feat: Add GRAPH_PTR_LIST and MATRIX_LIST type support to enable autogeneration of *_many functions by Copilot · Pull Request #2540 · igraph/rigraph

Copilot · 2026-01-24T12:45:01Z

Description

Implements complete two-layer type support (R validation + C conversion) for GRAPH_PTR_LIST and MATRIX_LIST to autogenerate functions operating on multiple graphs simultaneously. Previously ignored due to missing type support.

Changes

Type System - R Layer (types-RR.yaml)

Added GRAPH_PTR_LIST: Validates list of igraph objects with user-friendly error messages
Added MATRIX_LIST: Validates list of matrices, converts to numeric
All arguments are now checked in R before being passed to C

Type System - C Layer (types-RC.yaml)

Added GRAPH_PTR_LIST (wraps igraph_vector_ptr_t)
Implemented bidirectional conversions in rinterface_extra.c:
- Rz_SEXP_to_graph_ptr_list(): R list → C vector_ptr using non-copying conversion to avoid memory leaks
- Ry_igraph_graph_ptr_list_to_SEXP(): C vector_ptr → R list
Uses R_alloc() for graph storage and Rz_SEXP_to_igraph (non-copying) to match existing manual implementation patterns

Autogenerated Functions (4 new)

igraph_disjoint_union_many() - disjoint union of N graphs
igraph_union_many() - union with edge mapping
igraph_intersection_many() - intersection with edge mapping
igraph_layout_merge_dla() - merge layouts via DLA

Documentation

Added "Type Definitions" section to tools/README.md explaining:
- Role of types-RR.yaml (R-level validation)
- Role of types-RC.yaml (C-level conversion)
- How to add new type support

Tests

Added coverage for all 4 functions in test-aaa-auto.R

Example

# Previously required manual implementation, now autogenerated:
graphs <- list(make_ring(3), make_star(4), make_full_graph(2))
result <- disjoint_union_many(graphs)  # Works directly with validation

# Layout merging with coordinate validation:
coords <- list(matrix(c(0,0,1,0,2,0), ncol=2, byrow=TRUE),
               matrix(c(0,1,1,1,2,1), ncol=2, byrow=TRUE))
layout <- layout_merge_dla(graphs[1:2], coords)

Note: Functions with callbacks (7) and SPARSEMAT types (5) remain correctly excluded per requirements. Three functions (igraph_get_eid, igraph_community_voronoi, igraph_subisomorphic_lad) require custom implementations due to API mismatches.

Memory Management

The implementation uses Rz_SEXP_to_igraph (non-copying) rather than Rz_SEXP_to_igraph_copy to avoid memory leaks. The non-copying version only sets pointers to existing R graph objects without allocating new memory, eliminating the need for cleanup of copied graph structures. This approach matches the pattern used in existing manual implementations like Rx_igraph_disjoint_union.

By submitting this pull request, I assign the copyright of my contribution to The igraph development team.

Original prompt

This section details on the original issue you should resolve

<issue_title>Autogenerate all non-callback functions except SPARSEMAT</issue_title>
<issue_description>Needs conversions for a few more types, both in RR and RC. Do not worry about sparse matrices.</issue_description>

Comments on the Issue (you are @copilot in this section)

Fixes Autogenerate all non-callback functions except SPARSEMAT #2531

💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.

Co-authored-by: krlmlr <1741643+krlmlr@users.noreply.github.com>

krlmlr

@copilot: All arguments need a check/conversion in R, need to add corresponding definitions to types-RR.yaml -- also the coords argument. Document this in an appropriate place.

krlmlr · 2026-01-24T17:16:08Z

    # Needs custom handling - GRAPH_PTR_LIST type not properly supported
-    IGNORE: RR, RC
+    # IGNORE: RR, RC


Remove the comments, no longer needed.

