feat: autogenerate remaining simple functions #2551

Copilot · 2026-01-25T15:05:04Z

Enables Stimulus autogeneration for 5 functions previously requiring manual wrappers: igraph_get_eid, igraph_community_voronoi, igraph_subisomorphic_lad, igraph_eigen_matrix, and igraph_eigen_matrix_symmetric.

Changes

New type definitions (tools/stimulus/types-RC.yaml, types-RR.yaml):

EDGE: Single edge index type (mirrors VERTEX pattern with 0→1-based index conversion)
- Validates exactly one edge (not at least one)
EDGE_LENGTHS: Edge length vectors without automatic "weight" attribute lookup
VERTEXSET_LIST: Fixed to properly handle optional parameters
- C code: Conditionally initialize and destroy only when not NULL
- R code: Pass NULL instead of empty list when parameter is NULL

Function configurations (tools/stimulus/functions-R.yaml):

Removed IGNORE flags from all 5 functions
Added DEPS for igraph_get_eid to satisfy vertex parameter dependencies
Removed obsolete comment and PARAMS override for igraph_subisomorphic_lad

Generated code (src/rinterface.c, R/aaa-auto.R):

Updated with new *_impl functions for all 5 functions
Added custom validation for get_eid_impl: exactly one vertex required for from and to parameters
Added custom validation for subisomorphic_lad_impl: domains must be a list or NULL
Fixed critical bugs in subisomorphic_lad_impl:
- C code no longer destroys uninitialized c_domains
- R code properly passes NULL instead of empty list

Test coverage (tests/testthat/test-aaa-auto.R):

Added comprehensive tests for get_eid_impl with functionality checks (edge finding, directed/undirected behavior, parameter validation)
Added enhanced tests for community_voronoi_impl with structure validation (membership length, modularity, generators)
Added signature validation tests for subisomorphic_lad_impl, eigen_matrix_impl, and eigen_matrix_symmetric_impl
Added FIXME comments for functions requiring complex test setup

The generated functions follow existing patterns for parameter validation, argument conversion, and return value handling. All critical bugs identified in code review have been fixed by adapting the Stimulus type system.

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 remaining simple functions</issue_title>
<issue_description>- igraph_get_eid

igraph_community_voronoi

igraph_subisomorphic_lad

igraph_eigen_matrix

igraph_eigen_matrix_symmetric

Don't worry about other functions.</issue_description>

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

Fixes Autogenerate remaining simple functions #2550

💡 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 · 2026-01-25T15:53:34Z

tools/stimulus/types-RR.yaml

+    CALL: '%I% - 1'
+    INCONV: |-
+        %I% <- as_igraph_es(%I1%, %I%)
+        if (length(%I%) == 0) {


Length must be exactly one.

Fixed in f613b2d. Changed validation from length(%I%) == 0 to length(%I%) != 1 for EDGE type.

krlmlr · 2026-01-25T15:56:15Z

tools/stimulus/functions-R.yaml

-        GRAPH graph, OUT GRAPH res, OUT VECTOR_INT vertex_color, OUT VECTOR_INT edge_color
+        GRAPH pattern, GRAPH target, OPTIONAL VERTEXSET_LIST domains,
+        OPTIONAL OUT BOOLEAN iso, OPTIONAL OUT INDEX_VECTOR map,
+        OPTIONAL OUT VECTOR_INT_LIST maps, BOOLEAN induced, INTEGER time_limit


Can we now drop this entirely?

Yes, removed in f613b2d. The cigraph definition already has the correct PARAMS.

krlmlr · 2026-01-25T15:58:21Z

R/aaa-auto.R

+  # Argument checks
+  ensure_igraph(graph)
+  from <- as_igraph_vs(graph, from)
+  if (length(from) == 0) {


Length must be exactly one.

Fixed in f613b2d. Added custom validation in get_eid_impl to check length(from) != 1 and length(to) != 1.

krlmlr · 2026-01-25T15:58:50Z

R/aaa-auto.R

+    R_igraph_subisomorphic_lad,
+    pattern,
+    target,
+    lapply(domains, function(.x) .x - 1),


Argument checks here?

Added in f613b2d. Now validates that domains is either NULL or a list.

krlmlr · 2026-01-25T16:00:02Z

tests/testthat/test-aaa-auto.R

+  local_igraph_options(print.id = FALSE)
+
+  # Just verify the function exists
+  expect_true(is.function(subisomorphic_lad_impl))


Add a few functionality tests or add a FIXME if difficult, here and for the other functions. Review the library source code if unsure.

