@optave/codegraph 3.7.0 → 3.8.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (401) hide show
  1. package/README.md +28 -16
  2. package/dist/ast-analysis/engine.d.ts.map +1 -1
  3. package/dist/ast-analysis/engine.js +195 -30
  4. package/dist/ast-analysis/engine.js.map +1 -1
  5. package/dist/ast-analysis/metrics.d.ts +0 -3
  6. package/dist/ast-analysis/metrics.d.ts.map +1 -1
  7. package/dist/ast-analysis/metrics.js +30 -13
  8. package/dist/ast-analysis/metrics.js.map +1 -1
  9. package/dist/ast-analysis/rules/javascript.d.ts.map +1 -1
  10. package/dist/ast-analysis/rules/javascript.js +0 -1
  11. package/dist/ast-analysis/rules/javascript.js.map +1 -1
  12. package/dist/ast-analysis/shared.d.ts.map +1 -1
  13. package/dist/ast-analysis/shared.js +24 -19
  14. package/dist/ast-analysis/shared.js.map +1 -1
  15. package/dist/ast-analysis/visitor-utils.d.ts.map +1 -1
  16. package/dist/ast-analysis/visitor-utils.js +55 -39
  17. package/dist/ast-analysis/visitor-utils.js.map +1 -1
  18. package/dist/ast-analysis/visitor.d.ts.map +1 -1
  19. package/dist/ast-analysis/visitor.js +91 -70
  20. package/dist/ast-analysis/visitor.js.map +1 -1
  21. package/dist/ast-analysis/visitors/ast-store-visitor.d.ts.map +1 -1
  22. package/dist/ast-analysis/visitors/ast-store-visitor.js +52 -129
  23. package/dist/ast-analysis/visitors/ast-store-visitor.js.map +1 -1
  24. package/dist/ast-analysis/visitors/complexity-visitor.d.ts.map +1 -1
  25. package/dist/ast-analysis/visitors/complexity-visitor.js +32 -39
  26. package/dist/ast-analysis/visitors/complexity-visitor.js.map +1 -1
  27. package/dist/ast-analysis/visitors/dataflow-visitor.d.ts.map +1 -1
  28. package/dist/ast-analysis/visitors/dataflow-visitor.js +57 -38
  29. package/dist/ast-analysis/visitors/dataflow-visitor.js.map +1 -1
  30. package/dist/cli/commands/ast.js +2 -2
  31. package/dist/cli/commands/ast.js.map +1 -1
  32. package/dist/cli/commands/watch.d.ts.map +1 -1
  33. package/dist/cli/commands/watch.js +16 -2
  34. package/dist/cli/commands/watch.js.map +1 -1
  35. package/dist/db/connection.d.ts.map +1 -1
  36. package/dist/db/connection.js +29 -26
  37. package/dist/db/connection.js.map +1 -1
  38. package/dist/db/query-builder.d.ts.map +1 -1
  39. package/dist/db/query-builder.js +16 -5
  40. package/dist/db/query-builder.js.map +1 -1
  41. package/dist/db/repository/base.d.ts +10 -0
  42. package/dist/db/repository/base.d.ts.map +1 -1
  43. package/dist/db/repository/base.js +17 -0
  44. package/dist/db/repository/base.js.map +1 -1
  45. package/dist/db/repository/native-repository.d.ts +6 -1
  46. package/dist/db/repository/native-repository.d.ts.map +1 -1
  47. package/dist/db/repository/native-repository.js +77 -1
  48. package/dist/db/repository/native-repository.js.map +1 -1
  49. package/dist/db/repository/nodes.d.ts.map +1 -1
  50. package/dist/db/repository/nodes.js +8 -4
  51. package/dist/db/repository/nodes.js.map +1 -1
  52. package/dist/db/repository/sqlite-repository.d.ts +3 -0
  53. package/dist/db/repository/sqlite-repository.d.ts.map +1 -1
  54. package/dist/db/repository/sqlite-repository.js +26 -0
  55. package/dist/db/repository/sqlite-repository.js.map +1 -1
  56. package/dist/domain/analysis/brief.d.ts.map +1 -1
  57. package/dist/domain/analysis/brief.js +13 -17
  58. package/dist/domain/analysis/brief.js.map +1 -1
  59. package/dist/domain/analysis/context.d.ts.map +1 -1
  60. package/dist/domain/analysis/context.js +14 -11
  61. package/dist/domain/analysis/context.js.map +1 -1
  62. package/dist/domain/analysis/dependencies.d.ts.map +1 -1
  63. package/dist/domain/analysis/dependencies.js +53 -52
  64. package/dist/domain/analysis/dependencies.js.map +1 -1
  65. package/dist/domain/analysis/fn-impact.d.ts +2 -7
  66. package/dist/domain/analysis/fn-impact.d.ts.map +1 -1
  67. package/dist/domain/analysis/fn-impact.js +33 -31
  68. package/dist/domain/analysis/fn-impact.js.map +1 -1
  69. package/dist/domain/analysis/implementations.d.ts.map +1 -1
  70. package/dist/domain/analysis/implementations.js +11 -19
  71. package/dist/domain/analysis/implementations.js.map +1 -1
  72. package/dist/domain/analysis/module-map.d.ts.map +1 -1
