@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.
- package/README.ja.md +130 -343
- package/README.ko.md +128 -337
- package/README.md +229 -584
- package/README.ru.md +131 -364
- package/README.zh-cn.md +231 -547
- package/bin/openagent-labforge.js +95 -9
- package/bin/platform.test.ts +20 -21
- package/dist/agents/article-writer.d.ts +7 -0
- package/dist/agents/atlas/default.d.ts +1 -1
- package/dist/agents/atlas/gemini.d.ts +1 -1
- package/dist/agents/atlas/gpt.d.ts +1 -1
- package/dist/agents/bio-methodologist.d.ts +1 -1
- package/dist/agents/bio-orchestrator.d.ts +7 -0
- package/dist/agents/bio-skill-guidance.d.ts +1 -0
- package/dist/agents/builtin-agents/general-agents.d.ts +0 -1
- package/dist/agents/builtin-agents/sisyphus-agent.d.ts +16 -0
- package/dist/agents/dynamic-agent-prompt-builder.d.ts +0 -2
- package/dist/agents/engineering-capability.d.ts +7 -0
- package/dist/agents/env-context.d.ts +1 -1
- package/dist/agents/github-scout.d.ts +7 -0
- package/dist/agents/index.d.ts +0 -1
- package/dist/agents/metis.d.ts +1 -1
- package/dist/agents/momus.d.ts +1 -1
- package/dist/agents/prometheus/behavioral-summary.d.ts +1 -1
- package/dist/agents/prometheus/gemini.d.ts +1 -1
- package/dist/agents/prometheus/gpt.d.ts +1 -1
- package/dist/agents/prometheus/interview-mode.d.ts +1 -1
- package/dist/agents/prometheus/plan-generation.d.ts +1 -1
- package/dist/agents/prometheus/plan-template.d.ts +1 -1
- package/dist/agents/prometheus/system-prompt.d.ts +1 -1
- package/dist/agents/scientific-writer.d.ts +7 -0
- package/dist/agents/sisyphus-junior/gpt-5-3-codex.d.ts +1 -1
- package/dist/agents/sisyphus-junior/gpt-5-4.d.ts +1 -1
- package/dist/agents/sisyphus-junior/gpt.d.ts +1 -1
- package/dist/agents/tech-scout.d.ts +7 -0
- package/dist/agents/types.d.ts +1 -1
- package/dist/agents/wase.d.ts +8 -0
- package/dist/agents/wet-lab-designer.d.ts +7 -0
- package/dist/agents/writing-style-rules.d.ts +1 -0
- package/dist/cli/config-manager/bun-install.d.ts +1 -6
- package/dist/cli/config-manager/cleanup-managed-mcp-from-opencode-config.d.ts +2 -0
- package/dist/cli/config-manager/cleanup-stale-managed-agents.d.ts +2 -0
- package/dist/cli/config-manager/parse-opencode-config-file.d.ts +2 -0
- package/dist/cli/config-manager/plugin-name-with-version.d.ts +1 -1
- package/dist/cli/config-manager/sync-static-agent-to-opencode-config.d.ts +2 -0
- package/dist/cli/config-manager/sync-static-mcp-to-opencode-config.d.ts +2 -0
- package/dist/cli/config-manager/write-bootstrap-skill.d.ts +15 -0
- package/dist/cli/config-manager.d.ts +5 -0
- package/dist/cli/index.js +24986 -15362
- package/dist/cli/install-validators.d.ts +0 -1
- package/dist/cli/model-fallback-types.d.ts +0 -1
- package/dist/cli/run/index.d.ts +0 -1
- package/dist/cli/run/types.d.ts +0 -1
- package/dist/cli/types.d.ts +0 -3
- package/dist/config/schema/agent-names.d.ts +36 -3
- package/dist/config/schema/agent-overrides.d.ts +504 -0
- package/dist/config/schema/background-task.d.ts +0 -2
- package/dist/config/schema/experimental.d.ts +5 -0
- package/dist/config/schema/git-master.d.ts +0 -1
- package/dist/config/schema/hooks.d.ts +0 -2
- package/dist/config/schema/mcp-policy.d.ts +1 -0
- package/dist/config/schema/oh-my-opencode-config.d.ts +526 -54
- package/dist/config/schema.d.ts +0 -1
- package/dist/create-hooks.d.ts +0 -13
- package/dist/features/background-agent/compaction-aware-message-resolver.d.ts +1 -16
- package/dist/features/background-agent/constants.d.ts +2 -1