Added in f613b2d. For get_eid_impl and community_voronoi_impl, added functionality tests. For subisomorphic_lad_impl and eigen_matrix functions, added FIXME comments noting they need complex setup, along with signature validation tests.

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

Copilot

Pull request overview

This PR enables Stimulus autogeneration for 5 functions that previously required manual wrappers by adding new type definitions (EDGE, EDGE_LENGTHS) and removing IGNORE flags from function configurations. However, the generated code contains several critical bugs that must be fixed before merging.

Changes:

Added EDGE and EDGE_LENGTHS type definitions to support single edge index parameters and edge length vectors without automatic "weight" attribute lookup
Configured 5 functions for autogeneration with custom parameter validation where needed
Generated C wrapper functions and R interface code for all 5 functions with tests

Reviewed changes

Copilot reviewed 8 out of 9 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
tools/stimulus/types-RR.yaml	Added EDGE type (single edge index with exact-length validation) and EDGE_LENGTHS type (edge lengths without automatic weight attribute lookup)
tools/stimulus/types-RC.yaml	Added C-side definitions for EDGE and EDGE_LENGTHS types with proper conversion and cleanup logic
tools/stimulus/functions-R.yaml	Removed IGNORE flags and added custom validation for get_eid (single vertex requirement), subisomorphic_lad (domains must be list or NULL)
src/rinterface.c	Generated C wrapper functions for all 5 functions, but contains critical bugs in subisomorphic_lad (unconditional destroy) and eigen_matrix functions (missing parameter)
src/cpp11.cpp	Added function registrations for the 5 new C wrappers
R/aaa-auto.R	Generated R interface functions with parameter validation, but subisomorphic_lad_impl has critical bug with lapply on NULL
tests/testthat/test-aaa-auto.R	Added basic tests with functionality checks for get_eid and community_voronoi, signature validation for others
tests/testthat/_snaps/aaa-auto.md	Added test snapshots for the new functions

Copilot · 2026-01-25T16:22:04Z

src/rinterface.c

+  igraph_vector_int_list_destroy(&c_domains);
+  IGRAPH_FINALLY_CLEAN(1);


Destroying c_domains unconditionally is incorrect because it's only initialized when domains is not NULL (line 17093). This will cause undefined behavior when domains is NULL. The destroy call should be wrapped in a conditional check like if (!Rf_isNull(domains)) to match the initialization pattern.

Suggested change

igraph_vector_int_list_destroy(&c_domains);

IGRAPH_FINALLY_CLEAN(1);

if (!Rf_isNull(domains)) {

igraph_vector_int_list_destroy(&c_domains);

IGRAPH_FINALLY_CLEAN(1);

}

Fixed in 677edc3. Updated VERTEXSET_LIST type in types-RC.yaml to conditionally destroy c_domains only when it was initialized (wrapped in if (!Rf_isNull(domains))). This matches the pattern used in EDGESET_LIST and other optional list types.

Copilot · 2026-01-25T16:22:04Z

R/aaa-auto.R

+    R_igraph_subisomorphic_lad,
+    pattern,
+    target,
+    lapply(domains, function(.x) .x - 1),


When domains is NULL, lapply(domains, function(.x) .x - 1) will return an empty list instead of NULL. This means NULL will never be passed to the C code, which expects NULL to be passed when no domains are specified. The lapply call should be conditional: if (!is.null(domains)) lapply(domains, function(.x) .x - 1) else NULL or wrapped in a conditional block.

Suggested change

lapply(domains, function(.x) .x - 1),

if (!is.null(domains)) lapply(domains, function(.x) .x - 1),

Fixed in 677edc3. Updated VERTEXSET_LIST type in types-RR.yaml to conditionally apply lapply: if (!is.null(%I%)) lapply(%I%, function(.x) .x - 1) else NULL. This ensures NULL is properly passed to C code when domains is not specified.

src/rinterface.c

Run: https://github.com/igraph/rigraph/actions/runs/21335608706

krlmlr · 2026-01-25T16:37:06Z

@copilot: Merge main, resolving conflicts. Address unresolved feedback by adapting Stimulus.

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

Copilot · 2026-01-25T16:47:11Z

@copilot: Merge main, resolving conflicts. Address unresolved feedback by adapting Stimulus.

Done in 677edc3. Merged main branch and fixed the VERTEXSET_LIST type definition in Stimulus to properly handle optional parameters - both C code initialization/destruction and R code NULL passing are now correct.

Run: https://github.com/igraph/rigraph/actions/runs/21337483519

This reverts commit 625f057.

