@bohuyeshan/openagent-labforge-core 3.11.5 → 3.13.0

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 (272) hide show
  1. package/README.ja.md +130 -343
  2. package/README.ko.md +128 -337
  3. package/README.md +229 -584
  4. package/README.ru.md +131 -364
  5. package/README.zh-cn.md +231 -547
  6. package/bin/openagent-labforge.js +95 -9
  7. package/bin/platform.test.ts +20 -21
  8. package/dist/agents/article-writer.d.ts +7 -0
  9. package/dist/agents/atlas/default.d.ts +1 -1
  10. package/dist/agents/atlas/gemini.d.ts +1 -1
  11. package/dist/agents/atlas/gpt.d.ts +1 -1
  12. package/dist/agents/bio-methodologist.d.ts +1 -1
  13. package/dist/agents/bio-orchestrator.d.ts +7 -0
  14. package/dist/agents/bio-skill-guidance.d.ts +1 -0
  15. package/dist/agents/builtin-agents/general-agents.d.ts +0 -1
  16. package/dist/agents/builtin-agents/sisyphus-agent.d.ts +16 -0
  17. package/dist/agents/dynamic-agent-prompt-builder.d.ts +0 -2
  18. package/dist/agents/engineering-capability.d.ts +7 -0
  19. package/dist/agents/env-context.d.ts +1 -1
  20. package/dist/agents/github-scout.d.ts +7 -0
  21. package/dist/agents/index.d.ts +0 -1
  22. package/dist/agents/metis.d.ts +1 -1
  23. package/dist/agents/momus.d.ts +1 -1
  24. package/dist/agents/prometheus/behavioral-summary.d.ts +1 -1
  25. package/dist/agents/prometheus/gemini.d.ts +1 -1
  26. package/dist/agents/prometheus/gpt.d.ts +1 -1
  27. package/dist/agents/prometheus/interview-mode.d.ts +1 -1
  28. package/dist/agents/prometheus/plan-generation.d.ts +1 -1
  29. package/dist/agents/prometheus/plan-template.d.ts +1 -1
  30. package/dist/agents/prometheus/system-prompt.d.ts +1 -1
  31. package/dist/agents/scientific-writer.d.ts +7 -0
  32. package/dist/agents/sisyphus-junior/gpt-5-3-codex.d.ts +1 -1
  33. package/dist/agents/sisyphus-junior/gpt-5-4.d.ts +1 -1
  34. package/dist/agents/sisyphus-junior/gpt.d.ts +1 -1
  35. package/dist/agents/tech-scout.d.ts +7 -0
  36. package/dist/agents/types.d.ts +1 -1
  37. package/dist/agents/wase.d.ts +8 -0
  38. package/dist/agents/wet-lab-designer.d.ts +7 -0
  39. package/dist/agents/writing-style-rules.d.ts +1 -0
  40. package/dist/cli/config-manager/bun-install.d.ts +1 -6
  41. package/dist/cli/config-manager/cleanup-managed-mcp-from-opencode-config.d.ts +2 -0
  42. package/dist/cli/config-manager/cleanup-stale-managed-agents.d.ts +2 -0
  43. package/dist/cli/config-manager/parse-opencode-config-file.d.ts +2 -0
  44. package/dist/cli/config-manager/plugin-name-with-version.d.ts +1 -1
  45. package/dist/cli/config-manager/sync-static-agent-to-opencode-config.d.ts +2 -0
  46. package/dist/cli/config-manager/sync-static-mcp-to-opencode-config.d.ts +2 -0
  47. package/dist/cli/config-manager/write-bootstrap-skill.d.ts +15 -0
  48. package/dist/cli/config-manager.d.ts +5 -0
  49. package/dist/cli/index.js +24986 -15362
  50. package/dist/cli/install-validators.d.ts +0 -1
  51. package/dist/cli/model-fallback-types.d.ts +0 -1
  52. package/dist/cli/run/index.d.ts +0 -1
  53. package/dist/cli/run/types.d.ts +0 -1
  54. package/dist/cli/types.d.ts +0 -3
  55. package/dist/config/schema/agent-names.d.ts +36 -3
  56. package/dist/config/schema/agent-overrides.d.ts +504 -0
  57. package/dist/config/schema/background-task.d.ts +0 -2
  58. package/dist/config/schema/experimental.d.ts +5 -0
  59. package/dist/config/schema/git-master.d.ts +0 -1
  60. package/dist/config/schema/hooks.d.ts +0 -2
  61. package/dist/config/schema/mcp-policy.d.ts +1 -0
  62. package/dist/config/schema/oh-my-opencode-config.d.ts +526 -54
  63. package/dist/config/schema.d.ts +0 -1
  64. package/dist/create-hooks.d.ts +0 -13
  65. package/dist/features/background-agent/compaction-aware-message-resolver.d.ts +1 -16
  66. package/dist/features/background-agent/constants.d.ts +2 -1
  67. package/dist/features/background-agent/manager.d.ts +5 -20
  68. package/dist/features/background-agent/process-cleanup.d.ts +1 -1
  69. package/dist/features/background-agent/task-history.d.ts +0 -1
  70. package/dist/features/background-agent/task-poller.d.ts +0 -1
  71. package/dist/features/background-agent/types.d.ts +0 -4
  72. package/dist/features/builtin-commands/commands.d.ts +4 -1
  73. package/dist/features/builtin-skills/skills/bio-methods.d.ts +2 -0
  74. package/dist/features/builtin-skills/skills/bio-pipeline.d.ts +2 -0
  75. package/dist/features/builtin-skills/skills/bio-tools.d.ts +2 -0
  76. package/dist/features/builtin-skills/skills/bio-visualization.d.ts +2 -0
  77. package/dist/features/builtin-skills/skills/cell-annotation.d.ts +2 -0
  78. package/dist/features/builtin-skills/skills/differential-expression.d.ts +2 -0
  79. package/dist/features/builtin-skills/skills/geo-query.d.ts +2 -0
  80. package/dist/features/builtin-skills/skills/index.d.ts +14 -0
  81. package/dist/features/builtin-skills/skills/paper-evidence.d.ts +2 -0
  82. package/dist/features/builtin-skills/skills/pubmed-search.d.ts +2 -0
  83. package/dist/features/builtin-skills/skills/scrna-preprocessing.d.ts +2 -0
  84. package/dist/features/builtin-skills/skills/sequence-analysis.d.ts +2 -0
  85. package/dist/features/builtin-skills/skills/structural-biology.d.ts +2 -0
  86. package/dist/features/builtin-skills/skills/vector-design.d.ts +2 -0
  87. package/dist/features/builtin-skills/skills/wet-lab-design.d.ts +2 -0
  88. package/dist/features/claude-code-agent-loader/loader.d.ts +3 -3
  89. package/dist/features/claude-code-agent-loader/types.d.ts +1 -8
  90. package/dist/features/claude-code-mcp-loader/configure-allowed-env-vars.d.ts +5 -0
  91. package/dist/features/claude-code-mcp-loader/index.d.ts +1 -0
  92. package/dist/features/claude-code-mcp-loader/types.d.ts +3 -0