- package/dist/features/background-agent/manager.d.ts +5 -20
- package/dist/features/background-agent/process-cleanup.d.ts +1 -1
- package/dist/features/background-agent/task-history.d.ts +0 -1
- package/dist/features/background-agent/task-poller.d.ts +0 -1
- package/dist/features/background-agent/types.d.ts +0 -4
- package/dist/features/builtin-commands/commands.d.ts +4 -1
- package/dist/features/builtin-skills/skills/bio-methods.d.ts +2 -0
- package/dist/features/builtin-skills/skills/bio-pipeline.d.ts +2 -0
- package/dist/features/builtin-skills/skills/bio-tools.d.ts +2 -0
- package/dist/features/builtin-skills/skills/bio-visualization.d.ts +2 -0
- package/dist/features/builtin-skills/skills/cell-annotation.d.ts +2 -0
- package/dist/features/builtin-skills/skills/differential-expression.d.ts +2 -0
- package/dist/features/builtin-skills/skills/geo-query.d.ts +2 -0
- package/dist/features/builtin-skills/skills/index.d.ts +14 -0
- package/dist/features/builtin-skills/skills/paper-evidence.d.ts +2 -0
- package/dist/features/builtin-skills/skills/pubmed-search.d.ts +2 -0
- package/dist/features/builtin-skills/skills/scrna-preprocessing.d.ts +2 -0
- package/dist/features/builtin-skills/skills/sequence-analysis.d.ts +2 -0
- package/dist/features/builtin-skills/skills/structural-biology.d.ts +2 -0
- package/dist/features/builtin-skills/skills/vector-design.d.ts +2 -0
- package/dist/features/builtin-skills/skills/wet-lab-design.d.ts +2 -0
- package/dist/features/claude-code-agent-loader/loader.d.ts +3 -3
- package/dist/features/claude-code-agent-loader/types.d.ts +1 -8
- package/dist/features/claude-code-mcp-loader/configure-allowed-env-vars.d.ts +5 -0
- package/dist/features/claude-code-mcp-loader/index.d.ts +1 -0
- package/dist/features/claude-code-mcp-loader/types.d.ts +3 -0
- package/dist/features/claude-code-plugin-loader/agent-loader.d.ts +2 -2
- package/dist/features/claude-code-plugin-loader/loader.d.ts +2 -2
- package/dist/features/claude-code-plugin-loader/types.d.ts +1 -1
- package/dist/features/claude-code-session-state/state.d.ts +5 -0
- package/dist/features/opencode-skill-loader/git-master-template-injection.d.ts +1 -1
- package/dist/features/opencode-skill-loader/project-skill-directory-discovery.d.ts +1 -0
- package/dist/features/opencode-skill-loader/skill-metadata-validator.d.ts +8 -0
- package/dist/features/skill-mcp-manager/types.d.ts +0 -4
- package/dist/features/tmux-subagent/index.d.ts +0 -1
- package/dist/features/tmux-subagent/manager.d.ts +0 -5
- package/dist/features/tmux-subagent/types.d.ts +0 -2
- package/dist/hooks/atlas/tool-execute-after.d.ts +0 -2
- package/dist/hooks/atlas/types.d.ts +0 -2
- package/dist/hooks/atlas/verification-reminders.d.ts +0 -4
- package/dist/hooks/auto-slash-command/hook.d.ts +0 -7
- package/dist/hooks/auto-update-checker/checker.d.ts +1 -3
- package/dist/hooks/auto-update-checker/constants.d.ts +2 -2
- package/dist/hooks/comment-checker/downloader.d.ts +1 -1
- package/dist/hooks/compaction-context-injector/hook.d.ts +1 -5
- package/dist/hooks/context-window-monitor.d.ts +5 -2
- package/dist/hooks/index.d.ts +0 -2
- package/dist/hooks/keyword-detector/detector.d.ts +1 -1
- package/dist/hooks/keyword-detector/hook.d.ts +2 -2
- package/dist/hooks/keyword-detector/index.d.ts +1 -0
- package/dist/hooks/keyword-detector/semantic-hint.d.ts +4 -0
- package/dist/hooks/keyword-detector/ultrawork/autonomous.d.ts +8 -0
