Merge branch 'main' into again-cut.prob

CONTRIBUTING.md

@@ -154,6 +154,16 @@ pak::pak("igraph/igraph.r2cdocs")
 [roxygen2](https://roxygen2.r-lib.org/), and run `devtools::document()` or `make
 igraph` to update the `.Rd` files.
 
+- Links to C docs are added using the cdocs tag, for instance:
+
+```
+#' @cdocs igraph_assortativity
+```
+
+### Maintaining igraph.r2cdocs
+
+To update the data (when the C docs index has changed after a release) in https://github.com/igraph/igraph.r2cdocs/, run the script that is `data-raw`, commit the csv file and push.
+
 ### Test Cases
 
 Unless you change something trivial, please consider adding test cases.  This is

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: igraph
 Title: Network Analysis and Visualization
-Version: 2.1.4.9011
+Version: 2.1.4.9019
 Authors@R: c(
     person("Gábor", "Csárdi", , "[email protected]", role = "aut",
            comment = c(ORCID = "0000-0001-7098-9676")),
@@ -65,7 +65,7 @@ VignetteBuilder:
     knitr
 Config/Needs/build: roxygen2, devtools, irlba, pkgconfig, igraph/igraph.r2cdocs, moodymudskipper/devtag
 Config/Needs/coverage: covr
-Config/Needs/website: readr
+Config/Needs/website: here, readr, tibble, xmlparsedata, xml2
 Config/testthat/edition: 3
 Config/testthat/parallel: true
 Config/testthat/start-first: vs-es, scan, vs-operators, weakref,

NEWS.md

@@ -1,5 +1,119 @@
 <!-- NEWS.md is maintained by https://fledge.cynkra.com, contributors should not edit this file -->
 
+# igraph 2.1.4.9019
+
+## Testing
+
+- Added tests for untested files (@schochastics, #1728).
+
+- Merged and refactored other.R tests (@schochastics, #1727).
+
+- Merged and refactored structural.properties.R tests (@schochastics, #1726).
+
+
+# igraph 2.1.4.9018
+
+## Bug fixes
+
+- Use function instead of (x) in arrow.mode (@schochastics, #1722).
+
+## Documentation
+
+- Lifecycle table (#1525).
+
+## Refactoring
+
+- One less tmp use case (#1715).
+
+## Testing
+
+- Merged and refactored orphaned test files (@schochastics, #1724).
+
+- Merged and refactored iterators.R and operators.R tests (@schochastics, #1723).
+
+- Merged and refactored topology.R tests (@schochastics, #1720).
+
+- Merged and refactored embedding.R tests (@schochastics, #1721).
+
+- Merge all tests for foreign.R into one test file (#1713).
+
+
+# igraph 2.1.4.9017
+
+## Features
+
+- Added proper support for adding attributes via data.frames (@schochastics, #1373, #1669, #1716).
+
+
+# igraph 2.1.4.9016
+
+## doc
+
+- Fix typos in `laplacian_matrix` documentation.
+
+
+# igraph 2.1.4.9015
+
+## Chore
+
+- Run `devtools::document()` (#1710).
+
+
+# igraph 2.1.4.9014
+
+## Bug fixes
+
+- Duplicated arrowhead drawing (@schochastics, #640, #1709).
+
+- Correct mapping of edge label properties in plots when loops are present (@schochastics, #157, #1706).
+
+- NA attribute values are replaced with default values for plotting (@schochastics, #293, #1707).
+
+## vendor
+
+- Update vendored sources to igraph/igraph@10ef19bc2a61de6c6cfe76e5a068f82b1d29fff1 (#1694).
+
+
+# igraph 2.1.4.9013
+
+## Features
+
+- Hrg functions check their argument (#1074, #1699).
+
+## Documentation
+
+- Replace instances of `#' if` with `#' @examplesIf` (#1134, #1698).
+
+- Update graph saving rec (#1242, #1700).
+
+## Testing
+
+- Improve test-dot.product.game (#1396, #1705).
+
+
+# igraph 2.1.4.9012
+
+## Chore
+
+- Run {styler} (with {igraph.style}) (#1696).
+
+## Documentation
+
+- Add more about igraph.r2cdocs in the contributing guide (#1686, #1697).
+
+## Testing
+
+- Merged and refactored conversion.R tests (@schochastics, #1701).
+
+- Create helpers (#1691, #1695).
+
+- Merged and refactored make.R tests (@schochastics, #1685).
+
+- Merged and refactored community.R tests (@schochastics, #1689).
+
+- Merged and refactored indexing.R tests (@schochastics, #1687).
+
+
 # igraph 2.1.4.9011
 