  93. package/dist/features/claude-code-plugin-loader/agent-loader.d.ts +2 -2
  94. package/dist/features/claude-code-plugin-loader/loader.d.ts +2 -2
  95. package/dist/features/claude-code-plugin-loader/types.d.ts +1 -1
  96. package/dist/features/claude-code-session-state/state.d.ts +5 -0
  97. package/dist/features/opencode-skill-loader/git-master-template-injection.d.ts +1 -1
  98. package/dist/features/opencode-skill-loader/project-skill-directory-discovery.d.ts +1 -0
  99. package/dist/features/opencode-skill-loader/skill-metadata-validator.d.ts +8 -0
  100. package/dist/features/skill-mcp-manager/types.d.ts +0 -4
  101. package/dist/features/tmux-subagent/index.d.ts +0 -1
  102. package/dist/features/tmux-subagent/manager.d.ts +0 -5
  103. package/dist/features/tmux-subagent/types.d.ts +0 -2
  104. package/dist/hooks/atlas/tool-execute-after.d.ts +0 -2
  105. package/dist/hooks/atlas/types.d.ts +0 -2
  106. package/dist/hooks/atlas/verification-reminders.d.ts +0 -4
  107. package/dist/hooks/auto-slash-command/hook.d.ts +0 -7
  108. package/dist/hooks/auto-update-checker/checker.d.ts +1 -3
  109. package/dist/hooks/auto-update-checker/constants.d.ts +2 -2
  110. package/dist/hooks/comment-checker/downloader.d.ts +1 -1
  111. package/dist/hooks/compaction-context-injector/hook.d.ts +1 -5
  112. package/dist/hooks/context-window-monitor.d.ts +5 -2
  113. package/dist/hooks/index.d.ts +0 -2
  114. package/dist/hooks/keyword-detector/detector.d.ts +1 -1
  115. package/dist/hooks/keyword-detector/hook.d.ts +2 -2
  116. package/dist/hooks/keyword-detector/index.d.ts +1 -0
  117. package/dist/hooks/keyword-detector/semantic-hint.d.ts +4 -0
  118. package/dist/hooks/keyword-detector/ultrawork/autonomous.d.ts +8 -0
  119. package/dist/hooks/preemptive-compaction.d.ts +5 -2
  120. package/dist/hooks/runtime-fallback/hook.d.ts +3 -2
  121. package/dist/hooks/runtime-fallback/message-update-handler.d.ts +2 -1
  122. package/dist/hooks/runtime-fallback/types.d.ts +3 -56
  123. package/dist/hooks/session-notification-scheduler.d.ts +3 -5
  124. package/dist/hooks/session-notification.d.ts +0 -2
  125. package/dist/hooks/session-recovery/tool-pairing.d.ts +16 -0
  126. package/dist/hooks/start-work/index.d.ts +1 -1
  127. package/dist/hooks/start-work/worktree-detector.d.ts +0 -7
  128. package/dist/hooks/todo-continuation-enforcer/compaction-guard.d.ts +4 -0
  129. package/dist/hooks/todo-continuation-enforcer/constants.d.ts +6 -5
  130. package/dist/hooks/todo-continuation-enforcer/handler.d.ts +0 -1
  131. package/dist/hooks/todo-continuation-enforcer/idle-event.d.ts +0 -1
  132. package/dist/hooks/todo-continuation-enforcer/resolve-message-info.d.ts +3 -0
  133. package/dist/hooks/todo-continuation-enforcer/session-state.d.ts +1 -1
  134. package/dist/hooks/todo-continuation-enforcer/types.d.ts +8 -3
  135. package/dist/hooks/tool-output-truncator.d.ts +0 -1
  136. package/dist/index.js +56627 -56933
  137. package/dist/mcp/extended.d.ts +4 -2
  138. package/dist/mcp/index.d.ts +2 -1
  139. package/dist/mcp/types.d.ts +2 -3
  140. package/dist/openagent-labforge.schema.json +1362 -83
  141. package/dist/plugin/hooks/create-continuation-hooks.d.ts +1 -2
  142. package/dist/plugin/hooks/create-core-hooks.d.ts +0 -1
  143. package/dist/plugin/hooks/create-session-hooks.d.ts +1 -2
  144. package/dist/plugin/ultrawork-model-override.d.ts +11 -1
  145. package/dist/plugin-dispose.d.ts +12 -10
  146. package/dist/plugin-handlers/agent-config-handler.d.ts +0 -1
  147. package/dist/plugin-handlers/prometheus-agent-config-builder.d.ts +1 -1
  148. package/dist/plugin-state.d.ts +0 -5
  149. package/dist/shared/agent-display-names.d.ts +1 -0
  150. package/dist/shared/data-path.d.ts +1 -1
  151. package/dist/shared/dynamic-truncator.d.ts +7 -4
  152. package/dist/shared/external-plugin-detector.d.ts +7 -0
  153. package/dist/shared/index.d.ts +5 -3
  154. package/dist/shared/jsonc-parser.d.ts +4 -0
  155. package/dist/shared/mcp-local-command-normalizer.d.ts +1 -0
  156. package/dist/shared/migrate-legacy-config-file.d.ts +1 -0
  157. package/dist/shared/model-error-classifier.d.ts +1 -2
  158. package/dist/shared/opencode-command-dirs.d.ts +0 -1
  159. package/dist/shared/plugin-identity.d.ts +2 -3
  160. package/dist/shared/project-discovery-dirs.d.ts +4 -0
  161. package/dist/shared/session-model-state.d.ts +1 -2
  162. package/dist/shared/system-directive.d.ts +5 -6
  163. package/dist/tools/call-omo-agent/background-executor.d.ts +1 -2
  164. package/dist/tools/call-omo-agent/constants.d.ts +2 -2
  165. package/dist/tools/call-omo-agent/sync-executor.d.ts +3 -11
  166. package/dist/tools/call-omo-agent/tools.d.ts +2 -2
  167. package/dist/tools/call-omo-agent/types.d.ts +13 -0
  168. package/dist/tools/delegate-task/constants.d.ts +1 -1
  169. package/dist/tools/delegate-task/model-selection.d.ts +0 -1
  170. package/dist/tools/delegate-task/model-string-parser.d.ts +3 -1
  171. package/dist/tools/delegate-task/parent-context-resolver.d.ts +22 -0
  172. package/dist/tools/lsp/constants.d.ts +0 -1
  173. package/dist/tools/lsp/lsp-client-transport.d.ts +2 -4
  174. package/dist/tools/lsp/lsp-client-wrapper.d.ts +1 -2
  175. package/generated/skills-bundles/catalog.json +1 -1
  176. package/generated/skills-bundles/full/skills/data-analysis/experiment-monitoring/auto-claude__monitor-experiment/SKILL.md +56 -55
  177. package/generated/skills-bundles/full/skills/data-analysis/experiment-ops/auto-claude__run-experiment/SKILL.md +105 -104
  178. package/generated/skills-bundles/full/skills/data-analysis/optimization/auto-claude__dse-loop/SKILL.md +272 -271
