Merge branch 'main' into move-vignette

.Rbuildignore

@@ -32,3 +32,7 @@
 ^codecov\.yml$
 ^\.gitattributes$
 ^build$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/fledge.yaml

@@ -16,8 +16,20 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  check_fork:
+    runs-on: ubuntu-latest
+    outputs:
+      is_forked: ${{ steps.check.outputs.is_forked }}
+    steps:
+      - name: Check if the repo is forked
+        id: check
+        run: |
+          echo "is_forked=$(curl -s -H "Accept: application/vnd.github+json" -H 'Authorization: Bearer ${{ github.token }}' -H "X-GitHub-Api-Version: 2022-11-28" ${GITHUB_API_URL}/repos/${GITHUB_REPOSITORY} | jq .fork)" >> $GITHUB_OUTPUT
+
   fledge:
     runs-on: ubuntu-latest
+    needs: check_fork
+    if: needs.check_fork.outputs.is_forked == 'false'
     permissions:
       contents: write
     env:

.github/workflows/pkgdown.yaml

@@ -0,0 +1,46 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master, config-draft]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: igraph
-Version: 1.3.5.9100
+Version: 1.3.5.9104
 Title: Network Analysis and Visualization
 Author: See AUTHORS file.
 Maintainer: Tamás Nepusz <ntamas@gmail.com>

NAMESPACE

@@ -706,7 +706,6 @@ export(path.length.hist)
 export(permute)
 export(permute.vertices)
 export(piecewise.layout)
-export(plot.igraph)
 export(plotHierarchy)
 export(plot_dendrogram)
 export(plot_hierarchy)
@@ -715,7 +714,6 @@ export(power_centrality)
 export(predict_edges)
 export(pref)
 export(preference.game)
-export(print.igraph)
 export(print_all)
 export(printer_callback)
 export(r_pal)

NEWS.md

@@ -1,5 +1,37 @@
 <!-- NEWS.md is maintained by https://cynkra.github.io/fledge, do not edit -->
 
+# igraph 1.3.5.9104
+
+- Merge pull request #652 from wael-sadek/f-check-if-forked.
+
+skip fledge job if the repo is a fork
+
+
+# igraph 1.3.5.9103
+
+## Bug fixes
+
+- Iterators created with `E(P = ...)` or `E(path = ...)` are incomplete (#648).
+
+
+# igraph 1.3.5.9102
+
+## Chore
+
+- Avoid fledge workflow on forks.
+
+
+# igraph 1.3.5.9101
+
+## Documentation
+
+- Link to installation troubleshooting info (@maelle, #646).
+
+- Further polish print_all() docs.
+
+- Clarify print_all() output.
+
+
 # igraph 1.3.5.9100
 
 ## Chore

R/adjacency.R

@@ -435,5 +435,6 @@ graph_from_adjacency_matrix <- function(adjmatrix,
 
 #' @rdname graph_from_adjacency_matrix
 #' @param ... Passed to `graph_from_adjacency_matrix()`.
+#' @family adjacency
 #' @export
 from_adjacency <- function(...) constructor_spec(graph_from_adjacency_matrix, ...)

R/bipartite.R

@@ -66,6 +66,7 @@
 #'   default it will be removed.
 #' @return A list of two undirected graphs. See details above.
 #' @author Gabor Csardi \email{csardi.gabor@@gmail.com}
+#' @family bipartite
 #' @export
 #' @keywords graphs
 #' @examples
@@ -190,5 +191,6 @@ bipartite_projection <- function(graph, types = NULL,
 #' g3 <- make_ring(10)
 #' g3 <- add_edges(g3, c(1, 3))
 #' bipartite_mapping(g3)
+#' @family bipartite
 #' @export
 bipartite_mapping <- bipartite_mapping

R/centrality.R

@@ -24,6 +24,7 @@
 #'   calculated.
 #' @param cutoff The maximum path length to consider when calculating the
 #'   betweenness. If zero or negative then there is no such limit.
+#' @family centrality
 #' @export
 estimate_betweenness <- function(graph, vids = V(graph), directed = TRUE, cutoff, weights = NULL, nobigint = TRUE) {
   if (!missing(nobigint)) {
@@ -105,6 +106,7 @@ estimate_betweenness <- function(graph, vids = V(graph), directed = TRUE, cutoff
 #'
 #' Ulrik Brandes, A Faster Algorithm for Betweenness Centrality. *Journal
 #' of Mathematical Sociology* 25(2):163-177, 2001.
+#' @family centrality
 #' @export
 #' @keywords graphs
 #' @examples
@@ -154,6 +156,7 @@ betweenness <- function(graph, v = V(graph), directed = TRUE, weights = NULL,
 