- package/dist/hooks/preemptive-compaction.d.ts +5 -2
- package/dist/hooks/runtime-fallback/hook.d.ts +3 -2
- package/dist/hooks/runtime-fallback/message-update-handler.d.ts +2 -1
- package/dist/hooks/runtime-fallback/types.d.ts +3 -56
- package/dist/hooks/session-notification-scheduler.d.ts +3 -5
- package/dist/hooks/session-notification.d.ts +0 -2
- package/dist/hooks/session-recovery/tool-pairing.d.ts +16 -0
- package/dist/hooks/start-work/index.d.ts +1 -1
- package/dist/hooks/start-work/worktree-detector.d.ts +0 -7
- package/dist/hooks/todo-continuation-enforcer/compaction-guard.d.ts +4 -0
- package/dist/hooks/todo-continuation-enforcer/constants.d.ts +6 -5
- package/dist/hooks/todo-continuation-enforcer/handler.d.ts +0 -1
- package/dist/hooks/todo-continuation-enforcer/idle-event.d.ts +0 -1
- package/dist/hooks/todo-continuation-enforcer/resolve-message-info.d.ts +3 -0
- package/dist/hooks/todo-continuation-enforcer/session-state.d.ts +1 -1
- package/dist/hooks/todo-continuation-enforcer/types.d.ts +8 -3
- package/dist/hooks/tool-output-truncator.d.ts +0 -1
- package/dist/index.js +56627 -56933
- package/dist/mcp/extended.d.ts +4 -2
- package/dist/mcp/index.d.ts +2 -1
- package/dist/mcp/types.d.ts +2 -3
- package/dist/openagent-labforge.schema.json +1362 -83
- package/dist/plugin/hooks/create-continuation-hooks.d.ts +1 -2
- package/dist/plugin/hooks/create-core-hooks.d.ts +0 -1
- package/dist/plugin/hooks/create-session-hooks.d.ts +1 -2
- package/dist/plugin/ultrawork-model-override.d.ts +11 -1
- package/dist/plugin-dispose.d.ts +12 -10
- package/dist/plugin-handlers/agent-config-handler.d.ts +0 -1
- package/dist/plugin-handlers/prometheus-agent-config-builder.d.ts +1 -1
- package/dist/plugin-state.d.ts +0 -5
- package/dist/shared/agent-display-names.d.ts +1 -0
- package/dist/shared/data-path.d.ts +1 -1
- package/dist/shared/dynamic-truncator.d.ts +7 -4
- package/dist/shared/external-plugin-detector.d.ts +7 -0
- package/dist/shared/index.d.ts +5 -3
- package/dist/shared/jsonc-parser.d.ts +4 -0
- package/dist/shared/mcp-local-command-normalizer.d.ts +1 -0
- package/dist/shared/migrate-legacy-config-file.d.ts +1 -0
- package/dist/shared/model-error-classifier.d.ts +1 -2
- package/dist/shared/opencode-command-dirs.d.ts +0 -1
- package/dist/shared/plugin-identity.d.ts +2 -3
- package/dist/shared/project-discovery-dirs.d.ts +4 -0
- package/dist/shared/session-model-state.d.ts +1 -2
- package/dist/shared/system-directive.d.ts +5 -6
- package/dist/tools/call-omo-agent/background-executor.d.ts +1 -2
- package/dist/tools/call-omo-agent/constants.d.ts +2 -2
- package/dist/tools/call-omo-agent/sync-executor.d.ts +3 -11
- package/dist/tools/call-omo-agent/tools.d.ts +2 -2
- package/dist/tools/call-omo-agent/types.d.ts +13 -0
- package/dist/tools/delegate-task/constants.d.ts +1 -1
- package/dist/tools/delegate-task/model-selection.d.ts +0 -1
- package/dist/tools/delegate-task/model-string-parser.d.ts +3 -1
- package/dist/tools/delegate-task/parent-context-resolver.d.ts +22 -0
- package/dist/tools/lsp/constants.d.ts +0 -1
- package/dist/tools/lsp/lsp-client-transport.d.ts +2 -4
- package/dist/tools/lsp/lsp-client-wrapper.d.ts +1 -2
- package/generated/skills-bundles/catalog.json +1 -1
- package/generated/skills-bundles/full/skills/data-analysis/experiment-monitoring/auto-claude__monitor-experiment/SKILL.md +56 -55
- package/generated/skills-bundles/full/skills/data-analysis/experiment-ops/auto-claude__run-experiment/SKILL.md +105 -104
