Merge branch 'main' into copilot/autogenerate-callback-functions

Author: krlmlr

.github/copilot-instructions.md

@@ -2,11 +2,33 @@
 
 > **Note**: For general development guidelines, code style conventions, and AI agent instructions, see [`AGENTS.md`](../AGENTS.md) in the repository root.
 
+## Project Overview
+
+igraph/rigraph is an R package for network analysis and graph theory with a C/C++ backend.
+
 ## Common Commands for Copilot Chat
 
 - Load for development: `pkgload::load_all()`
 - Run tests: `testthat::test_local(reporter = "check")`
+- Run tests for a single file: `testthat::test_local(filter = "foo", reporter = "check")`
 - Format code: `air format .`
 - Update documentation: `devtools::document()`
+- Build package: `devtools::build()`
+- Check package: `devtools::check()`
+
+## Key Conventions
+
+- Use `snake_case` for functions and arguments
+- Follow tidyverse style guide
+- Use roxygen2 with Markdown for documentation
+- Run `air format .` before committing
+- Add tests for all new functionality
+- Use explicit package prefixes (e.g., `withr::local_db_connection()`)
+
+## Important Files
+
+- **Do not modify directly**: `src/rinterface.c`, `R/aaa-auto.R` (generated by Stimulus)
+- Update generated files: `make -f Makefile-cigraph src/rinterface.c R/aaa-auto.R`
+- See `tools/README.md` for Stimulus framework guidelines
 
-Refer to `AGENTS.md` for more instructions.
+Refer to `AGENTS.md` for complete instructions.

.github/workflows/copilot-setup-steps.yaml

@@ -6,10 +6,10 @@ on:
   workflow_dispatch:
   push:
     paths:
-      - .github/workflows/copilot-setup-steps.yml
+      - .github/workflows/copilot-setup-steps.yaml
   pull_request:
     paths:
-      - .github/workflows/copilot-setup-steps.yml
+      - .github/workflows/copilot-setup-steps.yaml
 
 jobs:
   # The job MUST be called `copilot-setup-steps` or it will not be picked up by Copilot.

.gitignore

@@ -27,3 +27,4 @@ cran
 /.vscode/launch.json
 /Rplots.pdf
 /_codeql_detected_source_root
+tests/testthat/_problems/

R/assortativity.R

@@ -237,7 +237,8 @@ assortativity_legacy <- function(
 
 #' @param types Vector giving the vertex types. They as assumed to be integer
 #'   numbers, starting with one. Non-integer values are converted to integers
-#'   with [as.integer()].
+#'   with [as.integer()]. Character vectors are converted to integers using
+#'   [as.factor()].
 #' @rdname assortativity
 #' @export
 #' @cdocs igraph_assortativity_nominal
@@ -247,6 +248,11 @@ assortativity_nominal <- function(
   directed = TRUE,
   normalized = TRUE
 ) {
+  # Convert character types to factor then to integer for categorical data
+  if (is.character(types)) {
+    types <- as.integer(as.factor(types))
+  }
+
   assortativity_nominal_impl(
     graph = graph,
     types = types,

R/utils.R

@@ -94,3 +94,23 @@ modify_list <- function(x, y) {
 
   utils::modifyList(x, y)
 }
+
+#' Test function to verify error formatting with file and line information
+#'
+#' @description
+#' This is a test function that throws an error from C code with file and line
+#' information.
+#' The error message should include the source file and line number where the
+#' error occurred.
+#'
+#' @return This function never returns; it always throws an error.
+#' @keywords internal
+#' @noRd
+#' @examples
+#' \dontrun{
+#' # This will throw an error with source location information
+#' test_error_with_source()
+#' }
+test_error_with_source <- function() {
+  .Call(Rx_igraph_test_error_with_source)
+}

