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refactor: Purge legacy alias formals via the migration registry #2863

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56 changes: 45 additions & 11 deletions R/community.R
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Original file line number Diff line number Diff line change
Expand Up @@ -1758,7 +1758,6 @@ cluster_spinglass <- function(
#' @param resolution The resolution parameter to use. Higher
#' resolutions lead to more smaller communities, while lower resolutions lead
#' to fewer larger communities.
#' @param resolution_parameter `r lifecycle::badge("superseded")` Use `resolution` instead.
#' @param beta Parameter affecting the randomness in the Leiden algorithm.
#' This affects only the refinement step of the algorithm.
#' @param initial_membership If provided, the Leiden algorithm
Expand Down Expand Up @@ -1809,22 +1808,57 @@ cluster_leiden <- function(
...,
weights = NULL,
resolution = 1,
resolution_parameter = deprecated(),
beta = 0.01,
initial_membership = NULL,
n_iterations = 2,
vertex_weights = NULL
) {
check_dots_empty()

if (lifecycle::is_present(resolution_parameter)) {
lifecycle::deprecate_warn(
"2.1.0",
"cluster_leiden(resolution_parameter)",
"cluster_leiden(resolution)"
)
resolution <- resolution_parameter
# BEGIN GENERATED ARG_HANDLE: cluster_leiden, do not edit, see tools/generate-migrations.R
# fmt: skip
if (...length() > 0L) {
.arg_ambiguous <- base::intersect(base::names(base::substitute(...())), base::c("r", "re", "res", "reso", "resol", "resolu", "resolut", "resoluti", "resolutio"))
if (base::length(.arg_ambiguous) > 0L) cli::cli_abort("Argument {.arg {(.arg_ambiguous[[1L]])}} matches multiple arguments of {.fn cluster_leiden}.")
# Pre-3.0.0 signature: cluster_leiden(graph, objective_function, weights, resolution_parameter, beta, initial_membership, n_iterations, vertex_weights)
.old_signature <- function(weights, resolution_parameter, beta, initial_membership, n_iterations, vertex_weights, ...) {
if (...length() > 0L) {
.arg_extra <- base::names(base::substitute(...()))
.arg_extra <- .arg_extra[base::nzchar(.arg_extra)]
if (base::length(.arg_extra) == 0L) cli::cli_abort("Too many arguments passed to {.fn cluster_leiden}.", call = base::parent.frame())
cli::cli_abort(base::c("Unexpected argument passed to {.fn cluster_leiden}: {.arg {(.arg_extra)}}.", i = "Arguments after {.arg ...} must be spelled out in full."), call = base::parent.frame())
}
base::c(
if (!base::missing(weights)) base::list(weights = weights),
if (!base::missing(resolution_parameter)) base::list(resolution = resolution_parameter),
if (!base::missing(beta)) base::list(beta = beta),
if (!base::missing(initial_membership)) base::list(initial_membership = initial_membership),
if (!base::missing(n_iterations)) base::list(n_iterations = n_iterations),
if (!base::missing(vertex_weights)) base::list(vertex_weights = vertex_weights)
)
}
.arg_handle <- .old_signature(...)
if (base::length(.arg_handle) > 0L) {
.arg_names <- base::names(.arg_handle)
.arg_conflict <- base::intersect(.arg_names, base::c(
if (!base::missing(weights)) "weights",
if (!base::missing(resolution)) "resolution",
if (!base::missing(beta)) "beta",
if (!base::missing(initial_membership)) "initial_membership",
if (!base::missing(n_iterations)) "n_iterations",
if (!base::missing(vertex_weights)) "vertex_weights"
))
if (base::length(.arg_conflict) > 0L) cli::cli_abort(base::c("Argument {.arg {(.arg_conflict)}} of {.fn cluster_leiden} was supplied more than once.", i = "Pass it exactly once, by its new name {.arg {(.arg_conflict)}}."))
base::list2env(.arg_handle, base::environment())
lifecycle::deprecate_soft(
"3.0.0",
what = base::I("Calling `cluster_leiden()` with positional or abbreviated arguments"),
details = base::c(
i = base::paste0("Detected call: cluster_leiden(", base::paste(base::c("graph", "objective_function", base::c(weights = "weights", resolution = "resolution_parameter", beta = "beta", initial_membership = "initial_membership", n_iterations = "n_iterations", vertex_weights = "vertex_weights")[.arg_names]), collapse = ", "), ")"),
i = base::paste0("Use instead: cluster_leiden(", base::paste(base::c("graph", "objective_function", base::paste0(.arg_names, " = ")), collapse = ", "), ")")
)
)
}
}
# END GENERATED ARG_HANDLE

ensure_igraph(graph)