 #' @rdname betweenness
 #' @param e The edges for which the edge betweenness will be calculated.
+#' @family centrality
 #' @export
 edge_betweenness <- function(graph, e = E(graph),
                              directed = TRUE, weights = NULL, cutoff = -1) {
@@ -183,6 +186,7 @@ edge_betweenness <- function(graph, e = E(graph),
   res[as.numeric(e)]
 }
 
+#' @family centrality
 #' @export
 estimate_edge_betweenness <- function(graph, e = E(graph),
                                       directed = TRUE, cutoff, weights = NULL) {
@@ -242,6 +246,7 @@ estimate_edge_betweenness <- function(graph, e = E(graph),
 #' @seealso [betweenness()], [degree()], [harmonic_centrality()]
 #' @references Freeman, L.C. (1979). Centrality in Social Networks I:
 #' Conceptual Clarification. *Social Networks*, 1, 215-239.
+#' @family centrality
 #' @export
 #' @keywords graphs
 #' @examples
@@ -291,12 +296,14 @@ closeness <- function(graph, vids = V(graph),
   res
 }
 
+#' @family centrality
 #' @export
 estimate_closeness <- function(graph, vids = V(graph), mode = c("out", "in", "all", "total"), cutoff, weights = NULL, normalized = FALSE) {
   closeness(graph, vids, mode = mode, weights = weights, normalized = normalized, cutoff = cutoff)
 }
 
 #' @rdname arpack
+#' @family centrality
 #' @export
 arpack_defaults <- list(
   bmat = "I", n = 0, which = "XX", nev = 1, tol = 0.0,
@@ -490,6 +497,7 @@ arpack_defaults <- list(
 #'     which = "LM", maxiter = 2000
 #'   ))
 #' }
+#' @family centrality
 #' @export
 arpack <- function(func, extra = NULL, sym = FALSE, options = arpack_defaults,
                    env = parent.frame(), complex = !sym) {
@@ -588,6 +596,7 @@ arpack.unpack.complex <- function(vectors, values, nev) {
 #' @seealso [eigen_centrality()], [page_rank()]
 #' @references Ernesto Estrada, Juan A. Rodriguez-Velazquez: Subgraph
 #' centrality in Complex Networks. *Physical Review E* 71, 056103 (2005).
+#' @family centrality
 #' @export
 #' @keywords graphs
 #' @examples
@@ -668,6 +677,7 @@ subgraph_centrality <- function(graph, diag = FALSE) {
 #' ## Smallest eigenvalues
 #' spectrum(kite, which = list(pos = "SM", howmany = 2))$values
 #'
+#' @family centrality
 #' @export
 spectrum <- spectrum
 
@@ -760,6 +770,7 @@ eigen_defaults <- list(
 #' g <- make_ring(10, directed = FALSE)
 #' # Compute eigenvector centrality scores
 #' eigen_centrality(g)
+#' @family centrality
 #' @export
 eigen_centrality <- eigen_centrality
 
@@ -798,6 +809,7 @@ eigen_centrality <- eigen_centrality
 #' # No weights, a warning is given
 #' g <- make_ring(10)
 #' strength(g)
+#' @family centrality
 #' @export
 strength <- strength
 
@@ -841,6 +853,7 @@ strength <- strength
 #' diversity(g1)
 #' diversity(g2)
 #' diversity(g3)
+#' @family centrality
 #' @export
 diversity <- diversity
 
@@ -1027,6 +1040,7 @@ authority_score <- authority_score
 #' page_rank(g3)$vector
 #' reset <- seq(vcount(g3))
 #' page_rank(g3, personalized = reset)$vector
+#' @family centrality
 #' @export
 page_rank <- page_rank
 