  73. package/dist/domain/analysis/module-map.js +55 -76
  74. package/dist/domain/analysis/module-map.js.map +1 -1
  75. package/dist/domain/analysis/query-helpers.d.ts +7 -0
  76. package/dist/domain/analysis/query-helpers.d.ts.map +1 -1
  77. package/dist/domain/analysis/query-helpers.js +15 -1
  78. package/dist/domain/analysis/query-helpers.js.map +1 -1
  79. package/dist/domain/graph/builder/pipeline.d.ts.map +1 -1
  80. package/dist/domain/graph/builder/pipeline.js +315 -43
  81. package/dist/domain/graph/builder/pipeline.js.map +1 -1
  82. package/dist/domain/graph/builder/stages/build-edges.d.ts.map +1 -1
  83. package/dist/domain/graph/builder/stages/build-edges.js +106 -1
  84. package/dist/domain/graph/builder/stages/build-edges.js.map +1 -1
  85. package/dist/domain/graph/builder/stages/collect-files.d.ts.map +1 -1
  86. package/dist/domain/graph/builder/stages/collect-files.js +17 -5
  87. package/dist/domain/graph/builder/stages/collect-files.js.map +1 -1
  88. package/dist/domain/graph/builder/stages/detect-changes.d.ts.map +1 -1
  89. package/dist/domain/graph/builder/stages/detect-changes.js +99 -51
  90. package/dist/domain/graph/builder/stages/detect-changes.js.map +1 -1
  91. package/dist/domain/graph/builder/stages/finalize.d.ts.map +1 -1
  92. package/dist/domain/graph/builder/stages/finalize.js +34 -7
  93. package/dist/domain/graph/builder/stages/finalize.js.map +1 -1
  94. package/dist/domain/graph/builder/stages/insert-nodes.d.ts.map +1 -1
  95. package/dist/domain/graph/builder/stages/insert-nodes.js +50 -26
  96. package/dist/domain/graph/builder/stages/insert-nodes.js.map +1 -1
  97. package/dist/domain/graph/builder/stages/resolve-imports.d.ts.map +1 -1
  98. package/dist/domain/graph/builder/stages/resolve-imports.js +95 -84
  99. package/dist/domain/graph/builder/stages/resolve-imports.js.map +1 -1
  100. package/dist/domain/graph/cycles.d.ts +6 -0
  101. package/dist/domain/graph/cycles.d.ts.map +1 -1
  102. package/dist/domain/graph/cycles.js +114 -22
  103. package/dist/domain/graph/cycles.js.map +1 -1
  104. package/dist/domain/graph/resolve.js +1 -1
  105. package/dist/domain/graph/resolve.js.map +1 -1
  106. package/dist/domain/graph/watcher.d.ts +2 -0
  107. package/dist/domain/graph/watcher.d.ts.map +1 -1
  108. package/dist/domain/graph/watcher.js +170 -75
  109. package/dist/domain/graph/watcher.js.map +1 -1
  110. package/dist/domain/parser.d.ts +1 -6
  111. package/dist/domain/parser.d.ts.map +1 -1
  112. package/dist/domain/parser.js +101 -32
  113. package/dist/domain/parser.js.map +1 -1
  114. package/dist/domain/search/generator.js +1 -1
  115. package/dist/domain/search/generator.js.map +1 -1
  116. package/dist/domain/search/models.d.ts +4 -3
  117. package/dist/domain/search/models.d.ts.map +1 -1
  118. package/dist/domain/search/models.js +18 -5
  119. package/dist/domain/search/models.js.map +1 -1
  120. package/dist/domain/search/search/hybrid.d.ts.map +1 -1
  121. package/dist/domain/search/search/hybrid.js +29 -18
  122. package/dist/domain/search/search/hybrid.js.map +1 -1
  123. package/dist/extractors/clojure.d.ts +12 -0
  124. package/dist/extractors/clojure.d.ts.map +1 -0
  125. package/dist/extractors/clojure.js +245 -0
  126. package/dist/extractors/clojure.js.map +1 -0
  127. package/dist/extractors/cuda.d.ts +11 -0
  128. package/dist/extractors/cuda.d.ts.map +1 -0
  129. package/dist/extractors/cuda.js +302 -0
  130. package/dist/extractors/cuda.js.map +1 -0
  131. package/dist/extractors/erlang.d.ts +14 -0
  132. package/dist/extractors/erlang.d.ts.map +1 -0
  133. package/dist/extractors/erlang.js +239 -0
  134. package/dist/extractors/erlang.js.map +1 -0
  135. package/dist/extractors/fsharp.d.ts +13 -0
  136. package/dist/extractors/fsharp.d.ts.map +1 -0
  137. package/dist/extractors/fsharp.js +218 -0
  138. package/dist/extractors/fsharp.js.map +1 -0
  139. package/dist/extractors/gleam.d.ts +14 -0
  140. package/dist/extractors/gleam.d.ts.map +1 -0
  141. package/dist/extractors/gleam.js +229 -0
  142. package/dist/extractors/gleam.js.map +1 -0
  143. package/dist/extractors/go.js +36 -33
