From 98357e2072b0d3a28f9aa12c491ba5f348293bab Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 27 Mar 2026 17:13:10 +0000
Subject: [PATCH 1/3] Initial plan


From 8ba0158818660f0141f344547562c0922971fea0 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 27 Mar 2026 17:23:33 +0000
Subject: [PATCH 2/3] fix: make cut_at() handle partial dendrograms from
 cluster_leading_eigen()"

Agent-Logs-Url: https://github.com/igraph/rigraph/sessions/058c68f4-d54e-4cfc-8444-530d274067e5

Co-authored-by: schochastics <17147355+schochastics@users.noreply.github.com>
---
 R/community.R                   | 33 +++++++++++++++++++++++--
 tests/testthat/test-community.R | 43 +++++++++++++++++++++++++++++++++
 2 files changed, 74 insertions(+), 2 deletions(-)

diff --git a/R/community.R b/R/community.R
index 352f534ba11..152efc69ce6 100644
--- a/R/community.R
+++ b/R/community.R
@@ -1241,15 +1241,44 @@ cut_at <- function(communities, no, steps) {
     cli::cli_abort("Please use either {.arg no} or {.arg steps} (but not both)")
   }
 
+  mm <- merges(communities)
+
+  # The leading eigenvector algorithm uses a different merges format:
+  # merges operate on communities rather than vertices, so we need the
+  # dedicated igraph_le_community_to_membership function.
+  if (isTRUE(communities$algorithm == "leading eigenvector")) {
+    n_initial <- max(communities$membership)
+    if (!missing(steps)) {
+      if (steps > nrow(mm)) {
+        cli::cli_warn("Cannot make that many steps.")
+        steps <- nrow(mm)
+      }
+    } else {
+      noc <- n_initial - nrow(mm) # minimum number of communities after all merges
+      if (no > n_initial) {
+        cli::cli_warn("Cannot have that many communities.")
+        no <- n_initial
+      } else if (no < noc) {
+        cli::cli_warn("Cannot have that few communities.")
+        no <- noc
+      }
+      steps <- n_initial - no
+    }
+    res <- le_community_to_membership_impl(
+      merges = mm - 1L,
+      steps = steps,
+      membership = communities$membership - 1L
+    )
+    return(res$membership + 1L)
+  }
+
   if (!missing(steps)) {
-    mm <- merges(communities)
     if (steps > nrow(mm)) {
       cli::cli_warn("Cannot make that many steps.")
       steps <- nrow(mm)
     }
     community.to.membership2(mm, communities$vcount, steps)
   } else {
-    mm <- merges(communities)
     noc <- communities$vcount - nrow(mm) # final number of communities
     if (no < noc) {
       cli::cli_warn("Cannot have that few communities.")
diff --git a/tests/testthat/test-community.R b/tests/testthat/test-community.R
index a5ba5644e72..aa8e3739092 100644
--- a/tests/testthat/test-community.R
+++ b/tests/testthat/test-community.R
@@ -304,6 +304,49 @@ test_that("cluster_leading_eigen is deterministic", {
   }
 })
 
+test_that("cut_at works with cluster_leading_eigen partial dendrograms", {
+  g <- make_full_graph(5) %du% make_full_graph(5) %du% make_full_graph(5)
+  g <- add_edges(g, c(1, 6, 1, 11, 6, 11))
+  lec <- cluster_leading_eigen(g)
+
+  # The algorithm finds 3 communities, with a partial dendrogram (2 merges)
+  expect_equal(max(membership(lec)), 3L)
+  expect_equal(nrow(lec$merges), 2L)
+
+  # cut_at with no= should return the original 3 communities
+  m3 <- cut_at(lec, no = 3)
+  expect_equal(length(unique(m3)), 3L)
+  expect_equal(m3, membership(lec))
+
+  # cut_at with no=2 should merge 2 of the 3 communities
+  m2 <- cut_at(lec, no = 2)
+  expect_equal(length(unique(m2)), 2L)
+
+  # cut_at with no=1 should put all vertices in one community
+  m1 <- cut_at(lec, no = 1)
+  expect_equal(length(unique(m1)), 1L)
+  expect_true(all(m1 == m1[1]))
+
+  # cut_at with steps= should work equivalently
+  expect_equal(cut_at(lec, steps = 0), cut_at(lec, no = 3))
+  expect_equal(cut_at(lec, steps = 1), cut_at(lec, no = 2))
+  expect_equal(cut_at(lec, steps = 2), cut_at(lec, no = 1))
+
+  # Asking for too many communities should warn and clamp
+  expect_warning(
+    m_excess <- cut_at(lec, no = 10),
+    "Cannot have that many communities"
+  )
+  expect_equal(m_excess, membership(lec))
+
+  # Asking for too many steps should warn and clamp
+  expect_warning(
+    m_excess_steps <- cut_at(lec, steps = 10),
+    "Cannot make that many steps"
+  )
+  expect_equal(m_excess_steps, cut_at(lec, no = 1))
+})
+
 test_that("cluster_leiden works", {
   withr::local_seed(42)
 

From 8198b93a76e2107a435a973df50d98314c119fbb Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 27 Mar 2026 17:24:26 +0000
Subject: [PATCH 3/3] fix: rename noc to min_communities in leading eigenvector
 cut_at block

Agent-Logs-Url: https://github.com/igraph/rigraph/sessions/058c68f4-d54e-4cfc-8444-530d274067e5

Co-authored-by: schochastics <17147355+schochastics@users.noreply.github.com>
---
 R/community.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/community.R b/R/community.R
index 152efc69ce6..04ac00f5e0e 100644
--- a/R/community.R
+++ b/R/community.R
@@ -1254,13 +1254,13 @@ cut_at <- function(communities, no, steps) {
         steps <- nrow(mm)
       }
     } else {
-      noc <- n_initial - nrow(mm) # minimum number of communities after all merges
+      min_communities <- n_initial - nrow(mm) # minimum number of communities after all merges
       if (no > n_initial) {
         cli::cli_warn("Cannot have that many communities.")
         no <- n_initial
-      } else if (no < noc) {
+      } else if (no < min_communities) {
         cli::cli_warn("Cannot have that few communities.")
-        no <- noc
+        no <- min_communities
       }
       steps <- n_initial - no
     }