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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  410. package/tools/generate_codex_claude_review_overrides.py +299 -0
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@@ -0,0 +1,129 @@
1
+ ---
2
+ name: embodiment-description
3
+ description: "Write detailed embodiment descriptions for patent specifications. Use when user says \"ๆ’ฐๅ†™ๅฎžๆ–ฝไพ‹\", \"write embodiment\", \"ๅฎžๆ–ฝไพ‹ๆ่ฟฐ\", \"detailed description\", or wants to describe how to practice an invention."
4
+ argument-hint: "[claims-path-or-embodiment-details]"
5
+ allowed-tools: Bash(*), Read, Write, Edit, Grep, Glob
6
+ ---
7
+
8
+ # Embodiment Description
9
+
10
+ Write detailed embodiments for: **$ARGUMENTS**
11
+
12
+ Embodiments describe HOW to make and use the invention -- they are the patent equivalent of experiment sections, but describe the invention rather than evaluating it empirically.
13
+
14
+ ## Constants
15
+
16
+ - `MIN_EMBODIMENTS = 1` โ€” At least one complete embodiment required
17
+ - `MAX_EMBODIMENTS = 3` โ€” Practical limit; more embodiments strengthen enablement
18
+ - `EMBODIMENT_STYLE = detailed` โ€” `detailed` (full working example) or `outline` (sketch)
19
+ - `REFERENCE_NUMERAL_PREFIX = 100` โ€” Starting reference numeral for first figure's components
20
+
21
+ ## Inputs
22
+
23
+ 1. `patent/INVENTION_DISCLOSURE.md` โ€” invention decomposition (core/supporting/optional features)
24
+ 2. `patent/CLAIMS.md` โ€” drafted claims that the embodiments must support
25
+ 3. User-provided figures (if any) in any directory
26
+ 4. `patent/figures/numeral_index.md` if it exists (from `/figure-description`)
27
+
28
+ ## Workflow
29
+
30
+ ### Step 1: Plan Embodiments
31
+
32
+ For each claim category (method, system, etc.), plan at least one embodiment:
33
+
34
+ | Embodiment | Covers Claims | Type | Key Variations |
35
+ |-----------|--------------|------|----------------|
36
+ | 1 | Claims 1, X | Best mode / preferred | [primary implementation] |
37
+ | 2 | Claims 2, 3 | Alternative | [different parameters/materials] |
38
+ | 3 | Claims 4, 5 | Additional alternative | [different configuration] |
39
+
40
+ ### Step 2: Write Each Embodiment
41
+
42
+ For each embodiment, write a detailed description following this structure:
43
+
44
+ **Opening paragraph**:
45
+ "In one embodiment, [invention summary with reference to what is being described]."
46
+
47
+ **Component/step-by-step description**:
48
+
49
+ For method embodiments:
50
+ - Describe each step in order
51
+ - Reference figure numerals: "As shown in FIG. 1, at step 202, the processor 102 receives the input data 104..."
52
+ - Include specific parameters, ranges, and conditions
53
+ - Describe what happens at each decision point
54
+
55
+ For system/apparatus embodiments:
56
+ - Describe each component
57
+ - Reference figure numerals: "Referring to FIG. 1, the system 100 comprises a processor 102, a memory 104, and a communication interface 106..."
58
+ - Describe interconnections between components
59
+ - Describe operation of the system step-by-step
60
+
61
+ **Variations and alternatives**:
62
+ - "In some embodiments, the processor 102 may be a GPU, an FPGA, or an ASIC."
63
+ - "In another embodiment, the memory 104 may be replaced with a distributed storage system."
64
+ - "The parameters described above are exemplary; other values within the range [X, Y] are also contemplated."
65
+
66
+ These variations are critical -- they support broader claim interpretation.
