@research-copilot/plugin 1.1.17 → 1.1.19

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 (800) hide show
  1. package/README.md +18 -9
  2. package/dist/.claude-plugin/plugin.json +1 -1
  3. package/dist/.codex-plugin/plugin.toml +1 -1
  4. package/dist/.cursor-plugin/plugin.json +1 -1
  5. package/dist/.gemini-plugin/plugin.json +1 -1
  6. package/dist/.opencode-plugin/plugin.json +1 -1
  7. package/dist/.windsurf-plugin/plugin.json +1 -1
  8. package/dist/skills/ablation-planner/SKILL.md +126 -0
  9. package/dist/skills/alphaxiv/SKILL.md +186 -0
  10. package/dist/skills/analyze-results/SKILL.md +45 -0
  11. package/dist/skills/arxiv/SKILL.md +210 -0
  12. package/dist/skills/auto-paper-improvement-loop/SKILL.md +574 -0
  13. package/dist/skills/auto-review-loop/SKILL.md +370 -0
  14. package/dist/skills/auto-review-loop-llm/SKILL.md +247 -0
  15. package/dist/skills/auto-review-loop-minimax/SKILL.md +290 -0
  16. package/dist/skills/benchmark-paper-template/SKILL.md +142 -0
  17. package/dist/skills/benchmark-paper-template/references/benchmark-design.md +180 -0
  18. package/dist/skills/benchmark-paper-template/references/checklist.md +113 -0
  19. package/dist/skills/benchmark-paper-template/references/construction-pipeline.md +127 -0
  20. package/dist/skills/benchmark-paper-template/references/experiments.md +159 -0
  21. package/dist/skills/benchmark-paper-template/references/gap-analysis.md +86 -0
  22. package/dist/skills/benchmark-paper-template/references/instantiation-template.md +194 -0
  23. package/dist/skills/benchmark-paper-template/references/orchestrator-notes.md +96 -0
  24. package/dist/skills/benchmark-paper-template/references/paper-structure.md +209 -0
  25. package/dist/skills/citation-audit/SKILL.md +494 -0
  26. package/dist/skills/claims-drafting/SKILL.md +239 -0
  27. package/dist/skills/comm-lit-review/SKILL.md +299 -0
  28. package/dist/skills/comm-lit-review/references/domain-taxonomy.md +57 -0
  29. package/dist/skills/comm-lit-review/references/output-template.md +37 -0
  30. package/dist/skills/comm-lit-review/references/source-policy.md +99 -0
  31. package/dist/skills/comm-lit-review/references/venue-tiering.md +112 -0
  32. package/dist/skills/composer/SKILL.md +840 -0
  33. package/dist/skills/composer/references/section_guides.md +675 -0
  34. package/dist/skills/composer/references/writing_standards.md +629 -0
  35. package/dist/skills/composer/scripts/chapter_quality_check.py +470 -0
  36. package/dist/skills/composer/scripts/final_evaluation.py +550 -0
  37. package/dist/skills/deepxiv/SKILL.md +142 -0
  38. package/dist/skills/dse-loop/SKILL.md +277 -0
  39. package/dist/skills/embodiment-description/SKILL.md +129 -0
  40. package/dist/skills/exa-search/SKILL.md +192 -0
  41. package/dist/skills/experiment-audit/SKILL.md +262 -0
  42. package/dist/skills/experiment-bridge/SKILL.md +316 -0
  43. package/dist/skills/experiment-plan/SKILL.md +249 -0
  44. package/dist/skills/experiment-queue/SKILL.md +380 -0
  45. package/dist/skills/experiment-queue/scripts/build_manifest.py +142 -0
  46. package/dist/skills/experiment-queue/scripts/queue_manager.py +426 -0
  47. package/dist/skills/feishu-notify/SKILL.md +155 -0
  48. package/dist/skills/figure-description/SKILL.md +138 -0
  49. package/dist/skills/figure-designer/SKILL.md +207 -0
  50. package/dist/skills/figure-designer/references/design-rules.md +99 -0
  51. package/dist/skills/figure-designer/references/experimental-results.md +127 -0
  52. package/dist/skills/figure-designer/references/motivated-example.md +138 -0
  53. package/dist/skills/figure-designer/references/solution-overview.md +145 -0
  54. package/dist/skills/figure-designer/references/tools.md +124 -0
  55. package/dist/skills/figure-spec/SKILL.md +252 -0
  56. package/dist/skills/figure-spec/scripts/figure_renderer.py +799 -0
  57. package/dist/skills/formula-derivation/SKILL.md +280 -0
  58. package/dist/skills/gemini-search/SKILL.md +205 -0
  59. package/dist/skills/grant-proposal/SKILL.md +625 -0
  60. package/dist/skills/humanizer/AGENTS.md +25 -0
  61. package/dist/skills/humanizer/SKILL.md +621 -0
  62. package/dist/skills/idea-creator/SKILL.md +311 -0
  63. package/dist/skills/idea-discovery/SKILL.md +340 -0
  64. package/dist/skills/idea-discovery-robot/SKILL.md +362 -0
  65. package/dist/skills/idea-evaluator/SKILL.md +265 -0
  66. package/dist/skills/idea-evaluator/references/fatal-flaws.md +192 -0
  67. package/dist/skills/idea-evaluator/references/five-dimensions.md +251 -0
  68. package/dist/skills/idea-evaluator/references/lifecycle-capability-matching.md +177 -0
