From db199d7ee648704fa1d02e8b3d4e900cd846efd9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 15 Sep 2026 12:24:44 +0200
Subject: [PATCH 1/2] docs: integrate the roclet to igraph proper

---
 DESCRIPTION        |   4 +-
 R/utils-roxygen2.R | 314 +++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 316 insertions(+), 2 deletions(-)
 create mode 100644 R/utils-roxygen2.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 8f902283bfe..d9fb605aadc 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -82,7 +82,7 @@ Config/comment/gha/extra-packages: graph is an optional Enhances
     4.4.0, where a published release still exists.
 Config/Needs/build: devtools, irlba, pkgconfig
 Config/Needs/coverage: covr
-Config/Needs/roxygen2: r-lib/roxygen2, igraph/igraph.r2cdocs,
+Config/Needs/roxygen2: r-lib/roxygen2, 
     moodymudskipper/devtag
 Config/Needs/website: here, readr, tibble, xmlparsedata, xml2
 Config/testthat/edition: 3
@@ -91,6 +91,6 @@ Config/testthat/start-first: aaa-auto, vs-es, scan, vs-operators, weakref,
     watts.strogatz.game
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE, roclets = c("collate", "namespace",
-    "igraph.r2cdocs::docs_rd", "devtag::dev_roclet"))
+    "igraph:::docs_rd", "devtag::dev_roclet"))
 SystemRequirements: libxml2 (optional), glpk (>= 4.57, optional)
 Config/roxygen2/version: 8.1.0.9000
diff --git a/R/utils-roxygen2.R b/R/utils-roxygen2.R
new file mode 100644
index 00000000000..d798c049a3f
--- /dev/null
+++ b/R/utils-roxygen2.R
@@ -0,0 +1,314 @@
+docs_rd <- function() {
+  roxygen2::roclet(c("docs_rd", "rd"))
+}
+
+roclet_process.roclet_docs_rd <- function(x, blocks, env, base_path) {
+  NextMethod()
+}
+
+roclet_output.roclet_docs_rd <- function(x, results, base_path, ...) {
+  results <- lapply_with_names(results, add_cdocs_section, base_path)
+  NextMethod()
+}
+
+# https://github.com/gaborcsardi/roxygenlabs/blob/5a7e4449c28f9e423de3f4e8e1be9bc9080f4e52/R/themed-rd.R#L26
+lapply_with_names <- function(X, FUN, ...) {
+  structure(
+    lapply(X, FUN, ...),
+    names = names(X) %||% (if (is.character(X)) X)
+  )
+}
+
+add_cdocs_section <- function(topic, base_path) {
+  alias <- topic$get_value("alias")
+  impl <- purrr::map(alias, find_impl, base_path = base_path) |> unlist()
+
+  if (length(impl) == 0) {
+    return(topic)
+  }
+
+  impl <- sub("_impl", "", impl)
+  impl <- sprintf("igraph_%s", impl)
+
+  content <- present_cdocs_link(impl, base_path)
+
+  # Only add section if there are actual links
+  if (content == "") {
+    return(topic)
+  }
+
+  topic$add_section(roxygen2::rd_section(
+    "section",
+    list(
+      title = "Related documentation in the C library",
+      content = content
+    )
+  ))
+
+  topic
+}
+
+present_cdocs_link <- function(value, base_path) {
+  strings <- map_chr(
+    unique(value),
+    format_cdocs_single_link,
+    base_path
+  )
+
+  # Filter out empty strings
+  strings <- strings[strings != ""]
+
+  paste(strings, collapse = ", ")
+}
+
+
+# rigraph's `src/rcallback.c` defines closure shims that exist on the R side
+# only: each one wraps a single C function, and none has a C entry of its own.
+# The wrapped name is mapped explicitly rather than derived by stripping the
+# `_closure` suffix, for two reasons.
+# `igraph_transitive_closure` and `igraph_transitive_closure_dag` are
+# graph-theory functions rather than wrappers, so a suffix rule would have to
+# know to leave them alone.
+# And `community_leading_eigenvector_callback_closure` wraps
+# `igraph_community_leading_eigenvector`, dropping `_callback` along with
+# `_closure`, where every other shim keeps it.
+# Mirrors `closure_map` in rigraph's `tools/rebuild-cats.R`.
+closure_map <- c(
+  "igraph_bfs_closure" = "igraph_bfs",
+  "igraph_dfs_closure" = "igraph_dfs",
+  "igraph_cliques_callback_closure" = "igraph_cliques_callback",
+  "igraph_maximal_cliques_callback_closure" = "igraph_maximal_cliques_callback",