67
+
68
+ ### Step 3: Reference Numeral Integration
69
+
70
+ Ensure consistent reference numeral usage:
71
+
72
+ 1. Every component mentioned must have a numeral
73
+ 2. Numeral must appear first in parentheses after the component name: "the processor (102)"
74
+ 3. Subsequent references: "the processor 102" (no parentheses)
75
+ 4. Numbering follows figure series: 100-series for FIG. 1, 200-series for FIG. 2
76
+
77
+ **Format**:
78
+ - First mention: "the processor (102)"
79
+ - Later in same embodiment: "the processor 102"
80
+ - Cross-figure: "the processor 102 (shown in both FIG. 1 and FIG. 2)"
81
+
82
+ ### Step 4: Claim Support Verification
83
+
84
+ For each claim element, verify it appears in at least one embodiment:
85
+
86
+ | Claim Element | Embodiment | Reference Numeral | Description Paragraph |
87
+ |---------------|-----------|-------------------|----------------------|
88
+ | [element] | [which] | [numeral] | [paragraph reference] |
89
+
90
+ If any claim element lacks embodiment support, add the necessary description.
91
+
92
+ ### Step 5: Software/Algorithm Embodiments (if applicable)
93
+
94
+ For method/software inventions, include:
95
+ - Pseudocode or algorithmic description (NOT actual code)
96
+ - Flowchart description tied to figures
97
+ - Data structure descriptions
98
+ - Interface specifications
99
+
100
+ Example:
101
+ ```
102
+ In one embodiment, the method comprises the following steps:
103
+ At step 202, the processor 102 receives input data from the input device 108.
104
+ At step 204, the processor 102 extracts feature vectors from the input data using a convolutional neural network.
105
+ At step 206, the processor 102 applies the attention mechanism 110 to the feature vectors...
106
+ ```
107
+
108
+ ### Step 6: Output
109
+
110
+ Embodiment sections are written to `patent/specification/detailed_description.md` (or appended to the specification structure).
111
+
112
+ Each embodiment section should be self-contained but cross-reference other embodiments when describing alternatives.
113
+
114
+ ## Key Rules
115
+
116
+ - Embodiments must teach a POSITA to make and use the invention without undue experimentation.
117
+ - Include at least one "best mode" embodiment (US requirement).
118
+ - Multiple embodiments strengthen the specification against enablement challenges.
119
+ - Describe the invention, do NOT evaluate it empirically ("The embodiment achieves 95% accuracy" is wrong; "The processor classifies the input data" is correct).
120
+ - **CRITICAL โ€” NO experimental data, test results, accuracy percentages, detection rates, precision values, or comparative performance data.** These belong in papers, not patents. The embodiment teaches HOW to make and use, not HOW WELL it performs.
121
+ - WRONG: "ไผ ๆ„Ÿๅ™จๅฏน็›ดๅพ„่ถ…่ฟ‡150ฮผm็š„้‡‘ๅฑž้ข—็ฒ’ๅฎž็Žฐไบ†100%็š„ๆฃ€ๆต‹็ฒพๅบฆ๏ผŒๅณไฝฟๅœจๆฃ€ๆต‹้™ๅค„ไปไฟๆŒ94%็š„้ซ˜็ฒพๅบฆใ€‚"
122
+ - RIGHT: "ๅฝ“ไธ้”ˆ้’ข้ข—็ฒ’้€š่ฟ‡้—ด้š™ไผ ๆ„ŸๅŒบๅŸŸๆ—ถ๏ผŒ่ฐๆŒฏ้ข‘็އไธ‹้™ใ€‚้ข—็ฒ’็›ดๅพ„่ถŠๅคง๏ผŒ้ข‘็އๅ็งปๅน…ๅบฆ่ถŠๅคงใ€‚"
123
+ - Do NOT include tables of experimental results, graphs of measurement data, or comparisons with prior art performance.
124
+ - **CRITICAL โ€” An embodiment is NOT an experiment.** Do NOT describe "repeated experiments", "accuracy evaluation", "precision testing", "calibration experiments", or "comparison with reference methods". An embodiment describes ONE way to make and use the invention โ€” it is a recipe, not a test report.
