Merge main and update make_tri_lattice() per updated AGENTS.md

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

Author: Copilot

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

@@ -76,7 +76,7 @@ jobs:
           ref: ${{ inputs.ref }}
 
       - name: Update status for rcc
-        if: github.actor != 'github-copilot[bot]'
+        if: github.actor != 'Copilot'
         # FIXME: Wrap into action
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -182,7 +182,7 @@ jobs:
 
       - name: Update status for rcc
         # FIXME: Wrap into action
-        if: always() && (github.actor != 'github-copilot[bot]')
+        if: always() && (github.actor != 'Copilot')
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
@@ -219,12 +219,16 @@ jobs:
 
       - name: Update status for rcc (Copilot)
         # Update status directly when triggered by Copilot or bots, since they can't dispatch workflows
-        if: always() && (github.actor == 'github-copilot[bot]')
+        if: always() && (github.actor == 'Copilot')
         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

@@ -22,4 +22,6 @@ cran
 /rchk
 /src/*.d
 /src/symbols.rds
+/tests/testthat/testthat-problems.rds
 /covr
+/.vscode/launch.json

AGENTS.md

@@ -31,15 +31,16 @@ pak::pak(dependencies = "Config/Needs/build")
 
 - When run on GitHub Actions, assume that R, the package in its current state and all dependencies are installed.
 - Only install new packages when needed for implementing new features or tests.
-- Run `R -q -e 'testthat::test_local(reporter = "check")'` to execute tests as a final step.
+- Run `R -q -e 'devtools::check()'` to execute all checks as a final step.
 
 ### Building and Testing
 
 - 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
@@ -54,21 +55,24 @@ pak::pak(dependencies = "Config/Needs/build")
 - Prefer expressive code over comments where possible
 - Add comments to utility functions that cannot be made immediately obvious
 - Focus comments on explaining the "why" and "how", the "what" should be clear from the code itself
-- Use line breaks after each sentence in multi-sentence comments
+- Use line breaks after each sentence
 
 ### R Code Conventions
 
-- Follow the [tidyverse style guide](https://style.tidyverse.org)
+- 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 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
 
 ### Documentation
 
 - Use roxygen2 with Markdown syntax for all function documentation
+- 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
 - Document internal functions using devtag (work in progress)
 - Link to C documentation using `@cdocs` tag: `#' @cdocs igraph_function_name`
 - Always run `devtools::document()` after updating documentation
@@ -77,6 +81,25 @@ pak::pak(dependencies = "Config/Needs/build")
 
 - Use `max` for maximal (graph theory term: a vertex is maximal if no other vertex dominates it) and `largest` for maximum (the biggest value in a set)
 
+### New functions
+
+All new functions must include:
+
+- Examples
+- Tests
+- 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
+- Add tests for the `_impl` function
+- Name all arguments in all calls to the `_impl` function
+
 ## File Structure and Organization
 
 ### Test Files
@@ -95,9 +118,19 @@ Update them using: `make -f Makefile-cigraph src/rinterface.c R/aaa-auto.R`
 
 See `tools/README.md` for guidelines on code generation using the Stimulus framework.
 
+### Build Artifacts
+
+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
 - For newly created autogenerated functions, always add a test to `test-aaa-auto.R`
 - Test file naming should mirror source file naming
+- Implement both structured and snapshot tests. For the latter, ensure stability by setting a random seed and calling `local_igraph_options(print.id = FALSE)` if graph IDs are involved.
+- When testing error behavior, prefer snapshot tests.
 - Run tests frequently during development and at the end: `testthat::test_local(reporter = "check")`
+- Run `devtools::check()` as a final step to ensure all checks pass.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: igraph
 Title: Network Analysis and Visualization
-Version: 2.2.1.9000
+Version: 2.2.1.9003
 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)
@@ -529,6 +533,7 @@ export(induced_subgraph)
 export(infomap.community)
 export(interconnected.islands.game)
 export(intersection)
+export(invalidate_cache)
 export(is.bipartite)
 export(is.chordal)
 export(is.connected)
@@ -648,6 +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)
@@ -657,6 +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)
@@ -666,6 +673,7 @@ export(make_ring)
 export(make_star)
 export(make_tree)
 export(make_tri_lattice)
+export(make_turan)
 export(make_undirected_graph)
 export(match_vertices)
 export(max_bipartite_match)
@@ -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)
@@ -866,12 +875,14 @@ export(topo_sort)
 export(topological.sort)
 export(traits)
 export(traits_callaway)
+export(transitive_closure)
 export(transitivity)
 export(tree)
 export(tri_lattice)
 export(triad.census)
 export(triad_census)
 export(triangles)
+export(turan)
 export(undirected_graph)
 export(unfold.tree)
 export(unfold_tree)