  179. package/generated/skills-bundles/full/skills/data-analysis/statistics/auto-claude__analyze-results/SKILL.md +40 -39
  180. package/generated/skills-bundles/full/skills/data-analysis/visualization/auto-claude__paper-figure/SKILL.md +274 -273
  181. package/generated/skills-bundles/full/skills/productivity/visual-design/auto-claude__pixel-art/SKILL.md +131 -130
  182. package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-compile/SKILL.md +245 -244
  183. package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-plan/SKILL.md +247 -246
  184. package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-write/SKILL.md +303 -302
  185. package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-write/templates/iclr2026.tex +84 -84
  186. package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-write/templates/icml2025.tex +87 -87
  187. package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-write/templates/math_commands.tex +48 -48
  188. package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-write/templates/neurips2025.tex +80 -80
  189. package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-writing/SKILL.md +31 -31
  190. package/generated/skills-bundles/full/skills/research/literature-and-web-search/auto-claude__arxiv/SKILL.md +126 -125
  191. package/generated/skills-bundles/full/skills/research/literature-and-web-search/auto-claude__novelty-check/SKILL.md +80 -79
  192. package/generated/skills-bundles/full/skills/research/literature-and-web-search/auto-claude__research-lit/SKILL.md +187 -186
  193. package/generated/skills-bundles/full/skills/research/research-ideation/auto-claude__idea-creator/SKILL.md +11 -11
  194. package/generated/skills-bundles/full/skills/research/research-ideation/auto-claude__idea-discovery/SKILL.md +18 -18
  195. package/generated/skills-bundles/full/skills/research/research-ideation/auto-claude__idea-discovery-robot/SKILL.md +20 -20
  196. package/generated/skills-bundles/full/skills/research/research-ideation/auto-claude__research-pipeline/SKILL.md +15 -15
  197. package/generated/skills-bundles/full/skills/research/theory-writing/auto-claude__proof-writer/SKILL.md +217 -216
  198. package/generated/skills-bundles/paper/skills/data-analysis/experiment-monitoring/auto-claude__monitor-experiment/SKILL.md +56 -55
  199. package/generated/skills-bundles/paper/skills/data-analysis/experiment-ops/auto-claude__run-experiment/SKILL.md +105 -104
  200. package/generated/skills-bundles/paper/skills/data-analysis/optimization/auto-claude__dse-loop/SKILL.md +272 -271
  201. package/generated/skills-bundles/paper/skills/data-analysis/statistics/auto-claude__analyze-results/SKILL.md +40 -39
  202. package/generated/skills-bundles/paper/skills/data-analysis/visualization/auto-claude__paper-figure/SKILL.md +274 -273
  203. package/generated/skills-bundles/paper/skills/productivity/visual-design/auto-claude__pixel-art/SKILL.md +131 -130
  204. package/generated/skills-bundles/paper/skills/research/document-authoring/auto-claude__paper-compile/SKILL.md +245 -244
  205. package/generated/skills-bundles/paper/skills/research/document-authoring/auto-claude__paper-plan/SKILL.md +247 -246
  206. package/generated/skills-bundles/paper/skills/research/document-authoring/auto-claude__paper-write/SKILL.md +303 -302
  207. package/generated/skills-bundles/paper/skills/research/document-authoring/auto-claude__paper-write/templates/iclr2026.tex +84 -84
  208. package/generated/skills-bundles/paper/skills/research/document-authoring/auto-claude__paper-write/templates/icml2025.tex +87 -87
  209. package/generated/skills-bundles/paper/skills/research/document-authoring/auto-claude__paper-write/templates/math_commands.tex +48 -48
  210. package/generated/skills-bundles/paper/skills/research/document-authoring/auto-claude__paper-write/templates/neurips2025.tex +80 -80
  211. package/generated/skills-bundles/paper/skills/research/document-authoring/auto-claude__paper-writing/SKILL.md +31 -31
  212. package/generated/skills-bundles/paper/skills/research/literature-and-web-search/auto-claude__arxiv/SKILL.md +126 -125
  213. package/generated/skills-bundles/paper/skills/research/literature-and-web-search/auto-claude__novelty-check/SKILL.md +80 -79
  214. package/generated/skills-bundles/paper/skills/research/literature-and-web-search/auto-claude__research-lit/SKILL.md +187 -186
  215. package/generated/skills-bundles/paper/skills/research/research-ideation/auto-claude__idea-creator/SKILL.md +11 -11
  216. package/generated/skills-bundles/paper/skills/research/research-ideation/auto-claude__idea-discovery/SKILL.md +18 -18
  217. package/generated/skills-bundles/paper/skills/research/research-ideation/auto-claude__idea-discovery-robot/SKILL.md +20 -20
  218. package/generated/skills-bundles/paper/skills/research/research-ideation/auto-claude__research-pipeline/SKILL.md +15 -15
  219. package/generated/skills-bundles/paper/skills/research/theory-writing/auto-claude__proof-writer/SKILL.md +217 -216
  220. package/package.json +36 -32
  221. package/dist/cli/openai-only-model-catalog.d.ts +0 -3
  222. package/dist/cli/run/model-resolver.d.ts +0 -4
  223. package/dist/config/schema/git-env-prefix.d.ts +0 -5
  224. package/dist/features/background-agent/remove-task-toast-tracking.d.ts +0 -1
  225. package/dist/features/background-agent/subagent-spawn-limits.d.ts +0 -23
  226. package/dist/features/claude-code-agent-loader/claude-model-mapper.d.ts +0 -4
  227. package/dist/features/tmux-subagent/pane-state-parser.d.ts +0 -8
  228. package/dist/features/tmux-subagent/tracked-session-state.d.ts +0 -8
  229. package/dist/hooks/atlas/boulder-session-lineage.d.ts +0 -6