  69. package/dist/skills/idea-evaluator/references/paradigm-elephant.md +112 -0
  70. package/dist/skills/idea-evaluator/references/paradigm-examples.md +107 -0
  71. package/dist/skills/idea-evaluator/references/paradigm-first-principles.md +115 -0
  72. package/dist/skills/idea-evaluator/references/paradigm-hamming.md +137 -0
  73. package/dist/skills/idea-evaluator/references/paradigm-shift-probe.md +160 -0
  74. package/dist/skills/idea-evaluator/references/paradigm-technology-cycle.md +116 -0
  75. package/dist/skills/idea-evaluator/references/worked-examples.md +206 -0
  76. package/dist/skills/interview-cheatsheet/SKILL.md +245 -0
  77. package/dist/skills/intro-drafter/SKILL.md +250 -0
  78. package/dist/skills/intro-drafter/references/contribution-patterns.md +116 -0
  79. package/dist/skills/intro-drafter/references/flowchart.md +204 -0
  80. package/dist/skills/intro-drafter/references/paper-types.md +155 -0
  81. package/dist/skills/intro-drafter/references/running-example.md +133 -0
  82. package/dist/skills/intro-drafter/references/worked-examples.md +161 -0
  83. package/dist/skills/invention-structuring/SKILL.md +188 -0
  84. package/dist/skills/jurisdiction-format/SKILL.md +192 -0
  85. package/dist/skills/kill-argument/SKILL.md +384 -0
  86. package/dist/skills/llm-wiki/.mise.toml +2 -0
  87. package/dist/skills/llm-wiki/.nvmrc +1 -0
  88. package/dist/skills/llm-wiki/AGENTS.md +132 -0
  89. package/dist/skills/llm-wiki/CHANGELOG.md +459 -0
  90. package/dist/skills/llm-wiki/CLAUDE.md +109 -0
  91. package/dist/skills/llm-wiki/HERMES.md +44 -0
  92. package/dist/skills/llm-wiki/SKILL.md +1133 -0
  93. package/dist/skills/llm-wiki/assets/graph-demo.gif +0 -0
  94. package/dist/skills/llm-wiki/assets/graph-preview.png +0 -0
  95. package/dist/skills/llm-wiki/deps/LICENSE-d3.txt +13 -0
  96. package/dist/skills/llm-wiki/deps/LICENSE-marked.txt +44 -0
  97. package/dist/skills/llm-wiki/deps/LICENSE-purify.txt +568 -0
  98. package/{LICENSE → dist/skills/llm-wiki/deps/LICENSE-roughjs.txt} +1 -1
  99. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/SKILL.md +261 -0
  100. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/references/config/first-time-setup.md +106 -0
  101. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/cdp.ts +179 -0
  102. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/constants.ts +13 -0
  103. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/defuddle-converter.ts +58 -0
  104. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/html-to-markdown.ts +135 -0
  105. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/legacy-converter.ts +629 -0
  106. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/main.ts +314 -0
  107. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/markdown-conversion-shared.ts +305 -0
  108. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/media-localizer.ts +317 -0
  109. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/package.json +14 -0
  110. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/paths.ts +29 -0
  111. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/vendor/baoyu-chrome-cdp/package.json +9 -0
  112. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/vendor/baoyu-chrome-cdp/src/index.test.ts +307 -0
  113. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/vendor/baoyu-chrome-cdp/src/index.ts +523 -0
  114. package/dist/skills/llm-wiki/deps/d3.min.js +2 -0
  115. package/dist/skills/llm-wiki/deps/marked.min.js +6 -0
  116. package/dist/skills/llm-wiki/deps/purify.min.js +3 -0
  117. package/dist/skills/llm-wiki/deps/rough.min.js +7 -0
  118. package/dist/skills/llm-wiki/deps/youtube-transcript/SKILL.md +47 -0
  119. package/dist/skills/llm-wiki/deps/youtube-transcript/scripts/get_transcript.py +72 -0
  120. package/dist/skills/llm-wiki/docs/design/oriental-atlas/DESIGN.md +183 -0
  121. package/dist/skills/llm-wiki/docs/design/oriental-atlas/design-brief.md +170 -0
  122. package/dist/skills/llm-wiki/docs/design/oriental-atlas/oriental-editorial-atlas.html +1908 -0
  123. package/dist/skills/llm-wiki/docs/design/oriental-atlas/reviews/result-review.md +68 -0
  124. package/dist/skills/llm-wiki/docs/plans/2026-06-15-omp-tool-status-events-phased-plan.md +655 -0
  125. package/dist/skills/llm-wiki/docs/plans/2026-06-15-omp-tool-status-events-progress.json +913 -0
  126. package/dist/skills/llm-wiki/docs/spark/2026-06-15-omp-tool-status-events-design.md +174 -0
  127. package/dist/skills/llm-wiki/install.ps1 +87 -0
  128. package/dist/skills/llm-wiki/install.sh +722 -0
  129. package/dist/skills/llm-wiki/package-lock.json +10309 -0