125
+ - Do NOT copy experimental sections from source papers verbatim. Transform the experimental setup into a manufacturing/operation description.
126
+ - If the source material is a paper, extract ONLY: (1) what was built, (2) what materials/parameters were used, (3) how it operates. Ignore all test methodology, results, and performance metrics.
127
+ - Include specific parameters where possible, but frame them as exemplary, not limiting.
128
+ - Reference numerals must be consistent with the figures.
129
+ - Do NOT use subjective language ("excellent", "surprising", "superior").
@@ -0,0 +1,192 @@
1
+ ---
2
+ name: exa-search
3
+ description: AI-powered web search via Exa with content extraction. Use when user says "exa search", "web search with content", "find similar pages", or needs broad web results beyond academic databases (arXiv, Semantic Scholar).
4
+ argument-hint: "[search-query-or-url]"
5
+ allowed-tools: Bash(*), Read, Write
6
+ ---
7
+
8
+ # Exa AI-Powered Web Search
9
+
10
+ Search query: $ARGUMENTS
11
+
12
+ ## Role & Positioning
13
+
14
+ Exa is the **broad web search** source with built-in content extraction:
15
+
16
+ | Skill | Best for |
17
+ |------|----------|
18
+ | `/arxiv` | Direct preprint search and PDF download |
19
+ | `/semantic-scholar` | Published venue papers (IEEE, ACM, Springer), citation counts |
20
+ | `/deepxiv` | Layered reading: search, brief, section map, section reads |
21
+ | `/exa-search` | Broad web search: blogs, docs, news, companies, research papers โ€” with content extraction |
22
+
23
+ Use Exa when you need results beyond academic databases, or when you want content (highlights, full text, summaries) extracted alongside search results.
24
+
25
+ ## Constants
26
+
27
+ - **EXA_FETCHER** โ€” canonical name `exa_search.py`, resolved per
28
+ [`shared-references/integration-contract.md`](../shared-references/integration-contract.md) ยง2
29
+ (Codex-side chain: `$ARIS_REPO/tools/` โ†’ `tools/` โ†’ `~/.codex/skills/exa-search/`).
30
+ Policy D1 โ€” standalone `/exa-search` has no documented fallback,
31
+ so unresolved helper terminates with an explicit error.
32
+ - **MAX_RESULTS = 10** โ€” Default number of results to return.
33
+
34
+ > Overrides (append to arguments):
35
+ > - `/exa-search "RAG pipelines" โ€” max: 5` โ€” top 5 results
36
+ > - `/exa-search "diffusion models" โ€” category: research paper` โ€” research papers only
37
+ > - `/exa-search "startup funding" โ€” category: news, start date: 2025-01-01` โ€” recent news
38
+ > - `/exa-search "transformer" โ€” content: text, max chars: 8000` โ€” full text mode
39
+ > - `/exa-search "transformer" โ€” content: summary` โ€” LLM-generated summaries
40
+ > - `/exa-search "transformer" โ€” domains: arxiv.org,huggingface.co` โ€” domain filter
41
+ > - `/exa-search "https://arxiv.org/abs/2301.07041" โ€” similar` โ€” find similar pages
42
+
43
+ ## Setup
44
+
45
+ Exa requires the `exa-py` SDK and an API key:
46
+
47
+ ```bash
48
+ pip install exa-py
49
+ ```
50
+
51
+ Set your API key:
52
+ ```bash
53
+ export EXA_API_KEY=your-key-here
54
+ ```
55
+
56
+ Get a key from [exa.ai](https://exa.ai).
