refactor: snake_case attr-comb options & arguments, soft-deprecate dotted names by schochastics · Pull Request #2742 · igraph/rigraph

schochastics · 2026-07-08T19:52:13Z

Split out from #2676 per review feedback ("I'd like to review the par code in a separate PR"). #2676 kept the original dotted option/argument names; this PR carries the naming refactor on its own so it can be reviewed in isolation.

What this does

igraph options: rename vertex.attr.comb → vertex_attr_combine, edge.attr.comb → edge_attr_combine, and the new graph.attr.comb → graph_attr_combine. Reading/setting the old dotted keys still works via back-compatible aliasing in igraph_opt() / igraph_options(), emitting a single lifecycle::deprecate_soft() warning (R/par.R).
Function arguments: simplify(), as_undirected() and contract() gain snake_case edge_attr_combine / vertex_attr_combine arguments via the argument-migration infrastructure (registry entries in tools/migrations/attr-comb.R, spliced by Rscript tools/generate-migrations.R; schema in tools/migrations/README.md); the dotted names keep working and soft-deprecate.
Graph operators: union() / intersection() / compose() / disjoint_union() use the snake_case *_combine argument names.
Updates the stimulus codegen defaults (types-RR.yaml), regenerated *_impl defaults, and the affected tests/snapshots.
Points the stale tools/migrations.R schema references in sibling registry files and helper comments at tools/migrations/README.md, where the schema documentation lives since the registry split (refactor(migrations): split the registry into per-topic files #2779).

Base branch

#2676 has merged, so this PR is based on main and rebased into a single commit on top of it; the attr-comb migration entries live in their own registry file tools/migrations/attr-comb.R so that the open per-topic migration PRs can append to conversion.R, community.R, etc. without conflicting here.

github-actions · 2026-07-08T20:07:12Z

This is how benchmark results would change (along with a 95% confidence interval in relative change) if 1453158 is merged into feat-attrib_comb:

✔️as_adjacency_matrix: 706ms -> 701ms [-2.32%, +0.95%]
✔️as_biadjacency_matrix: 734ms -> 736ms [-1.27%, +1.75%]
✔️as_data_frame_both: 1.48ms -> 1.56ms [-8.29%, +19.78%]
✔️as_long_data_frame: 3.85ms -> 3.91ms [-1.87%, +5.16%]
✔️es_attr_filter: 2.84ms -> 2.88ms [-1.61%, +4.71%]
✔️graph_from_adjacency_matrix: 147ms -> 148ms [-1.36%, +2.48%]
✔️graph_from_data_frame: 3.38ms -> 3.44ms [-1.16%, +4.6%]
✔️vs_attr_filter: 1.54ms -> 1.56ms [-3.55%, +5.83%]
✔️vs_by_name: 983µs -> 983µs [-3.85%, +3.81%]
Further explanation regarding interpretation and methodology can be found in the documentation.

github-actions · 2026-07-15T19:26:09Z

This is how benchmark results would change (along with a 95% confidence interval in relative change) if 2f878f3 is merged into main:

✔️as_adjacency_matrix: 924ms -> 934ms [-1.4%, +3.52%]
✔️as_biadjacency_matrix: 899ms -> 899ms [-1.57%, +1.56%]
✔️as_data_frame_both: 1.68ms -> 1.67ms [-3.86%, +2.57%]
✔️as_long_data_frame: 4.38ms -> 4.22ms [-13.07%, +5.49%]
✔️es_attr_filter: 3.16ms -> 3.09ms [-5.92%, +1.93%]
✔️graph_from_adjacency_matrix: 164ms -> 168ms [-1.87%, +6.71%]
❗🐌graph_from_data_frame: 3.63ms -> 3.77ms [+1.29%, +6.67%]
✔️vs_attr_filter: 1.84ms -> 1.81ms [-7.05%, +3.86%]
✔️vs_by_name: 1.11ms -> 1.11ms [-4.04%, +3.9%]
Further explanation regarding interpretation and methodology can be found in the documentation.