  230. package/dist/hooks/atlas/final-wave-approval-gate.d.ts +0 -4
  231. package/dist/hooks/atlas/idle-event.d.ts +0 -8
  232. package/dist/hooks/atlas/resolve-active-boulder-session.d.ts +0 -11
  233. package/dist/hooks/auto-slash-command/processed-command-store.d.ts +0 -7
  234. package/dist/hooks/auto-update-checker/checker/sync-package-json.d.ts +0 -7
  235. package/dist/hooks/compaction-context-injector/compaction-context-prompt.d.ts +0 -1
  236. package/dist/hooks/compaction-context-injector/constants.d.ts +0 -5
  237. package/dist/hooks/compaction-context-injector/recovery-prompt-config.d.ts +0 -6
  238. package/dist/hooks/compaction-context-injector/recovery.d.ts +0 -6
  239. package/dist/hooks/compaction-context-injector/session-id.d.ts +0 -2
  240. package/dist/hooks/compaction-context-injector/session-prompt-config-resolver.d.ts +0 -16
  241. package/dist/hooks/compaction-context-injector/tail-monitor.d.ts +0 -13
  242. package/dist/hooks/compaction-context-injector/types.d.ts +0 -43
  243. package/dist/hooks/compaction-context-injector/validated-model.d.ts +0 -13
  244. package/dist/hooks/delegate-task-english-directive/hook.d.ts +0 -14
  245. package/dist/hooks/delegate-task-english-directive/index.d.ts +0 -1
  246. package/dist/hooks/gpt-permission-continuation/assistant-message.d.ts +0 -23
  247. package/dist/hooks/gpt-permission-continuation/constants.d.ts +0 -4
  248. package/dist/hooks/gpt-permission-continuation/detector.d.ts +0 -1
  249. package/dist/hooks/gpt-permission-continuation/handler.d.ts +0 -12
  250. package/dist/hooks/gpt-permission-continuation/index.d.ts +0 -13
  251. package/dist/hooks/gpt-permission-continuation/session-state.d.ts +0 -15
  252. package/dist/hooks/ralph-loop/pending-verification-handler.d.ts +0 -16
  253. package/dist/hooks/runtime-fallback/fallback-bootstrap-model.d.ts +0 -10
  254. package/dist/hooks/runtime-fallback/fallback-retry-dispatcher.d.ts +0 -11
  255. package/dist/hooks/runtime-fallback/last-user-retry-parts.d.ts +0 -4
  256. package/dist/hooks/runtime-fallback/retry-model-payload.d.ts +0 -7
  257. package/dist/hooks/runtime-fallback/session-messages.d.ts +0 -9
  258. package/dist/hooks/runtime-fallback/session-status-handler.d.ts +0 -3
  259. package/dist/hooks/runtime-fallback/visible-assistant-response.d.ts +0 -3
  260. package/dist/hooks/session-notification-content.d.ts +0 -30
  261. package/dist/plugin/normalize-tool-arg-schemas.d.ts +0 -2
  262. package/dist/plugin/ultrawork-variant-availability.d.ts +0 -6
  263. package/dist/shared/compaction-agent-config-checkpoint.d.ts +0 -11
  264. package/dist/shared/context-limit-resolver.d.ts +0 -5
  265. package/dist/shared/fallback-chain-from-models.d.ts +0 -3
  266. package/dist/shared/question-denied-session-permission.d.ts +0 -6
  267. package/dist/shared/retry-status-utils.d.ts +0 -2
  268. package/dist/shared/vision-capable-models-cache.d.ts +0 -4
  269. package/dist/tools/delegate-task/cancel-unstable-agent-task.d.ts +0 -2
  270. package/dist/tools/look-at/multimodal-fallback-chain.d.ts +0 -4
  271. package/dist/tools/lsp/directory-diagnostics.d.ts +0 -1
  272. package/dist/tools/lsp/server-path-bases.d.ts +0 -1
@@ -6,276 +6,277 @@ allowed-tools: "Bash(*), Read, Write, Edit, Grep, Glob, Agent, mcp__codex__codex
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  metadata:
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  category: "data-analysis/visualization"
8
8
  ---
9
- # Paper Figure: Publication-Quality Plots from Experiment Data
10
-
11
- Generate all figures and tables for a paper based on: **$ARGUMENTS**
12
-
13
- ## Scope: What This Skill Can and Cannot Do
14
-
15
- | Category | Can auto-generate? | Examples |
16
- |----------|-------------------|----------|
17
- | **Data-driven plots** | ✅ Yes | Line plots (training curves), bar charts (method comparison), scatter plots, heatmaps, box/violin plots |
18
- | **Comparison tables** | ✅ Yes | LaTeX tables comparing prior bounds, method features, ablation results |
19
- | **Multi-panel figures** | ✅ Yes | Subfigure grids combining multiple plots (e.g., 3×3 dataset × method) |
20
- | **Architecture/pipeline diagrams** | No — manual | Model architecture, data flow diagrams, system overviews. At best can generate a rough TikZ skeleton, but **expect to draw these yourself** using tools like draw.io, Figma, or TikZ |
21
- | **Generated image grids** | ❌ No — manual | Grids of generated samples (e.g., GAN/diffusion outputs). These come from running your model, not from this skill |
22
- | **Photographs / screenshots** | ❌ No — manual | Real-world images, UI screenshots, qualitative examples |
23
-
24
- **In practice:** For a typical ML paper, this skill handles ~60% of figures (all data plots + tables). The remaining ~40% (hero figure, architecture diagram, qualitative results) need to be created manually and placed in `figures/` before running `/paper-write`. The skill will detect these as "existing figures" and preserve them.
25
-
26
- ## Constants
27
-
28
- - **STYLE = `publication`** — Visual style preset. Options: `publication` (default, clean for print), `poster` (larger fonts), `slide` (bold colors)
29
- - **DPI = 300**Output resolution
30
- - **FORMAT = `pdf`** — Output format. Options: `pdf` (vector, best for LaTeX), `png` (raster fallback)
31
- - **COLOR_PALETTE = `tab10`** — Default matplotlib color cycle. Options: `tab10`, `Set2`, `colorblind` (deuteranopia-safe)
32
- - **FONT_SIZE = 10**Base font size (matches typical conference body text)
33
- - **FIG_DIR = `figures/`**Output directory for generated figures
34
- - **REVIEWER_MODEL = `gpt-5.4`**Model used via Codex MCP for figure quality review.