  144. package/dist/extractors/go.js.map +1 -1
  145. package/dist/extractors/groovy.d.ts +10 -0
  146. package/dist/extractors/groovy.d.ts.map +1 -0
  147. package/dist/extractors/groovy.js +304 -0
  148. package/dist/extractors/groovy.js.map +1 -0
  149. package/dist/extractors/helpers.d.ts.map +1 -1
  150. package/dist/extractors/helpers.js +40 -29
  151. package/dist/extractors/helpers.js.map +1 -1
  152. package/dist/extractors/index.d.ts +11 -0
  153. package/dist/extractors/index.d.ts.map +1 -1
  154. package/dist/extractors/index.js +11 -0
  155. package/dist/extractors/index.js.map +1 -1
  156. package/dist/extractors/java.js +58 -46
  157. package/dist/extractors/java.js.map +1 -1
  158. package/dist/extractors/javascript.js +46 -45
  159. package/dist/extractors/javascript.js.map +1 -1
  160. package/dist/extractors/julia.d.ts +16 -0
  161. package/dist/extractors/julia.d.ts.map +1 -0
  162. package/dist/extractors/julia.js +287 -0
  163. package/dist/extractors/julia.js.map +1 -0
  164. package/dist/extractors/kotlin.js +84 -78
  165. package/dist/extractors/kotlin.js.map +1 -1
  166. package/dist/extractors/objc.d.ts +9 -0
  167. package/dist/extractors/objc.d.ts.map +1 -0
  168. package/dist/extractors/objc.js +406 -0
  169. package/dist/extractors/objc.js.map +1 -0
  170. package/dist/extractors/ocaml.js +74 -0
  171. package/dist/extractors/ocaml.js.map +1 -1
  172. package/dist/extractors/python.js +29 -24
  173. package/dist/extractors/python.js.map +1 -1
  174. package/dist/extractors/r.d.ts +13 -0
  175. package/dist/extractors/r.d.ts.map +1 -0
  176. package/dist/extractors/r.js +251 -0
  177. package/dist/extractors/r.js.map +1 -0
  178. package/dist/extractors/rust.js +41 -32
  179. package/dist/extractors/rust.js.map +1 -1
  180. package/dist/extractors/solidity.d.ts +9 -0
  181. package/dist/extractors/solidity.d.ts.map +1 -0
  182. package/dist/extractors/solidity.js +365 -0
  183. package/dist/extractors/solidity.js.map +1 -0
  184. package/dist/extractors/swift.js +83 -81
  185. package/dist/extractors/swift.js.map +1 -1
  186. package/dist/extractors/verilog.d.ts +9 -0
  187. package/dist/extractors/verilog.d.ts.map +1 -0
  188. package/dist/extractors/verilog.js +286 -0
  189. package/dist/extractors/verilog.js.map +1 -0
  190. package/dist/extractors/zig.js +58 -60
  191. package/dist/extractors/zig.js.map +1 -1
  192. package/dist/features/ast.d.ts +16 -14
  193. package/dist/features/ast.d.ts.map +1 -1
  194. package/dist/features/ast.js +84 -83
  195. package/dist/features/ast.js.map +1 -1
  196. package/dist/features/audit.d.ts.map +1 -1
  197. package/dist/features/audit.js +8 -6
  198. package/dist/features/audit.js.map +1 -1
  199. package/dist/features/branch-compare.d.ts.map +1 -1
  200. package/dist/features/branch-compare.js +69 -72
  201. package/dist/features/branch-compare.js.map +1 -1
  202. package/dist/features/communities.d.ts.map +1 -1
  203. package/dist/features/communities.js +19 -7
  204. package/dist/features/communities.js.map +1 -1
  205. package/dist/features/complexity.d.ts.map +1 -1
  206. package/dist/features/complexity.js +120 -125
  207. package/dist/features/complexity.js.map +1 -1
  208. package/dist/features/dataflow.d.ts.map +1 -1
  209. package/dist/features/dataflow.js +136 -137
  210. package/dist/features/dataflow.js.map +1 -1
  211. package/dist/features/flow.d.ts.map +1 -1
  212. package/dist/features/flow.js +84 -79
  213. package/dist/features/flow.js.map +1 -1
  214. package/dist/features/structure-query.d.ts.map +1 -1
  215. package/dist/features/structure-query.js +69 -65
  216. package/dist/features/structure-query.js.map +1 -1
  217. package/dist/graph/algorithms/bfs.d.ts +2 -0
  218. package/dist/graph/algorithms/bfs.d.ts.map +1 -1
  219. package/dist/graph/algorithms/bfs.js +27 -0
  220. package/dist/graph/algorithms/bfs.js.map +1 -1
  221. package/dist/graph/algorithms/centrality.d.ts +2 -0
  222. package/dist/graph/algorithms/centrality.d.ts.map +1 -1
  223. package/dist/graph/algorithms/centrality.js +28 -0
  224. package/dist/graph/algorithms/centrality.js.map +1 -1
  225. package/dist/graph/algorithms/leiden/optimiser.d.ts.map +1 -1
