   heuristic = c("colored_neighbors", "dsatur")
 ) {
+  # BEGIN GENERATED ARG_HANDLE: greedy_vertex_coloring, do not edit, see tools/generate-migrations.R
+  if (...length() > 0L) {
+    .arg_handle <- migrate_recover_args(
+      list(...),
+      current = list(heuristic = heuristic),
+      recover_new = c("heuristic"),
+      recover_old = c("heuristic"),
+      match_names = c("heuristic"),
+      match_to = c("heuristic"),
+      defaults = list(heuristic = c("colored_neighbors", "dsatur")),
+      head_args = c("graph"),
+      fn_name = "greedy_vertex_coloring"
+    )
+    list2env(.arg_handle$values, environment())
+    lifecycle::deprecate_soft(
+      "3.0.0",
+      what = I(.arg_handle$what),
+      details = .arg_handle$details
+    )
+  }
+  # END GENERATED ARG_HANDLE
+
   vertex_coloring_greedy_impl(
     graph = graph,
     heuristic = heuristic

R/cycles.R

@@ -31,6 +31,7 @@
 #' a specific cycle.
 #'
 #' @param graph The input graph.
+#' @inheritParams rlang::args_dots_empty
 #' @param mode Character constant specifying how to handle directed graphs.
 #'   `out` follows edge directions, `in` follows edges in the reverse direction,
 #'   and `all` ignores edge directions. Ignored in undirected graphs.

R/epi.R

@@ -20,16 +20,43 @@
 ###################################################################
 
 #' @rdname sir
+#' @inheritParams rlang::args_dots_empty
 #' @export
-time_bins <- function(x, middle = TRUE) {
+time_bins <- function(
+  x,
+  ...,
+  middle = TRUE
+) {
   UseMethod("time_bins")
 }
 
 #' @method time_bins sir
 #' @rdname sir
 #' @export
 #' @importFrom stats IQR
-time_bins.sir <- function(x, middle = TRUE) {
+time_bins.sir <- function(x, ..., middle = TRUE) {
+  # BEGIN GENERATED ARG_HANDLE: time_bins, do not edit, see tools/generate-migrations.R
+  if (...length() > 0L) {
+    .arg_handle <- migrate_recover_args(
+      list(...),
+      current = list(middle = middle),
+      recover_new = c("middle"),
+      recover_old = c("middle"),
+      match_names = c("middle"),
+      match_to = c("middle"),
+      defaults = list(middle = TRUE),
+      head_args = c("x"),
+      fn_name = "time_bins"
+    )
+    list2env(.arg_handle$values, environment())
+    lifecycle::deprecate_soft(
+      "3.0.0",
+      what = I(.arg_handle$what),
+      details = .arg_handle$details
+    )
+  }
+  # END GENERATED ARG_HANDLE
+
   sir <- x
 
   big.time <- unlist(sapply(sir, "[[", "times"))

R/foreign.R

@@ -794,6 +794,7 @@ write.graph.dot <- function(graph, file) {
 #' for the actual format of a graph database file and other information.
 #'
 #' @param url Complete URL with the file to import. Default: `NULL`.
+#' @inheritParams rlang::args_dots_empty
 #' @param prefix Gives the prefix. See details below. Possible values:
 #'   `iso`, `i2`, `si4`, `si6`, `mcs10`, `mcs30`,
 #'   `mcs50`, `mcs70`, `mcs90`.
@@ -825,6 +826,7 @@ write.graph.dot <- function(graph, file) {
 #' @keywords graphs
 graph_from_graphdb <- function(
   url = NULL,
+  ...,
   prefix = "iso",
   type = "r001",
   nodes = NULL,
@@ -834,6 +836,82 @@ graph_from_graphdb <- function(
   compressed = TRUE,
   directed = TRUE
 ) {
+  # BEGIN GENERATED ARG_HANDLE: graph_from_graphdb, do not edit, see tools/generate-migrations.R
+  if (...length() > 0L) {
+    .arg_handle <- migrate_recover_args(
+      list(...),
+      current = list(
+        prefix = prefix,
+        type = type,
+        nodes = nodes,
+        pair = pair,
+        which = which,
+        base = base,
+        compressed = compressed,
+        directed = directed
+      ),
+      recover_new = c(
+        "prefix",
+        "type",
+        "nodes",
+        "pair",
+        "which",
+        "base",
+        "compressed",
+        "directed"
+      ),
+      recover_old = c(
+        "prefix",
+        "type",
+        "nodes",
+        "pair",
+        "which",
+        "base",
+        "compressed",
+        "directed"
+      ),
+      match_names = c(
+        "prefix",
+        "type",
+        "nodes",
+        "pair",
+        "which",
+        "base",
+        "compressed",
+        "directed"
+      ),
+      match_to = c(
+        "prefix",
+        "type",
+        "nodes",
+        "pair",
+        "which",
+        "base",
+        "compressed",
+        "directed"
+      ),
+      defaults = list(
+        prefix = "iso",
+        type = "r001",
+        nodes = NULL,
+        pair = "A",
+        which = 0,
+        base = "https://github.com/igraph/graphsdb/raw/refs/heads/main",
+        compressed = TRUE,
+        directed = TRUE
+      ),
+      head_args = c("url"),
+      fn_name = "graph_from_graphdb"
+    )
+    list2env(.arg_handle$values, environment())
+    lifecycle::deprecate_soft(
+      "3.0.0",
+      what = I(.arg_handle$what),
+      details = .arg_handle$details
+    )
+  }
+  # END GENERATED ARG_HANDLE
+
   if (is.null(nodes) && is.null(url)) {
     cli::cli_abort("Either {.arg nodes}' or `{.arg url}' must be non-null.")
   }