@@ -1063,6 +1077,7 @@ page_rank <- page_rank
 #' @seealso [betweenness()], [closeness()]
 #' @references M. Marchiori and V. Latora, Harmony in the small-world,
 #' *Physica A* 285, pp. 539-546 (2000).
+#' @family centrality
 #' @export
 #' @keywords graphs
 #' @examples
@@ -1210,6 +1225,7 @@ bonpow.sparse <- function(graph, nodes = V(graph), loops = FALSE,
 #' Bonacich, P.  (1987).  ``Power and Centrality: A Family of Measures.''
 #' *American Journal of Sociology*, 92, 1170-1182.
 #' @keywords graphs
+#' @family centrality
 #' @export
 #' @examples
 #'
@@ -1393,6 +1409,7 @@ alpha.centrality.sparse <- function(graph, nodes = V(graph), alpha = 1,
 #' @references Bonacich, P. and Lloyd, P. (2001). ``Eigenvector-like
 #' measures of centrality for asymmetric relations'' *Social Networks*,
 #' 23, 191-201.
+#' @family centrality
 #' @export
 #' @keywords graphs
 #' @examples

R/cliques.R

@@ -74,6 +74,7 @@
 #' @references For maximal cliques the following algorithm is implemented:
 #' David Eppstein, Maarten Loffler, Darren Strash: Listing All Maximal Cliques
 #' in Sparse Graphs in Near-optimal Time.  <https://arxiv.org/abs/1006.5440>
+#' @family cliques
 #' @export
 #' @keywords graphs
 #' @examples
@@ -89,6 +90,7 @@
 #' max_cliques(g)
 cliques <- cliques
 
+#' @family cliques
 #' @export
 largest_cliques <- largest_cliques
 
@@ -103,6 +105,7 @@ largest_cliques <- largest_cliques
 #'   it exists, then it will be overwritten.) Each clique will be a separate line
 #'   in the file, given with the numeric ids of its vertices, separated by
 #'   whitespace.
+#' @family cliques
 #' @export
 max_cliques <- function(graph, min = NULL, max = NULL, subset = NULL, file = NULL) {
   if (!is_igraph(graph)) {
@@ -156,6 +159,7 @@ max_cliques <- function(graph, min = NULL, max = NULL, subset = NULL, file = NUL
   }
 }
 
+#' @family cliques
 #' @export
 count_max_cliques <- function(graph, min = NULL, max = NULL,
                               subset = NULL) {
@@ -184,6 +188,7 @@ count_max_cliques <- function(graph, min = NULL, max = NULL,
   res
 }
 
+#' @family cliques
 #' @export
 clique_num <- clique_num
 
@@ -236,6 +241,7 @@ clique_num <- clique_num
 #' @author Tamas Nepusz \email{ntamas@@gmail.com} and Gabor Csardi
 #' \email{csardi.gabor@@gmail.com}
 #' @seealso [ivs()]
+#' @family cliques
 #' @export
 #' @keywords graphs
 #' @examples
@@ -299,6 +305,7 @@ weighted_clique_num <- weighted_clique_num
 #' @references S. Tsukiyama, M. Ide, H. Ariyoshi and I. Shirawaka. A new
 #' algorithm for generating all the maximal independent sets. *SIAM J
 #' Computing*, 6:505--517, 1977.
+#' @family cliques
 #' @export
 #' @keywords graphs
 #' @examples
@@ -342,6 +349,7 @@ ivs <- function(graph, min = NULL, max = NULL) {
   res
 }
 
+#' @family cliques
 #' @export
 largest_ivs <- function(graph) {
   if (!is_igraph(graph)) {
@@ -359,6 +367,7 @@ largest_ivs <- function(graph) {
   res
 }
 
+#' @family cliques
 #' @export
 maximal_ivs <- function(graph) {
   if (!is_igraph(graph)) {
@@ -376,6 +385,7 @@ maximal_ivs <- function(graph) {
   res
 }
 
+#' @family cliques
 #' @export
 ivs_size <- function(graph) {
   if (!is_igraph(graph)) {
@@ -386,6 +396,7 @@ ivs_size <- function(graph) {
   .Call(C_R_igraph_independence_number, graph)
 }
 
+#' @family cliques
 #' @export
 clique_size_counts <- function(graph, min = 0, max = 0, maximal = FALSE, ...) {
   if (maximal) {

R/cocitation.R

@@ -47,6 +47,7 @@
 #'   `vcount(graph)` columns. Element `(i,j)` contains the cocitation
 #'   or bibliographic coupling for vertices `v[i]` and `j`.
 #' @author Gabor Csardi \email{csardi.gabor@@gmail.com}
+#' @family cocitation
 #' @export
 #' @keywords graphs
 #' @examples
@@ -69,6 +70,7 @@ cocitation <- function(graph, v = V(graph)) {
   res
 }
 
+#' @family cocitation
 #' @export
 bibcoupling <- function(graph, v = V(graph)) {
   if (!is_igraph(graph)) {