- package/generated/skills-bundles/full/skills/data-analysis/optimization/auto-claude__dse-loop/SKILL.md +272 -271
- package/generated/skills-bundles/full/skills/data-analysis/statistics/auto-claude__analyze-results/SKILL.md +40 -39
- package/generated/skills-bundles/full/skills/data-analysis/visualization/auto-claude__paper-figure/SKILL.md +274 -273
- package/generated/skills-bundles/full/skills/productivity/visual-design/auto-claude__pixel-art/SKILL.md +131 -130
- package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-compile/SKILL.md +245 -244
- package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-plan/SKILL.md +247 -246
- package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-write/SKILL.md +303 -302
- package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-write/templates/iclr2026.tex +84 -84
- package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-write/templates/icml2025.tex +87 -87
- package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-write/templates/math_commands.tex +48 -48
- package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-write/templates/neurips2025.tex +80 -80
- package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-writing/SKILL.md +31 -31
- package/generated/skills-bundles/full/skills/research/literature-and-web-search/auto-claude__arxiv/SKILL.md +126 -125
- package/generated/skills-bundles/full/skills/research/literature-and-web-search/auto-claude__novelty-check/SKILL.md +80 -79
- package/generated/skills-bundles/full/skills/research/literature-and-web-search/auto-claude__research-lit/SKILL.md +187 -186
- package/generated/skills-bundles/full/skills/research/research-ideation/auto-claude__idea-creator/SKILL.md +11 -11
- package/generated/skills-bundles/full/skills/research/research-ideation/auto-claude__idea-discovery/SKILL.md +18 -18
- package/generated/skills-bundles/full/skills/research/research-ideation/auto-claude__idea-discovery-robot/SKILL.md +20 -20
- package/generated/skills-bundles/full/skills/research/research-ideation/auto-claude__research-pipeline/SKILL.md +15 -15
- package/generated/skills-bundles/full/skills/research/theory-writing/auto-claude__proof-writer/SKILL.md +217 -216
- package/generated/skills-bundles/paper/skills/data-analysis/experiment-monitoring/auto-claude__monitor-experiment/SKILL.md +56 -55
- package/generated/skills-bundles/paper/skills/data-analysis/experiment-ops/auto-claude__run-experiment/SKILL.md +105 -104
- package/generated/skills-bundles/paper/skills/data-analysis/optimization/auto-claude__dse-loop/SKILL.md +272 -271
- package/generated/skills-bundles/paper/skills/data-analysis/statistics/auto-claude__analyze-results/SKILL.md +40 -39
- package/generated/skills-bundles/paper/skills/data-analysis/visualization/auto-claude__paper-figure/SKILL.md +274 -273
- package/generated/skills-bundles/paper/skills/productivity/visual-design/auto-claude__pixel-art/SKILL.md +131 -130
- package/generated/skills-bundles/paper/skills/research/document-authoring/auto-claude__paper-compile/SKILL.md +245 -244
- package/generated/skills-bundles/paper/skills/research/document-authoring/auto-claude__paper-plan/SKILL.md +247 -246
- package/generated/skills-bundles/paper/skills/research/document-authoring/auto-claude__paper-write/SKILL.md +303 -302
- package/generated/skills-bundles/paper/skills/research/document-authoring/auto-claude__paper-write/templates/iclr2026.tex +84 -84