35
-
36
- ## Inputs
37
-
38
- 1. **PAPER_PLAN.md** — figure plan table (from `/paper-plan`)
39
- 2. **Experiment data** — JSON files, CSV files, or screen logs in `figures/` or project root
40
- 3. **Existing figures** — any manually created figures to preserve
41
-
42
- If no PAPER_PLAN.md exists, scan for data files and ask the user which figures to generate.
43
-
44
- ## Workflow
45
-
46
- ### Step 1: Read Figure Plan
47
-
48
- Parse the Figure Plan table from PAPER_PLAN.md:
49
-
50
- ```markdown
51
- | ID | Type | Description | Data Source | Priority |
52
- |----|------|-------------|-------------|----------|
53
- | Fig 1 | Architecture | ... | manual | HIGH |
54
- | Fig 2 | Line plot | ... | figures/exp.json | HIGH |
55
- ```
56
-
57
- Identify:
58
- - Which figures can be auto-generated from data
59
- - Which need manual creation (architecture diagrams, etc.)
60
- - Which are comparison tables (generate as LaTeX)
61
-
62
- ### Step 2: Set Up Plotting Environment
63
-
64
- Create a shared style configuration script:
65
-
66
- ```python
67
- # paper_plot_style.py — shared across all figure scripts
68
- import matplotlib.pyplot as plt
69
- import matplotlib
70
- matplotlib.rcParams.update({
71
- 'font.size': FONT_SIZE,
72
- 'font.family': 'serif',
73
- 'font.serif': ['Times New Roman', 'Times', 'DejaVu Serif'],
74
- 'axes.labelsize': FONT_SIZE,
75
- 'axes.titlesize': FONT_SIZE + 1,
76
- 'xtick.labelsize': FONT_SIZE - 1,
77
- 'ytick.labelsize': FONT_SIZE - 1,
78
- 'legend.fontsize': FONT_SIZE - 1,
79
- 'figure.dpi': DPI,
80
- 'savefig.dpi': DPI,
81
- 'savefig.bbox': 'tight',
82
- 'savefig.pad_inches': 0.05,
83
- 'axes.grid': False,
84
- 'axes.spines.top': False,
85
- 'axes.spines.right': False,
86
- 'text.usetex': False, # set True if LaTeX is available
87
- 'mathtext.fontset': 'stix',
88
- })
89
-
90
- # Color palette
91
- COLORS = plt.cm.tab10.colors # or Set2, or colorblind-safe
92
-
93
- def save_fig(fig, name, fmt=FORMAT):
94
- """Save figure to FIG_DIR with consistent naming."""
95
- fig.savefig(f'{FIG_DIR}/{name}.{fmt}')
96
- print(f'Saved: {FIG_DIR}/{name}.{fmt}')
97
- ```
98
-
99
- ### Step 3: Auto-Select Figure Type
100
-
101
- Use this decision tree for data-driven figures (inspired by Imbad0202/academic-research-skills):
102
-
103
- | Data Pattern | Recommended Type | Size |
104
- |-------------|-----------------|------|
105
- | X=time/steps, Y=metric | Line plot | 0.48\textwidth |
106
- | Methods × 1 metric | Bar chart | 0.48\textwidth |
107
- | Methods × multiple metrics | Grouped bar / radar | 0.95\textwidth |
108
- | Two continuous variables | Scatter plot | 0.48\textwidth |
109
- | Matrix / grid values | Heatmap | 0.48\textwidth |
110
- | Distribution comparison | Box/violin plot | 0.48\textwidth |
111
- | Multi-dataset results | Multi-panel (subfigure) | 0.95\textwidth |
112
- | Prior work comparison | LaTeX table | |
113
-
114
- ### Step 4: Generate Each Figure
115
-
116
- For each figure in the plan, create a standalone Python script:
117
-
118
- **Line plots** (training curves, scaling):
119
- ```python
120
- # gen_fig2_training_curves.py
121
- from paper_plot_style import *
122
- import json
123
-
124
- with open('figures/exp_results.json') as f:
125
- data = json.load(f)
126
-
127
- fig, ax = plt.subplots(1, 1, figsize=(5, 3.5))
128
- ax.plot(data['steps'], data['fac_loss'], label='Factorized', color=COLORS[0])
129
- ax.plot(data['steps'], data['crf_loss'], label='CRF-LR', color=COLORS[1])
130
- ax.set_xlabel('Training Steps')
131
- ax.set_ylabel('Cross-Entropy Loss')
132
- ax.legend(frameon=False)
133
- save_fig(fig, 'fig2_training_curves')
134
- ```
135
-
136
- **Bar charts** (comparison, ablation):
137
- ```python
138
- fig, ax = plt.subplots(1, 1, figsize=(5, 3))
139
- methods = ['Baseline', 'Method A', 'Method B', 'Ours']
140
- values = [82.3, 85.1, 86.7, 89.2]
141
- bars = ax.bar(methods, values, color=[COLORS[i] for i in range(len(methods))])
142
- ax.set_ylabel('Accuracy (%)')
143
- # Add value labels on bars
144
- for bar, val in zip(bars, values):
145
- ax.text(bar.get_x() + bar.get_width()/2, bar.get_height() + 0.3,
146
- f'{val:.1f}', ha='center', va='bottom', fontsize=FONT_SIZE-1)
147
- save_fig(fig, 'fig3_comparison')
148
- ```
149
-
150
- **Comparison tables** (LaTeX, for theory papers):
151
- ```latex
152
- \begin{table}[t]
153
- \centering
154
- \caption{Comparison of estimation error bounds. $n$: sample size, $D$: ambient dim, $d$: latent dim, $K$: subspaces, $n_k$: modes.}
155
- \label{tab:bounds}
156
- \begin{tabular}{lccc}
157
- \toprule
158
- Method & Rate & Depends on $D$? & Multi-modal? \\
159
- \midrule
160
- \citet{MinimaxOkoAS23} & $n^{-s'/D}$ & Yes (curse) & No \\
161
- \citet{ScoreMatchingdistributionrecovery} & $n^{-2/d}$ & No & No \\
162
- \textbf{Ours} & $\sqrt{\sum n_k d_k / n}$ & No & Yes \\
163
- \bottomrule
164
- \end{tabular}
165
- \end{table}
166
- ```
167
-
168
- **Architecture/pipeline diagrams** (MANUAL — outside this skill's scope):
169
- - These require manual creation using draw.io, Figma, Keynote, or TikZ
170
- - This skill can generate a rough TikZ skeleton as a starting point, but **do not expect publication-quality results**
171
- - If the figure already exists in `figures/`, preserve it and generate only the LaTeX `\includegraphics` snippet
172
- - Flag as `[MANUAL]` in the figure plan and `latex_includes.tex`
173
-
174
- ### Step 5: Run All Scripts
175
-
176
- ```bash
177
- # Run all figure generation scripts
178
- for script in gen_fig*.py; do
179
- python "$script"
180
- done
181
- ```
182
-
183
- Verify all output files exist and are non-empty.