 ## Testing

R/aaa-auto.R

@@ -2712,14 +2712,25 @@ triad_census_impl <- function(graph) {
   res
 }
 
-adjacent_triangles_impl <- function(graph, vids=V(graph)) {
+count_adjacent_triangles_impl <- function(graph, vids=V(graph)) {
   # Argument checks
   ensure_igraph(graph)
   vids <- as_igraph_vs(graph, vids)
 
   on.exit( .Call(R_igraph_finalizer) )
   # Function call
-  res <- .Call(R_igraph_adjacent_triangles, graph, vids-1)
+  res <- .Call(R_igraph_count_adjacent_triangles, graph, vids-1)
+
+  res
+}
+
+count_triangles_impl <- function(graph) {
+  # Argument checks
+  ensure_igraph(graph)
+
+  on.exit( .Call(R_igraph_finalizer) )
+  # Function call
+  res <- .Call(R_igraph_count_triangles, graph)
 
   res
 }

R/adjacency.R

@@ -375,8 +375,8 @@ mysummary <- function(x) {
   result
 }
 
-pmax_AB <- function(A,B) {
-  change <- A < B  
+pmax_AB <- function(A, B) {
+  change <- A < B
   A[change] <- B[change]
   A
 }

R/assortativity.R

@@ -1,4 +1,3 @@
-
 #' Assortativity coefficient
 #'
 #' @description

R/attributes.R

@@ -1,4 +1,3 @@
-
 #' Set vertex attributes
 #'
 #' @description
@@ -350,6 +349,9 @@ graph.attributes <- function(graph) {
 "graph.attributes<-" <- function(graph, value) {
   ensure_igraph(graph)
   assert_named_list(value)
+  if (inherits(value, "data.frame")) {
+    value <- as.list(value)
+  }
 
   .Call(R_igraph_mybracket2_set, graph, igraph_t_idx_attr, igraph_attr_idx_graph, value)
 }
@@ -391,7 +393,6 @@ vertex_attr <- function(graph, name, index = V(graph)) {
   }
   index <- as_igraph_vs(graph, index)
   myattr[index]
-
 }
 
 #' Set one or more vertex attributes
@@ -489,12 +490,8 @@ i_set_vertex_attr <- function(graph, name, index = V(graph), value, check = TRUE
     } else if (length(value) == length(index)) {
       value_in <- unname(value)
     } else {
-      stop(
-        "Length of new attribute value must be ",
-        if (length(index) != 1) "1 or ",
-        length(index),
-        ", the number of target vertices, not ",
-        length(value)
+      cli::cli_abort(
+        "Length of new attribute value must be {if (length(index) != 1) '1 or '}{length(index)}, the number of target vertices, not {length(value)}."
       )
     }
 
@@ -520,8 +517,8 @@ vertex.attributes <- function(graph, index = V(graph)) {
 
   if (!missing(index)) {
     index_is_natural_sequence <- (length(index) == vcount(graph) &&
-        identical(index, seq(1, vcount(graph))))
-    if  (!index_is_natural_sequence) {
+      identical(index, seq(1, vcount(graph))))
+    if (!index_is_natural_sequence) {
       for (i in seq_along(res)) {
         res[[i]] <- res[[i]][index]
       }
@@ -543,16 +540,19 @@ set_value_at <- function(value, idx, length_out) {
   ensure_igraph(graph)
 
   assert_named_list(value)
+  if (inherits(value, "data.frame")) {
+    value <- as.list(value)
+  }
 
   if (!all(lengths(value) == length(index))) {
-    stop("Invalid attribute value length, must match number of vertices")
+    cli::cli_abort("Invalid attribute value length, must match number of vertices.")
   }
 
   if (!missing(index)) {
     index <- as_igraph_vs(graph, index)
 
     if (anyDuplicated(index) || anyNA(index)) {
-      stop("Invalid vertices in index")
+      cli::cli_abort("{.arg index} contains duplicated vertices or NAs.")
     }
   }
 