  130. package/dist/skills/llm-wiki/package.json +24 -0
  131. package/dist/skills/llm-wiki/packages/graph-engine/package.json +33 -0
  132. package/dist/skills/llm-wiki/packages/graph-engine/src/anim/.gitkeep +1 -0
  133. package/dist/skills/llm-wiki/packages/graph-engine/src/anim/index.ts +179 -0
  134. package/dist/skills/llm-wiki/packages/graph-engine/src/diff.ts +121 -0
  135. package/dist/skills/llm-wiki/packages/graph-engine/src/graph-node.ts +37 -0
  136. package/dist/skills/llm-wiki/packages/graph-engine/src/index.ts +140 -0
  137. package/dist/skills/llm-wiki/packages/graph-engine/src/model/atlas.ts +18 -0
  138. package/dist/skills/llm-wiki/packages/graph-engine/src/model/index.ts +6 -0
  139. package/dist/skills/llm-wiki/packages/graph-engine/src/model/labels.ts +11 -0
  140. package/dist/skills/llm-wiki/packages/graph-engine/src/model/learning.ts +8 -0
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  143. package/dist/skills/llm-wiki/packages/graph-engine/src/model/storage.ts +4 -0
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  148. package/dist/skills/llm-wiki/packages/graph-engine/src/render/model.ts +593 -0
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  178. package/dist/skills/llm-wiki/platforms/claude/CLAUDE.md +37 -0
  179. package/dist/skills/llm-wiki/platforms/claude/companions/llm-wiki-upgrade/SKILL.md +95 -0
  180. package/dist/skills/llm-wiki/platforms/codex/AGENTS.md +23 -0
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  800. package/package.json +1 -1
@@ -0,0 +1,7 @@
1
+ export {
2
+ defaultQueue,
3
+ normalizeQueue,
4
+ toggleQueueFavorite,
5
+ appendQueueNote,
6
+ summarizeQueue
7
+ } from './legacy-helpers';
@@ -0,0 +1,4 @@
1
+ export {
2
+ createSafeStorage,
3
+ getWikiStorageNamespace
4
+ } from './legacy-helpers';
@@ -0,0 +1,9 @@
1
+ export {
2
+ buildSearchHaystack,
3
+ buildSearchIndex,
4
+ filterLinksByTypes,
5
+ applySearchToNodeIds,
6
+ applyFocusMode,
7
+ resolveVisibleSnapshot,
8
+ shouldAutoOpenDrawer
9
+ } from './legacy-helpers';
@@ -0,0 +1,59 @@
1
+ export {
2
+ buildRenderableGraph,
3
+ createRenderPathCache,
4
+ edgeOpacity,
5
+ edgeRelationClass,
6
+ edgeStrokeWidth,
7
+ edgeVisualOpacity,
8
+ edgeVisualStrokeWidth,
9
+ makeEdgePath,
10
+ makeEdgePathFromPoints,
11
+ nodeDisplayModeForDensity,
12
+ screenEffectiveDensityMode
13
+ } from "./model";
14
+ export type {
15
+ DensityMode,
16
+ NodeDisplayMode,
17
+ NodeVisualRole,
18
+ RenderableCommunity,
19
+ RenderableEdge,
20
+ RenderableGraph,
21
+ RenderableMinimap,
22
+ RenderableNode,
23
+ RenderPathCache,
24
+ RenderPosition,
25
+ RenderPositionMap
26
+ } from "./model";
27
+ export { buildCommunityLegend } from "./legend";
28
+ export type { CommunityLegendRow } from "./legend";
29
+ export {
30
+ GRAPH_TOOLBAR_PANEL_KEY,
31
+ nextToolbarPanelState,
32
+ normalizeToolbarPanelState,
33
+ readToolbarPanelState,
34
+ shouldBlankClickCloseToolbar,
35
+ toolbarPanelStateAfterBlankClick,
36
+ writeToolbarPanelState
37
+ } from "./toolbar";
38
+ export type { GraphToolbarPanelState, GraphToolbarStorage } from "./toolbar";
39
+ export { createStaticGraphRenderer } from "./static-renderer";
40
+ export type { StaticGraphRenderer } from "./static-renderer";
41
+ export { resolveGraphSearchState, resolveNextGraphSearchFocus } from "./search";
42
+ export type { GraphSearchFocus, GraphSearchNodeState, GraphSearchNodeView, GraphSearchState } from "./search";
43
+ export { buildHoverPreview, firstUsefulParagraph, previewSummary } from "./preview";
44
+ export type { GraphHoverPreview } from "./preview";
45
+ export {
46
+ DEFAULT_RENDERER_VIEWPORT,
47
+ applyRendererViewportTransform,
48
+ centerRendererViewportOnPoint,
49
+ createViewportFrameCommitter,
50
+ fitRendererViewportToPoints,
51
+ normalizeRendererViewport,
52
+ normalizeWheelDelta,
53
+ panRendererViewport,
54
+ rendererViewportToMinimapRect,
55
+ rendererViewportToTransform,
56
+ viewportAfterResize,
57
+ viewportAfterWheelZoom
58
+ } from "./viewport";
59
+ export type { RafScheduler, RendererPoint, RendererViewport, RendererViewportOptions, RendererViewportResizeOptions, RendererViewportSize, WheelDeltaLike } from "./viewport";
@@ -0,0 +1,25 @@
1
+ import type { NodeId } from "../types";
2
+ import type { RenderableCommunity, RenderableNode } from "./model";
3
+
4
+ export interface CommunityLegendRow {
5
+ id: string;
6
+ label: string;
7
+ color: string;
8
+ pageCount: number;
9
+ nodeIds: NodeId[];
10
+ }
11
+
12
+ export function buildCommunityLegend(
13
+ communities: Array<Pick<RenderableCommunity, "id" | "label" | "color" | "nodeCount" | "wash">>,