Expand Down
28 changes: 11 additions & 17 deletions R/layout.R
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -1766,7 +1766,6 @@ with_dh <- function(...) layout_spec(layout_with_dh, ...)
#' @param coolexp,maxdelta,area,repulserad `r lifecycle::badge("deprecated")` These
#' arguments are not supported from igraph version 0.8.0 and are ignored
#' (with a warning).
#' @param maxiter A deprecated synonym of `niter`, for compatibility.
#' @return A two- or three-column matrix, each row giving the coordinates of a
#' vertex, according to the IDs of the vertex IDs.
#' @author Gabor Csardi \email{csardi.gabor@@gmail.com}
Expand Down Expand Up @@ -1817,15 +1816,14 @@ layout_with_fr <- function(
coolexp = deprecated(),
maxdelta = deprecated(),
area = deprecated(),
repulserad = deprecated(),
maxiter = deprecated()
repulserad = deprecated()
) {
# BEGIN GENERATED ARG_HANDLE: layout_with_fr, do not edit, see tools/generate-migrations.R
# fmt: skip
if (...length() > 0L) {
.arg_forbidden <- base::intersect(base::names(base::sys.call()), base::c("g", "gr"))
if (base::length(.arg_forbidden) > 0L) cli::cli_abort(base::c("Argument {.arg {(.arg_forbidden)}} matches multiple formal arguments of {.fn layout_with_fr}.", i = "Spell out the full argument name."))
.arg_ambiguous <- base::intersect(base::names(base::substitute(...())), base::c("c", "co", "coo", "m", "mi", "min", "ma", "max"))
.arg_ambiguous <- base::intersect(base::names(base::substitute(...())), base::c("m", "ma", "max", "c", "co", "coo", "mi", "min"))
if (base::length(.arg_ambiguous) > 0L) cli::cli_abort("Argument {.arg {(.arg_ambiguous[[1L]])}} matches multiple arguments of {.fn layout_with_fr}.")
# Pre-3.0.0 signature: layout_with_fr(graph, coords, dim, niter, start.temp, grid, weights, minx, maxx, miny, maxy, minz, maxz, coolexp, maxdelta, area, repulserad, maxiter)
.old_signature <- function(coords, dim, niter, start.temp, grid, weights, minx, maxx, miny, maxy, minz, maxz, coolexp, maxdelta, area, repulserad, maxiter, ...) {
Expand All @@ -1852,7 +1850,7 @@ layout_with_fr <- function(
if (!base::missing(maxdelta)) base::list(maxdelta = maxdelta),
if (!base::missing(area)) base::list(area = area),
if (!base::missing(repulserad)) base::list(repulserad = repulserad),
if (!base::missing(maxiter)) base::list(maxiter = maxiter)
if (!base::missing(maxiter)) base::list(niter = maxiter)
)
}
.arg_handle <- .old_signature(...)
Expand All @@ -1875,15 +1873,15 @@ layout_with_fr <- function(
if (!base::missing(maxdelta)) "maxdelta",
if (!base::missing(area)) "area",
if (!base::missing(repulserad)) "repulserad",
if (!base::missing(maxiter)) "maxiter"
if (!base::missing(niter)) "niter"
))
if (base::length(.arg_conflict) > 0L) cli::cli_abort(base::c("Argument {.arg {(.arg_conflict)}} of {.fn layout_with_fr} was supplied more than once.", i = "Pass it exactly once, by its new name {.arg {(.arg_conflict)}}."))
base::list2env(.arg_handle, base::environment())
lifecycle::deprecate_soft(
"3.0.0",
what = base::I("Calling `layout_with_fr()` with positional or abbreviated arguments"),
details = base::c(
i = base::paste0("Detected call: layout_with_fr(", base::paste(base::c("graph", .arg_names), collapse = ", "), ")"),
i = base::paste0("Detected call: layout_with_fr(", base::paste(base::c("graph", base::c(coords = "coords", dim = "dim", niter = "niter", start.temp = "start.temp", grid = "grid", weights = "weights", minx = "minx", maxx = "maxx", miny = "miny", maxy = "maxy", minz = "minz", maxz = "maxz", coolexp = "coolexp", maxdelta = "maxdelta", area = "area", repulserad = "repulserad", niter = "maxiter")[.arg_names]), collapse = ", "), ")"),
i = base::paste0("Use instead: layout_with_fr(", base::paste(base::c("graph", base::paste0(.arg_names, " = ")), collapse = ", "), ")")
)
)
Expand All @@ -1899,15 +1897,6 @@ layout_with_fr <- function(