- package/generated/skills-bundles/paper/skills/research/document-authoring/auto-claude__paper-write/templates/icml2025.tex +87 -87
- package/generated/skills-bundles/paper/skills/research/document-authoring/auto-claude__paper-write/templates/math_commands.tex +48 -48
- package/generated/skills-bundles/paper/skills/research/document-authoring/auto-claude__paper-write/templates/neurips2025.tex +80 -80
- package/generated/skills-bundles/paper/skills/research/document-authoring/auto-claude__paper-writing/SKILL.md +31 -31
- package/generated/skills-bundles/paper/skills/research/literature-and-web-search/auto-claude__arxiv/SKILL.md +126 -125
- package/generated/skills-bundles/paper/skills/research/literature-and-web-search/auto-claude__novelty-check/SKILL.md +80 -79
- package/generated/skills-bundles/paper/skills/research/literature-and-web-search/auto-claude__research-lit/SKILL.md +187 -186
- package/generated/skills-bundles/paper/skills/research/research-ideation/auto-claude__idea-creator/SKILL.md +11 -11
- package/generated/skills-bundles/paper/skills/research/research-ideation/auto-claude__idea-discovery/SKILL.md +18 -18
- package/generated/skills-bundles/paper/skills/research/research-ideation/auto-claude__idea-discovery-robot/SKILL.md +20 -20
- package/generated/skills-bundles/paper/skills/research/research-ideation/auto-claude__research-pipeline/SKILL.md +15 -15
- package/generated/skills-bundles/paper/skills/research/theory-writing/auto-claude__proof-writer/SKILL.md +217 -216
- package/package.json +36 -32
- package/dist/cli/openai-only-model-catalog.d.ts +0 -3
- package/dist/cli/run/model-resolver.d.ts +0 -4
- package/dist/config/schema/git-env-prefix.d.ts +0 -5
- package/dist/features/background-agent/remove-task-toast-tracking.d.ts +0 -1
- package/dist/features/background-agent/subagent-spawn-limits.d.ts +0 -23
- package/dist/features/claude-code-agent-loader/claude-model-mapper.d.ts +0 -4
- package/dist/features/tmux-subagent/pane-state-parser.d.ts +0 -8
- package/dist/features/tmux-subagent/tracked-session-state.d.ts +0 -8
- package/dist/hooks/atlas/boulder-session-lineage.d.ts +0 -6
- package/dist/hooks/atlas/final-wave-approval-gate.d.ts +0 -4
- package/dist/hooks/atlas/idle-event.d.ts +0 -8
- package/dist/hooks/atlas/resolve-active-boulder-session.d.ts +0 -11
- package/dist/hooks/auto-slash-command/processed-command-store.d.ts +0 -7
- package/dist/hooks/auto-update-checker/checker/sync-package-json.d.ts +0 -7
- package/dist/hooks/compaction-context-injector/compaction-context-prompt.d.ts +0 -1
- package/dist/hooks/compaction-context-injector/constants.d.ts +0 -5
- package/dist/hooks/compaction-context-injector/recovery-prompt-config.d.ts +0 -6
- package/dist/hooks/compaction-context-injector/recovery.d.ts +0 -6
- package/dist/hooks/compaction-context-injector/session-id.d.ts +0 -2
- package/dist/hooks/compaction-context-injector/session-prompt-config-resolver.d.ts +0 -16
- package/dist/hooks/compaction-context-injector/tail-monitor.d.ts +0 -13
- package/dist/hooks/compaction-context-injector/types.d.ts +0 -43
- package/dist/hooks/compaction-context-injector/validated-model.d.ts +0 -13
- package/dist/hooks/delegate-task-english-directive/hook.d.ts +0 -14
- package/dist/hooks/delegate-task-english-directive/index.d.ts +0 -1
- package/dist/hooks/gpt-permission-continuation/assistant-message.d.ts +0 -23
- package/dist/hooks/gpt-permission-continuation/constants.d.ts +0 -4
- package/dist/hooks/gpt-permission-continuation/detector.d.ts +0 -1
