dsh-aris-panel 0.1.0

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 (442) hide show
  1. package/LICENSE +21 -0
  2. package/README.md +98 -0
  3. package/README_CN.md +87 -0
  4. package/dsh/checkout.patch.yml +38 -0
  5. package/dsh/client.js +634 -0
  6. package/dsh/cordis.patch.yml +44 -0
  7. package/dsh/index.mjs +76 -0
  8. package/dsh/run-status.mjs +182 -0
  9. package/dsh/scope-limits.mjs +50 -0
  10. package/dsh/workbench.mjs +291 -0
  11. package/mcp-servers/claude-review/README.md +93 -0
  12. package/mcp-servers/claude-review/run_with_claude_aws.sh +49 -0
  13. package/mcp-servers/claude-review/server.py +718 -0
  14. package/mcp-servers/codex-image2/README.md +65 -0
  15. package/mcp-servers/codex-image2/server.py +893 -0
  16. package/mcp-servers/feishu-bridge/requirements.txt +1 -0
  17. package/mcp-servers/feishu-bridge/server.py +240 -0
  18. package/mcp-servers/gemini-review/README.md +171 -0
  19. package/mcp-servers/gemini-review/server.py +1856 -0
  20. package/mcp-servers/llm-chat/requirements.txt +1 -0
  21. package/mcp-servers/llm-chat/server.py +664 -0
  22. package/mcp-servers/manual-review/README.md +133 -0
  23. package/mcp-servers/manual-review/server.py +910 -0
  24. package/mcp-servers/manual-review/ui.html +279 -0
  25. package/mcp-servers/minimax-chat/requirements.txt +1 -0
  26. package/mcp-servers/minimax-chat/server.py +381 -0
  27. package/package.json +51 -0
  28. package/skills/ablation-planner/SKILL.md +123 -0
  29. package/skills/alphaxiv/SKILL.md +196 -0
  30. package/skills/analyze-results/SKILL.md +46 -0
  31. package/skills/arxiv/SKILL.md +248 -0
  32. package/skills/auto-paper-improvement-loop/SKILL.md +651 -0
  33. package/skills/auto-review-loop/SKILL.md +1137 -0
  34. package/skills/auto-review-loop-llm/SKILL.md +259 -0
  35. package/skills/auto-review-loop-minimax/SKILL.md +302 -0
  36. package/skills/citation-audit/SKILL.md +502 -0
  37. package/skills/claims-drafting/SKILL.md +227 -0
  38. package/skills/comm-lit-review/SKILL.md +297 -0
  39. package/skills/deepxiv/SKILL.md +263 -0
  40. package/skills/dse-loop/SKILL.md +296 -0
  41. package/skills/embodiment-description/SKILL.md +129 -0
  42. package/skills/exa-search/SKILL.md +205 -0
  43. package/skills/experiment-audit/SKILL.md +311 -0
  44. package/skills/experiment-bridge/SKILL.md +376 -0
  45. package/skills/experiment-plan/SKILL.md +249 -0
  46. package/skills/experiment-queue/SKILL.md +431 -0
  47. package/skills/experiment-queue/scripts/build_manifest.py +142 -0
  48. package/skills/experiment-queue/scripts/queue_manager.py +433 -0
  49. package/skills/feishu-notify/SKILL.md +156 -0
  50. package/skills/figure-description/SKILL.md +138 -0
  51. package/skills/figure-spec/SKILL.md +262 -0
  52. package/skills/figure-spec/scripts/figure_renderer.py +799 -0
  53. package/skills/formula-derivation/SKILL.md +280 -0
  54. package/skills/gemini-search/SKILL.md +231 -0
  55. package/skills/grant-proposal/SKILL.md +698 -0
  56. package/skills/idea-creator/SKILL.md +542 -0
  57. package/skills/idea-discovery/SKILL.md +521 -0
  58. package/skills/idea-discovery-robot/SKILL.md +363 -0
  59. package/skills/integrity-forensics/SKILL.md +284 -0
  60. package/skills/interview-cheatsheet/SKILL.md +245 -0
  61. package/skills/invention-structuring/SKILL.md +188 -0
  62. package/skills/jurisdiction-format/SKILL.md +192 -0
  63. package/skills/kill-argument/SKILL.md +437 -0
  64. package/skills/mermaid-diagram/SKILL.md +419 -0
  65. package/skills/meta-apply/SKILL.md +141 -0
  66. package/skills/meta-optimize/SKILL.md +437 -0
  67. package/skills/monitor-experiment/SKILL.md +140 -0
  68. package/skills/novelty-check/SKILL.md +101 -0
  69. package/skills/openalex/SKILL.md +237 -0
  70. package/skills/overleaf-sync/SKILL.md +220 -0
  71. package/skills/paper-claim-audit/SKILL.md +348 -0
  72. package/skills/paper-compile/SKILL.md +266 -0
  73. package/skills/paper-figure/SKILL.md +312 -0
  74. package/skills/paper-illustration/SKILL.md +736 -0
  75. package/skills/paper-illustration-image2/SKILL.md +391 -0
  76. package/skills/paper-illustration-image2/scripts/paper_illustration_image2.py +255 -0
  77. package/skills/paper-plan/SKILL.md +386 -0
  78. package/skills/paper-poster/SKILL.md +19 -0
  79. package/skills/paper-poster-html/DESIGN_FINAL.md +176 -0
  80. package/skills/paper-poster-html/IMPLEMENTATION_CONVENTIONS.md +161 -0
  81. package/skills/paper-poster-html/LICENSES/posterly-MIT.txt +21 -0
  82. package/skills/paper-poster-html/NOTICE.md +57 -0
  83. package/skills/paper-poster-html/SKILL.md +323 -0
  84. package/skills/paper-poster-html/scripts/_posterly/__init__.py +0 -0
  85. package/skills/paper-poster-html/scripts/_posterly/canvas.py +200 -0
  86. package/skills/paper-poster-html/scripts/_posterly/measure.py +588 -0
  87. package/skills/paper-poster-html/scripts/_posterly/polish.py +498 -0