  226. package/dist/graph/algorithms/leiden/optimiser.js +70 -55
  227. package/dist/graph/algorithms/leiden/optimiser.js.map +1 -1
  228. package/dist/graph/algorithms/leiden/partition.d.ts.map +1 -1
  229. package/dist/graph/algorithms/leiden/partition.js +288 -266
  230. package/dist/graph/algorithms/leiden/partition.js.map +1 -1
  231. package/dist/graph/algorithms/louvain.d.ts +3 -4
  232. package/dist/graph/algorithms/louvain.d.ts.map +1 -1
  233. package/dist/graph/algorithms/louvain.js +29 -0
  234. package/dist/graph/algorithms/louvain.js.map +1 -1
  235. package/dist/graph/algorithms/shortest-path.d.ts +2 -0
  236. package/dist/graph/algorithms/shortest-path.d.ts.map +1 -1
  237. package/dist/graph/algorithms/shortest-path.js +18 -1
  238. package/dist/graph/algorithms/shortest-path.js.map +1 -1
  239. package/dist/graph/model.d.ts.map +1 -1
  240. package/dist/graph/model.js +5 -1
  241. package/dist/graph/model.js.map +1 -1
  242. package/dist/infrastructure/config.d.ts.map +1 -1
  243. package/dist/infrastructure/config.js +6 -4
  244. package/dist/infrastructure/config.js.map +1 -1
  245. package/dist/infrastructure/suppress.d.ts +25 -0
  246. package/dist/infrastructure/suppress.d.ts.map +1 -0
  247. package/dist/infrastructure/suppress.js +43 -0
  248. package/dist/infrastructure/suppress.js.map +1 -0
  249. package/dist/mcp/server.d.ts.map +1 -1
  250. package/dist/mcp/server.js +29 -24
  251. package/dist/mcp/server.js.map +1 -1
  252. package/dist/presentation/dataflow.d.ts.map +1 -1
  253. package/dist/presentation/dataflow.js +47 -38
  254. package/dist/presentation/dataflow.js.map +1 -1
  255. package/dist/presentation/diff-impact-mermaid.d.ts.map +1 -1
  256. package/dist/presentation/diff-impact-mermaid.js +60 -51
  257. package/dist/presentation/diff-impact-mermaid.js.map +1 -1
  258. package/dist/presentation/queries-cli/exports.d.ts.map +1 -1
  259. package/dist/presentation/queries-cli/exports.js +20 -14
  260. package/dist/presentation/queries-cli/exports.js.map +1 -1
  261. package/dist/presentation/queries-cli/impact.d.ts.map +1 -1
  262. package/dist/presentation/queries-cli/impact.js +15 -13
  263. package/dist/presentation/queries-cli/impact.js.map +1 -1
  264. package/dist/presentation/queries-cli/inspect.d.ts.map +1 -1
  265. package/dist/presentation/queries-cli/inspect.js +101 -79
  266. package/dist/presentation/queries-cli/inspect.js.map +1 -1
  267. package/dist/presentation/queries-cli/overview.d.ts.map +1 -1
  268. package/dist/presentation/queries-cli/overview.js +25 -16
  269. package/dist/presentation/queries-cli/overview.js.map +1 -1
  270. package/dist/presentation/queries-cli/path.js +26 -20
  271. package/dist/presentation/queries-cli/path.js.map +1 -1
  272. package/dist/presentation/result-formatter.d.ts +10 -0
  273. package/dist/presentation/result-formatter.d.ts.map +1 -1
  274. package/dist/presentation/result-formatter.js +16 -1
  275. package/dist/presentation/result-formatter.js.map +1 -1
  276. package/dist/presentation/viewer.d.ts.map +1 -1
  277. package/dist/presentation/viewer.js +18 -12
  278. package/dist/presentation/viewer.js.map +1 -1
  279. package/dist/shared/errors.d.ts +5 -0
  280. package/dist/shared/errors.d.ts.map +1 -1
  281. package/dist/shared/errors.js +5 -0
  282. package/dist/shared/errors.js.map +1 -1
  283. package/dist/shared/hierarchy.d.ts +8 -2
  284. package/dist/shared/hierarchy.d.ts.map +1 -1
  285. package/dist/shared/hierarchy.js +42 -1
  286. package/dist/shared/hierarchy.js.map +1 -1
  287. package/dist/shared/normalize.d.ts +6 -1
  288. package/dist/shared/normalize.d.ts.map +1 -1
  289. package/dist/shared/normalize.js +20 -12
  290. package/dist/shared/normalize.js.map +1 -1
  291. package/dist/shared/paginate.d.ts +0 -9
  292. package/dist/shared/paginate.d.ts.map +1 -1
  293. package/dist/shared/paginate.js +0 -15
  294. package/dist/shared/paginate.js.map +1 -1
  295. package/dist/types.d.ts +129 -3
  296. package/dist/types.d.ts.map +1 -1
  297. package/grammars/tree-sitter-clojure.wasm +0 -0
  298. package/grammars/tree-sitter-cuda.wasm +0 -0
  299. package/grammars/tree-sitter-erlang.wasm +0 -0
