Merge main, resolve conflicts, remove spurious .dd system headers

Author: Copilot

.github/workflows/R-CMD-check.yaml

@@ -223,8 +223,12 @@ jobs:
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          # Check status of this workflow
-          state="pending"
+          # Set status to success if job succeeded, failure otherwise
+          if [ "${{ job.status }}" == "success" ]; then
+            state="success"
+          else
+            state="failure"
+          fi
           sha=${{ inputs.ref }}
           if [ -z "${sha}" ]; then
             sha=${{ github.sha }}

.github/workflows/vendor.yaml

@@ -7,7 +7,7 @@ on:
       - "vendor-one.sh"
   workflow_dispatch:
   schedule:
-    - cron: "0 * * * *"
+    - cron: "* 0 * * *"
 
 concurrency:
   group: ${{ github.workflow }}

.gitignore

@@ -25,3 +25,4 @@ cran
 /tests/testthat/testthat-problems.rds
 /covr
 /.vscode/launch.json
+/_codeql_detected_source_root

AGENTS.md

@@ -37,9 +37,10 @@ pak::pak(dependencies = "Config/Needs/build")
 
 - Load package for development: `pkgload::load_all()`
 - Run tests: `testthat::test_local(reporter = "check")`
+- Run tests for a single file `test-foo.R`: `testthat::test_local(filter = "foo", reporter = "check")`
 - Build package: `devtools::build()`
 - Check package: `devtools::check()`
-- Update documentation: `devtools::document()`
+- Update `.Rd` documentation: `devtools::document()`
 - Format code: `air format .`
 
 ## Code Style and Documentation
@@ -48,6 +49,7 @@ pak::pak(dependencies = "Config/Needs/build")
 
 - IMPORTANT: PR titles end up in `NEWS.md` grouped by conventional commit label. PRs and commits use the conventional commit style with backticks for code references such as `function_call()`
 - PRs are generally squashed, a clean history within a PR is not necessary
+- Before resuming work on a PR, always merge the current base branch (typically `main`)
 
 ### Comment Style
 
@@ -59,15 +61,18 @@ pak::pak(dependencies = "Config/Needs/build")
 ### R Code Conventions
 
 - Follow the [tidyverse style guide](https://style.tidyverse.org) and the [tidyverse design guide](https://design.tidyverse.org)
-- Use `snake_case` for new functions
+- Use `snake_case` for new functions and all arguments
 - Use explicit package prefixes (e.g., `withr::local_db_connection()`) for clarity
 - Maintain consistent indentation (2 spaces) and spacing patterns
 - Use meaningful variable names that reflect context
 - Run `air format .` before committing changes to ensure consistent formatting
+- Never change deprecated functions
+- Avoid `.Call()` outside `*_impl()` in `aaa-auto.R`
 
 ### Documentation
 
 - Use roxygen2 with Markdown syntax for all function documentation
+- Use explicit `@description` and `@details` sections, aim for a complete description and move only excess details to `@details`
 - Use math notation for formulas: `\eqn{...}` for inline, `\deqn{...}` for display equations
 - Keep each sentence on its own line in roxygen2 comments for better readability
 - Document all arguments and return values
@@ -88,8 +93,16 @@ All new functions must include:
 - Proper documentation, including arguments and return values
 - A concept so that it exists in the pkgdown reference index
 - An "experimental" badge via `r lifecycle::badge("experimental")`
+- All arguments in `snake_case`, with documentation and suitable defaults
+- An ellipsis guarded with `check_dots_empty()` separating mandatory and optional arguments
+- Argument validation using built-in `check_*()` functions or `igraph_arg_match()`
 
-If exporting a new function from the C library, ensure it is autogenerated and add tests for the `_impl` function.
+If exporting a new function from the C library:
+
+- Ensure it is autogenerated
+- Add tests for the `_impl` function
+- Name all arguments in all calls to the `_impl` function
+- For graph constructors, prefer `GATTR` and `GATTR-PARAM` in Stimulus over manually assigning attributes
 
 ## File Structure and Organization
 
@@ -111,9 +124,11 @@ See `tools/README.md` for guidelines on code generation using the Stimulus frame
 
 ### Build Artifacts
 
-Do not commit: `*.dd`, `*.d`, `*.o`, `*.so` files in `src/`, and `tests/testthat/testthat-problems.rds`.
+Do not commit: `*.d`, `*.o`, `*.so` files in `src/`, and `tests/testthat/testthat-problems.rds`.
 These are build artifacts that are regenerated automatically (see `src/README.md` for details on dependency tracking).
 
+Careful with changes to `*.dd`, keep system headers out, only expect changes if new source files are added or their local dependencies change.
+
 ## Testing
 
 - Add test cases for all new functionality

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: igraph
 Title: Network Analysis and Visualization
-Version: 2.2.1.9000
+Version: 2.2.1.9006
 Authors@R: c(
     person("Gábor", "Csárdi", , "csardi.gabor@gmail.com", role = "aut",
            comment = c(ORCID = "0000-0001-7098-9676")),

NAMESPACE

@@ -222,6 +222,7 @@ export(centralize)
 export(centralize.scores)
 export(chordal_ring)
 export(chung_lu)
+export(circulant)
 export(cit_cit_types)
 export(cit_types)
 export(cited.type.game)
@@ -272,9 +273,11 @@ export(count.multiple)
 export(count_automorphisms)
 export(count_components)
 export(count_isomorphisms)
+export(count_loops)
 export(count_max_cliques)
 export(count_motifs)
 export(count_multiple)
+export(count_reachable)
 export(count_subgraph_isomorphisms)
 export(count_triangles)
 export(create.communities)
@@ -366,6 +369,7 @@ export(from_prufer)
 export(full_bipartite_graph)
 export(full_citation_graph)
 export(full_graph)
+export(full_multipartite)
 export(get.adjacency)
 export(get.adjedgelist)
 export(get.adjlist)
@@ -649,6 +653,7 @@ export(local_scan)
 export(make_)
 export(make_bipartite_graph)
 export(make_chordal_ring)
+export(make_circulant)
 export(make_clusters)
 export(make_de_bruijn_graph)
 export(make_directed_graph)
@@ -658,6 +663,7 @@ export(make_from_prufer)
 export(make_full_bipartite_graph)
 export(make_full_citation_graph)
 export(make_full_graph)
+export(make_full_multipartite)
 export(make_graph)
 export(make_kautz_graph)
 export(make_lattice)
@@ -666,7 +672,9 @@ export(make_neighborhood_graph)
 export(make_ring)
 export(make_star)
 export(make_tree)
+export(make_turan)
 export(make_undirected_graph)
+export(make_wheel)
 export(match_vertices)
 export(max_bipartite_match)
 export(max_cardinality)
@@ -682,6 +690,7 @@ export(maximal.independent.vertex.sets)
 export(maximal_ivs)
 export(maximum.bipartite.matching)
 export(maximum.cardinality.search)
+export(mean_degree)
 export(mean_distance)
 export(membership)
 export(merge_coords)
@@ -866,11 +875,13 @@ export(topo_sort)
 export(topological.sort)
 export(traits)
 export(traits_callaway)
+export(transitive_closure)
 export(transitivity)
 export(tree)
 export(triad.census)
 export(triad_census)
 export(triangles)
+export(turan)
 export(undirected_graph)
 export(unfold.tree)
 export(unfold_tree)
@@ -892,6 +903,7 @@ export(walktrap.community)
 export(watts.strogatz.game)
 export(weighted_clique_num)
 export(weighted_cliques)
+export(wheel)
 export(which_loop)
 export(which_multiple)
 export(which_mutual)