  88. package/skills/paper-poster-html/scripts/_posterly/preflight.py +489 -0
  89. package/skills/paper-poster-html/scripts/_posterly/render.py +215 -0
  90. package/skills/paper-poster-html/scripts/_posterly/textutil.py +16 -0
  91. package/skills/paper-poster-html/scripts/_posterly/verify_final.py +171 -0
  92. package/skills/paper-poster-html/scripts/asset_check.py +897 -0
  93. package/skills/paper-poster-html/scripts/extract_pdf_figures.py +666 -0
  94. package/skills/paper-poster-html/scripts/poster_check.py +251 -0
  95. package/skills/paper-poster-html/scripts/preprocess_figures.py +238 -0
  96. package/skills/paper-poster-html/scripts/render_preview.py +217 -0
  97. package/skills/paper-poster-html/scripts/run_gates.py +556 -0
  98. package/skills/paper-poster-html/scripts/style_check.py +1324 -0
  99. package/skills/paper-poster-html/templates/COMPONENTS.md +462 -0
  100. package/skills/paper-poster-html/templates/README.md +170 -0
  101. package/skills/paper-poster-html/templates/landscape_4col.html +1032 -0
  102. package/skills/paper-poster-html/templates/landscape_hero.html +1046 -0
  103. package/skills/paper-poster-html/templates/portrait_2col.html +947 -0
  104. package/skills/paper-poster-html/templates/tokens/acl.json +9 -0
  105. package/skills/paper-poster-html/templates/tokens/cvpr.json +9 -0
  106. package/skills/paper-poster-html/templates/tokens/generic.json +9 -0
  107. package/skills/paper-poster-html/templates/tokens/iclr.json +9 -0
  108. package/skills/paper-poster-html/templates/tokens/icml.json +9 -0
  109. package/skills/paper-poster-html/templates/tokens/neurips.json +9 -0
  110. package/skills/paper-slides/SKILL.md +635 -0
  111. package/skills/paper-talk/SKILL.md +381 -0
  112. package/skills/paper-write/SKILL.md +604 -0
  113. package/skills/paper-write/templates/IEEEtran.bst +2409 -0
  114. package/skills/paper-write/templates/IEEEtran.cls +6347 -0
  115. package/skills/paper-write/templates/iclr2026.tex +84 -0
  116. package/skills/paper-write/templates/icml2025.tex +87 -0
  117. package/skills/paper-write/templates/ieee_conference.tex +89 -0
  118. package/skills/paper-write/templates/ieee_journal.tex +93 -0
  119. package/skills/paper-write/templates/math_commands.tex +48 -0
  120. package/skills/paper-write/templates/neurips2025.tex +80 -0
  121. package/skills/paper-writing/SKILL.md +916 -0
  122. package/skills/patent-novelty-check/SKILL.md +153 -0
  123. package/skills/patent-pipeline/SKILL.md +344 -0
  124. package/skills/patent-review/SKILL.md +203 -0
  125. package/skills/pixel-art/SKILL.md +137 -0
  126. package/skills/prior-art-search/SKILL.md +146 -0
  127. package/skills/proof-checker/SKILL.md +866 -0
  128. package/skills/proof-orchestrator/NOTICE.md +24 -0
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  130. package/skills/proof-orchestrator/references/audit-output-contract.md +126 -0
  131. package/skills/proof-orchestrator/references/deepseek-routing.md +74 -0
  132. package/skills/proof-orchestrator/references/dispatch-prompts.md +227 -0
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  140. package/skills/render-html/scripts/render_html.py +1006 -0
  141. package/skills/render-html/scripts/templates/academic.html +703 -0
  142. package/skills/render-html/scripts/templates/dashboard.html +333 -0
  143. package/skills/research-lit/SKILL.md +756 -0
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  145. package/skills/research-refine/SKILL.md +770 -0
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  158. package/skills/shared-references/compute-env-contract.md +163 -0
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  160. package/skills/shared-references/evidence-precheck.md +65 -0
  161. package/skills/shared-references/experiment-integrity.md +49 -0
  162. package/skills/shared-references/external-cadence.md +326 -0
  163. package/skills/shared-references/fan-out-pattern.md +366 -0
  164. package/skills/shared-references/injection-hygiene.md +127 -0
  165. package/skills/shared-references/integration-contract.md +461 -0
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@@ -0,0 +1,289 @@
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+ ---
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+ name: "paper-figure"
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+ description: "Generate publication-quality figures and tables from experiment results. Use when user says \"画图\", \"作图\", \"generate figures\", \"paper figures\", or needs plots for a paper."
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+ ---
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+
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+ > Override for Codex users who want **Gemini**, not a second Codex agent, to act as the reviewer. Install this package **after** `skills/skills-codex/*`.