184
-
185
- ### Step 6: Generate LaTeX Include Snippets
186
-
187
- For each figure, output the LaTeX code to include it:
188
-
189
- ```latex
190
- % === Fig 2: Training Curves ===
191
- \begin{figure}[t]
192
- \centering
193
- \includegraphics[width=0.48\textwidth]{figures/fig2_training_curves.pdf}
194
- \caption{Training curves comparing factorized and CRF-LR denoising.}
195
- \label{fig:training_curves}
196
- \end{figure}
197
- ```
198
-
199
- Save all snippets to `figures/latex_includes.tex` for easy copy-paste into the paper.
200
-
201
- ### Step 7: Figure Quality Review with REVIEWER_MODEL
202
-
203
- Send figure descriptions and captions to GPT-5.4 for review:
204
-
205
- ```
206
- mcp__codex__codex:
207
- model: gpt-5.4
208
- config: {"model_reasoning_effort": "xhigh"}
209
- prompt: |
210
- Review these figure/table plans for a [VENUE] submission.
211
-
212
- For each figure:
213
- 1. Is the caption informative and self-contained?
214
- 2. Does the figure type match the data being shown?
215
- 3. Is the comparison fair and clear?
216
- 4. Any missing baselines or ablations?
217
- 5. Would a different visualization be more effective?
218
-
219
- [list all figures with captions and descriptions]
220
- ```
221
-
222
- ### Step 8: Quality Checklist
223
-
224
- Before finishing, verify each figure (from pedrohcgs/claude-code-my-workflow):
225
-
226
- - [ ] Font size readable at printed paper size (not too small)
227
- - [ ] Colors distinguishable in grayscale (print-friendly)
228
- - [ ] **No title inside figures** — titles go only in LaTeX `\caption{}` (from pedrohcgs)
229
- - [ ] Legend does not overlap data
230
- - [ ] Axis labels have units where applicable
231
- - [ ] Axis labels are publication-quality (not variable names like `emp_rate`)
232
- - [ ] Figure width fits single column (0.48\textwidth) or full width (0.95\textwidth)
233
- - [ ] PDF output is vector (not rasterized text)
234
- - [ ] No matplotlib default title (remove `plt.title` for publications)
235
- - [ ] Serif font matches paper body text (Times / Computer Modern)
236
- - [ ] Colorblind-accessible (if using colorblind palette)
237
-
238
- ## Output
239
-
240
- ```
241
- figures/
242
- ├── paper_plot_style.py # shared style config
243
- ├── gen_fig1_architecture.py # per-figure scripts
244
- ├── gen_fig2_training_curves.py
245
- ├── gen_fig3_comparison.py
246
- ├── fig1_architecture.pdf # generated figures
247
- ├── fig2_training_curves.pdf
248
- ├── fig3_comparison.pdf
249
- ├── latex_includes.tex # LaTeX snippets for all figures
250
- └── TABLE_*.tex # standalone table LaTeX files
251
- ```
252
-
253
- ## Key Rules
254
-
255
- - **Every figure must be reproducible** — save the generation script alongside the output
256
- - **Do NOT hardcode data** — always read from JSON/CSV files
257
- - **Use vector format (PDF)** for all plots PNG only as fallback
258
- - **No decorative elements** no background colors, no 3D effects, no chart junk
259
- - **Consistent style across all figures** — same fonts, colors, line widths
260
- - **Colorblind-safe** — verify with https://davidmathlogic.com/colorblind/ if needed
261
- - **One script per figure** — easy to re-run individual figures when data changes
262
- - **No titles inside figures** — captions are in LaTeX only
263
- - **Comparison tables count as figures** — generate them as standalone .tex files
264
-
265
- ## Figure Type Reference
266
-
267
- | Type | When to Use | Typical Size |
268
- |------|------------|--------------|
269
- | Line plot | Training curves, scaling trends | 0.48\textwidth |
270
- | Bar chart | Method comparison, ablation | 0.48\textwidth |
271
- | Grouped bar | Multi-metric comparison | 0.95\textwidth |
272
- | Scatter plot | Correlation analysis | 0.48\textwidth |
273
- | Heatmap | Attention, confusion matrix | 0.48\textwidth |
274
- | Box/violin | Distribution comparison | 0.48\textwidth |
275
- | Architecture | System overview | 0.95\textwidth |
276
- | Multi-panel | Combined results (subfigures) | 0.95\textwidth |
277
- | Comparison table | Prior bounds vs. ours (theory) | full width |
278
-
279
- ## Acknowledgements
280
-
281
- Design pattern (type × style matrix) inspired by [baoyu-skills](https://github.com/jimliu/baoyu-skills). Publication style defaults and figure rules from [pedrohcgs/claude-code-my-workflow](https://github.com/pedrohcgs/claude-code-my-workflow). Visualization decision tree from [Imbad0202/academic-research-skills](https://github.com/Imbad0202/academic-research-skills).
9
+
10
+ # Paper Figure: Publication-Quality Plots from Experiment Data
11
+
12
+ Generate all figures and tables for a paper based on: **$ARGUMENTS**
13
+
14
+ ## Scope: What This Skill Can and Cannot Do
15
+
16
+ | Category | Can auto-generate? | Examples |
17
+ |----------|-------------------|----------|
18
+ | **Data-driven plots** | ✅ Yes | Line plots (training curves), bar charts (method comparison), scatter plots, heatmaps, box/violin plots |
19
+ | **Comparison tables** | ✅ Yes | LaTeX tables comparing prior bounds, method features, ablation results |
20
+ | **Multi-panel figures** | Yes | Subfigure grids combining multiple plots (e.g., 3×3 dataset × method) |
21
+ | **Architecture/pipeline diagrams** | ❌ No — manual | Model architecture, data flow diagrams, system overviews. At best can generate a rough TikZ skeleton, but **expect to draw these yourself** using tools like draw.io, Figma, or TikZ |
22
+ | **Generated image grids** | ❌ No — manual | Grids of generated samples (e.g., GAN/diffusion outputs). These come from running your model, not from this skill |
23
+ | **Photographs / screenshots** | ❌ No — manual | Real-world images, UI screenshots, qualitative examples |
24
+
25
+ **In practice:** For a typical ML paper, this skill handles ~60% of figures (all data plots + tables). The remaining ~40% (hero figure, architecture diagram, qualitative results) need to be created manually and placed in `figures/` before running `/paper-write`. The skill will detect these as "existing figures" and preserve them.