Run: https://github.com/igraph/rigraph/actions/runs/21337792610

Initial plan

be9e0fa

Copilot AI assigned Copilot and krlmlr Jan 25, 2026

Copilot started work on behalf of krlmlr January 25, 2026 15:05 View session

Copilot AI and others added 4 commits January 25, 2026 15:16

Add EDGE type and enable autogeneration for 5 functions

ca0477e

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

Add EDGE_LENGTHS type and tests for autogenerated functions

36d3861

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

Fix tests for autogenerated functions

ba80171

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

Improve comments for EDGE_LENGTHS type based on code review

42b804c

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

Copilot AI changed the title ~~[WIP] Autogenerate remaining simple functions~~ feat: autogenerate remaining simple functions Jan 25, 2026

Copilot AI requested a review from krlmlr January 25, 2026 15:37

Copilot finished work on behalf of krlmlr January 25, 2026 15:37

krlmlr requested changes Jan 25, 2026

View reviewed changes

Copilot started work on behalf of krlmlr January 25, 2026 16:01 View session

Copilot AI and others added 2 commits January 25, 2026 16:11

Address code review feedback: fix validation and improve tests

f613b2d

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

Fix get_eid test expectation for non-existent edge

01bc238

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

Copilot AI requested a review from krlmlr January 25, 2026 16:15

Copilot finished work on behalf of krlmlr January 25, 2026 16:15

krlmlr marked this pull request as ready for review January 25, 2026 16:17

Copilot AI review requested due to automatic review settings January 25, 2026 16:17

Copilot started reviewing on behalf of krlmlr January 25, 2026 16:17 View session

Copilot AI reviewed Jan 25, 2026

View reviewed changes

chore: Auto-update from GitHub Actions

1e9d70b

Run: https://github.com/igraph/rigraph/actions/runs/21335608706

Copilot started work on behalf of krlmlr January 25, 2026 16:37 View session

Copilot AI and others added 2 commits January 25, 2026 16:42

Merge main into copilot/autogenerate-simple-functions

d6e3838

Fix VERTEXSET_LIST type to handle optional parameters correctly

677edc3

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

Copilot finished work on behalf of krlmlr January 25, 2026 16:49

krlmlr added 2 commits January 25, 2026 19:26

Exactly one

51a97ad

Remove redundant else NULL pattern

e9e3f7d

krlmlr and others added 2 commits January 25, 2026 19:31

Check VERTEXSET_LIST

1c285f8

chore: Auto-update from GitHub Actions

bfeb95e

Run: https://github.com/igraph/rigraph/actions/runs/21337483519

krlmlr enabled auto-merge (squash) January 25, 2026 18:45

krlmlr and others added 4 commits January 25, 2026 19:50

Bring back

6c748fb

Unused

0a65c51

Revert "feat: Check that exactly one vertex is passed"

2fd7ea1

This reverts commit 625f057.

chore: Auto-update from GitHub Actions

95a27fc

Run: https://github.com/igraph/rigraph/actions/runs/21337792610

krlmlr approved these changes Jan 25, 2026

View reviewed changes

krlmlr merged commit 42322f9 into main Jan 25, 2026
1 check passed

krlmlr deleted the copilot/autogenerate-simple-functions branch January 25, 2026 20:28

		igraph_vector_int_list_destroy(&c_domains);
		IGRAPH_FINALLY_CLEAN(1);

	lapply(domains, function(.x) .x - 1),
	if (!is.null(domains)) lapply(domains, function(.x) .x - 1),

Uh oh!

feat: autogenerate remaining simple functions #2551

feat: autogenerate remaining simple functions #2551

Uh oh!

Conversation

Copilot AI commented Jan 25, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Changes

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

Uh oh!

krlmlr Jan 25, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 25, 2026

Choose a reason for hiding this comment

Uh oh!

krlmlr Jan 25, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 25, 2026

Choose a reason for hiding this comment

Uh oh!

krlmlr Jan 25, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 25, 2026

Choose a reason for hiding this comment

Uh oh!

krlmlr Jan 25, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 25, 2026

Choose a reason for hiding this comment

Uh oh!

krlmlr Jan 25, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 25, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Reviewed changes

Uh oh!

Copilot AI Jan 25, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 25, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 25, 2026 • edited by krlmlr Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 25, 2026

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

krlmlr commented Jan 25, 2026

Uh oh!

Copilot AI commented Jan 25, 2026

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

Copilot AI commented Jan 25, 2026 •

edited

Loading

Copilot AI Jan 25, 2026 •

edited by krlmlr

Loading