Removed obsolete comments from functions-R.yaml for all *_many functions and layout_merge_dla. (commit bfb9caf)

- Added GRAPH_PTR_LIST and MATRIX_LIST to types-RR.yaml with proper argument validation - Ensures all list arguments contain correct object types before passing to C - Removed obsolete comments from functions-R.yaml - Documented type definition system in tools/README.md Co-authored-by: krlmlr <1741643+krlmlr@users.noreply.github.com>

Copilot · 2026-01-24T17:27:13Z

@copilot: All arguments need a check/conversion in R, need to add corresponding definitions to types-RR.yaml -- also the coords argument. Document this in an appropriate place.

Added GRAPH_PTR_LIST and MATRIX_LIST type definitions to types-RR.yaml with proper argument validation. All list arguments now have R-level type checks before being passed to C. Documented the type definition system in tools/README.md. (commit bfb9caf)

…again

Run: https://github.com/igraph/rigraph/actions/runs/21319096358

Copilot

Pull request overview

This PR adds support for GRAPH_PTR_LIST and MATRIX_LIST types to the Stimulus code generation framework, enabling autogeneration of 4 functions that operate on multiple graphs: disjoint_union_many, union_many, intersection_many, and layout_merge_dla.

Changes:

Added two-layer type validation system: R-level validation in types-RR.yaml and C-level conversion in types-RC.yaml
Implemented C conversion functions in rinterface_extra.c for bidirectional GRAPH_PTR_LIST transformations
Removed IGNORE directives from functions-R.yaml to enable autogeneration of 4 previously manual functions
Added comprehensive tests for all 4 newly autogenerated functions

Reviewed changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tools/stimulus/types-RR.yaml	Added R-level validation for GRAPH_PTR_LIST and MATRIX_LIST with user-friendly error messages
tools/stimulus/types-RC.yaml	Added C-level type definitions for GRAPH_PTR_LIST with conversion infrastructure
src/rinterface_extra.c	Implemented bidirectional conversion functions between R lists and igraph_vector_ptr_t
src/rinterface.h	Added function declarations for new conversion functions
src/rinterface.c	Autogenerated C wrapper functions for 4 *_many operations
R/aaa-auto.R	Autogenerated R wrapper functions with argument validation
tools/stimulus/functions-R.yaml	Removed IGNORE directives to enable autogeneration
tools/README.md	Added documentation explaining the two-layer type system
tests/testthat/test-aaa-auto.R	Added basic tests for all 4 newly autogenerated functions

Copilot · 2026-01-24T17:55:55Z

+            IGRAPH_FINALLY(igraph_vector_ptr_destroy, &%C%);
+        OUT: |-
+            IGRAPH_R_CHECK(igraph_vector_ptr_init(&%C%, 0));
+            IGRAPH_FINALLY(igraph_vector_ptr_destroy, &%C%);
+    OUTCONV:
+        IN: |-
+            igraph_vector_ptr_destroy(&%C%);
+            IGRAPH_FINALLY_CLEAN(1);
+        OUT: |-
+            PROTECT(%I%=Ry_igraph_graph_ptr_list_to_SEXP(&%C%));
+            igraph_vector_ptr_destroy(&%C%);


Missing cleanup registration for copied graphs. The GRAPH_PTR_LIST type definition only registers cleanup for the vector_ptr container itself, but not for the individual graph copies created by Rz_SEXP_to_igraph_copy. This will cause memory leaks when errors occur after graph conversion but before normal cleanup in the calling function.

The type definition should either:

Use Rz_SEXP_to_igraph (non-copying) instead of Rz_SEXP_to_igraph_copy, matching the pattern in existing manual implementations like Rx_igraph_disjoint_union in rinterface_extra.c:4981, or

Add proper cleanup handlers that destroy all copied graphs when errors occur.

