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Resolve the last input-contract and plotting inconsistencies - #5
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Oct 3, 2026
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- Fix five runtime defects and add a testthat suite
- Prepare DESCRIPTION, LICENSE and .Rbuildignore for CRAN
- Make all examples executable
- Replace deprecated ggplot2 and igraph calls
- Extract shared graph validator and collapse duplicate diffusion kernel
- Add release infrastructure and fix documentation typos
- Do not claim untested platforms in cran-comments.md
- Adopt the .9000 development-version convention
- Stop setting a future plan inside network_diffusion_with_pvalues()
- Make the plot return slot uniform across the package
- Fix silently wrong participation coefficients in calculate_roles()
- Fix NaN AUC in robustness_analysis() and audit the surrounding pattern
- Resolve the last input-contract and plotting inconsistencies
Two small items, both long-standing. calculate_roles() and layout_horizontal_tree() were the only exports not implementing the data.frame branch of the input preamble: they errored on an edge list with igraph's internal "Must provide a graph object" rather than netkit's own message. Both now route through as_netkit_graph() like the other twelve, so the flexible-input convention holds across the whole public API. calculate_roles() passes backfill_names = TRUE because it keys results by vertex name. Both @PARAM blocks updated. highlight_nodes() set frame.color to NA for every vertex whenever "outline" was not among the requested methods, which made plot.igraph warn "vertex attribute frame.color contains NAs. Replacing with default value black" on every such call. Note this fired for method = "label" and method = "fill", not for "outline" -- the opposite of what the earlier note in CLAUDE.md claimed. plot_Net() already falls back to the fill colour when given no frame.color, which renders an invisible frame, so the attribute is now simply left unset (and any stale one deleted) instead of being set to NA. Test-suite warnings go from 5 to 1. The remaining one is "package 'future' was built under R version 4.4.3", an artifact of the local R installation rather than anything in netkit. Getting there also meant asserting the warnings that are deliberate rather than leaving them as ambient noise in the summary: assign_attributes() announcing an overwrite, and the pair raised on the spinglass path (find_modules() falling back to the largest connected component, and calculate_roles() reporting the resulting partial coverage). Tests go from 411 to 425. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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