14
+ nodes: Array<Pick<RenderableNode, "id" | "community">>
15
+ ): CommunityLegendRow[] {
16
+ return communities
17
+ .filter((community) => community.nodeCount > 0)
18
+ .map((community) => ({
19
+ id: community.id,
20
+ label: community.label || community.id,
21
+ color: community.color,
22
+ pageCount: community.nodeCount,
23
+ nodeIds: nodes.filter((node) => node.community === community.id).map((node) => node.id)
24
+ }));
25
+ }
@@ -0,0 +1,593 @@
1
+ import type { GraphData, GraphFocusInput, GraphTypeFilters, NodeId, PinMap, SelectionInput, ThemeId, WikiPath } from "../types";
2
+ import {
3
+ atlasNodePoint,
4
+ atlasPointToMinimap,
5
+ buildAtlasModel,
6
+ deriveAtlasLayout,
7
+ getAtlasDensityMode,
8
+ resolveAtlasVisibleSnapshot
9
+ } from "../model";
10
+ import { wikiPathForGraphNode } from "../graph-node";
11
+ import { getCommunityColor } from "../themes";
12
+
13
+ export type DensityMode = "card" | "compact-card" | "point-plus-focus" | "overview";
14
+ export type NodeDisplayMode = "card" | "compact-card" | "point" | "overview";
15
+ export type NodeVisualRole = "landmark" | "index-slip" | "cinnabar-note" | "map-pin";
16
+
17
+ export interface RenderableGraph {
18
+ model: Record<string, unknown>;
19
+ layout: Record<string, unknown>;
20
+ selectedNodeId: string | null;
21
+ focus: GraphFocusInput;
22
+ typeFilters: GraphTypeFilters;
23
+ densityMode: DensityMode;
24
+ counts: {
25
+ visibleNodes: number;
26
+ visibleEdges: number;
27
+ totalNodes: number;
28
+ totalEdges: number;
29
+ totalCommunities: number;
30
+ };
31
+ nodes: RenderableNode[];
32
+ edges: RenderableEdge[];
33
+ communities: RenderableCommunity[];
34
+ minimap: RenderableMinimap;
35
+ }
36
+
37
+ export interface RenderableNode {
38
+ id: string;
39
+ label: string;
40
+ type: string;
41
+ kind: string;
42
+ community: string;
43
+ sourcePath: string;
44
+ x: number;
45
+ y: number;
46
+ point: { x: number; y: number };
47
+ displayMode: NodeDisplayMode;
48
+ visualRole: NodeVisualRole;
49
+ priority: number;
50
+ weight: number;
51
+ unavailable: boolean;
52
+ selected: boolean;
53
+ startNode: boolean;
54
+ previewStart: boolean;
55
+ labelVisible: boolean;
56
+ }
57
+
58
+ export interface RenderableEdge {
59
+ id: string;
60
+ source: string;
61
+ target: string;
62
+ type: string;
63
+ confidence: string;
64
+ relationType: string;
65
+ relationClass: string;
66
+ path: string;
67
+ curveOffset: number;
68
+ strokeWidth: number;
69
+ opacity: number;
70
+ simulationWeight: number;
71
+ }
72
+
73
+ export interface RenderableCommunity {
74
+ id: string;
75
+ label: string;
76
+ color: string;
77
+ nodeCount: number;
78
+ wash: {
79
+ cx: number;
80
+ cy: number;
81
+ rx: number;
82
+ ry: number;
83
+ opacity: number;
84
+ } | null;
85
+ }
86
+
87
+ export interface RenderableMinimap {
88
+ path: string;
89
+ nodes: Array<{ id: string; x: number; y: number; r: number; fill: string; selected: boolean }>;
90
+ }
91
+
92
+ interface BuildRenderableGraphOptions {
93
+ pins?: PinMap;
94
+ theme?: ThemeId;
95
+ selectedNodeId?: string | null;
96
+ selection?: SelectionInput | null;
97
+ focus?: GraphFocusInput;
98
+ typeFilters?: GraphTypeFilters;
99
+ positions?: RenderPositionMap;
100
+ pathCache?: RenderPathCache;
101
+ }
102
+
103
+ type AtlasNode = {
104
+ id: string;
105
+ label: string;
106
+ type: string;
107
+ kind: string;
108
+ community: string;
109
+ source_path?: string;
110
+ x: number;
111
+ y: number;
112
+ priority?: number;
113
+ weight?: number;
114
+ unavailable?: boolean;
115
+ };
116
+
117
+ type AtlasEdge = {
118
+ id: string;
119
+ source: string;
120
+ target: string;
121
+ type: string;
122
+ confidence?: string;
123
+ relation_type?: string;
124
+ weight?: number;
125
+ };
126
+
127
+ type AtlasCommunity = {
128
+ id: string;
129
+ label?: string;
130
+ node_count?: number;
131
+ color_index?: number;
132
+ };
133
+
134
+ export interface RenderPosition {
135
+ x: number;
136
+ y: number;
137
+ }
138
+
139
+ export type RenderPositionMap = Record<NodeId, RenderPosition>;
140
+
141
+ export interface RenderPathCache {
142
+ getEdgeCurve(edge: { id: string; source: string; target: string; weight?: number }, source: RenderPosition, target: RenderPosition): number;
143
+ clear(): void;
144
+ }
145
+
146
+ const WORLD_WIDTH = 1000;
147
+ const WORLD_HEIGHT = 680;
148
+ const MINIMAP_PATH = "M8 40 C34 20 54 36 76 22 C98 8 118 24 150 12";
149
+
150
+ export function createRenderPathCache(): RenderPathCache {
151
+ const edgeCurves = new Map<string, number>();
152
+ return {
153
+ getEdgeCurve(edge, source, target): number {