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+
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+ # Paper Figure: Publication-Quality Plots from Experiment Data
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+
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+ > **Gemini overlay assurance:** `review_independence: cross-family` and `acceptance_status: accepted`.
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+
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+ Generate all figures and tables for a paper based on: **$ARGUMENTS**
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+
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+ ## Scope: What This Skill Can and Cannot Do
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+
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+ | Category | Can auto-generate? | Examples |
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+ |----------|-------------------|----------|
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+ | **Data-driven plots** | ✅ Yes | Line plots (training curves), bar charts (method comparison), scatter plots, heatmaps, box/violin plots |
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+ | **Comparison tables** | ✅ Yes | LaTeX tables comparing prior bounds, method features, ablation results |
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+ | **Multi-panel figures** | ✅ Yes | Subfigure grids combining multiple plots (e.g., 3×3 dataset × method) |
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+ | **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 |
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+ | **Generated image grids** | ❌ No — manual | Grids of generated samples (e.g., GAN/diffusion outputs). These come from running your model, not from this skill |
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+ | **Photographs / screenshots** | ❌ No — manual | Real-world images, UI screenshots, qualitative examples |
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+
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+ **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.
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+
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+ ## Constants
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+
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+ - **STYLE = `publication`** — Visual style preset. Options: `publication` (default, clean for print), `poster` (larger fonts), `slide` (bold colors)
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+ - **DPI = 300** — Output resolution
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+ - **FORMAT = `pdf`** — Output format. Options: `pdf` (vector, best for LaTeX), `png` (raster fallback)
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+ - **COLOR_PALETTE = `tab10`** — Default matplotlib color cycle. Options: `tab10`, `Set2`, `colorblind` (deuteranopia-safe)
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+ - **FONT_SIZE = 10** — Base font size (matches typical conference body text)
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+ - **FIG_DIR = `figures/`** — Output directory for generated figures
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+ - **REVIEWER_MODEL = `gemini-review`** — Gemini reviewer invoked through the local `gemini-review` MCP bridge. Set `GEMINI_REVIEW_MODEL` if you need a specific Gemini model override.
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+
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+ ## Inputs
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+
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+ 1. **PAPER_PLAN.md** — figure plan table (from `/paper-plan`)
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+ 2. **Experiment data** — JSON files, CSV files, or screen logs in `figures/` or project root
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+ 3. **Existing figures** — any manually created figures to preserve
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+
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+ If no PAPER_PLAN.md exists, scan for data files and ask the user which figures to generate.
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+
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+ ## Workflow
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+
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+ ### Step 1: Read Figure Plan
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+
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+ Parse the Figure Plan table from PAPER_PLAN.md:
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+
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+ ```markdown
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+ | ID | Type | Description | Data Source | Priority |
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+ |----|------|-------------|-------------|----------|
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+ | Fig 1 | Architecture | ... | manual | HIGH |
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+ | Fig 2 | Line plot | ... | figures/exp.json | HIGH |
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+ ```
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+
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+ Identify:
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+ - Which figures can be auto-generated from data
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+ - Which need manual creation (architecture diagrams, etc.)
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+ - Which are comparison tables (generate as LaTeX)
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+
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+ ### Step 2: Set Up Plotting Environment
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+
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+ Create a shared style configuration script:
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+
67
+ ```python
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+ # paper_plot_style.py — shared across all figure scripts
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+ import matplotlib.pyplot as plt
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+ import matplotlib
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+ matplotlib.rcParams.update({
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+ 'font.size': FONT_SIZE,
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+ 'font.family': 'serif',
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+ 'font.serif': ['Times New Roman', 'Times', 'DejaVu Serif'],
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+ 'axes.labelsize': FONT_SIZE,
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+ 'axes.titlesize': FONT_SIZE + 1,
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+ 'xtick.labelsize': FONT_SIZE - 1,
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+ 'ytick.labelsize': FONT_SIZE - 1,
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+ 'legend.fontsize': FONT_SIZE - 1,
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+ 'figure.dpi': DPI,
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+ 'savefig.dpi': DPI,
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+ 'savefig.bbox': 'tight',
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+ 'savefig.pad_inches': 0.05,
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+ 'axes.grid': False,
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+ 'axes.spines.top': False,
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+ 'axes.spines.right': False,
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+ 'text.usetex': False, # set True if LaTeX is available
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+ 'mathtext.fontset': 'stix',
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+ })
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+
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+ # Color palette
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+ COLORS = plt.cm.tab10.colors # or Set2, or colorblind-safe
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+
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}')
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+ print(f'Saved: {FIG_DIR}/{name}.{fmt}')
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+ ```
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+
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+ ### Step 3: Auto-Select Figure Type
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+