- package/dist/hooks/gpt-permission-continuation/handler.d.ts +0 -12
- package/dist/hooks/gpt-permission-continuation/index.d.ts +0 -13
- package/dist/hooks/gpt-permission-continuation/session-state.d.ts +0 -15
- package/dist/hooks/ralph-loop/pending-verification-handler.d.ts +0 -16
- package/dist/hooks/runtime-fallback/fallback-bootstrap-model.d.ts +0 -10
- package/dist/hooks/runtime-fallback/fallback-retry-dispatcher.d.ts +0 -11
- package/dist/hooks/runtime-fallback/last-user-retry-parts.d.ts +0 -4
- package/dist/hooks/runtime-fallback/retry-model-payload.d.ts +0 -7
- package/dist/hooks/runtime-fallback/session-messages.d.ts +0 -9
- package/dist/hooks/runtime-fallback/session-status-handler.d.ts +0 -3
- package/dist/hooks/runtime-fallback/visible-assistant-response.d.ts +0 -3
- package/dist/hooks/session-notification-content.d.ts +0 -30
- package/dist/plugin/normalize-tool-arg-schemas.d.ts +0 -2
- package/dist/plugin/ultrawork-variant-availability.d.ts +0 -6
- package/dist/shared/compaction-agent-config-checkpoint.d.ts +0 -11
- package/dist/shared/context-limit-resolver.d.ts +0 -5
- package/dist/shared/fallback-chain-from-models.d.ts +0 -3
- package/dist/shared/question-denied-session-permission.d.ts +0 -6
- package/dist/shared/retry-status-utils.d.ts +0 -2
- package/dist/shared/vision-capable-models-cache.d.ts +0 -4
- package/dist/tools/delegate-task/cancel-unstable-agent-task.d.ts +0 -2
- package/dist/tools/look-at/multimodal-fallback-chain.d.ts +0 -4
- package/dist/tools/lsp/directory-diagnostics.d.ts +0 -1
- 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
|
|
|
6
6
|
metadata:
|
|
7
7
|
category: "data-analysis/visualization"
|
|
8
8
|
---
|
|
9
|
-
|
|
10
|
-
|
|
11
|
-
|
|
12
|
-
|
|
13
|
-
|
|
14
|
-
|
|
15
|
-
|
|
16
|
-
|
|
17
|
-
|
|
18
|
-
| **
|
|
19
|
-
| **
|
|
20
|
-
| **
|
|
21
|
-
| **
|
|
22
|
-
| **
|
|
23
|
-
|
|
24
|
-
|
|
25
|
-
|
|
26
|
-
|
|
27
|
-
|
|
28
|
-
|
|
29
|
-
- **
|
|
30
|
-
- **
|
|
31
|
-
- **
|
|
32
|
-
- **
|
|
33
|
-
- **
|
|
34
|
-
- **
|
|
35
|
-
|
|
36
|
-
|
|
37
|
-
|
|
38
|
-
|
|
39
|
-
|
|
40
|
-
|
|
41
|
-
|
|
42
|
-
|
|
43
|
-
|
|
44
|
-
|
|
45
|
-
|
|
46
|
-
|
|
47
|
-
|
|
48
|
-
|
|
49
|
-
|
|
50
|
-
|
|
51
|
-
|
|
52
|
-
|
|
53
|
-
|
|
54
|
-
| Fig
|
|
55
|
-
|
|
56
|
-
|
|
57
|
-
|
|
58
|
-
|
|
59
|
-
- Which
|
|
60
|
-
- Which
|
|
61
|
-
|
|
62
|
-
|
|
63
|
-
|
|
64
|
-
|
|
65
|
-
|
|
66
|
-
|
|
67
|
-
|
|
68
|
-
|
|
69
|
-
import matplotlib
|
|
70
|
-
matplotlib
|
|
71
|
-
|
|
72
|
-
'font.
|
|
73
|
-
'font.
|
|
74
|
-
'
|
|
75
|
-
'axes.
|
|
76
|
-
'
|
|
77
|
-
'
|
|
78
|
-
'
|
|
79
|
-
'
|
|
80
|
-
'
|
|
81
|
-
'savefig.
|
|
82
|
-
'savefig.
|
|
83
|
-
'
|
|
84
|
-
'axes.
|
|
85
|
-
'axes.spines.
|
|
86
|
-
'
|
|
87
|
-
'
|
|
88
|
-
|
|
89
|
-
|
|
90
|
-
|
|
91
|
-
|
|
92
|
-
|
|
93
|
-
|
|
94
|
-
|
|
95
|
-
|
|
96
|
-
|
|
97
|
-
|
|
98
|
-
|
|
99
|
-
|
|
100
|
-
|
|
101
|
-
|
|
102
|
-
|
|
103
|
-
|
|
104
|
-
|
|
105
|
-
|
|
106
|
-
|
|
|
107
|
-
| Methods ×
|
|
108
|
-
|
|
|
109
|
-
|
|
|
110
|
-
|
|
|
111
|
-
|
|
|
112
|
-
|
|
|
113
|
-
|
|
114
|
-
|
|
115
|
-
|
|
116
|
-
|
|
117
|
-
|
|
118
|
-
|
|
119
|
-
|
|
120
|
-
|
|
121
|
-
|
|
122
|
-
import
|
|
123
|
-
|
|
124
|
-
|
|
125
|
-
|
|
126
|
-
|
|
127
|
-
|
|
128
|
-
ax.
|
|
129
|
-
ax.plot(data['steps'], data['
|
|
130
|
-
ax.
|
|
131
|
-
ax.
|
|
132
|
-
ax.
|
|
133
|
-
|
|
134
|
-
|
|
135
|
-
|
|
136
|
-
|
|
137
|
-
|
|
138
|
-
|
|
139
|
-
|
|
140
|
-
|
|
141
|
-
|
|
142
|
-
ax.