man/assortativity.Rd

@@ -602,6 +602,7 @@ extern SEXP Rx_igraph_st_vertex_connectivity(SEXP, SEXP, SEXP);
 extern SEXP Rx_igraph_star(SEXP, SEXP, SEXP);
 extern SEXP Rx_igraph_subcomponent(SEXP, SEXP, SEXP);
 extern SEXP Rx_igraph_subisomorphic_lad(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
+extern SEXP Rx_igraph_test_error_with_source(void);
 extern SEXP Rx_igraph_transitivity_local_undirected_all(SEXP, SEXP);
 extern SEXP Rx_igraph_union(SEXP, SEXP);
 extern SEXP Rx_igraph_vcount(SEXP);
@@ -1200,6 +1201,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"Rx_igraph_star",                                      (DL_FUNC) &Rx_igraph_star,                                       3},
     {"Rx_igraph_subcomponent",                              (DL_FUNC) &Rx_igraph_subcomponent,                               3},
     {"Rx_igraph_subisomorphic_lad",                         (DL_FUNC) &Rx_igraph_subisomorphic_lad,                          7},
+    {"Rx_igraph_test_error_with_source",                    (DL_FUNC) &Rx_igraph_test_error_with_source,                     0},
     {"Rx_igraph_transitivity_local_undirected_all",         (DL_FUNC) &Rx_igraph_transitivity_local_undirected_all,          2},
     {"Rx_igraph_union",                                     (DL_FUNC) &Rx_igraph_union,                                      2},
     {"Rx_igraph_vcount",                                    (DL_FUNC) &Rx_igraph_vcount,                                     1},

man/assortativity.nominal.Rd

@@ -2315,6 +2315,18 @@ static inline const char* maybe_add_punctuation(const char* msg, const char* pun
   return is_punctuated(msg) ? "" : punctuation;
 }
 
+/* Strip vendor/cigraph/src/ prefix from file path. This prefix depends on the
+ * build procedure, namely on the directory that the compiler is invoked from. */
+static inline const char* simplify_file_path(const char *file) {
+  const char prefix[] = "vendor/cigraph/src/";
+  const size_t prefix_len = sizeof(prefix) - 1;
+
+  if (strncmp(file, prefix, prefix_len) == 0) {
+    return file + prefix_len;
+  }
+  return file;
+}
+
 void Rx_igraph_fatal_handler(const char *reason, const char *file, int line) {
 #ifdef IGRAPH_SANITIZER_AVAILABLE
     __sanitizer_print_stack_trace();
@@ -2336,10 +2348,12 @@ void Rx_igraph_error_handler(const char *reason, const char *file,
    * IGRAPH_FINALLY_FREE() can then clean it up. */
 
   if (Rx_igraph_errors_count == 0 || !Rx_igraph_in_r_check) {
+    const char* simplified_path = simplify_file_path(file);
     snprintf(Rx_igraph_error_reason, sizeof(Rx_igraph_error_reason),
-      "At %s:%i : %s%s %s", file, line, reason,
-      maybe_add_punctuation(reason, ","),
-      igraph_strerror(igraph_errno));
+      "%s%s %s\nSource: %s:%i", reason,
+      maybe_add_punctuation(reason, "."),
+      igraph_strerror(igraph_errno),
+      simplified_path, line);
     Rx_igraph_error_reason[sizeof(Rx_igraph_error_reason) - 1] = 0;
 
     // FIXME: This is a hack, we should replace all memory allocations in the
@@ -2356,8 +2370,10 @@ void Rx_igraph_error_handler(const char *reason, const char *file,
 
 void Rx_igraph_warning_handler(const char *reason, const char *file, int line) {
   if (Rx_igraph_warnings_count == 0) {
+    const char* simplified_path = simplify_file_path(file);
     snprintf(Rx_igraph_warning_reason, sizeof(Rx_igraph_warning_reason),
-      "At %s:%i : %s%s", file, line, reason, maybe_add_punctuation(reason, "."));
+      "%s%s\nSource: %s:%i", reason, maybe_add_punctuation(reason, "."),
+      simplified_path, line);
     Rx_igraph_warning_reason[sizeof(Rx_igraph_warning_reason) - 1] = 0;
   }
   Rx_igraph_warnings_count++;

src/cpp11.cpp

@@ -1 +1 @@
-GLUE_C_SOURCES=rcallback.o rinterface.o rinterface_extra.o rrandom.o uuid.o
+GLUE_C_SOURCES=rcallback.o rinterface.o rinterface_extra.o rrandom.o test_error_with_source.o uuid.o