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+ Use this decision tree for data-driven figures (inspired by Imbad0202/academic-research-skills):
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+
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+ | Data Pattern | Recommended Type | Size |
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+ |-------------|-----------------|------|
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+ | X=time/steps, Y=metric | Line plot | 0.48\textwidth |
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+ | Methods × 1 metric | Bar chart | 0.48\textwidth |
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+ | Methods × multiple metrics | Grouped bar / radar | 0.95\textwidth |
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+ | Two continuous variables | Scatter plot | 0.48\textwidth |
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+ | Matrix / grid values | Heatmap | 0.48\textwidth |
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+ | Distribution comparison | Box/violin plot | 0.48\textwidth |
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+ | Multi-dataset results | Multi-panel (subfigure) | 0.95\textwidth |
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+ | Prior work comparison | LaTeX table | — |
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+
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+ ### Step 4: Generate Each Figure
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+
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+ For each figure in the plan, create a standalone Python script:
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+
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+ **Line plots** (training curves, scaling):
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+ ```python
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+ # gen_fig2_training_curves.py
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+ from paper_plot_style import *
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+ import json
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+
125
+ with open('figures/exp_results.json') as f:
126
+ data = json.load(f)
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+
128
+ fig, ax = plt.subplots(1, 1, figsize=(5, 3.5))
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+ ax.plot(data['steps'], data['fac_loss'], label='Factorized', color=COLORS[0])
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+ ax.plot(data['steps'], data['crf_loss'], label='CRF-LR', color=COLORS[1])
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+ ax.set_xlabel('Training Steps')
132
+ ax.set_ylabel('Cross-Entropy Loss')
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+ ax.legend(frameon=False)
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+ save_fig(fig, 'fig2_training_curves')
135
+ ```
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+
137
+ **Bar charts** (comparison, ablation):
138
+ ```python
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+ fig, ax = plt.subplots(1, 1, figsize=(5, 3))
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+ methods = ['Baseline', 'Method A', 'Method B', 'Ours']
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+ values = [82.3, 85.1, 86.7, 89.2]
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+ bars = ax.bar(methods, values, color=[COLORS[i] for i in range(len(methods))])
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+ ax.set_ylabel('Accuracy (%)')
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+ # Add value labels on bars
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+ for bar, val in zip(bars, values):
146
+ ax.text(bar.get_x() + bar.get_width()/2, bar.get_height() + 0.3,
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+ f'{val:.1f}', ha='center', va='bottom', fontsize=FONT_SIZE-1)
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+ save_fig(fig, 'fig3_comparison')
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+ ```
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+
151
+ **Comparison tables** (LaTeX, for theory papers):
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+ ```latex
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+ \begin{table}[t]
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+ \centering
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+ \caption{Comparison of estimation error bounds. $n$: sample size, $D$: ambient dim, $d$: latent dim, $K$: subspaces, $n_k$: modes.}
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+ \label{tab:bounds}
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+ \begin{tabular}{lccc}
158
+ \toprule
159
+ Method & Rate & Depends on $D$? & Multi-modal? \\
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+ \midrule
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+ \citet{MinimaxOkoAS23} & $n^{-s'/D}$ & Yes (curse) & No \\
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+ \citet{ScoreMatchingdistributionrecovery} & $n^{-2/d}$ & No & No \\
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+ \textbf{Ours} & $\sqrt{\sum n_k d_k / n}$ & No & Yes \\
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+ \bottomrule
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+ \end{tabular}
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+ \end{table}
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+ ```
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+
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+ **Architecture/pipeline diagrams** (MANUAL — outside this skill's scope):
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+ - These require manual creation using draw.io, Figma, Keynote, or TikZ
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+ - This skill can generate a rough TikZ skeleton as a starting point, but **do not expect publication-quality results**
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+ - If the figure already exists in `figures/`, preserve it and generate only the LaTeX `\includegraphics` snippet
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+ - Flag as `[MANUAL]` in the figure plan and `latex_includes.tex`
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+
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+ ### Step 5: Run All Scripts
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+
177
+ ```bash
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+ # Run all figure generation scripts
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+ for script in gen_fig*.py; do
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+ python "$script"
181
+ done
182
+ ```
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+
184
+ Verify all output files exist and are non-empty.
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+
186
+ ### Step 6: Generate LaTeX Include Snippets
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+
188
+ For each figure, output the LaTeX code to include it:
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+
190
+ ```latex
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+ % === Fig 2: Training Curves ===
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+ \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.}
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+ \label{fig:training_curves}
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+ \end{figure}
198
+ ```
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+
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+ 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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+
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+ Send figure descriptions and captions to Gemini for review:
205
+
206
+ ```
207
+ mcp__gemini-review__review_start:
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+ prompt: |
209
+ Review these figure/table plans for a [VENUE] submission.
210
+
211
+ For each figure:
212
+ 1. Is the caption informative and self-contained?
213
+ 2. Does the figure type match the data being shown?
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+ 3. Is the comparison fair and clear?
215
+ 4. Any missing baselines or ablations?
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+ 5. Would a different visualization be more effective?
217
+
218
+ [list all figures with captions and descriptions]
219
+ ```
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+
221
+ After this start call, immediately save the returned `jobId` and poll `mcp__gemini-review__review_status` with a bounded `waitSeconds` until `done=true`. Treat the completed status payload's `response` as the reviewer output, and save the completed `threadId` for any follow-up round.