coords[] <- as.numeric(coords)
dim <- igraph_match_arg(dim)
if (!missing(niter) && !missing(maxiter)) {
cli::cli_abort(c(
"{.arg niter} and {.arg maxiter} must not be specified at the same time.",
i = "Specify only {.arg niter}, {.arg maxiter} is deprecated."
))
}
if (!missing(maxiter)) {
niter <- maxiter
}
niter <- as.numeric(niter)
start.temp <- as.numeric(start.temp)

Expand Down Expand Up @@ -2322,7 +2311,7 @@ with_graphopt <- function(...) layout_spec(layout_with_graphopt, ...)
#' \sQuote{z} coordinates.
#' @param niter,sigma,initemp,coolexp `r lifecycle::badge("deprecated")` These
#' arguments are not supported from igraph version 0.8.0 and are ignored (with a warning).
#' @param start Deprecated synonym for `coords`, for compatibility.
#' @param start `r lifecycle::badge("deprecated")` Use `coords` instead.
#' @return A numeric matrix with two (dim=2) or three (dim=3) columns, and as
#' many rows as the number of vertices, the x, y and potentially z coordinates
#' of the vertices.
Expand Down Expand Up @@ -2445,6 +2434,11 @@ layout_with_kk <- function(
))
}
if (!missing(start)) {
lifecycle::deprecate_soft(
"3.0.0",
"layout_with_kk(start = )",
"layout_with_kk(coords = )"
)
coords <- start
}

Expand Down
72 changes: 8 additions & 64 deletions R/structural-properties.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -461,8 +461,7 @@ graph.dfs <- function(
in.callback = NULL,
out.callback = NULL,
extra = NULL,
rho = parent.frame(),
neimode
rho = parent.frame()
) {
# nocov start
lifecycle::deprecate_warn("2.0.0", "graph.dfs()", "dfs()")
Expand All @@ -478,8 +477,7 @@ graph.dfs <- function(
in.callback = in.callback,
out.callback = out.callback,
extra = extra,
rho = rho,
neimode = neimode
rho = rho
)
} # nocov end

Expand Down Expand Up @@ -540,8 +538,7 @@ graph.bfs <- function(
dist = FALSE,
callback = NULL,
extra = NULL,
rho = parent.frame(),
neimode
rho = parent.frame()
) {
# nocov start
lifecycle::deprecate_warn("2.0.0", "graph.bfs()", "bfs()")
Expand All @@ -559,8 +556,7 @@ graph.bfs <- function(
dist = dist,
callback = callback,
extra = extra,
rho = rho,
neimode = neimode
rho = rho
)
} # nocov end

Expand Down Expand Up @@ -3642,7 +3638,6 @@ count_loops <- function(graph) {
#' given vertices.
#' @param order Logical, whether to return the ordering of the vertices.
#' @param rank Logical, whether to return the rank of the vertices.
#' @param father `r lifecycle::badge("deprecated")` Use `parent` instead.
#' @param parent Logical, whether to return the parent of the vertices.
#' @param pred Logical, whether to return the predecessors of the
#' vertices.
Expand All @@ -3657,16 +3652,14 @@ count_loops <- function(graph) {
#' @param extra Additional argument to supply to the callback function.
#' @param rho The environment in which the callback function is evaluated.
#' The default `NULL` uses the caller's environment.
#' @param neimode `r lifecycle::badge("deprecated")` This argument is deprecated
#' from igraph 1.3.0; use `mode` instead.
#' @inheritParams rlang::args_dots_empty
#' @return A named list with the following entries:
#' \describe{
#' \item{root}{
#' Numeric vector. The root vertex (or vertices) that was used as the
#' starting point of the search, as supplied in the `root` argument.
#' }
#' \item{neimode}{
#' \item{mode}{
#' Character scalar. The `mode` argument of the function call.
#' Note that for undirected graphs this is always \sQuote{all}, irrespectively of the supplied value.
#' }
Expand All @@ -3683,9 +3676,6 @@ count_loops <- function(graph) {
#' A vertex sequence (`igraph.vs`), or a numeric vector if the
#' `return.vs.es` option is `FALSE`.
#' }
#' \item{father}{
#' Like parent, kept for compatibility for now.
#' }
#' \item{pred}{
#' The previously visited vertex for each vertex, or 0 if there was no such vertex.
#' A vertex sequence (`igraph.vs`), or a numeric vector if the
Expand Down Expand Up @@ -3751,9 +3741,7 @@ bfs <- function(
dist = FALSE,
callback = NULL,
extra = NULL,
rho = NULL,
neimode = deprecated(),
father = deprecated()
rho = NULL
) {
rlang::check_dots_empty()