R/sir.R

@@ -53,6 +53,7 @@
 #' @param gamma Positive scalar. The rate of recovery of an infected
 #'   individual. Formally, this is the rate parameter of an exponential
 #'   distribution.
+#' @inheritParams rlang::args_dots_empty
 #' @param no.sim Integer scalar, the number simulation runs to perform.
 #' @param x A `sir` object, returned by the `sir()` function.
 #' @param middle Logical, whether to return the middle of the time bins,
@@ -108,7 +109,35 @@
 #' plot(sm)
 #' @family processes
 #' @export
-sir <- function(graph, beta, gamma, no.sim = 100) {
+sir <- function(
+  graph,
+  beta,
+  gamma,
+  ...,
+  no.sim = 100
+) {
+  # BEGIN GENERATED ARG_HANDLE: sir, do not edit, see tools/generate-migrations.R
+  if (...length() > 0L) {
+    .arg_handle <- migrate_recover_args(
+      list(...),
+      current = list(no.sim = no.sim),
+      recover_new = c("no.sim"),
+      recover_old = c("no.sim"),
+      match_names = c("no.sim"),
+      match_to = c("no.sim"),
+      defaults = list(no.sim = 100),
+      head_args = c("graph", "beta", "gamma"),
+      fn_name = "sir"
+    )
+    list2env(.arg_handle$values, environment())
+    lifecycle::deprecate_soft(
+      "3.0.0",
+      what = I(.arg_handle$what),
+      details = .arg_handle$details
+    )
+  }
+  # END GENERATED ARG_HANDLE
+
   sir_impl(
     graph = graph,
     beta = beta,

R/stochastic_matrix.R

@@ -51,6 +51,7 @@ get.stochastic <- function(
 #' matrices are defined in a symmetric way.
 #'
 #' @param graph The input graph. Must be of class `igraph`.
+#' @inheritParams rlang::args_dots_empty
 #' @param column.wise If `FALSE`, then the rows of the stochastic matrix
 #'   sum up to one; otherwise it is the columns.
 #' @param sparse Logical, whether to return a sparse matrix. The
@@ -76,9 +77,35 @@ get.stochastic <- function(
 #'
 stochastic_matrix <- function(
   graph,
+  ...,
   column.wise = FALSE,
   sparse = igraph_opt("sparsematrices")
 ) {
+  # BEGIN GENERATED ARG_HANDLE: stochastic_matrix, do not edit, see tools/generate-migrations.R
+  if (...length() > 0L) {
+    .arg_handle <- migrate_recover_args(
+      list(...),
+      current = list(column.wise = column.wise, sparse = sparse),
+      recover_new = c("column.wise", "sparse"),
+      recover_old = c("column.wise", "sparse"),
+      match_names = c("column.wise", "sparse"),
+      match_to = c("column.wise", "sparse"),
+      defaults = list(
+        column.wise = FALSE,
+        sparse = igraph_opt("sparsematrices")
+      ),
+      head_args = c("graph"),
+      fn_name = "stochastic_matrix"
+    )
+    list2env(.arg_handle$values, environment())
+    lifecycle::deprecate_soft(
+      "3.0.0",
+      what = I(.arg_handle$what),
+      details = .arg_handle$details
+    )
+  }
+  # END GENERATED ARG_HANDLE
+
   ensure_igraph(graph)
 
   column.wise <- as.logical(column.wise)

tests/testthat/test-coloring.R

@@ -32,3 +32,15 @@ test_that("simplify_and_colorize works", {
   expect_equal(V(result)$color, c(0, 0, 0, 0, 1))
   expect_equal(E(result)$color, c(1, 4, 1, 2))
 })
+
+# ---- ellipsis migration: argument coverage ----------------------------------
+# The `heuristic` tail argument is already exercised by name in the tests above,
+# so here we only cover the legacy positional recovery path.
+
+test_that("greedy_vertex_coloring() recovers a legacy positional `heuristic`", {
+  g <- make_star(10, mode = "undirected")
+  lifecycle::expect_deprecated(
+    col <- greedy_vertex_coloring(g, "dsatur")
+  )
+  expect_identical(col, greedy_vertex_coloring(g, heuristic = "dsatur"))
+})