NEWS.md

@@ -1,5 +1,144 @@
 <!-- NEWS.md is maintained by https://fledge.cynkra.com, contributors should not edit this file -->
 
+# igraph 2.2.1.9003
+
+## Bug fixes
+
+- Fix `alpha_centrality()` crash when `weights` is a custom attribute name (#915, #2403).
+
+## Features
+
+- Add `make_full_multipartite()` and `make_turan()` graph constructors (#1562, #2406).
+
+- Add `count_loops()` to R interface (#1379, #2414).
+
+- Add `make_circulant()` to expose `igraph_circulant()` (#1563, #2407).
+
+- Add `mean_degree()` to R (#1380, #2415).
+
+- `vertices()` errors on duplicate attribute names (#1248, #2430).
+
+- Add `count_reachable()` function to R (#1349, #2412).
+
+## Chore
+
+- Auto-update from GitHub Actions (#2454).
+
+
+# igraph 2.2.1.9002
+
+## Bug fixes
+
+- Use `LC_ALL=C` instead of `LOCALE=C` in `deps.mk` (#2446, #2447).
+
+## Features
+
+- Add autogeneration for all C functions currently in use (#2424, #2442).
+
+## Chore
+
+- Format.
+
+- Ensure args are named.
+
+## Continuous integration
+
+- Fix final status as set by Copilot \[ci skip\].
+
+## Documentation
+
+- More instructions \[ci skip\].
+
+## Refactoring
+
+- Switch from `.Call()` to autogenerated `_impl` functions (#2434, #2443).
+
+## Testing
+
+- Add structured tests alongside snapshot tests for ALL \_impl functions in test-aaa-auto.R (#2448, #2449).
+
+## Uncategorized
+
+- Merge branch 'cran-2.2.1'.
+
+
+# igraph 2.2.1.9001
+
+## Bug fixes
+
+- Fix matrix lists for output.
+
+## Features
+
+- Add `invalidate_cache()` to R interface (#1387, #2416).
+
+- All arguments in calls to `_impl()` functions are named (#2423).
+
+## Chore
+
+- Use `Rx_` prefix for manually generated functions.
+
+- Clarify error testing preference \[ci skip\].
+
+- Ignore \[ci skip\].
+
+- Use `_impl` variants instead of inline `.Call()` for five functions with changed C signatures (#2428, #2429).
+
+- Format \[ci skip\].
+
+- Expand remaining `_impl` aliases (#2422).
+
+- Remove unused `NTIMER` and `NPRINT` macro definitions (#1095, #2405).
+
+- Cleanup.
+
+- Request math notation.
+
+### deps
+
+- Bump jinja2 from 3.1.2 to 3.1.6 in /tools/py-stimulus (#2401).
+
+- Replace `_impl` aliases in `R/flow.R` (#2347, #2379).
+
+- Autogenerated file looks more like as if it was formatted with `air` (#2395).
+
+## Continuous integration
+
+- Run daily vendoring to avoid noise \[ci skip\].
+
+- Snapshots \[ci skip\].
+
+- Use proper actor name \[ci skip\].
+
+- Reduce contention by running big matrices overnight.
+
+- Add workflow to auto-assign to Copilot.
+
+- Run running sanitizer only on cran branches to avoid pipeline contention.
+
+## Documentation
+
+- More instructions \[ci skip\].
+
+- More instructions \[ci skip\].
+
+- More instructions \[ci skip\].
+
+- More instructions \[ci skip\].
+
+- Experimental.
+
+- New code \[ci skip\].
+
+- Add GitHub Copilot instructions and expand AGENTS.md (#2397, #2400).
+
+## Refactoring
+
+- Replace `_impl` aliases with explicit wrapper functions in `R/topology.R` (#2366, #2398).
+
+- Replace \_impl aliases in R/other.R (#2355, #2388).
+
+
 # igraph 2.2.1.9000
 
 ## Chore