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+
223
+ ### Step 8: Quality Checklist
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+
225
+ Before finishing, verify each figure (from pedrohcgs/claude-code-my-workflow):
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+
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
+ ## Output Protocols
255
+
256
+ > Follow these shared protocols for all output files:
257
+ > - **[Output Versioning Protocol](../../shared-references/output-versioning.md)** — write timestamped file first, then copy to fixed name
258
+ > - **[Output Manifest Protocol](../../shared-references/output-manifest.md)** — log every output to MANIFEST.md
259
+ > - **[Output Language Protocol](../../shared-references/output-language.md)** — respect the project's language setting
260
+
261
+ ## Key Rules
262
+
263
+ - **Every figure must be reproducible** — save the generation script alongside the output
264
+ - **Do NOT hardcode data** — always read from JSON/CSV files
265
+ - **Use vector format (PDF)** for all plots — PNG only as fallback
266
+ - **No decorative elements** — no background colors, no 3D effects, no chart junk
267
+ - **Consistent style across all figures** — same fonts, colors, line widths
268
+ - **Colorblind-safe** — verify with https://davidmathlogic.com/colorblind/ if needed
269
+ - **One script per figure** — easy to re-run individual figures when data changes
270
+ - **No titles inside figures** — captions are in LaTeX only
271
+ - **Comparison tables count as figures** — generate them as standalone .tex files
272
+
273
+ ## Figure Type Reference
274
+
275
+ | Type | When to Use | Typical Size |
276
+ |------|------------|--------------|
277
+ | Line plot | Training curves, scaling trends | 0.48\textwidth |
278
+ | Bar chart | Method comparison, ablation | 0.48\textwidth |
279
+ | Grouped bar | Multi-metric comparison | 0.95\textwidth |
280
+ | Scatter plot | Correlation analysis | 0.48\textwidth |
281
+ | Heatmap | Attention, confusion matrix | 0.48\textwidth |
282
+ | Box/violin | Distribution comparison | 0.48\textwidth |
283
+ | Architecture | System overview | 0.95\textwidth |
284
+ | Multi-panel | Combined results (subfigures) | 0.95\textwidth |
285
+ | Comparison table | Prior bounds vs. ours (theory) | full width |
286
+
287
+ ## Acknowledgements
288
+
289
+ 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).
@@ -0,0 +1,265 @@
1
+ ---
2
+ name: "paper-plan"
3
+ description: "Generate a structured paper outline from review conclusions and experiment results. Use when user says \"写大纲\", \"paper outline\", \"plan the paper\", \"论文规划\", or wants to create a paper plan before writing."
4
+ ---
5
+
6
+ > Override for Codex users who want **Gemini**, not a second Codex agent, to act as the reviewer. Install this package **after** `skills/skills-codex/*`.
7
+
8
+ # Paper Plan: From Review Conclusions to Paper Outline
9
+
10
+ > **Gemini overlay assurance:** `review_independence: cross-family` and `acceptance_status: accepted`.
11
+
12
+ Generate a structured, section-by-section paper outline from: **$ARGUMENTS**
13
+
14
+ ## Constants
15
+
16
+ - **REVIEWER_MODEL = `gemini-review`** — Gemini reviewer invoked through the local `gemini-review` MCP bridge. Set `GEMINI_REVIEW_MODEL` if you need a specific Gemini model override.
17
+ - **TARGET_VENUE = `ICLR`** — Default venue. User can override (e.g., `/paper-plan "topic" — venue: NeurIPS`). Supported: `ICLR`, `NeurIPS`, `ICML`.
18
+ - **MAX_PAGES** — Main body page limit, measured from first page to end of Conclusion section (excluding references, appendix, and acknowledgements). ICLR=9, NeurIPS=9, ICML=8.
19
+
20
+ ## Inputs
21
+
22
+ The skill expects one or more of these in the project directory:
23
+
24
+ 1. **NARRATIVE_REPORT.md** or **STORY.md** — research narrative with claims and evidence
25
+ 2. **review-stage/AUTO_REVIEW.md** — auto-review loop conclusions *(fall back to `./AUTO_REVIEW.md` if not found)*
26
+ 3. **Experiment results** — JSON files in `figures/`, screen logs, tables
27
+ 4. **idea-stage/IDEA_REPORT.md** — from idea-discovery pipeline (if applicable) *(fall back to `./IDEA_REPORT.md` if not found)*
28
+
29
+ If none exist, ask the user to describe the paper's contribution in 3-5 sentences.
30
+
31
+ ## Workflow
32
+
33
+ ### Step 1: Extract Claims and Evidence
34
+
35
+ Read all available narrative documents and extract:
36
+
37
+ 1. **Core claims** (3-5 main contributions)
38
+ 2. **Evidence** for each claim (which experiments, which metrics, which figures)
39
+ 3. **Known weaknesses** (from reviewer feedback)
40
+ 4. **Suggested framing** (from review conclusions)
41
+
42
+ Build a **Claims-Evidence Matrix**:
43
+
44
+ ```markdown
45
+ | Claim | Evidence | Status | Section |
46
+ |-------|----------|--------|---------|
47
+ | [claim 1] | [exp A, metric B] | Supported | §3.2 |
48
+ | [claim 2] | [exp C] | Partially supported | §4.1 |
49
+ ```
50
+
51
+ ### Step 2: Determine Paper Type and Structure
52
+
53
+ Based on TARGET_VENUE and paper content, classify and select structure.
54
+
55
+ **IMPORTANT**: The section count is FLEXIBLE (5-8 sections). Choose what fits the content best. The templates below are starting points, not rigid constraints.
56
+
57
+ **Empirical/Diagnostic paper:**
58
+ ```
59
+ 1. Introduction (1.5 pages)
60
+ 2. Related Work (1 page)
61
+ 3. Method / Setup (1.5 pages)
62
+ 4. Experiments (3 pages)
63
+ 5. Analysis / Discussion (1 page)
64
+ 6. Conclusion (0.5 pages)
65
+ ```
66
+
67
+ **Theory + Experiments paper:**
68
+ ```
69
+ 1. Introduction (1.5 pages)
70
+ 2. Related Work (1 page)
71
+ 3. Preliminaries & Modeling (1.5 pages)
72
+ 4. Experiments (1.5 pages)
73
+ 5. Theory Part A (1.5 pages)
74
+ 6. Theory Part B (1.5 pages)
75
+ 7. Conclusion (0.5 pages)
76
+ — Total: 9 pages
77
+ ```
78
+ Theory papers often need 7 sections (splitting theory into estimation + optimization, or setup + analysis). The total page budget MUST sum to MAX_PAGES.