57
+
58
+ ## Workflow
59
+
60
+ ### Step 1: Parse Arguments
61
+
62
+ Parse `$ARGUMENTS` for:
63
+ - **query**: The search query (required) or a URL (for `find-similar` mode)
64
+ - **similar**: If present, use `find-similar` mode instead of search
65
+ - **max**: Override MAX_RESULTS
66
+ - **category**: `research paper`, `news`, `company`, `personal site`, `financial report`, `people`
67
+ - **content**: `highlights` (default), `text`, `summary`, `none`
68
+ - **max chars**: Max characters for content extraction
69
+ - **type**: Search type โ€” `auto` (default), `neural`, `fast`, `instant`
70
+ - **domains**: Comma-separated include domains
71
+ - **exclude domains**: Comma-separated exclude domains
72
+ - **include text**: Phrase that must appear in results
73
+ - **exclude text**: Phrase to exclude from results
74
+ - **start date**: ISO 8601 date โ€” only results after this
75
+ - **end date**: ISO 8601 date โ€” only results before this
76
+ - **location**: Two-letter ISO country code
77
+
78
+ ### Step 2: Locate Script
79
+
80
+ ```bash
81
+ # Resolve $EXA_FETCHER via the canonical strict-safe Codex chain.
82
+ if [ -z "${ARIS_REPO:-}" ] && [ -f .aris/installed-skills-codex.txt ]; then
83
+ ARIS_REPO=$(awk -F'\t' '$1=="repo_root"{print $2; exit}' .aris/installed-skills-codex.txt 2>/dev/null) || true
84
+ fi
85
+ EXA_FETCHER=""
86
+ [ -n "${ARIS_REPO:-}" ] && [ -f "$ARIS_REPO/tools/exa_search.py" ] && EXA_FETCHER="$ARIS_REPO/tools/exa_search.py"
87
+ [ -z "$EXA_FETCHER" ] && [ -f tools/exa_search.py ] && EXA_FETCHER="tools/exa_search.py"
88
+ [ -z "$EXA_FETCHER" ] && [ -f ~/.codex/skills/exa-search/exa_search.py ] && EXA_FETCHER="$HOME/.codex/skills/exa-search/exa_search.py"
89
+ [ -z "$EXA_FETCHER" ] && {
90
+ echo "ERROR: exa_search.py not resolved at \$ARIS_REPO/tools/, tools/, or ~/.codex/skills/exa-search/." >&2
91
+ echo " Fix: rerun tools/install_aris_codex.sh, export ARIS_REPO, or copy the helper to ~/.codex/skills/exa-search/." >&2
92
+ echo " Also ensure 'exa-py' is installed: pip install exa-py" >&2
93
+ exit 1
94
+ }
95
+ ```
96
+
97
+ If not found, tell the user:
98
+ ```
99
+ exa_search.py not found. Run install_aris_codex.sh, set ARIS_REPO to your ARIS repo root, or install/copy the helper into the project/global Codex skill path; then install exa-py:
100
+ pip install exa-py
101
+ ```
102
+
103
+ ### Step 3: Execute Search
104
+
105
+ **Standard search:**
106
+ ```bash
107
+ python3 "$EXA_FETCHER" search "QUERY" --max 10 --content highlights
108
+ ```
109
+
110
+ **With filters:**
111
+ ```bash
112
+ python3 "$EXA_FETCHER" search "QUERY" --max 10 \
113
+ --category "research paper" \
114
+ --start-date 2025-01-01 \
115
+ --content text --max-chars 8000
116
+ ```
117
+
118
+ **Find similar pages:**
119
+ ```bash
120
+ python3 "$EXA_FETCHER" find-similar "URL" --max 5 --content highlights
121
+ ```
122
+
123
+ **Get content for known URLs:**
124
+ ```bash
125
+ python3 "$EXA_FETCHER" get-contents "URL1" "URL2" --content text
126
+ ```
127
+
128
+ ### Step 4: Present Results
129
+
130
+ Format results as a structured table:
131
+
132
+ ```
133
+ | # | Title | Authors | Venue/Publisher | URL | Date | Key Content |
134
+ |---|-------|---------|-----------------|-----|------|-------------|
135
+ ```
136
+
137
+ For each result:
138
+ - Show title and URL
139
+ - Show published date if available
140
+ - Show highlights, text excerpt, or summary depending on content mode
141
+ - Flag particularly relevant results
142
+ - **For `category: "research paper"` hits only** โ€” also record authors
143
+ (from Exa's `author`/`authors` fields, or fallback: parse from the
144
+ result snippet) and venue/publisher (from `publisher`, `source`, or
145
+ the domain hosting the paper). These are needed by Step 6's wiki
146
+ hook; if either is unavailable for a given hit, skip wiki ingest
147
+ for that one hit and log a note.