154
+ const key = edge.id || `${edge.source}->${edge.target}`;
155
+ const existing = edgeCurves.get(key);
156
+ if (existing != null) return existing;
157
+ const curve = edgeCurveOffset(source, target, edge);
158
+ edgeCurves.set(key, curve);
159
+ return curve;
160
+ },
161
+ clear(): void {
162
+ edgeCurves.clear();
163
+ }
164
+ };
165
+ }
166
+
167
+ export function buildRenderableGraph(data: GraphData, options: BuildRenderableGraphOptions = {}): RenderableGraph {
168
+ const theme = options.theme || "shan-shui";
169
+ const dataWithPins = applyPinsToGraphData(data, options.pins || {});
170
+ const model = buildAtlasModel(dataWithPins) as {
171
+ nodes: AtlasNode[];
172
+ edges: AtlasEdge[];
173
+ byId: Record<string, AtlasNode>;
174
+ communities: AtlasCommunity[];
175
+ communityById: Record<string, AtlasCommunity>;
176
+ };
177
+ const layout = deriveAtlasLayout(model) as Record<string, unknown>;
178
+ const selectedNodeIds = resolveSelectedNodeIds(model, options);
179
+ const selectedNodeSet = new Set(selectedNodeIds);
180
+ const selectedNodeId = selectedNodeIds.length === 1 ? selectedNodeIds[0] : null;
181
+ const focus = normalizeGraphFocus(options.focus, model);
182
+ const typeFilters = normalizeGraphTypeFilters(options.typeFilters, model.nodes);
183
+ const visible = resolveAtlasVisibleSnapshot(model, layout, {
184
+ activeCommunityId: focus?.kind === "community" ? focus.id : "all",
185
+ selectedNodeId
186
+ }) as {
187
+ nodes: AtlasNode[];
188
+ edges: AtlasEdge[];
189
+ densityMode: DensityMode;
190
+ labelNodeIds: Record<string, boolean>;
191
+ importantNodeIds: Record<string, boolean>;
192
+ startNodeIds: Record<string, boolean>;
193
+ starts: Array<{ node: AtlasNode }>;
194
+ counts: {
195
+ visible_nodes: number;
196
+ visible_edges: number;
197
+ total_nodes: number;
198
+ total_edges: number;
199
+ total_communities: number;
200
+ };
201
+ };
202
+ const previewNodeId = selectedNodeId ? null : firstPreviewNodeId(visible);
203
+ const importantIds = visible.importantNodeIds || {};
204
+ const labelIds = visible.labelNodeIds || {};
205
+ const startIds = visible.startNodeIds || {};
206
+
207
+ const filteredVisibleNodes = applyNodeTypeFilters(visible.nodes, typeFilters);
208
+ const filteredVisibleNodeIds = new Set(filteredVisibleNodes.map((node) => node.id));
209
+ const filteredVisibleEdges = visible.edges.filter((edge) => filteredVisibleNodeIds.has(edge.source) && filteredVisibleNodeIds.has(edge.target));
210
+ const filteredDensityMode = getAtlasDensityMode(filteredVisibleNodes.length) as DensityMode;
211
+ const filteredVisibleCounts = {
212
+ visible_nodes: filteredVisibleNodes.length,
213
+ visible_edges: filteredVisibleEdges.length,
214
+ total_nodes: visible.counts.total_nodes,
215
+ total_edges: visible.counts.total_edges,
216
+ total_communities: visible.counts.total_communities
217
+ };
218
+
219
+ const nodes = filteredVisibleNodes.map((node) => {
220
+ const isSelected = selectedNodeSet.has(node.id);
221
+ const displayMode = isSelected
222
+ ? "card"
223
+ : nodeDisplayMode(node, filteredDensityMode, selectedNodeId, previewNodeId, labelIds, importantIds);
224
+ const point = renderPointForNode(node, options.positions);
225
+ return {
226
+ id: node.id,
227
+ label: node.label,
228
+ type: node.type,
229
+ kind: node.kind,
230
+ community: node.community,
231
+ sourcePath: wikiPathForGraphNode(node),
232
+ x: pointToPercentX(point.x),
233
+ y: pointToPercentY(point.y),
234
+ point,
235
+ displayMode,
236
+ visualRole: nodeVisualRole(node, displayMode, isSelected ? node.id : selectedNodeId, previewNodeId, importantIds),
237
+ priority: Number(node.priority || 0),
238
+ weight: Number(node.weight || 0),
239
+ unavailable: node.unavailable === true,
240
+ selected: isSelected,
241
+ startNode: startIds[node.id] === true,
242
+ previewStart: node.id === previewNodeId,
243
+ labelVisible: labelIds[node.id] === true
244
+ };
245
+ });
246
+
247
+ const nodeById = new Map(nodes.map((node) => [node.id, node]));
248
+ const isFocusedView = focus?.kind === "community";
249
+ const edges = filteredVisibleEdges.flatMap((edge) => {
250
+ const source = nodeById.get(edge.source);
251
+ const target = nodeById.get(edge.target);
252
+ if (!source || !target) return [];
253
+ const curveOffset = options.pathCache?.getEdgeCurve(edge, source.point, target.point) ?? edgeCurveOffset(source.point, target.point, edge);
254
+ const confidence = normalizeEdgeConfidence(edge);
255
+ const relationType = normalizeEdgeRelationType(edge);
256
+ return [{
257
+ id: edge.id,
258
+ source: edge.source,
259
+ target: edge.target,