github-actions · 2026-07-26T17:24:23Z

This is how benchmark results would change (along with a 95% confidence interval in relative change) if ba22989 is merged into main:

✔️as_adjacency_matrix: 760ms -> 758ms [-0.87%, +0.2%]
✔️as_biadjacency_matrix: 742ms -> 740ms [-0.98%, +0.45%]
✔️as_data_frame_both: 1.46ms -> 1.47ms [-1.02%, +1.2%]
✔️as_long_data_frame: 3.87ms -> 3.87ms [-0.66%, +1.04%]
✔️es_attr_filter: 2.77ms -> 2.75ms [-2.88%, +1.57%]
✔️graph_from_adjacency_matrix: 118ms -> 117ms [-1.93%, +1.58%]
❗🐌graph_from_data_frame: 3.32ms -> 3.38ms [+1.01%, +2.53%]
✔️vs_attr_filter: 1.5ms -> 1.5ms [-1.86%, +0.59%]
✔️vs_by_name: 1ms -> 987µs [-4.57%, +1.83%]
Further explanation regarding interpretation and methodology can be found in the documentation.

…tted names Rename the attribute-combination options and arguments to snake_case: `edge.attr.comb` -> `edge_attr_combine` and `vertex.attr.comb` -> `vertex_attr_combine`, both as igraph options and as arguments to `simplify()`, `as_undirected()`, and `contract()`. The dotted argument names keep working behind `...` under a single soft-deprecation, via generated ARG_HANDLE blocks driven by the new tools/migrations/attr-comb.R registry file. Dotted option names are soft-deprecated with a warning shim. Also point the stale schema references in sibling registry files and helper comments at tools/migrations/README.md, where the schema documentation lives since the registry was split into per-topic files. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016M32izVHZPfxAqemAe4BrX

Resolve the R/par.R conflict by keeping main's migrated igraph_opt(x, ..., default = NULL) signature and generated ARG_HANDLE block, followed by this branch's dotted-name aliasing (igraph_normalize_par_name()). Declare the compose() dotted -> snake_case argument rename in tools/migrations/operators.R so the regenerated block recovers graph.attr.comb/vertex.attr.comb/edge.attr.comb into the new *_combine arguments; regenerated with tools/generate-migrations.R (idempotent on the second run) and formatted with air. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016M32izVHZPfxAqemAe4BrX

Run: https://github.com/igraph/rigraph/actions/runs/30298235003

github-actions · 2026-07-27T19:40:07Z

This is how benchmark results would change (along with a 95% confidence interval in relative change) if c3cf816 is merged into main:

✔️as_adjacency_matrix: 753ms -> 753ms [-1.42%, +1.22%]
✔️as_biadjacency_matrix: 723ms -> 724ms [-0.92%, +1.07%]
✔️as_data_frame_both: 1.54ms -> 1.53ms [-2.27%, +0.28%]
✔️as_long_data_frame: 3.85ms -> 3.85ms [-0.94%, +0.93%]
✔️es_attr_filter: 2.81ms -> 2.8ms [-1.78%, +1.06%]
✔️graph_from_adjacency_matrix: 143ms -> 142ms [-1.65%, +1.25%]
❗🐌graph_from_data_frame: 3.44ms -> 3.5ms [+0.51%, +3.2%]
✔️vs_attr_filter: 1.52ms -> 1.51ms [-2.31%, +1.06%]
✔️vs_by_name: 1ms -> 988µs [-3.25%, +0.42%]
Further explanation regarding interpretation and methodology can be found in the documentation.

krlmlr

Thanks! Almost good to merge. The one snapshot flagged could be just a symptom of a pattern across the codebase.

krlmlr · 2026-09-03T09:33:51Z

Needs conflict resolution.

