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chore!: Hard-deprecate as_adjacency_matrix(edges = ) #1080

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Merged
aviator-app merged 4 commits into from
Jan 21, 2024
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chore!: Hard-deprecate as_adjacency_matrix(edges = ) #1080

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84dbc20
chore: Hard-deprecate `as_adjacency_matrix(edges = )`
krlmlr Jan 8, 2024
2609103
docs: add deprecated badge for the edges argument of as_adjacency_mat…
maelle Jan 8, 2024
6c4cb68
rm tests of now unsupported behaviour
maelle Jan 16, 2024
89a1d4b
revdepcheck results
krlmlr Jan 21, 2024
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12 changes: 6 additions & 6 deletions R/conversion.R
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Expand Up @@ -317,7 +317,7 @@ get.adjacency.sparse <- function(graph, type = c("both", "upper", "lower"),
#' numeric. If the `sparse` argument is `FALSE`, then character is
#' also allowed. The reason for the difference is that the `Matrix`
#' package does not support character sparse matrices yet.
#' @param edges Logical scalar, whether to return the edge ids in the matrix.
#' @param edges `r lifecycle::badge("deprecated")` Logical scalar, whether to return the edge ids in the matrix.
#' For non-existant edges zero is returned.
Comment on lines +320 to 321
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@krlmlr krlmlr Jan 20, 2024

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Should we just mention that this must be omitted?

#' @param names Logical constant, whether to assign row and column names
#' to the matrix. These are only assigned if the `name` vertex attribute
Expand All @@ -344,14 +344,14 @@ as_adjacency_matrix <- function(graph, type = c("both", "upper", "lower"),
sparse = igraph_opt("sparsematrices")) {
ensure_igraph(graph)

if (!missing(edges)) {
warning("The `edges` argument of `as_adjacency_matrix` is deprecated; it will be removed in igraph 1.4.0")
if (!missing(edges) && isTRUE(edges)) {
lifecycle::deprecate_stop("2.0.0", "as_adjacency_matrix(edges = )")
}
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@krlmlr krlmlr Jan 20, 2024

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Add a deprecate_soft() if edges is FALSE ?


if (!sparse) {
get.adjacency.dense(graph, type = type, attr = attr, weights = NULL, names = names)
} else {
if (sparse) {
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maelle marked this conversation as resolved.
get.adjacency.sparse(graph, type = type, attr = attr, edges = edges, names = names)
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@krlmlr krlmlr Jan 20, 2024 •
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Passing edges now looks like dead code, but get.adjacency.sparse() will be implemented in C anyway, perhaps no need to act.

} else {
get.adjacency.dense(graph, type = type, attr = attr, weights = NULL, names = names)
}
}

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2 changes: 1 addition & 1 deletion man/as_adjacency_matrix.Rd
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2 changes: 1 addition & 1 deletion man/get.adjacency.Rd
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12 changes: 12 additions & 0 deletions revdep/README.md
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@@ -1,5 +1,17 @@
# Revdeps

## Failed to check (7)

|package |version |error |warning |note |
|:----------|:-------|:-----|:-------|:----|
|geostan |0.5.3 |1 | | |
|HLSM |? | | | |
|Seurat |? | | | |
|streamDAG |? | | | |
|TDA |1.9 |1 | | |
|TestAnaAPP |0.1.5 |1 | | |
|treestats |1.0.3 |1 | | |

## New problems (22)

|package |version |error |warning |note |
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12 changes: 10 additions & 2 deletions revdep/cran.md
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@@ -1,9 +1,9 @@
## revdepcheck results

We checked 22 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
We checked 30 reverse dependencies (29 from CRAN + 1 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.

* We saw 22 new problems
* We failed to check 0 packages
* We failed to check 6 packages

Issues with CRAN packages are summarised below.

Expand Down Expand Up @@ -80,3 +80,11 @@ Issues with CRAN packages are summarised below.
* VertexSort
checking examples ... ERROR

### Failed to check

* geostan (NA)
* Seurat (NA)
* streamDAG (NA)
* TDA (NA)
* TestAnaAPP (NA)
* treestats (NA)
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