Suggested change

IGRAPH_FINALLY(igraph_vector_ptr_destroy, &%C%);

OUT: |-

IGRAPH_R_CHECK(igraph_vector_ptr_init(&%C%, 0));

IGRAPH_FINALLY(igraph_vector_ptr_destroy, &%C%);

OUTCONV:

IN: |-

igraph_vector_ptr_destroy(&%C%);

IGRAPH_FINALLY_CLEAN(1);

OUT: |-

PROTECT(%I%=Ry_igraph_graph_ptr_list_to_SEXP(&%C%));

igraph_vector_ptr_destroy(&%C%);

IGRAPH_FINALLY(igraph_vector_ptr_destroy_all, &%C%);

OUT: |-

IGRAPH_R_CHECK(igraph_vector_ptr_init(&%C%, 0));

IGRAPH_FINALLY(igraph_vector_ptr_destroy_all, &%C%);

OUTCONV:

IN: |-

igraph_vector_ptr_destroy_all(&%C%);

IGRAPH_FINALLY_CLEAN(1);

OUT: |-

PROTECT(%I%=Ry_igraph_graph_ptr_list_to_SEXP(&%C%));

igraph_vector_ptr_destroy_all(&%C%);

Fixed by changing to use Rz_SEXP_to_igraph (non-copying) instead of Rz_SEXP_to_igraph_copy. The non-copying version doesn't allocate new graph structures, eliminating the memory leak. This matches the pattern in existing manual implementations like Rx_igraph_disjoint_union. (commit 089ef94)

Copilot · 2026-01-24T17:55:55Z

+/* Convert SEXP list of graphs to igraph_vector_ptr_t */
+igraph_error_t Rz_SEXP_to_graph_ptr_list(SEXP graphlist, igraph_vector_ptr_t *ptr, 
+                                          igraph_t **storage) {
+  igraph_integer_t n = Rf_xlength(graphlist);
+
+  /* Allocate storage for the graphs */
+  *storage = (igraph_t*) R_alloc(n, sizeof(igraph_t));
+
+  /* Initialize the vector_ptr */
+  IGRAPH_R_CHECK(igraph_vector_ptr_init(ptr, n));
+
+  /* Convert each graph */
+  for (igraph_integer_t i = 0; i < n; i++) {
+    SEXP item = VECTOR_ELT(graphlist, i);
+    IGRAPH_R_CHECK(Rz_SEXP_to_igraph_copy(item, &(*storage)[i]));
+    VECTOR(*ptr)[i] = &(*storage)[i];
+  }
+
+  return IGRAPH_SUCCESS;
+}


Memory leak: The graphs copied by Rz_SEXP_to_igraph_copy at line 3072 are never destroyed. When igraph_copy is called inside Rz_SEXP_to_igraph_copy, it allocates internal graph structures that must be explicitly freed with igraph_destroy. However, the current implementation only registers cleanup for igraph_vector_ptr_destroy (which doesn't free the graph contents), and the c_graphs_storage array is allocated with R_alloc (which only frees the array itself, not the graph structures it contains).

The existing manual implementations (e.g., Rx_igraph_disjoint_union at line 4981) correctly use Rz_SEXP_to_igraph without copy, which only references existing graph structures and requires no cleanup. Consider changing this function to use Rz_SEXP_to_igraph instead of Rz_SEXP_to_igraph_copy, or add a loop to call igraph_destroy on each graph in the storage array when errors occur or after successful completion.

Fixed by using Rz_SEXP_to_igraph (non-copying) instead of Rz_SEXP_to_igraph_copy. This avoids the memory leak since no new graph structures are allocated that would need cleanup. (commit 089ef94)

krlmlr

@copilot: The review remarks seem to be consistent with the test failures. Review and fix.

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-aaa-auto.R:11139:3'): disjoint_union_many_impl basic ───────────
Error in `disjoint_union_many_impl(graphs = list(g1, g2, g3))`: object 'R_igraph_disjoint_union_many' not found
Backtrace:
    ▆
 1. └─igraph:::disjoint_union_many_impl(graphs = list(g1, g2, g3))
── Error ('test-aaa-auto.R:11158:3'): union_many_impl basic ────────────────────
Error in `union_many_impl(graphs = list(g1, g2, g3))`: object 'R_igraph_union_many' not found
Backtrace:
    ▆
 1. └─igraph:::union_many_impl(graphs = list(g1, g2, g3))
── Error ('test-aaa-auto.R:11177:3'): intersection_many_impl basic ─────────────
Error in `intersection_many_impl(graphs = list(g1, g2, g3))`: object 'R_igraph_intersection_many' not found
Backtrace:
    ▆
 1. └─igraph:::intersection_many_impl(graphs = list(g1, g2, g3))
── Error ('test-aaa-auto.R:11197:3'): layout_merge_dla_impl basic ──────────────
Error in `layout_merge_dla_impl(graphs = list(g1, g2), coords = list(coords1, coords2))`: object 'R_igraph_layout_merge_dla' not found
Backtrace:
    ▆
 1. └─igraph:::layout_merge_dla_impl(...)