260
+ type: confidence,
261
+ confidence,
262
+ relationType,
263
+ relationClass: edgeRelationClass(relationType),
264
+ path: makeEdgePathFromPoints(source.point, target.point, curveOffset),
265
+ curveOffset,
266
+ strokeWidth: edgeVisualStrokeWidth(edge, isFocusedView),
267
+ opacity: edgeVisualOpacity(edge, isFocusedView),
268
+ simulationWeight: edgeStrokeWidth(edge)
269
+ }];
270
+ });
271
+
272
+ const allFilteredNodes = applyNodeTypeFilters(model.nodes, typeFilters);
273
+ const communities = model.communities.map((community, index) => {
274
+ const communityNodes = nodes.filter((node) => node.community === community.id);
275
+ const allCommunityNodes = allFilteredNodes.filter((node) => node.community === community.id);
276
+ return {
277
+ id: community.id,
278
+ label: community.label || community.id,
279
+ color: getCommunityColor(theme, Number(community.color_index ?? index)),
280
+ nodeCount: Number(community.node_count ?? allCommunityNodes.length),
281
+ wash: computeCommunityWash(communityNodes)
282
+ };
283
+ });
284
+ const communityById = new Map(communities.map((community) => [community.id, community]));
285
+
286
+ return {
287
+ model,
288
+ layout,
289
+ selectedNodeId,
290
+ focus,
291
+ typeFilters,
292
+ densityMode: filteredDensityMode,
293
+ counts: {
294
+ visibleNodes: filteredVisibleCounts.visible_nodes,
295
+ visibleEdges: filteredVisibleCounts.visible_edges,
296
+ totalNodes: filteredVisibleCounts.total_nodes,
297
+ totalEdges: filteredVisibleCounts.total_edges,
298
+ totalCommunities: filteredVisibleCounts.total_communities
299
+ },
300
+ nodes,
301
+ edges,
302
+ communities,
303
+ minimap: {
304
+ path: MINIMAP_PATH,
305
+ nodes: nodes.slice(0, 60).map((node) => {
306
+ const point = atlasPointToMinimap(node.point) as { x: number; y: number };
307
+ return {
308
+ id: node.id,
309
+ x: point.x,
310
+ y: point.y,
311
+ r: node.selected ? 3.2 : 2.2,
312
+ fill: communityById.get(node.community)?.color || getCommunityColor(theme, 0),
313
+ selected: node.selected
314
+ };
315
+ })
316
+ }
317
+ };
318
+ }
319
+
320
+ export function makeEdgePath(source: AtlasNode, target: AtlasNode, edge: { weight?: number }): string {
321
+ const sourcePoint = atlasNodePoint(source) as { x: number; y: number };
322
+ const targetPoint = atlasNodePoint(target) as { x: number; y: number };
323
+ return makeEdgePathFromPoints(sourcePoint, targetPoint, edgeCurveOffset(sourcePoint, targetPoint, edge));
324
+ }
325
+
326
+ export function makeEdgePathFromPoints(sourcePoint: RenderPosition, targetPoint: RenderPosition, curveOffset: number): string {
327
+ const x1 = sourcePoint.x;
328
+ const y1 = sourcePoint.y;
329
+ const x2 = targetPoint.x;
330
+ const y2 = targetPoint.y;
331
+ const mx = (x1 + x2) / 2;
332
+ const my = (y1 + y2) / 2;
333
+ return `M ${round(x1)} ${round(y1)} Q ${round(mx + curveOffset)} ${round(my - 22)} ${round(x2)} ${round(y2)}`;
334
+ }
335
+
336
+ export function edgeStrokeWidth(edge: { weight?: number }): number {
337
+ return round(1.1 + clampWeight(edge.weight) * 1.8);
338
+ }
339
+
340
+ export function edgeOpacity(edge: { weight?: number }): number {
341
+ return round(0.32 + clampWeight(edge.weight) * 0.44);
342
+ }
343
+
344
+ export function edgeVisualStrokeWidth(edge: { weight?: number }, focusedView: boolean): number {
345
+ if (focusedView) return edgeStrokeWidth(edge);
346
+ return round(0.95 + clampWeight(edge.weight) * 0.75);
347
+ }
348
+
349
+ export function edgeVisualOpacity(edge: { weight?: number }, focusedView: boolean): number {
350
+ if (focusedView) return edgeOpacity(edge);
351
+ return round(0.2 + clampWeight(edge.weight) * 0.22);
352
+ }
353
+
354
+ export function edgeRelationClass(relationType: unknown): string {
355
+ switch (normalizeEdgeRelationText(relationType)) {
356
+ case "实现":
357
+ return "relation-implementation";
358
+ case "依赖":
359
+ return "relation-dependency";
360
+ case "衍生":
361
+ return "relation-derivation";
362
+ case "对比":
363
+ return "relation-contrast";
364
+ case "矛盾":
365
+ return "relation-conflict";
366
+ default:
367
+ return "relation-dependency";
368
+ }
369
+ }
370
+
371
+ export function screenEffectiveDensityMode(visibleNodeCount: number, viewportScale: number): DensityMode {
372
+ const count = Number.isFinite(Number(visibleNodeCount)) ? Math.max(0, Number(visibleNodeCount)) : 0;
373
+ const scale = Number.isFinite(Number(viewportScale)) ? clamp(Number(viewportScale), 0.25, 4) : 1;
374
+ return getAtlasDensityMode(Math.ceil(count / (scale * scale))) as DensityMode;
375
+ }
376
+
377
+ export function nodeDisplayModeForDensity(