@@ -700,12 +700,8 @@ i_set_edge_attr <- function(graph, name, index = E(graph), value, check = TRUE)
     } else if (length(value) == length(index)) {
       value_in <- unname(value)
     } else {
-      stop(
-        "Length of new attribute value must be ",
-        if (length(index) != 1) "1 or ",
-        length(index),
-        ", the number of target edges, not ",
-        length(value)
+      cli::cli_abort(
+        "Length of new attribute value must be {if (length(index) != 1) '1 or '}{length(index)}, the number of target edges, not {length(value)}."
       )
     }
 
@@ -743,15 +739,18 @@ edge.attributes <- function(graph, index = E(graph)) {
   ensure_igraph(graph)
 
   assert_named_list(value)
+  if (inherits(value, "data.frame")) {
+    value <- as.list(value)
+  }
 
   if (any(sapply(value, length) != length(index))) {
-    stop("Invalid attribute value length, must match number of edges")
+    cli::cli_abort("Invalid attribute value length, must match number of edges")
   }
 
   if (!missing(index)) {
     index <- as_igraph_es(graph, index)
     if (any(duplicated(index)) || any(is.na(index))) {
-      stop("Invalid edges in index")
+      cli::cli_abort("{.arg index} contains duplicated edges or NAs.")
     }
   }
 
@@ -857,7 +856,7 @@ delete_graph_attr <- function(graph, name) {
 
   name <- as.character(name)
   if (!name %in% graph_attr_names(graph)) {
-    stop("No such graph attribute: ", name)
+    cli::cli_abort("No graph attribute {.arg {name}} found.")
   }
 
   gattr <- .Call(R_igraph_mybracket2, graph, igraph_t_idx_attr, igraph_attr_idx_graph)
@@ -886,7 +885,7 @@ delete_vertex_attr <- function(graph, name) {
 
   name <- as.character(name)
   if (!name %in% vertex_attr_names(graph)) {
-    stop("No such vertex attribute: ", name)
+    cli::cli_abort("No vertex attribute {.arg {name}} found.")
   }
 
   vattr <- .Call(R_igraph_mybracket2, graph, igraph_t_idx_attr, igraph_attr_idx_vertex)
@@ -915,7 +914,7 @@ delete_edge_attr <- function(graph, name) {
 
   name <- as.character(name)
   if (!name %in% edge_attr_names(graph)) {
-    stop("No such edge attribute: ", name)
+    cli::cli_abort("No edge attribute {.arg {name}} found.")
   }
 
   eattr <- .Call(R_igraph_mybracket2, graph, igraph_t_idx_attr, igraph_attr_idx_edge)
@@ -1022,7 +1021,7 @@ igraph.i.attribute.combination <- function(comb) {
   if (any(!sapply(comb, function(x) {
     is.function(x) || (is.character(x) && length(x) == 1)
   }))) {
-    stop("Attribute combination element must be a function or character scalar")
+    cli::cli_abort("Attribute combination element must be a function or character scalar.")
   }
   if (is.null(names(comb))) {
     names(comb) <- rep("", length(comb))
@@ -1043,7 +1042,7 @@ igraph.i.attribute.combination <- function(comb) {
       )
       x <- pmatch(tolower(x), known[, 1])
       if (is.na(x)) {
-        stop("Unknown/unambigous attribute combination specification")
+        cli::cli_abort("Unknown/unambigous attribute combination specification.")
       }
       known[, 2][x]
     }
@@ -1187,18 +1186,15 @@ NULL
 }
 
 assert_named_list <- function(value) {
-  error_msg <- "{.arg value} must be a named list with unique names"
-
   if (!is.list(value)) {
-    rlang::abort(error_msg)
+    cli::cli_abort("{.arg value} must be a named list with unique names")
   }
 
   if (length(value) == 0) {
     return()
   }
 
   if (!rlang::is_named(value) || anyDuplicated(names(value)) > 0) {
-
-    rlang::abort(error_msg)
+    cli::cli_abort("{.arg value} must be a named list with unique names")
   }
 }

R/basic.R

@@ -1,4 +1,3 @@
-
 #' Is this object an igraph graph?
 #'
 #' @description

R/bipartite.R

@@ -1,4 +1,3 @@
-
 #' Project a bipartite graph
 #'
 #' @description