Resolve the conflicts against the migration infrastructure that moved under this branch while it was open: - #2812 removed the `migrate_recover_args()` runtime helper, so the ARG_HANDLE blocks are now self-contained. Accept the deletion of R/migrate-args.R and regenerate all 231 blocks. - #2784 requires migrated (`new`) defaults to be constant expressions. Express the attr-comb defaults as `NULL` in tools/migrations/attr-comb.R and tools/migrations/operators.R and resolve them in the bodies, as main already does for the dotted names. - main migrated `simplify()`, `as_undirected()`, `contract()` and `compose()` in the meantime; re-apply the snake_case rename on top of main's versions rather than the pre-migration ones. Also address the review feedback on the tests/testthat/_snaps/conversion.md snapshot, where `as.undirected()` emitted two deprecations the caller had not triggered: - The deprecated wrappers `as.undirected()` and `contract.vertices()` read the dotted igraph option and forwarded the dotted argument name, tripping both the option alias and the argument migration on their own behalf. Keep their public dotted arguments and read/forward the canonical names. - `igraph_opt()` / `igraph_options()` never actually emitted the option alias deprecation: `deprecate_soft()` takes its `user_env` from `caller_env(2)`, which resolved to a frame inside igraph and marked every use as indirect. Thread the real caller down to `igraph_normalize_par_name()`. - `graph.attr.comb` was missing from `.igraph.pars.aliases`, so reading the option under its old name returned NULL instead of the renamed value. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

Run: https://github.com/igraph/rigraph/actions/runs/33753104238

github-actions · 2026-09-03T12:18:47Z

This is how benchmark results would change (along with a 95% confidence interval in relative change) if ec159bd is merged into main:

✔️as_adjacency_matrix: 718ms -> 708ms [-3.86%, +1.13%]
✔️as_biadjacency_matrix: 726ms -> 726ms [-2.2%, +2.2%]
✔️as_data_frame_both: 1.36ms -> 1.36ms [-1.36%, +1.51%]
✔️as_long_data_frame: 3.25ms -> 3.26ms [-0.72%, +1.84%]
❗🐌es_attr_filter: 2.44ms -> 2.52ms [+0.05%, +6.8%]
✔️graph_from_adjacency_matrix: 157ms -> 155ms [-3.11%, +0.93%]
❗🐌graph_from_data_frame: 3.08ms -> 3.15ms [+0.65%, +3.53%]
✔️vs_attr_filter: 1.49ms -> 1.42ms [-11.47%, +2.3%]
✔️vs_by_name: 941µs -> 960µs [-1.94%, +6.16%]
Further explanation regarding interpretation and methodology can be found in the documentation.

Base automatically changed from feat-attrib_comb to main July 9, 2026 08:42

schochastics force-pushed the par-attr-comb-options branch from 1453158 to 2f878f3 Compare July 15, 2026 19:10

schochastics added the hackathon-topic 📆 label Jul 15, 2026

This was referenced Jul 26, 2026

docs: zoning rules for arguments around the ellipsis #2757

Merged

refactor(migrations): split the registry into per-topic files #2779

Merged

krlmlr force-pushed the par-attr-comb-options branch from ba22989 to c5de7bb Compare July 26, 2026 19:29

krlmlr mentioned this pull request Jul 26, 2026

Comprehensive plan: argument renames for 3.0.0 #2788

Open

12 tasks

claude and others added 2 commits July 27, 2026 19:26

chore: Auto-update from GitHub Actions

741f1f0

Run: https://github.com/igraph/rigraph/actions/runs/30298235003

krlmlr reviewed Jul 28, 2026

View reviewed changes

Comment thread tests/testthat/_snaps/conversion.md Outdated

krlmlr removed the hackathon-topic 📆 label Sep 3, 2026

schochastics added the hackathon-topic 📆 label Sep 3, 2026

chore: Auto-update from GitHub Actions

c87ec37

Run: https://github.com/igraph/rigraph/actions/runs/33753104238

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refactor: snake_case attr-comb options & arguments, soft-deprecate dotted names - #2742

refactor: snake_case attr-comb options & arguments, soft-deprecate dotted names#2742
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