378
+ node: Pick<RenderableNode, "selected" | "labelVisible" | "visualRole">,
379
+ densityMode: DensityMode
380
+ ): NodeDisplayMode {
381
+ if (node.selected) return "card";
382
+ if (densityMode === "card") return "card";
383
+ if (densityMode === "compact-card") return "compact-card";
384
+ const shouldShowLabel = node.labelVisible || node.visualRole !== "map-pin";
385
+ if (densityMode === "point-plus-focus") return shouldShowLabel ? "compact-card" : "point";
386
+ return shouldShowLabel ? "compact-card" : "overview";
387
+ }
388
+
389
+ function applyPinsToGraphData(data: GraphData, pins: PinMap): GraphData {
390
+ if (!Object.keys(pins).length) return data;
391
+ return {
392
+ ...data,
393
+ nodes: data.nodes.map((node) => {
394
+ const pin = pins[pinKeyForNode(node)];
395
+ if (!pin) return node;
396
+ return {
397
+ ...node,
398
+ x: normalizePinnedX(pin.x),
399
+ y: normalizePinnedY(pin.y)
400
+ };
401
+ })
402
+ };
403
+ }
404
+
405
+ function normalizeGraphFocus(
406
+ focus: GraphFocusInput | undefined,
407
+ model: { communityById: Record<string, AtlasCommunity> }
408
+ ): GraphFocusInput {
409
+ if (!focus || focus.kind !== "community") return null;
410
+ const id = String(focus.id || "");
411
+ return id && model.communityById[id] ? { kind: "community", id } : null;
412
+ }
413
+
414
+ function normalizeGraphTypeFilters(filters: GraphTypeFilters | undefined, nodes: AtlasNode[]): GraphTypeFilters {
415
+ const normalized: GraphTypeFilters = {};
416
+ for (const node of nodes) {
417
+ normalized[node.type] = filters?.[node.type] !== false;
418
+ }
419
+ return normalized;
420
+ }
421
+
422
+ function applyNodeTypeFilters(nodes: AtlasNode[], filters: GraphTypeFilters): AtlasNode[] {
423
+ return nodes.filter((node) => filters[node.type] !== false);
424
+ }
425
+
426
+ function normalizeEdgeConfidence(edge: AtlasEdge): string {
427
+ const value = String(edge.confidence || edge.type || "EXTRACTED").toUpperCase();
428
+ if (value === "INFERRED" || value === "AMBIGUOUS" || value === "UNVERIFIED") return value.toLowerCase();
429
+ return "extracted";
430
+ }
431
+
432
+ function normalizeEdgeRelationType(edge: AtlasEdge): string {
433
+ return normalizeEdgeRelationText(edge.relation_type || "依赖");
434
+ }
435
+
436
+ function normalizeEdgeRelationText(relationType: unknown): string {
437
+ const value = String(relationType || "依赖").trim();
438
+ return value || "依赖";
439
+ }
440
+
441
+ function pinKeyForNode(node: { source_path?: unknown; path?: unknown; source?: unknown; id: string }): WikiPath {
442
+ return wikiPathForGraphNode(node);
443
+ }
444
+
445
+ function renderPointForNode(node: AtlasNode, positions?: RenderPositionMap): RenderPosition {
446
+ const position = positions?.[node.id];
447
+ if (position) {
448
+ return {
449
+ x: clamp(position.x, 0, WORLD_WIDTH),
450
+ y: clamp(position.y, 0, WORLD_HEIGHT)
451
+ };
452
+ }
453
+ return atlasNodePoint(node) as RenderPosition;
454
+ }
455
+
456
+ function pointToPercentX(value: number): number {
457
+ return round(clamp(value, 0, WORLD_WIDTH) / WORLD_WIDTH * 100);
458
+ }
459
+
460
+ function pointToPercentY(value: number): number {
461
+ return round(clamp(value, 0, WORLD_HEIGHT) / WORLD_HEIGHT * 100);
462
+ }
463
+
464
+ function edgeCurveOffset(sourcePoint: RenderPosition, targetPoint: RenderPosition, edge: { weight?: number }): number {
465
+ const sourceYPercent = sourcePoint.y / WORLD_HEIGHT * 100;
466
+ const targetYPercent = targetPoint.y / WORLD_HEIGHT * 100;
467
+ return Math.max(-76, Math.min(76, (sourceYPercent - targetYPercent) * 1.8 + (clampWeight(edge.weight) - 0.5) * 24));
468
+ }
469
+
470
+ function normalizePinnedX(value: number): number {
471
+ return value > 100 ? clamp(value / WORLD_WIDTH * 100, 0, 100) : clamp(value, 0, 100);
472
+ }
473
+
474
+ function normalizePinnedY(value: number): number {
475
+ return value > 100 ? clamp(value / WORLD_HEIGHT * 100, 0, 100) : clamp(value, 0, 100);
476
+ }
477
+
478
+ function resolveSelectedNodeIds(
479
+ model: { byId: Record<string, AtlasNode>; nodes: AtlasNode[] },
480
+ options: BuildRenderableGraphOptions
481
+ ): string[] {
482
+ if (options.selection?.kind === "node" && model.byId[options.selection.id]) return [options.selection.id];
483
+ if (options.selection?.kind === "community") {
484
+ const communityId = options.selection.id;
485
+ return model.nodes.filter((node) => node.community === communityId).map((node) => node.id);
486
+ }
487
+ if (options.selection?.kind === "nodes") {
488
+ const selected = new Set(options.selection.ids);
489
+ return model.nodes.map((node) => node.id).filter((id) => selected.has(id));