79
+
80
+ Theory papers should:
81
+ - Include **proof sketch** locations (not just theorem statements)
82
+ - Plan a **comparison table** of prior theoretical bounds vs. this paper's bounds
83
+ - Identify which proofs go in appendix vs. main body
84
+
85
+ **Method paper:**
86
+ ```
87
+ 1. Introduction (1.5 pages)
88
+ 2. Related Work (1 page)
89
+ 3. Method (2 pages)
90
+ 4. Experiments (2.5 pages)
91
+ 5. Ablation / Analysis (1 page)
92
+ 6. Conclusion (0.5 pages)
93
+ ```
94
+
95
+ ### Step 3: Section-by-Section Planning
96
+
97
+ For each section, specify:
98
+
99
+ ```markdown
100
+ ### §0 Abstract
101
+ - **One-sentence problem**: [what gap this paper addresses]
102
+ - **Approach**: [what we do, in one sentence]
103
+ - **Key result**: [most compelling quantitative finding]
104
+ - **Implication**: [why it matters]
105
+ - **Estimated length**: 150-250 words
106
+ - **Self-contained check**: can a reader understand this without the paper?
107
+
108
+ ### §1 Introduction
109
+ - **Opening hook**: [1-2 sentences that motivate the problem]
110
+ - **Gap**: [what's missing in prior work]
111
+ - **Key questions**: [the research questions this paper answers]
112
+ - **Contributions**: [numbered list, matching Claims-Evidence Matrix]
113
+ - **Hero figure**: [describe what Figure 1 should show — MUST include clear comparison if applicable]
114
+ - **Estimated length**: 1.5 pages
115
+ - **Key citations**: [3-5 papers to cite here]
116
+
117
+ ### §2 Related Work
118
+ - **Subtopics**: [2-4 categories of related work]
119
+ - **Positioning**: [how this paper differs from each category]
120
+ - **Minimum length**: 1 full page (at least 3-4 paragraphs with substantive synthesis)
121
+ - **Must NOT be just a list** — synthesize, compare, and position
122
+
123
+ ### §3 Method / Setup / Preliminaries
124
+ - **Notation**: [key symbols and their meanings]
125
+ - **Problem formulation**: [formal setup]
126
+ - **Method description**: [algorithm, model, or experimental design]
127
+ - **Formal statements**: [theorems, propositions if applicable]
128
+ - **Proof sketch locations**: [which key steps appear here vs. appendix]
129
+ - **Estimated length**: 1.5-2 pages
130
+
131
+ ### §4 Experiments / Main Results
132
+ - **Figures planned**:
133
+ - Fig 1: [description, type: bar/line/table/architecture, WHAT COMPARISON it shows]
134
+ - Fig 2: [description]
135
+ - Table 1: [what it shows, which methods/baselines compared]
136
+ - **Data source**: [which JSON files / experiment results]
137
+
138
+ ### §5 Conclusion
139
+ - **Restatement**: [contributions rephrased, not copy-pasted from intro]
140
+ - **Limitations**: [honest assessment — reviewers value this]
141
+ - **Future work**: [1-2 concrete directions]
142
+ - **Estimated length**: 0.5 pages
143
+ ```
144
+
145
+ ### Step 4: Figure Plan
146
+
147
+ List every figure and table:
148
+
149
+ ```markdown
150
+ ## Figure Plan
151
+
152
+ | ID | Type | Description | Data Source | Priority |
153
+ |----|------|-------------|-------------|----------|
154
+ | Fig 1 | Hero/Architecture | System overview + comparison | manual | HIGH |
155
+ | Fig 2 | Line plot | Training curves comparison | figures/exp_A.json | HIGH |
156
+ | Fig 3 | Bar chart | Ablation results | figures/ablation.json | MEDIUM |
157
+ | Table 1 | Comparison table | Main results vs. baselines | figures/main_results.json | HIGH |
158
+ | Table 2 | Theory comparison | Prior bounds vs. ours | manual | HIGH (theory papers) |
159
+ ```
160
+
161
+ **CRITICAL for Figure 1 / Hero Figure**: Describe in detail what the figure should contain, including:
162
+ - Which methods are being compared
163
+ - What the visual difference should demonstrate
164
+ - Caption draft that clearly states the comparison
165
+
166
+ ### Step 5: Citation Scaffolding
167
+
168
+ For each section, list required citations:
169
+
170
+ ```markdown
171
+ ## Citation Plan
172
+ - §1 Intro: [paper1], [paper2], [paper3] (problem motivation)
173
+ - §2 Related: [paper4]-[paper10] (categorized by subtopic)
174
+ - §3 Method: [paper11] (baseline), [paper12] (technique we build on)
175
+ ```
176
+
177
+ **Citation rules** (from claude-scholar + Imbad0202/academic-research-skills):
178
+ 1. NEVER generate BibTeX from memory — always verify via search or existing .bib files
179
+ 2. Every citation must be verified: correct authors, year, venue
180
+ 3. Flag any citation you're unsure about with `[VERIFY]`
181
+ 4. Prefer published versions over arXiv preprints when available
182
+
183
+ ### Step 6: Cross-Review with REVIEWER_MODEL
184
+
185
+ Send the complete outline to Gemini review for feedback:
186
+
187
+ ```
188
+ mcp__gemini-review__review_start:
189
+ prompt: |
190
+ Review this paper outline for a [VENUE] submission.