26
+
27
+ ## Constants
28
+
29
+ - **STYLE = `publication`**Visual style preset. Options: `publication` (default, clean for print), `poster` (larger fonts), `slide` (bold colors)
30
+ - **DPI = 300** — Output resolution
31
+ - **FORMAT = `pdf`** — Output format. Options: `pdf` (vector, best for LaTeX), `png` (raster fallback)
32
+ - **COLOR_PALETTE = `tab10`**Default matplotlib color cycle. Options: `tab10`, `Set2`, `colorblind` (deuteranopia-safe)
33
+ - **FONT_SIZE = 10**Base font size (matches typical conference body text)
34
+ - **FIG_DIR = `figures/`**Output directory for generated figures
35
+ - **REVIEWER_MODEL = `gpt-5.4`** — Model used via Codex MCP for figure quality review.
36
+
37
+ ## Inputs
38
+
39
+ 1. **PAPER_PLAN.md** — figure plan table (from `/paper-plan`)
40
+ 2. **Experiment data** — JSON files, CSV files, or screen logs in `figures/` or project root
41
+ 3. **Existing figures** — any manually created figures to preserve
42
+
43
+ If no PAPER_PLAN.md exists, scan for data files and ask the user which figures to generate.
44
+
45
+ ## Workflow
46
+
47
+ ### Step 1: Read Figure Plan
48
+
49
+ Parse the Figure Plan table from PAPER_PLAN.md:
50
+
51
+ ```markdown
52
+ | ID | Type | Description | Data Source | Priority |
53
+ |----|------|-------------|-------------|----------|
54
+ | Fig 1 | Architecture | ... | manual | HIGH |
55
+ | Fig 2 | Line plot | ... | figures/exp.json | HIGH |
56
+ ```
57
+
58
+ Identify:
59
+ - Which figures can be auto-generated from data
60
+ - Which need manual creation (architecture diagrams, etc.)
61
+ - Which are comparison tables (generate as LaTeX)
62
+
63
+ ### Step 2: Set Up Plotting Environment
64
+
65
+ Create a shared style configuration script:
66
+
67
+ ```python
68
+ # paper_plot_style.py shared across all figure scripts
69
+ import matplotlib.pyplot as plt
70
+ import matplotlib
71
+ matplotlib.rcParams.update({
72
+ 'font.size': FONT_SIZE,
73
+ 'font.family': 'serif',
74
+ 'font.serif': ['Times New Roman', 'Times', 'DejaVu Serif'],
75
+ 'axes.labelsize': FONT_SIZE,
76
+ 'axes.titlesize': FONT_SIZE + 1,
77
+ 'xtick.labelsize': FONT_SIZE - 1,
78
+ 'ytick.labelsize': FONT_SIZE - 1,
79
+ 'legend.fontsize': FONT_SIZE - 1,
80
+ 'figure.dpi': DPI,
81
+ 'savefig.dpi': DPI,
82
+ 'savefig.bbox': 'tight',
83
+ 'savefig.pad_inches': 0.05,
84
+ 'axes.grid': False,
85
+ 'axes.spines.top': False,
86
+ 'axes.spines.right': False,
87
+ 'text.usetex': False, # set True if LaTeX is available
88
+ 'mathtext.fontset': 'stix',
89
+ })
90
+
91
+ # Color palette
92
+ COLORS = plt.cm.tab10.colors # or Set2, or colorblind-safe
93
+
94
+ def save_fig(fig, name, fmt=FORMAT):
95
+ """Save figure to FIG_DIR with consistent naming."""
96
+ fig.savefig(f'{FIG_DIR}/{name}.{fmt}')
97
+ print(f'Saved: {FIG_DIR}/{name}.{fmt}')
98
+ ```
99
+
100
+ ### Step 3: Auto-Select Figure Type
101
+
102
+ Use this decision tree for data-driven figures (inspired by Imbad0202/academic-research-skills):
103
+
104
+ | Data Pattern | Recommended Type | Size |
105
+ |-------------|-----------------|------|
106
+ | X=time/steps, Y=metric | Line plot | 0.48\textwidth |
107
+ | Methods × 1 metric | Bar chart | 0.48\textwidth |
108
+ | Methods × multiple metrics | Grouped bar / radar | 0.95\textwidth |
109
+ | Two continuous variables | Scatter plot | 0.48\textwidth |
110
+ | Matrix / grid values | Heatmap | 0.48\textwidth |
111
+ | Distribution comparison | Box/violin plot | 0.48\textwidth |
112
+ | Multi-dataset results | Multi-panel (subfigure) | 0.95\textwidth |
113
+ | Prior work comparison | LaTeX table | — |
114
+
115
+ ### Step 4: Generate Each Figure
116
+
117
+ For each figure in the plan, create a standalone Python script:
118
+
119
+ **Line plots** (training curves, scaling):
120
+ ```python
121
+ # gen_fig2_training_curves.py
122
+ from paper_plot_style import *
123
+ import json
124
+
125
+ with open('figures/exp_results.json') as f:
126
+ data = json.load(f)
127
+
128
+ fig, ax = plt.subplots(1, 1, figsize=(5, 3.5))
129
+ ax.plot(data['steps'], data['fac_loss'], label='Factorized', color=COLORS[0])
130
+ ax.plot(data['steps'], data['crf_loss'], label='CRF-LR', color=COLORS[1])
131
+ ax.set_xlabel('Training Steps')
132
+ ax.set_ylabel('Cross-Entropy Loss')
133
+ ax.legend(frameon=False)
134
+ save_fig(fig, 'fig2_training_curves')
135
+ ```
136
+
137
+ **Bar charts** (comparison, ablation):
138
+ ```python
139
+ fig, ax = plt.subplots(1, 1, figsize=(5, 3))
140
+ methods = ['Baseline', 'Method A', 'Method B', 'Ours']
141
+ values = [82.3, 85.1, 86.7, 89.2]
142
+ bars = ax.bar(methods, values, color=[COLORS[i] for i in range(len(methods))])
143
+ ax.set_ylabel('Accuracy (%)')
144
+ # Add value labels on bars
145
+ for bar, val in zip(bars, values):
146
+ ax.text(bar.get_x() + bar.get_width()/2, bar.get_height() + 0.3,
147
+ f'{val:.1f}', ha='center', va='bottom', fontsize=FONT_SIZE-1)
148
+ save_fig(fig, 'fig3_comparison')
149
+ ```
150
+
151
+ **Comparison tables** (LaTeX, for theory papers):
152
+ ```latex
153
+ \begin{table}[t]
154
+ \centering
155
+ \caption{Comparison of estimation error bounds. $n$: sample size, $D$: ambient dim, $d$: latent dim, $K$: subspaces, $n_k$: modes.}
156
+ \label{tab:bounds}
157
+ \begin{tabular}{lccc}
158
+ \toprule
159
+ Method & Rate & Depends on $D$? & Multi-modal? \\
160
+ \midrule
161
+ \citet{MinimaxOkoAS23} & $n^{-s'/D}$ & Yes (curse) & No \\
162
+ \citet{ScoreMatchingdistributionrecovery} & $n^{-2/d}$ & No & No \\
163
+ \textbf{Ours} & $\sqrt{\sum n_k d_k / n}$ & No & Yes \\
164
+ \bottomrule
165
+ \end{tabular}
166
+ \end{table}
167
+ ```
168
+
169
+ **Architecture/pipeline diagrams** (MANUAL outside this skill's scope):
170
+ - These require manual creation using draw.io, Figma, Keynote, or TikZ
171
+ - This skill can generate a rough TikZ skeleton as a starting point, but **do not expect publication-quality results**
172
+ - If the figure already exists in `figures/`, preserve it and generate only the LaTeX `\includegraphics` snippet
173
+ - Flag as `[MANUAL]` in the figure plan and `latex_includes.tex`
174
+
175
+ ### Step 5: Run All Scripts
176
+
177
+ ```bash
178
+ # Run all figure generation scripts
179
+ for script in gen_fig*.py; do
180
+ python "$script"
181
+ done
182
+ ```
183
+
184
+ Verify all output files exist and are non-empty.