490
+ }
491
+ if (options.selectedNodeId && model.byId[options.selectedNodeId]) return [options.selectedNodeId];
492
+ return [];
493
+ }
494
+
495
+ function firstPreviewNodeId(visible: { starts: Array<{ node: AtlasNode }>; nodes: AtlasNode[] }): string | null {
496
+ const firstStart = visible.starts.find((entry) => entry?.node);
497
+ if (firstStart?.node) return firstStart.node.id;
498
+ const fallback = visible.nodes.slice().sort((left, right) => Number(right.priority || 0) - Number(left.priority || 0))[0];
499
+ return fallback ? fallback.id : null;
500
+ }
501
+
502
+ function nodeDisplayMode(
503
+ node: AtlasNode,
504
+ densityMode: DensityMode,
505
+ selectedNodeId: string | null,
506
+ previewNodeId: string | null,
507
+ labelNodeIds: Record<string, boolean>,
508
+ importantNodeIds: Record<string, boolean>
509
+ ): NodeDisplayMode {
510
+ if (node.id === selectedNodeId) return "card";
511
+ if (previewNodeId && node.id === previewNodeId && (densityMode === "overview" || densityMode === "point-plus-focus")) return "compact-card";
512
+ if (importantNodeIds[node.id] && (densityMode === "overview" || densityMode === "point-plus-focus")) return "compact-card";
513
+ if (densityMode === "overview") return labelNodeIds[node.id] ? "compact-card" : "overview";
514
+ if (densityMode === "point-plus-focus") return labelNodeIds[node.id] ? "compact-card" : "point";
515
+ return densityMode;
516
+ }
517
+
518
+ function nodeVisualRole(
519
+ node: AtlasNode,
520
+ displayMode: NodeDisplayMode,
521
+ selectedNodeId: string | null,
522
+ previewNodeId: string | null,
523
+ importantNodeIds: Record<string, boolean>
524
+ ): NodeVisualRole {
525
+ if (node.id === selectedNodeId) return "cinnabar-note";
526
+ if (displayMode === "point" || displayMode === "overview") return "map-pin";
527
+ if (previewNodeId && node.id === previewNodeId) return "index-slip";
528
+ if (importantNodeIds[node.id]) return "index-slip";
529
+ return "landmark";
530
+ }
531
+
532
+ function computeCommunityWash(nodes: RenderableNode[]): RenderableCommunity["wash"] {
533
+ if (!nodes.length) return null;
534
+ const points = communityWashCorePoints(nodes);
535
+ const minX = Math.min(...points.map((point) => point.x));
536
+ const maxX = Math.max(...points.map((point) => point.x));
537
+ const minY = Math.min(...points.map((point) => point.y));
538
+ const maxY = Math.max(...points.map((point) => point.y));
539
+ return {
540
+ cx: round((minX + maxX) / 2),
541
+ cy: round((minY + maxY) / 2),
542
+ rx: round(Math.max(54, (maxX - minX) / 2 + 46)),
543
+ ry: round(Math.max(36, (maxY - minY) / 2 + 34)),
544
+ opacity: nodes.length > 1 ? 0.11 : 0.06
545
+ };
546
+ }
547
+
548
+ function communityWashCorePoints(nodes: RenderableNode[]): RenderPosition[] {
549
+ const points = nodes.map((node) => node.point);
550
+ if (points.length <= 3) return points;
551
+ const scored = points
552
+ .map((point) => ({
553
+ point,
554
+ neighborScore: nearestNeighborScore(point, points)
555
+ }))
556
+ .sort((left, right) => left.neighborScore - right.neighborScore);
557
+ const coreCount = Math.max(2, Math.ceil(points.length * 0.75));
558
+ const core = scored.slice(0, coreCount);
559
+ const excluded = scored.slice(coreCount);
560
+ const coreMax = Math.max(...core.map((item) => item.neighborScore));
561
+ const excludedMin = Math.min(...excluded.map((item) => item.neighborScore));
562
+ if (!Number.isFinite(excludedMin) || excludedMin <= Math.max(180, coreMax * 2.5)) {
563
+ return points;
564
+ }
565
+ return core.map((item) => item.point);
566
+ }
567
+
568
+ function nearestNeighborScore(point: RenderPosition, points: RenderPosition[]): number {
569
+ const distances = points
570
+ .filter((candidate) => candidate !== point)
571
+ .map((candidate) => distance(point, candidate))
572
+ .sort((left, right) => left - right);
573
+ const nearest = distances.slice(0, Math.min(2, distances.length));
574
+ return nearest.reduce((sum, value) => sum + value, 0) / Math.max(1, nearest.length);
575
+ }
576
+
577
+ function distance(left: RenderPosition, right: RenderPosition): number {
578
+ return Math.hypot(left.x - right.x, left.y - right.y);
579
+ }
580
+
581
+ function clampWeight(value: unknown): number {
582
+ const numeric = Number(value);
583
+ if (!Number.isFinite(numeric)) return 0.6;
584
+ return clamp(numeric, 0, 1);
585
+ }
586
+
587
+ function clamp(value: number, min: number, max: number): number {
588
+ return Math.max(min, Math.min(max, value));
589
+ }
590
+
591
+ function round(value: number): number {
592
+ return Math.round(value * 1000) / 1000;
593
+ }