191
+ [full outline including Claims-Evidence Matrix]
192
+
193
+ Score 1-10 on:
194
+ 1. Logical flow — does the story build naturally?
195
+ 2. Claim-evidence alignment — every claim backed?
196
+ 3. Missing experiments or analysis
197
+ 4. Positioning relative to prior work
198
+ 5. Page budget feasibility (MAX_PAGES = main body to Conclusion end, excluding refs/appendix)
199
+
200
+ For each weakness, suggest the MINIMUM fix.
201
+ Be specific and actionable — "add X" not "consider more experiments".
202
+ ```
203
+
204
+ After this start call, immediately save the returned `jobId` and poll `mcp__gemini-review__review_status` with a bounded `waitSeconds` until `done=true`. Treat the completed status payload's `response` as the reviewer output, and save the completed `threadId` for any follow-up round.
205
+
206
+ Apply feedback before finalizing.
207
+
208
+ ### Step 7: Output
209
+
210
+ Save the final outline to `PAPER_PLAN.md` in the project root:
211
+
212
+ ```markdown
213
+ # Paper Plan
214
+
215
+ **Title**: [working title]
216
+ **Venue**: [target venue]
217
+ **Type**: [empirical/theory/method]
218
+ **Date**: [today]
219
+ **Page budget**: [MAX_PAGES] pages (main body to Conclusion end, excluding references & appendix)
220
+ **Section count**: [N] (must match the number of section files that will be created)
221
+
222
+ ## Claims-Evidence Matrix
223
+ [from Step 1]
224
+
225
+ ## Structure
226
+ [from Step 2-3, section by section]
227
+
228
+ ## Figure Plan
229
+ [from Step 4, with detailed hero figure description]
230
+
231
+ ## Citation Plan
232
+ [from Step 5]
233
+
234
+ ## Reviewer Feedback
235
+ [from Step 6, summarized]
236
+
237
+ ## Next Steps
238
+ - [ ] /paper-figure to generate all figures
239
+ - [ ] /paper-write to draft LaTeX
240
+ - [ ] /paper-compile to build PDF
241
+ ```
242
+
243
+ ## Output Protocols
244
+
245
+ > Follow these shared protocols for all output files:
246
+ > - **[Output Versioning Protocol](../../shared-references/output-versioning.md)** — write timestamped file first, then copy to fixed name
247
+ > - **[Output Manifest Protocol](../../shared-references/output-manifest.md)** — log every output to MANIFEST.md
248
+ > - **[Output Language Protocol](../../shared-references/output-language.md)** — respect the project's language setting
249
+
250
+ ## Key Rules
251
+
252
+ - **Large file handling**: If the Write tool fails due to file size, immediately retry using Bash (`cat << 'EOF' > file`) to write in chunks. Do NOT ask the user for permission — just do it silently.
253
+
254
+ - **Do NOT generate author information** — leave author block as placeholder or anonymous
255
+ - **Be honest about evidence gaps** — mark claims as "needs experiment" rather than overclaiming
256
+ - **Page budget is hard** — if content exceeds MAX_PAGES, suggest what to move to appendix
257
+ - **MAX_PAGES counts main body only** — from first page to end of Conclusion. References and appendix are NOT counted.
258
+ - **Venue-specific norms** — all three venues (ICLR/NeurIPS/ICML) use `natbib` (`\citep`/`\citet`)
259
+ - **Claims-Evidence Matrix is the backbone** — every claim must map to evidence, every experiment must support a claim
260
+ - **Figures need detailed descriptions** — especially the hero figure, which must clearly specify comparisons and visual expectations
261
+ - **Section count is flexible** — 5-8 sections depending on paper type. Don't force content into a rigid 5-section template.
262
+
263
+ ## Acknowledgements
264
+
265
+ Outline methodology inspired by [Research-Paper-Writing-Skills](https://github.com/Master-cai/Research-Paper-Writing-Skills) (claim-evidence mapping), [claude-scholar](https://github.com/Galaxy-Dawn/claude-scholar) (citation verification), and [Imbad0202/academic-research-skills](https://github.com/Imbad0202/academic-research-skills) (claim verification protocol).
@@ -0,0 +1,102 @@
1
+ ---
2
+ name: paper-poster-html
3
+ description: "DEFAULT poster pipeline — build an academic conference poster (ICML/NeurIPS/ICLR/CVPR/...) as a single HTML/CSS file with measurement-driven hard gates, real paper figures, a two-hue design-token system, and print-ready PDF via headless Chromium. Use when the user says \"做海报\", \"poster\", \"conference poster\", \"paper poster\", or asks to design/redo a research poster."
4
+ argument-hint: "[paper-dir-or-pdf] [— venue: ICLR, canvas: 185x90cm landscape, venue-colors: true]"
5
+ allowed-tools: Bash(*), Read, Write, Edit, Grep, Glob, mcp__gemini-review__review, mcp__gemini-review__review_start, mcp__gemini-review__review_reply_start, mcp__gemini-review__review_status
6
+ ---
7
+
8
+ > Override for Codex users who want **Gemini**, not a second Codex/Codex-MCP reviewer, to act as the reviewer. Install this package **after** `skills/skills-codex/*`.