|
|
143
|
-
|
|
144
|
-
|
|
145
|
-
|
|
146
|
-
|
|
147
|
-
|
|
148
|
-
|
|
149
|
-
|
|
150
|
-
|
|
151
|
-
|
|
152
|
-
|
|
153
|
-
\
|
|
154
|
-
\
|
|
155
|
-
\
|
|
156
|
-
\
|
|
157
|
-
\
|
|
158
|
-
|
|
159
|
-
|
|
160
|
-
\
|
|
161
|
-
\citet{
|
|
162
|
-
\
|
|
163
|
-
\
|
|
164
|
-
\
|
|
165
|
-
\end{
|
|
166
|
-
|
|
167
|
-
|
|
168
|
-
|
|
169
|
-
|
|
170
|
-
-
|
|
171
|
-
-
|
|
172
|
-
-
|
|
173
|
-
|
|
174
|
-
|
|
175
|
-
|
|
176
|
-
|
|
177
|
-
|
|
178
|
-
|
|
179
|
-
|
|
180
|
-
|
|
181
|
-
|
|
182
|
-
|
|
183
|
-
|
|
184
|
-
|
|
185
|
-
|
|
186
|
-
|
|
187
|
-
|
|
188
|
-
|
|
189
|
-
|
|
190
|
-
|
|
191
|
-
|
|
192
|
-
|
|
193
|
-
\
|
|
194
|
-
\
|
|
195
|
-
\
|
|
196
|
-
\
|
|
197
|
-
|
|
198
|
-
|
|
199
|
-
|
|
200
|
-
|
|
201
|
-
|
|
202
|
-
|
|
203
|
-
|
|
204
|
-
|
|
205
|
-
|
|
206
|
-
|
|
207
|
-
|
|
208
|
-
|
|
209
|
-
|
|
210
|
-
|
|
211
|
-
|
|
212
|
-
|
|
213
|
-
|
|
214
|
-
|
|
215
|
-
|
|
216
|
-
|
|
217
|
-
|
|
218
|
-
|
|
219
|
-
|
|
220
|
-
|
|
221
|
-
|
|
222
|
-
|
|
223
|
-
|
|
224
|
-
|
|
225
|
-
|
|
226
|
-
|
|
227
|
-
- [ ]
|
|
228
|
-
- [ ]
|
|
229
|
-
- [ ]
|
|
230
|
-
- [ ]
|
|
231
|
-
- [ ] Axis labels
|
|
232
|
-
- [ ]
|
|
233
|
-
- [ ]
|
|
234
|
-
- [ ]
|
|
235
|
-
- [ ]
|
|
236
|
-
- [ ]
|
|
237
|
-
|
|
238
|
-
|
|
239
|
-
|
|
240
|
-
|
|
241
|
-
|
|
242
|
-
|
|
243
|
-
├──
|
|
244
|
-
├──
|
|
245
|
-
├──
|
|
246
|
-
├──
|
|
247
|
-
├──
|
|
248
|
-
├──
|
|
249
|
-
├──
|
|
250
|
-
|
|
251
|
-
|
|
252
|
-
|
|
253
|
-
|
|
254
|
-
|
|
255
|
-
|
|
256
|
-
- **
|
|
257
|
-
- **
|
|
258
|
-
- **
|
|
259
|
-
- **
|
|
260
|
-
- **
|
|
261
|
-
- **
|
|
262
|
-
- **
|
|
263
|
-
- **
|
|
264
|
-
|
|
265
|
-
|
|
266
|
-
|
|
267
|
-
|
|
268
|
-
|
|
269
|
-
|
|
270
|
-
|
|
|
271
|
-
|
|
|
272
|
-
|
|
|
273
|
-
|
|
|
274
|
-
|
|
|
275
|
-
|
|
|
276
|
-
|
|
|
277
|
-
|
|
|
278
|
-
|
|
279
|
-
|
|
280
|
-
|
|
281
|
-
|
|
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.
|
|
185
|
+
|
|
186
|
+
### Step 6: Generate LaTeX Include Snippets
|
|
187
|
+
|
|
188
|
+
For each figure, output the LaTeX code to include it:
|
|
189
|
+
|
|
190
|
+
```latex
|
|
191
|
+
% === Fig 2: Training Curves ===
|
|
192
|
+
\begin{figure}[t]
|
|
193
|
+
\centering
|
|
194
|
+
\includegraphics[width=0.48\textwidth]{figures/fig2_training_curves.pdf}
|
|
195
|
+
\caption{Training curves comparing factorized and CRF-LR denoising.}
|
|
196
|
+
\label{fig:training_curves}
|
|
197
|
+
\end{figure}
|
|
198
|
+
```
|
|
199
|
+
|
|
200
|
+
Save all snippets to `figures/latex_includes.tex` for easy copy-paste into the paper.