  300. package/grammars/tree-sitter-fsharp.wasm +0 -0
  301. package/grammars/tree-sitter-gleam.wasm +0 -0
  302. package/grammars/tree-sitter-groovy.wasm +0 -0
  303. package/grammars/tree-sitter-julia.wasm +0 -0
  304. package/grammars/tree-sitter-objc.wasm +0 -0
  305. package/grammars/tree-sitter-ocaml_interface.wasm +0 -0
  306. package/grammars/tree-sitter-r.wasm +0 -0
  307. package/grammars/tree-sitter-solidity.wasm +0 -0
  308. package/grammars/tree-sitter-verilog.wasm +0 -0
  309. package/package.json +18 -7
  310. package/src/ast-analysis/engine.ts +245 -42
  311. package/src/ast-analysis/metrics.ts +33 -11
  312. package/src/ast-analysis/rules/javascript.ts +0 -1
  313. package/src/ast-analysis/shared.ts +33 -24
  314. package/src/ast-analysis/visitor-utils.ts +52 -32
  315. package/src/ast-analysis/visitor.ts +132 -71
  316. package/src/ast-analysis/visitors/ast-store-visitor.ts +49 -119
  317. package/src/ast-analysis/visitors/complexity-visitor.ts +35 -40
  318. package/src/ast-analysis/visitors/dataflow-visitor.ts +87 -43
  319. package/src/cli/commands/ast.ts +2 -2
  320. package/src/cli/commands/watch.ts +16 -2
  321. package/src/db/connection.ts +29 -28
  322. package/src/db/query-builder.ts +15 -3
  323. package/src/db/repository/base.ts +20 -0
  324. package/src/db/repository/native-repository.ts +79 -1
  325. package/src/db/repository/nodes.ts +13 -8
  326. package/src/db/repository/sqlite-repository.ts +29 -0
  327. package/src/domain/analysis/brief.ts +15 -25
  328. package/src/domain/analysis/context.ts +17 -10
  329. package/src/domain/analysis/dependencies.ts +67 -76
  330. package/src/domain/analysis/fn-impact.ts +36 -43
  331. package/src/domain/analysis/implementations.ts +11 -17
  332. package/src/domain/analysis/module-map.ts +58 -92
  333. package/src/domain/analysis/query-helpers.ts +18 -1
  334. package/src/domain/graph/builder/pipeline.ts +366 -41
  335. package/src/domain/graph/builder/stages/build-edges.ts +162 -1
  336. package/src/domain/graph/builder/stages/collect-files.ts +18 -7
  337. package/src/domain/graph/builder/stages/detect-changes.ts +110 -56
  338. package/src/domain/graph/builder/stages/finalize.ts +41 -11
  339. package/src/domain/graph/builder/stages/insert-nodes.ts +75 -39
  340. package/src/domain/graph/builder/stages/resolve-imports.ts +122 -100
  341. package/src/domain/graph/cycles.ts +110 -23
  342. package/src/domain/graph/resolve.ts +1 -1
  343. package/src/domain/graph/watcher.ts +202 -96
  344. package/src/domain/parser.ts +122 -28
  345. package/src/domain/search/generator.ts +1 -1
  346. package/src/domain/search/models.ts +17 -4
  347. package/src/domain/search/search/hybrid.ts +69 -51
  348. package/src/extractors/clojure.ts +273 -0
  349. package/src/extractors/cuda.ts +316 -0
  350. package/src/extractors/erlang.ts +252 -0
  351. package/src/extractors/fsharp.ts +253 -0
  352. package/src/extractors/gleam.ts +246 -0
  353. package/src/extractors/go.ts +43 -33
  354. package/src/extractors/groovy.ts +332 -0
  355. package/src/extractors/helpers.ts +37 -23
  356. package/src/extractors/index.ts +11 -0
  357. package/src/extractors/java.ts +66 -47
  358. package/src/extractors/javascript.ts +45 -46
  359. package/src/extractors/julia.ts +318 -0
  360. package/src/extractors/kotlin.ts +84 -77
  361. package/src/extractors/objc.ts +431 -0
  362. package/src/extractors/ocaml.ts +78 -0
  363. package/src/extractors/python.ts +31 -25
  364. package/src/extractors/r.ts +253 -0
  365. package/src/extractors/rust.ts +37 -29
  366. package/src/extractors/solidity.ts +394 -0
  367. package/src/extractors/swift.ts +81 -80
  368. package/src/extractors/verilog.ts +315 -0
  369. package/src/extractors/zig.ts +58 -61
  370. package/src/features/ast.ts +131 -112
  371. package/src/features/audit.ts +8 -6
  372. package/src/features/branch-compare.ts +105 -79
  373. package/src/features/communities.ts +25 -10
  374. package/src/features/complexity.ts +171 -134
  375. package/src/features/dataflow.ts +165 -175
  376. package/src/features/flow.ts +129 -92
  377. package/src/features/structure-query.ts +79 -64
  378. package/src/graph/algorithms/bfs.ts +34 -0