[ FAIL 4 | WARN 0 | SKIP 4 | PASS 7512 ]

Changed Rz_SEXP_to_graph_ptr_list to use Rz_SEXP_to_igraph (non-copying) instead of Rz_SEXP_to_igraph_copy. The non-copying version just sets pointers to existing R graph objects, avoiding memory leaks that would occur with copied graphs. This matches the pattern used in existing manual implementations like Rx_igraph_disjoint_union. Co-authored-by: krlmlr <1741643+krlmlr@users.noreply.github.com>

Copilot · 2026-01-24T18:14:59Z

@copilot: The review remarks seem to be consistent with the test failures. Review and fix.

...

Fixed the memory leak by changing to non-copying graph conversion (Rz_SEXP_to_igraph). The test failures were due to missing regeneration of src/rinterface.c after the last commit - this has been resolved and the package now builds and tests successfully. (commit 089ef94)

…again

…non-callback-functions-again

Run: https://github.com/igraph/rigraph/actions/runs/21319867721

Initial plan

354ef6d

Copilot AI assigned Copilot and krlmlr Jan 24, 2026

Copilot started work on behalf of krlmlr January 24, 2026 12:45 View session

Copilot AI and others added 5 commits January 24, 2026 12:59

Enable igraph_community_voronoi autogeneration

22bf108

Co-authored-by: krlmlr <1741643+krlmlr@users.noreply.github.com>

Enable igraph_subisomorphic_lad and igraph_get_eid autogeneration

a2e5838

Co-authored-by: krlmlr <1741643+krlmlr@users.noreply.github.com>

Add GRAPH_PTR_LIST support and enable *_many functions

54eb3d3

Co-authored-by: krlmlr <1741643+krlmlr@users.noreply.github.com>

Add tests for newly autogenerated *_many functions

f188bdb

Co-authored-by: krlmlr <1741643+krlmlr@users.noreply.github.com>

fix: Add error handling in Rz_SEXP_to_graph_ptr_list

008cf3d

Co-authored-by: krlmlr <1741643+krlmlr@users.noreply.github.com>

Copilot AI changed the title ~~[WIP] Autogenerate all non-callback functions except SPARSEMAT~~ feat: Add GRAPH_PTR_LIST type support to enable autogeneration of *_many functions Jan 24, 2026

Copilot AI requested a review from krlmlr January 24, 2026 13:11

Copilot finished work on behalf of krlmlr January 24, 2026 13:11

krlmlr requested changes Jan 24, 2026

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Copilot AI changed the title ~~feat: Add GRAPH_PTR_LIST type support to enable autogeneration of *_many functions~~ feat: Add GRAPH_PTR_LIST and MATRIX_LIST type support to enable autogeneration of *_many functions Jan 24, 2026

Copilot AI requested a review from krlmlr January 24, 2026 17:28

Copilot finished work on behalf of krlmlr January 24, 2026 17:28

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

c8e00eb

…again

krlmlr marked this pull request as ready for review January 24, 2026 17:47

Copilot AI review requested due to automatic review settings January 24, 2026 17:47

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chore: Auto-update from GitHub Actions

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Run: https://github.com/igraph/rigraph/actions/runs/21319096358

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

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krlmlr and others added 3 commits January 24, 2026 19:48

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chore: Auto-update from GitHub Actions

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Run: https://github.com/igraph/rigraph/actions/runs/21319867721

krlmlr merged commit afca211 into main Jan 24, 2026
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feat: Add GRAPH_PTR_LIST and MATRIX_LIST type support to enable autogeneration of *_many functions#2540

feat: Add GRAPH_PTR_LIST and MATRIX_LIST type support to enable autogeneration of *_many functions#2540
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