148
+
149
+ ### Step 5: Offer Follow-up
150
+
151
+ After presenting results, suggest:
152
+ - **Deepen**: "I can fetch full text for any of these results"
153
+ - **Find similar**: "I can find pages similar to any result"
154
+ - **Narrow**: "I can re-search with domain/date/text filters"
155
+
156
+ ### Step 6: Update Research Wiki (if active, research-paper results only)
157
+
158
+ **Required when `research-wiki/` exists AND the search returned
159
+ results of `category: "research paper"`**; skip silently otherwise.
160
+ General web results (blog posts, docs, news) are **not** ingested โ€”
161
+ the wiki is for papers only.
162
+
163
+ For each research paper hit, try to recover an arXiv ID from the URL
164
+ (`arxiv.org/abs/<id>`); if present, use `--arxiv-id`. Otherwise fall
165
+ back to manual metadata:
166
+
167
+ ```
168
+ if [ -d research-wiki/ ] and query category was "research paper":
169
+ WIKI_SCRIPT=""
170
+ [ -n "$ARIS_REPO" ] && [ -f "$ARIS_REPO/tools/research_wiki.py" ] && WIKI_SCRIPT="$ARIS_REPO/tools/research_wiki.py"
171
+ [ -z "$WIKI_SCRIPT" ] && [ -f tools/research_wiki.py ] && WIKI_SCRIPT="tools/research_wiki.py"
172
+ [ -z "$WIKI_SCRIPT" ] && [ -f ~/.codex/skills/research-wiki/research_wiki.py ] && WIKI_SCRIPT="$HOME/.codex/skills/research-wiki/research_wiki.py"
173
+ for each research-paper hit in results:
174
+ if URL matches arxiv.org/abs/<id>:
175
+ [ -n "$WIKI_SCRIPT" ] && python3 "$WIKI_SCRIPT" ingest_paper research-wiki/ \
176
+ --arxiv-id "<id>"
177
+ else:
178
+ [ -n "$WIKI_SCRIPT" ] && python3 "$WIKI_SCRIPT" ingest_paper research-wiki/ \
179
+ --title "<title>" --authors "<authors joined by , >" \
180
+ --year <year> --venue "<venue or publisher>"
181
+ ```
182
+
183
+ The helper handles slug / dedup / page / index / log โ€” **do not
184
+ handwrite `papers/<slug>.md`**. See
185
+ [`shared-references/integration-contract.md`](../shared-references/integration-contract.md).
186
+
187
+ ## Key Rules
188
+ - Always check that `EXA_API_KEY` is set before searching
189
+ - Default to `highlights` content mode for a good balance of speed and context
190
+ - Use `category: "research paper"` when the user is clearly looking for academic content
191
+ - Use `text` content mode when the user needs full page content
192
+ - Combine with `/arxiv` or `/semantic-scholar` for comprehensive literature coverage
@@ -0,0 +1,286 @@
1
+ ---
2
+ name: experiment-audit
3
+ description: "Audit experiment integrity before claiming results. Uses fresh-agent GPT-5.6-Sol review (same-family provisional in the base Codex mirror) to check for fake ground truth, score normalization fraud, phantom results, and insufficient scope. Use when user says \"ๅฎก่ฎกๅฎž้ชŒ\", \"check experiment integrity\", \"audit results\", \"ๅฎž้ชŒ่ฏšๅฎžๅบฆ\", or after experiments complete before writing claims."
4
+ argument-hint: "[experiment-dir-or-results-path]"
5
+ allowed-tools: Bash(*), Read, Write, Edit, Grep, Glob
6
+ ---
7
+
8
+ # Experiment Audit: Fresh-Agent Integrity Verification
9
+
10
+ > **Codex assurance:** base semantic audit results record
11
+ > `review_independence: same-family` and `acceptance_status: provisional`.