  379. package/src/graph/algorithms/centrality.ts +30 -0
  380. package/src/graph/algorithms/leiden/optimiser.ts +99 -55
  381. package/src/graph/algorithms/leiden/partition.ts +359 -294
  382. package/src/graph/algorithms/louvain.ts +31 -4
  383. package/src/graph/algorithms/shortest-path.ts +20 -1
  384. package/src/graph/model.ts +6 -1
  385. package/src/infrastructure/config.ts +6 -4
  386. package/src/infrastructure/suppress.ts +47 -0
  387. package/src/mcp/server.ts +53 -37
  388. package/src/presentation/dataflow.ts +50 -44
  389. package/src/presentation/diff-impact-mermaid.ts +104 -62
  390. package/src/presentation/queries-cli/exports.ts +21 -13
  391. package/src/presentation/queries-cli/impact.ts +15 -13
  392. package/src/presentation/queries-cli/inspect.ts +100 -81
  393. package/src/presentation/queries-cli/overview.ts +26 -16
  394. package/src/presentation/queries-cli/path.ts +33 -25
  395. package/src/presentation/result-formatter.ts +19 -1
  396. package/src/presentation/viewer.ts +42 -14
  397. package/src/shared/errors.ts +6 -0
  398. package/src/shared/hierarchy.ts +50 -2
  399. package/src/shared/normalize.ts +31 -12
  400. package/src/shared/paginate.ts +0 -17
  401. package/src/types.ts +138 -3
@@ -0,0 +1,253 @@
1
+ import type { ExtractorOutput, SubDeclaration, TreeSitterNode, TreeSitterTree } from '../types.js';
2
+ import { findChild, nodeEndLine } from './helpers.js';
3
+
4
+ /**
5
+ * Extract symbols from R files.
6
+ *
7
+ * tree-sitter-r grammar (r-lib/tree-sitter-r) notes:
8
+ * - Assignments: binary_operator with `<-` or `=` operator
9
+ * - Functions: function_definition as RHS of assignment
10
+ * - Calls: call node with function/arguments fields
11
+ * - Imports: library() and require() calls
12
+ * - S4 classes: setClass(), setRefClass()
13
+ */
14
+ export function extractRSymbols(tree: TreeSitterTree, _filePath: string): ExtractorOutput {
15
+ const ctx: ExtractorOutput = {
16
+ definitions: [],
17
+ calls: [],
18
+ imports: [],
19
+ classes: [],
20
+ exports: [],
21
+ typeMap: new Map(),
22
+ };
23
+
24
+ walkRNode(tree.rootNode, ctx);
25
+ return ctx;
26
+ }
27
+
28
+ function walkRNode(node: TreeSitterNode, ctx: ExtractorOutput): void {
29
+ switch (node.type) {
30
+ case 'binary_operator':
31
+ handleBinaryOp(node, ctx);
32
+ break;
33
+ case 'call':
34
+ handleCall(node, ctx);
35
+ break;
36
+ }
37
+
38
+ for (let i = 0; i < node.childCount; i++) {
39
+ const child = node.child(i);
40
+ if (child) walkRNode(child, ctx);
41
+ }
42
+ }
43
+
44
+ function handleBinaryOp(node: TreeSitterNode, ctx: ExtractorOutput): void {
45
+ // binary_operator: child[0]=LHS, child[1]=operator (<- or =), child[2]=RHS
46
+ if (node.childCount < 3) return;
47
+
48
+ const lhs = node.child(0);
49
+ const op = node.child(1);
50
+ const rhs = node.child(2);
51
+
52
+ if (!lhs || !op || !rhs) return;
53
+ if (op.text !== '<-' && op.text !== '=' && op.text !== '<<-') return;
54
+ if (lhs.type !== 'identifier') return;
55
+
56
+ if (rhs.type === 'function_definition') {
57
+ const params = extractRParams(rhs);
58
+ ctx.definitions.push({
59
+ name: lhs.text,
60
+ kind: 'function',
61
+ line: node.startPosition.row + 1,
62
+ endLine: nodeEndLine(node),
63
+ children: params.length > 0 ? params : undefined,
64
+ });
65
+ } else {
66
+ // Variable assignment — only record top-level
67
+ if (node.parent?.type === 'program') {
68
+ ctx.definitions.push({
69
+ name: lhs.text,
70
+ kind: 'variable',
71
+ line: node.startPosition.row + 1,
72
+ endLine: nodeEndLine(node),
73
+ });
74
+ }
75
+ }
76
+ }
77
+
78
+ function extractRParams(funcDef: TreeSitterNode): SubDeclaration[] {
79
+ const params: SubDeclaration[] = [];
80
+ const paramsNode = findChild(funcDef, 'parameters');
81
+ if (!paramsNode) return params;
82
+
83
+ for (let i = 0; i < paramsNode.childCount; i++) {
84
+ const child = paramsNode.child(i);
85
+ if (!child) continue;
86
+ if (child.type === 'parameter') {
87
+ // parameter node has name and possibly default value
88
+ const nameNode = child.childForFieldName('name') || findChild(child, 'identifier');
89
+ if (nameNode) {
90
+ params.push({ name: nameNode.text, kind: 'parameter', line: child.startPosition.row + 1 });