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+
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+ ### Step 6: Generate LaTeX Include Snippets
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+
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+ For each figure, output the LaTeX code to include it:
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+
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+ ```latex
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+ % === Fig 2: Training Curves ===
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+ \begin{figure}[t]
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+ \centering
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+ \includegraphics[width=0.48\textwidth]{figures/fig2_training_curves.pdf}
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+ \caption{Training curves comparing factorized and CRF-LR denoising.}
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+ \label{fig:training_curves}
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+ \end{figure}
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+ ```
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+
200
+ Save all snippets to `figures/latex_includes.tex` for easy copy-paste into the paper.
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+
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+ ### Step 7: Figure Quality Review with REVIEWER_MODEL
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+
204
+ Send figure descriptions and captions to GPT-5.4 for review:
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+
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+ ```
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+ mcp__codex__codex:
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+ model: gpt-5.4
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+ config: {"model_reasoning_effort": "xhigh"}
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+ prompt: |
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+ Review these figure/table plans for a [VENUE] submission.
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+
213
+ For each figure:
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+ 1. Is the caption informative and self-contained?
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+ 2. Does the figure type match the data being shown?
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+ 3. Is the comparison fair and clear?
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+ 4. Any missing baselines or ablations?
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+ 5. Would a different visualization be more effective?
219
+
220
+ [list all figures with captions and descriptions]
221
+ ```
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+
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+ ### Step 8: Quality Checklist
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+
225
+ Before finishing, verify each figure (from pedrohcgs/claude-code-my-workflow):
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+
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+ - [ ] Font size readable at printed paper size (not too small)
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+ - [ ] Colors distinguishable in grayscale (print-friendly)
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+ - [ ] **No title inside figures** — titles go only in LaTeX `\caption{}` (from pedrohcgs)
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+ - [ ] Legend does not overlap data
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+ - [ ] Axis labels have units where applicable
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+ - [ ] Axis labels are publication-quality (not variable names like `emp_rate`)
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+ - [ ] Figure width fits single column (0.48\textwidth) or full width (0.95\textwidth)
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+ - [ ] PDF output is vector (not rasterized text)
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+ - [ ] No matplotlib default title (remove `plt.title` for publications)
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+ - [ ] Serif font matches paper body text (Times / Computer Modern)
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+ - [ ] Colorblind-accessible (if using colorblind palette)
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+
239
+ ## Output
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+
241
+ ```
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+ figures/
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+ ├── paper_plot_style.py # shared style config
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+ ├── gen_fig1_architecture.py # per-figure scripts
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+ ├── gen_fig2_training_curves.py
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+ ├── gen_fig3_comparison.py
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+ ├── fig1_architecture.pdf # generated figures
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+ ├── fig2_training_curves.pdf
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+ ├── fig3_comparison.pdf
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+ ├── latex_includes.tex # LaTeX snippets for all figures
251
+ └── TABLE_*.tex # standalone table LaTeX files
252
+ ```
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+
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+ ## Key Rules
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+
256
+ - **Every figure must be reproducible** — save the generation script alongside the output
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+ - **Do NOT hardcode data** always read from JSON/CSV files
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+ - **Use vector format (PDF)** for all plots PNG only as fallback
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+ - **No decorative elements** — no background colors, no 3D effects, no chart junk
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+ - **Consistent style across all figures** — same fonts, colors, line widths
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+ - **Colorblind-safe** — verify with https://davidmathlogic.com/colorblind/ if needed
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+ - **One script per figure** — easy to re-run individual figures when data changes
263
+ - **No titles inside figures** — captions are in LaTeX only
264
+ - **Comparison tables count as figures** — generate them as standalone .tex files
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+
266
+ ## Figure Type Reference
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+
268
+ | Type | When to Use | Typical Size |
269
+ |------|------------|--------------|
270
+ | Line plot | Training curves, scaling trends | 0.48\textwidth |
271
+ | Bar chart | Method comparison, ablation | 0.48\textwidth |
272
+ | Grouped bar | Multi-metric comparison | 0.95\textwidth |
273
+ | Scatter plot | Correlation analysis | 0.48\textwidth |
274
+ | Heatmap | Attention, confusion matrix | 0.48\textwidth |
275
+ | Box/violin | Distribution comparison | 0.48\textwidth |
276
+ | Architecture | System overview | 0.95\textwidth |
277
+ | Multi-panel | Combined results (subfigures) | 0.95\textwidth |
278
+ | Comparison table | Prior bounds vs. ours (theory) | full width |
279
+
280
+ ## Acknowledgements
281
+
282
+ Design pattern (type × style matrix) inspired by [baoyu-skills](https://github.com/jimliu/baoyu-skills). Publication style defaults and figure rules from [pedrohcgs/claude-code-my-workflow](https://github.com/pedrohcgs/claude-code-my-workflow). Visualization decision tree from [Imbad0202/academic-research-skills](https://github.com/Imbad0202/academic-research-skills).