9
+
10
+ # Paper Poster (HTML): measurement-gated poster generation
11
+
12
+ > **Gemini overlay assurance:** `review_independence: cross-family` and `acceptance_status: accepted`.
13
+
14
+ One HTML file styled for an exact print canvas (`@page { size: W H }`), rendered to PDF
15
+ via Playwright print emulation. **Iterate by measuring, not eyeballing** — the screen
16
+ preview lies; only print emulation at the correct viewport tells the truth. Core gate
17
+ machinery is adapted from [posterly](https://github.com/Chenruishuo/posterly) (MIT, ©
18
+ 2026 Ruishuo Chen — see `NOTICE.md` and `LICENSES/posterly-MIT.txt` in the mainline
19
+ skill directory); ARIS adds style discipline gates, figure-provenance gates, the
20
+ cross-model review loop, and the anti-patch-loop fix vocabulary.
21
+
22
+ This overlay is identical to `skills/skills-codex/paper-poster-html/` except that the
23
+ two cross-model review calls go to **Gemini** through the local `gemini-review` MCP
24
+ bridge instead of a spawned GPT reviewer agent. Follow the base mirror for everything
25
+ not restated here (phases, gates, fix vocabulary, figure provenance, output contract).
26
+
27
+ ## Reviewer constants (overlay)
28
+
29
+ - **REVIEWER_MODEL = `gemini-review`** — Gemini invoked through the local
30
+ `gemini-review` MCP bridge.
31
+ - **Fresh review job per call** — start each review with
32
+ `mcp__gemini-review__review_start`; never reuse a prior review job across review
33
+ boundaries. Save the returned `jobId`, poll `mcp__gemini-review__review_status` with
34
+ a bounded `waitSeconds` until `done=true`, and treat the completed payload's
35
+ `response` as the reviewer output.
36
+ - The Gemini bridge cannot read your local files — paste the relevant content into the
37
+ prompt, and pass rendered posters via `imagePaths`.
38
+ - If the `gemini-review` bridge is unavailable, stop and tell the user what to
39
+ configure. Do not silently degrade the cross-model reviews into self-review.
40
+
41
+ ## Phase 1 step 2 — Cross-model content audit (Gemini)
42
+
43
+ ```text
44
+ mcp__gemini-review__review_start:
45
+ prompt: |
46
+ Audit a conference-poster content plan against its source paper.
47
+
48
+ ## Poster content plan
49
+ [PASTE poster_html/POSTER_CONTENT_PLAN.md]
50
+
51
+ ## Paper source (relevant sections)
52
+ [PASTE the paper sections backing the plan's claims — abstract, headline
53
+ results tables, method equations, theorem statements]
54
+
55
+ For EVERY claim, number, equation, and attribution in the plan, output one row:
56
+ | claim on poster | paper location | paper says (verbatim) | match? |
57
+ with match ∈ {OK, NUMERIC-MISMATCH, OVERCLAIM, MISSING-PRECONDITION,
58
+ NOT-IN-PAPER, SCOPE-NARROWED}. End with a count per category.
59
+ ```
60
+
61
+ Poll `review_status` until `done=true`; save the response to
62
+ `poster_html/CLAIM_EVIDENCE.md`. Fix every non-OK row or record it as a
63
+ user-acknowledged tradeoff.
64
+
65
+ ## Phase 6 — Final review (Gemini, multimodal)
66
+
67
+ All hard gates PASS + polish warnings zero-or-waived + executor visual score ≥ 9
68
+ first. Then:
69
+
70
+ ```text
71
+ mcp__gemini-review__review_start:
72
+ imagePaths: ["poster_html/poster_preview.png"]
73
+ prompt: |
74
+ Final print-readiness audit of a conference poster (image attached).
75
+
76
+ ## Final poster text content
77
+ [PASTE the text content extracted from poster_html/poster.html]
78
+
79
+ ## Gate report summary
80
+ [PASTE the overall/hard_failures/warnings fields of poster_html/GATE_REPORT.json]
81
+
82
+ ## Claim→evidence audit
83
+ [PASTE poster_html/CLAIM_EVIDENCE.md]
84
+
85
+ Check: (1) fidelity & overclaims RE-CHECKED on the final text (polish introduces
86
+ new claims), (2) residue (\ref{, TODO, raw < in math, missing images, remote
87
+ URLs), (3) visual rhetoric (headline numbers prominent, banner readable from
88
+ 2 m, two-hue discipline, real paper figures central and inside their cards),
89
+ (4) gate-log coherence.
90
+ Verdict: PRINT-READY or NEEDS-FIX with a numbered, severity-ordered issue list.
91
+ ```
92
+
93
+ Poll `mcp__gemini-review__review_status` with a bounded `waitSeconds` until `done=true`;
94
+ treat the completed payload's `response` as the reviewer verdict.
95
+
96
+ The reviewer recommends; it does not edit. Any fix → back through Phase 4/5 gates —
97
+ never straight to re-review.
98
+
99
+ ## Review tracing
100
+
101
+ Save both review jobs' raw responses per `../../shared-references/review-tracing.md` to
102
+ `.aris/traces/paper-poster-html/<date>_run<NN>/`.