91
+ } else if (child.text && child.text !== ',' && child.text !== '(' && child.text !== ')') {
92
+ // Some grammars have the param as plain text
93
+ params.push({ name: child.text, kind: 'parameter', line: child.startPosition.row + 1 });
94
+ }
95
+ }
96
+ if (child.type === 'identifier') {
97
+ params.push({ name: child.text, kind: 'parameter', line: child.startPosition.row + 1 });
98
+ }
99
+ }
100
+ return params;
101
+ }
102
+
103
+ function handleCall(node: TreeSitterNode, ctx: ExtractorOutput): void {
104
+ // call: child[0]=function, then arguments
105
+ const funcNode = node.child(0);
106
+ if (!funcNode) return;
107
+
108
+ const funcName = funcNode.text;
109
+
110
+ // library() and require() are imports
111
+ if (funcName === 'library' || funcName === 'require') {
112
+ handleLibraryCall(node, ctx);
113
+ return;
114
+ }
115
+
116
+ // source() is a file import
117
+ if (funcName === 'source') {
118
+ handleSourceCall(node, ctx);
119
+ return;
120
+ }
121
+
122
+ // setClass / setRefClass for S4
123
+ if (funcName === 'setClass' || funcName === 'setRefClass') {
124
+ handleSetClass(node, ctx);
125
+ return;
126
+ }
127
+
128
+ if (funcName === 'setGeneric' || funcName === 'setMethod') {
129
+ handleSetGeneric(node, ctx);
130
+ return;
131
+ }
132
+
133
+ // Regular call
134
+ if (funcNode.type === 'identifier') {
135
+ ctx.calls.push({ name: funcName, line: node.startPosition.row + 1 });
136
+ } else if (funcNode.type === 'namespace_operator') {
137
+ // pkg::func
138
+ const parts = funcName.split('::');
139
+ if (parts.length >= 2) {
140
+ ctx.calls.push({
141
+ name: parts[parts.length - 1]!,
142
+ receiver: parts.slice(0, -1).join('::'),
143
+ line: node.startPosition.row + 1,
144
+ });
145
+ }
146
+ }
147
+ }
148
+
149
+ function handleLibraryCall(node: TreeSitterNode, ctx: ExtractorOutput): void {
150
+ // Find the package name in arguments
151
+ for (let i = 0; i < node.childCount; i++) {
152
+ const child = node.child(i);
153
+ if (!child) continue;
154
+ if (child.type === 'arguments') {
155
+ for (let j = 0; j < child.childCount; j++) {
156
+ const arg = child.child(j);
157
+ if (!arg) continue;
158
+ if (arg.type === 'identifier') {
159
+ ctx.imports.push({
160
+ source: arg.text,
161
+ names: [arg.text],
162
+ line: node.startPosition.row + 1,
163
+ });
164
+ return;
165
+ }
166
+ if (arg.type === 'string' || arg.type === 'string_content') {
167
+ const text = arg.text.replace(/^["']|["']$/g, '');
168
+ ctx.imports.push({
169
+ source: text,
170
+ names: [text],
171
+ line: node.startPosition.row + 1,
172
+ });
173
+ return;
174
+ }
175
+ // Argument might be wrapped
176
+ if (arg.type === 'argument') {
177
+ const id = findChild(arg, 'identifier') || findChild(arg, 'string');
178
+ if (id) {
179
+ const text = id.text.replace(/^["']|["']$/g, '');
180
+ ctx.imports.push({
181
+ source: text,
182
+ names: [text],
183
+ line: node.startPosition.row + 1,
184
+ });
185
+ return;
186
+ }
187
+ }
188
+ }
189
+ }
190
+ }
191
+ }
192
+
193
+ function handleSourceCall(node: TreeSitterNode, ctx: ExtractorOutput): void {
194
+ for (let i = 0; i < node.childCount; i++) {
195
+ const child = node.child(i);
196
+ if (!child || child.type !== 'arguments') continue;
197
+ for (let j = 0; j < child.childCount; j++) {
198
+ const arg = child.child(j);
199
+ if (!arg) continue;
200
+ if (arg.type === 'string') {
201
+ const text = arg.text.replace(/^["']|["']$/g, '');
202
+ ctx.imports.push({
203
+ source: text,
204
+ names: ['source'],
205
+ line: node.startPosition.row + 1,
206
+ });
207
+ return;
208
+ }
209
+ }
210
+ }
211
+ }
212
+
213
+ function handleSetClass(node: TreeSitterNode, ctx: ExtractorOutput): void {
214
+ for (let i = 0; i < node.childCount; i++) {
215
+ const child = node.child(i);
216
+ if (!child || child.type !== 'arguments') continue;
217
+ for (let j = 0; j < child.childCount; j++) {
218
+ const arg = child.child(j);
219
+ if (!arg) continue;
220
+ if (arg.type === 'string') {
221
+ const name = arg.text.replace(/^["']|["']$/g, '');
222
+ ctx.definitions.push({
223
+ name,
224
+ kind: 'class',
225
+ line: node.startPosition.row + 1,
226