+  "igraph_simple_cycles_callback_closure" = "igraph_simple_cycles_callback",
+  "igraph_get_isomorphisms_vf2_callback_closure" = "igraph_get_isomorphisms_vf2_callback",
+  "igraph_get_subisomorphisms_vf2_callback_closure" = "igraph_get_subisomorphisms_vf2_callback",
+  "igraph_motifs_randesu_callback_closure" = "igraph_motifs_randesu_callback",
+  "igraph_community_leading_eigenvector_callback_closure" = "igraph_community_leading_eigenvector"
+)
+
+# C functions that a public header exports but the C manual does not document,
+# so the index can never carry an entry for them.
+# Reported with a message rather than a warning:
+# the gap is upstream in the C library's own documentation,
+# and neither this package nor the R package calling it can close it.
+# Checked against the `doxrox-include` directives in igraph/igraph's `doc/`.
+undocumented_c_functions <- c(
+  "igraph_eigen_adjacency",
+  "igraph_eigen_matrix",
+  "igraph_eigen_matrix_symmetric",
+  "igraph_has_attribute_table",
+  "igraph_hrg_sample_many",
+  "igraph_residual_graph",
+  "igraph_reverse_residual_graph",
+  "igraph_solve_lsap",
+  "igraph_transitive_closure_dag",
+  "igraph_weighted_sparsemat"
+)
+
+format_cdocs_single_link <- function(x, base_path) {
+  if (x %in% names(closure_map)) {
+    x <- closure_map[[x]]
+  }
+
+  clinks <- c_links(base_path)
+
+  # we can use igraph_ or not
+  df <- clinks[clinks$method %in% c(x, sprintf("igraph_%s", x)), ]
+  if (nrow(df) == 0) {
+    if (x %in% undocumented_c_functions) {
+      cli::cli_inform("No C entry for {x}, the C manual does not document it.")
+    } else {
+      cli::cli_warn("Can't find C entry for {x}!")
+    }
+    return("")
+  }
+  sprintf("\\href{%s}{\\code{%s()}}", df$url, sub("igraph_", "", df$method))
+}
+
+find_impl <- function(topic, base_path) {
+  treesitter_graph <- treesitter_graph(base_path)
+
+  # Get vertex names properly
+  vertex_names <- V(treesitter_graph)$name
+  vertex <- which(vertex_names == topic)
+
+  # If topic not found, return empty character vector
+  if (length(vertex) == 0) {
+    return(character(0))
+  }
+
+  subcomponent <- names(subcomponent(
+    treesitter_graph,
+    vertex,
+    mode = "out"
+  ))
+  subcomponent[endsWith(subcomponent, "_impl")]
+}
+
+
+# https://blog.r-hub.io/2021/07/30/cache/#function-factory
+treesitter_graph_factory <- function() {
+  cache <- list()
+
+  function(base_path) {
+    if (!is.null(cache[[base_path]])) {
+      return(cache[[base_path]])
+    }
+
+    all_r_scripts <- fs::dir_ls(fs::path(base_path, "R"), glob = "*R")
+    all_r_code <- purrr::map_chr(
+      all_r_scripts,
+      \(x) readLines(x) |> paste(collapse = "\n")
+    ) |>
+      paste(collapse = "\n")
+
+    r_language <- treesitter.r::language()
+    r_parser <- treesitter::parser(language = r_language)
+    tree <- treesitter::parser_parse(r_parser, all_r_code)
+
+    # Query to find all function definitions with their names
+    func_def_query <- treesitter::query(
+      r_language,
+      '(binary_operator
+        lhs: (identifier) @func_name
+        rhs: (function_definition) @func_def
+      )'
+    )
+
+    # Extract all function definitions
+    root_node <- treesitter::tree_root_node(tree)
+    all_matches <- treesitter::query_matches(func_def_query, root_node)[[1]]
+
+    # Extract function names and definition nodes from matches
+    # Each match contains paired func_name and func_def captures
+    func_names <- purrr::map_chr(all_matches, \(m) {
+      treesitter::node_text(m$node[[which(m$name == "func_name")]])
+    })
+    func_def_nodes <- purrr::map(all_matches, \(m) {
+      m$node[[which(m$name == "func_def")]]
+    })
+
+    # Query to find all function calls
+    func_call_query <- treesitter::query(
+      r_language,
+      '(call
+        function: (identifier) @call_name
+      )'
+    )
+
+    # Build the call graph table
+    call_graph_df <- purrr::map2_dfr(