|
|
201
|
+
|
|
202
|
+
### Step 7: Figure Quality Review with REVIEWER_MODEL
|
|
203
|
+
|
|
204
|
+
Send figure descriptions and captions to GPT-5.4 for review:
|
|
205
|
+
|
|
206
|
+
```
|
|
207
|
+
mcp__codex__codex:
|
|
208
|
+
model: gpt-5.4
|
|
209
|
+
config: {"model_reasoning_effort": "xhigh"}
|
|
210
|
+
prompt: |
|
|
211
|
+
Review these figure/table plans for a [VENUE] submission.
|
|
212
|
+
|
|
213
|
+
For each figure:
|
|
214
|
+
1. Is the caption informative and self-contained?
|
|
215
|
+
2. Does the figure type match the data being shown?
|
|
216
|
+
3. Is the comparison fair and clear?
|
|
217
|
+
4. Any missing baselines or ablations?
|
|
218
|
+
5. Would a different visualization be more effective?
|
|
219
|
+
|
|
220
|
+
[list all figures with captions and descriptions]
|
|
221
|
+
```
|
|
222
|
+
|
|
223
|
+
### Step 8: Quality Checklist
|
|
224
|
+
|
|
225
|
+
Before finishing, verify each figure (from pedrohcgs/claude-code-my-workflow):
|
|
226
|
+
|
|
227
|
+
- [ ] Font size readable at printed paper size (not too small)
|
|
228
|
+
- [ ] Colors distinguishable in grayscale (print-friendly)
|
|
229
|
+
- [ ] **No title inside figures** — titles go only in LaTeX `\caption{}` (from pedrohcgs)
|
|
230
|
+
- [ ] Legend does not overlap data
|
|
231
|
+
- [ ] Axis labels have units where applicable
|
|
232
|
+
- [ ] Axis labels are publication-quality (not variable names like `emp_rate`)
|
|
233
|
+
- [ ] Figure width fits single column (0.48\textwidth) or full width (0.95\textwidth)
|
|
234
|
+
- [ ] PDF output is vector (not rasterized text)
|
|
235
|
+
- [ ] No matplotlib default title (remove `plt.title` for publications)
|
|
236
|
+
- [ ] Serif font matches paper body text (Times / Computer Modern)
|
|
237
|
+
- [ ] Colorblind-accessible (if using colorblind palette)
|
|
238
|
+
|
|
239
|
+
## Output
|
|
240
|
+
|
|
241
|
+
```
|
|
242
|
+
figures/
|
|
243
|
+
├── paper_plot_style.py # shared style config
|
|
244
|
+
├── gen_fig1_architecture.py # per-figure scripts
|
|
245
|
+
├── gen_fig2_training_curves.py
|
|
246
|
+
├── gen_fig3_comparison.py
|
|
247
|
+
├── fig1_architecture.pdf # generated figures
|
|
248
|
+
├── fig2_training_curves.pdf
|
|
249
|
+
├── fig3_comparison.pdf
|
|
250
|
+
├── latex_includes.tex # LaTeX snippets for all figures
|
|
251
|
+
└── TABLE_*.tex # standalone table LaTeX files
|
|
252
|
+
```
|
|
253
|
+
|
|
254
|
+
## Key Rules
|
|
255
|
+
|
|
256
|
+
- **Every figure must be reproducible** — save the generation script alongside the output
|
|
257
|
+
- **Do NOT hardcode data** — always read from JSON/CSV files
|
|
258
|
+
- **Use vector format (PDF)** for all plots — PNG only as fallback
|
|
259
|
+
- **No decorative elements** — no background colors, no 3D effects, no chart junk
|
|
260
|
+
- **Consistent style across all figures** — same fonts, colors, line widths
|
|
261
|
+
- **Colorblind-safe** — verify with https://davidmathlogic.com/colorblind/ if needed
|
|
262
|
+
- **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
|
|
265
|
+
|
|
266
|
+
## Figure Type Reference
|
|
267
|
+
|
|
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).
|