+ endLine: nodeEndLine(node),
227
+ });
228
+ return;
229
+ }
230
+ }
231
+ }
232
+ }
233
+
234
+ function handleSetGeneric(node: TreeSitterNode, ctx: ExtractorOutput): void {
235
+ for (let i = 0; i < node.childCount; i++) {
236
+ const child = node.child(i);
237
+ if (!child || child.type !== 'arguments') continue;
238
+ for (let j = 0; j < child.childCount; j++) {
239
+ const arg = child.child(j);
240
+ if (!arg) continue;
241
+ if (arg.type === 'string') {
242
+ const name = arg.text.replace(/^["']|["']$/g, '');
243
+ ctx.definitions.push({
244
+ name,
245
+ kind: 'function',
246
+ line: node.startPosition.row + 1,
247
+ endLine: nodeEndLine(node),
248
+ });
249
+ return;
250
+ }
251
+ }
252
+ }
253
+ }
@@ -138,19 +138,22 @@ function handleRustTraitItem(node: TreeSitterNode, ctx: ExtractorOutput): void {
138
138
  endLine: nodeEndLine(node),
139
139
  });
140
140
  const body = node.childForFieldName('body');
141
- if (body) {
142
- for (let i = 0; i < body.childCount; i++) {
143
- const child = body.child(i);
144
- if (child && (child.type === 'function_signature_item' || child.type === 'function_item')) {
145
- const methName = child.childForFieldName('name');
146
- if (methName) {
147
- ctx.definitions.push({
148
- name: `${nameNode.text}.${methName.text}`,
149
- kind: 'method',
150
- line: child.startPosition.row + 1,
151
- endLine: child.endPosition.row + 1,
152
- });
153
- }
141
+ if (body) extractTraitMethods(body, nameNode.text, ctx);
142
+ }
143
+
144
+ /** Extract method signatures/definitions from a trait body. */
145
+ function extractTraitMethods(body: TreeSitterNode, traitName: string, ctx: ExtractorOutput): void {
146
+ for (let i = 0; i < body.childCount; i++) {
147
+ const child = body.child(i);
148
+ if (child && (child.type === 'function_signature_item' || child.type === 'function_item')) {
149
+ const methName = child.childForFieldName('name');
150
+ if (methName) {
151
+ ctx.definitions.push({
152
+ name: `${traitName}.${methName.text}`,
153
+ kind: 'method',
154
+ line: child.startPosition.row + 1,
155
+ endLine: child.endPosition.row + 1,
156
+ });
154
157
  }
155
158
  }
156
159
  }
@@ -185,25 +188,30 @@ function handleRustUseDecl(node: TreeSitterNode, ctx: ExtractorOutput): void {
185
188
  function handleRustCallExpr(node: TreeSitterNode, ctx: ExtractorOutput): void {
186
189
  const fn = node.childForFieldName('function');
187
190
  if (!fn) return;
188
- if (fn.type === 'identifier') {
189
- ctx.calls.push({ name: fn.text, line: node.startPosition.row + 1 });
190
- } else if (fn.type === 'field_expression') {
191
+ const call = extractRustCallInfo(fn, node.startPosition.row + 1);
192
+ if (call) ctx.calls.push(call);
193
+ }
194
+
195
+ /** Extract call info from a Rust call function node. */
196
+ function extractRustCallInfo(fn: TreeSitterNode, line: number): Call | null {
197
+ if (fn.type === 'identifier') return { name: fn.text, line };
198
+ if (fn.type === 'field_expression') {
191
199
  const field = fn.childForFieldName('field');
192
- if (field) {
193
- const value = fn.childForFieldName('value');
194
- const call: Call = { name: field.text, line: node.startPosition.row + 1 };
195
- if (value) call.receiver = value.text;
196
- ctx.calls.push(call);
197
- }
198
- } else if (fn.type === 'scoped_identifier') {
200
+ if (!field) return null;
201
+ const value = fn.childForFieldName('value');
202
+ const call: Call = { name: field.text, line };
203
+ if (value) call.receiver = value.text;
204
+ return call;
205
+ }
206
+ if (fn.type === 'scoped_identifier') {
199
207
  const name = fn.childForFieldName('name');
200
- if (name) {
201
- const path = fn.childForFieldName('path');
202
- const call: Call = { name: name.text, line: node.startPosition.row + 1 };
203
- if (path) call.receiver = path.text;
204
- ctx.calls.push(call);
205
- }
208
+ if (!name) return null;
209
+ const path = fn.childForFieldName('path');
210
+ const call: Call = { name: name.text, line };
211
+ if (path) call.receiver = path.text;
212
+ return call;
206
213
  }
214
+ return null;
207
215
  }
208
216
 
209
217
  function handleRustMacroInvocation(node: TreeSitterNode, ctx: ExtractorOutput): void {