Expand All @@ -3763,18 +3751,6 @@ bfs <- function(
rho <- parent.frame()
}

if (lifecycle::is_present(neimode)) {
lifecycle::deprecate_stop(
"1.3.0",
"bfs(neimode = )",
"bfs(mode = )"
)
}

if (lifecycle::is_present(father)) {
lifecycle::deprecate_stop("2.2.0", "bfs(father = )", "bfs(parent = )")
}

if (length(root) == 1) {
root <- as_igraph_vs(graph, root) - 1
roots <- NULL
Expand Down Expand Up @@ -3827,9 +3803,6 @@ bfs <- function(
# https://github.com/igraph/rigraph/issues/1639
res$root <- requested_roots

# Remove in 1.4.0
res$neimode <- res$mode

if (order) {
res$order <- res$order + 1
}
Expand Down Expand Up @@ -3885,9 +3858,6 @@ bfs <- function(
res$dist[is.nan(res$dist)] <- -3
}

# Remove this later? https://github.com/igraph/rigraph/issues/1576
res$father <- res$parent

res
}

Expand Down Expand Up @@ -3927,7 +3897,6 @@ bfs <- function(
#' vertices.
#' @param order.out Logical, whether to return the ordering based on
#' leaving the subtree of the vertex.
#' @param father `r lifecycle::badge("deprecated")`, use `parent` instead.
#' @param parent Logical, whether to return the parent of the vertices.
#' @param dist Logical, whether to return the distance from the root of
#' the search tree.
Expand All @@ -3941,15 +3910,13 @@ bfs <- function(
#' @param extra Additional argument to supply to the callback function.
#' @param rho The environment in which the callback function is evaluated.
#' The default `NULL` uses the caller's environment.
#' @param neimode `r lifecycle::badge("deprecated")` This argument is deprecated from igraph 1.3.0; use
#' `mode` instead.
#' @inheritParams rlang::args_dots_empty
#' @return A named list with the following entries:
#' \describe{
#' \item{root}{
#' Numeric scalar. The root vertex that was used as the starting point of the search.
#' }
#' \item{neimode}{
#' \item{mode}{
#' Character scalar. The `mode` argument of the function call.
#' Note that for undirected graphs this is always \sQuote{all}, irrespectively of the supplied value.
#' }
Expand All @@ -3962,9 +3929,6 @@ bfs <- function(
#' \item{parent}{
#' Numeric vector. The parent of each vertex, i.e. the vertex it was discovered from.
#' }
#' \item{father}{
#' Like parent, kept for compatibility for now.
#' }
#' \item{dist}{
#' Numeric vector, for each vertex its distance from the root of the search tree.
#' }
Expand Down Expand Up @@ -4028,9 +3992,7 @@ dfs <- function(
in.callback = NULL,
out.callback = NULL,
extra = NULL,
rho = NULL,
neimode = deprecated(),
father = deprecated()
rho = NULL
) {
rlang::check_dots_empty()

Expand All @@ -4039,18 +4001,6 @@ dfs <- function(
rho <- parent.frame()
}

if (lifecycle::is_present(neimode)) {
lifecycle::deprecate_stop(
"1.3.0",
"dfs(neimode = )",
"dfs(mode = )"
)
}

if (lifecycle::is_present(father)) {
lifecycle::deprecate_stop("2.2.0", "dfs(father = )", "dfs(parent = )")
}

root <- as_igraph_vs(graph, root) - 1
mode <- switch(
igraph_match_arg(mode),
Expand Down Expand Up @@ -4084,9 +4034,6 @@ dfs <- function(
rho
)

# Remove in 1.4.0
res$neimode <- res$mode

if (order) {
res$order <- res$order + 1
}
Expand Down Expand Up @@ -4119,9 +4066,6 @@ dfs <- function(
if (dist) names(res$dist) <- V(graph)$name
}

# Remove this later? https://github.com/igraph/rigraph/issues/1576
res$father <- res$parent

res
}

Expand Down
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