+      func_def_nodes,
+      func_names,
+      \(func_def_node, func_name) {
+        # Query for function calls within this function definition
+        calls <- treesitter::query_captures(func_call_query, func_def_node)
+
+        if (length(calls$node) > 0) {
+          call_names <- purrr::map_chr(calls$node, treesitter::node_text)
+          data.frame(
+            from = func_name,
+            to = call_names,
+            stringsAsFactors = FALSE
+          )
+        } else {
+          data.frame(from = character(), to = character())
+        }
+      }
+    )
+
+    graph <- graph_from_data_frame(call_graph_df)
+    cache[[base_path]] <<- graph
+    graph
+  }
+}
+treesitter_graph <- treesitter_graph_factory()
+
+igraph_c_version_factory <- function() {
+  cache <- list()
+
+  function(base_path) {
+    if (!is.null(cache[[base_path]])) {
+      return(cache[[base_path]])
+    }
+
+    c_lines <- readLines(file.path(
+      base_path,
+      "src",
+      "vendor",
+      "igraph_version.h"
+    ))
+    version_line <- c_lines[startsWith(c_lines, "#define IGRAPH_VERSION ")]
+
+    c_version <- regmatches(
+      version_line,
+      regexec('"([^"]+)"', version_line)
+    )[[1]][2]
+    cache[[base_path]] <<- c_version
+    c_version
+  }
+}
+igraph_c_version <- igraph_c_version_factory()
+
+c_links_factory <- function() {
+  cache <- list()
+
+  function(base_path) {
+    if (!is.null(cache[[base_path]])) {
+      return(cache[[base_path]])
+    }
+
+    igraph_version <- igraph_c_version(base_path)
+
+    local_cache_dir <- file.path(
+      tools::R_user_dir("igraph", "data"),
+      "links",
+      igraph_version
+    )
+    local_cache <- file.path(local_cache_dir, "clinks.csv")
+    if (file.exists(local_cache)) {
+      clinks <- read.csv(local_cache)
+      cache[[base_path]] <<- clinks
+      return(clinks)
+    }
+
+    dir.create(local_cache_dir, recursive = TRUE)
+
+    index_url <- sprintf(
+      "https://igraph.org/c/html/%s/ix01.html",
+      igraph_version
+    )
+    index <- xml2::read_html(index_url)
+
+    entries <- xml2::xml_find_all(index, ".//dt")
+
+    clinks <- purrr::map_df(entries, handle_dt, igraph_version = igraph_version)
+    write.csv(clinks, local_cache, row.names = FALSE)
+
+    cache[[base_path]] <<- clinks
+    clinks
+  }
+}
+c_links <- c_links_factory()
+
+handle_dt <- function(dt, igraph_version) {
+  href <- xml2::xml_attr(xml2::xml_child(dt), "href")
+  url <- sprintf("https://igraph.org/c/html/%s/%s", igraph_version, href)
+  method <- sub(".*#", "", href)
+  tibble::tibble(
+    method = method,
+    url = url
+  )
+}
+
+on_load({
+  vctrs::s3_register(
+    "roxygen2::roclet_process",
+    "roclet_docs_rd",
+    roclet_process.roclet_docs_rd
+  )
+  vctrs::s3_register(
+    "roxygen2::roclet_output",
+    "roclet_docs_rd",
+    roclet_output.roclet_docs_rd
+  )
+})

From 63f3088fd2a523c2f53531e80b7f492284d4c6d8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Tue, 15 Sep 2026 15:38:47 +0200
Subject: [PATCH 2/2] namespace

---
 R/utils-roxygen2.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/utils-roxygen2.R b/R/utils-roxygen2.R
index d798c049a3f..2879c78711a 100644
--- a/R/utils-roxygen2.R
+++ b/R/utils-roxygen2.R
@@ -266,7 +266,7 @@ c_links_factory <- function() {
     )
     local_cache <- file.path(local_cache_dir, "clinks.csv")
     if (file.exists(local_cache)) {
-      clinks <- read.csv(local_cache)
+      clinks <- utils::read.csv(local_cache)
       cache[[base_path]] <<- clinks
       return(clinks)
     }
@@ -282,7 +282,7 @@ c_links_factory <- function() {
     entries <- xml2::xml_find_all(index, ".//dt")
 
     clinks <- purrr::map_df(entries, handle_dt, igraph_version = igraph_version)
-    write.csv(clinks, local_cache, row.names = FALSE)
+    utils::write.csv(clinks, local_cache, row.names = FALSE)
 
     cache[[base_path]] <<- clinks
     clinks