12
+ > Deterministic evidence checks may be accepted; unavailable reviewer calls emit
13
+ > BLOCKED/ERROR rather than a provisional PASS.
14
+
15
+ Audit experiment integrity for: **$ARGUMENTS**
16
+
17
+ ## Why This Exists
18
+
19
+ LLM agents can produce fraudulent experimental results through:
20
+ 1. **Fake ground truth** โ€” creating synthetic "reference" from model outputs, then reporting high agreement as performance
21
+ 2. **Score normalization** โ€” dividing metrics by the model's own max to get 0.99+
22
+ 3. **Phantom results** โ€” claiming numbers from files that don't exist or functions never called
23
+ 4. **Insufficient scope** โ€” reporting 2-scene pilots as "comprehensive evaluation"
24
+
25
+ These are NOT intentional deception โ€” they are failure modes of optimizing agents that lack integrity constraints. This skill adds that constraint.
26
+
27
+ ## Core Principle
28
+
29
+ **The executor (Codex) collects file paths. A fresh Codex reviewer reads code and judges integrity. The executor does NOT participate in integrity judgment; this base route is same-family/provisional.**
30
+
31
+ This follows `shared-references/reviewer-independence.md` and `shared-references/experiment-integrity.md`.
32
+
33
+ ## Constants
34
+
35
+ - **REVIEWER_BACKEND = `codex`** โ€” Default: Codex reviewer agent (`spawn_agent`, ultra โ€” deep-audit tier). Override with `โ€” reviewer: oracle-pro` for GPT-5.5 Pro via Oracle MCP. See `shared-references/reviewer-routing.md`.
36
+
37
+ ## Workflow
38
+
39
+ ### Step 1: Collect Artifacts (Executor โ€” Codex)
40
+
41
+ Locate and list these files WITHOUT reading or summarizing their content:
42
+
43
+ ```
44
+ Scan project directory for:
45
+ 1. Evaluation scripts: *eval*.py, *metric*.py, *test*.py, *benchmark*.py
46
+ 2. Result files: *.json, *.csv in results/, outputs/, logs/
47
+ 3. Ground truth paths: look in eval scripts for data loading (dataset paths, GT references)
48
+ 4. Experiment tracker: EXPERIMENT_TRACKER.md, EXPERIMENT_LOG.md
49
+ 5. Paper claims: NARRATIVE_REPORT.md, paper/sections/*.tex, PAPER_PLAN.md
50
+ 6. Config files: *.yaml, *.toml, *.json configs with metric definitions
51
+ ```
52
+
53
+ **DO NOT summarize, interpret, or explain any file content.** Only collect paths.
54
+
55
+ ### Step 2: Send to Reviewer (GPT-5.6-Sol via Codex MCP)
56
+
57
+ Pass ONLY file paths and the audit checklist to the reviewer. The reviewer reads everything directly.
58
+
59
+ ```text
60
+ spawn_agent:
61
+ model: gpt-5.6-sol
62
+ reasoning_effort: ultra
63
+ message: |
64
+ You are an experiment integrity auditor. Start from the assumption that the
65
+ evaluation is compromised somewhere โ€” your job is to find where. Be
66
+ adversarial. Trust nothing the author tells you โ€” verify everything
67
+ yourself. Read ALL files listed below and check for the following fraud
68
+ patterns.
69
+
70
+ Files to read:
71
+ - Evaluation scripts: [list paths]
72
+ - Result files: [list paths]
73
+ - Experiment tracker: [list paths]
74
+ - Paper claims: [list paths]
75
+ - Config files: [list paths]
76
+
77
+ ## Audit Checklist
78
+
79
+ ### A. Ground Truth Provenance
80
+ For each evaluation script:
81
+ 1. Where does "ground truth" / "reference" / "target" come from?
82
+ 2. Is it loaded from the DATASET, or generated/derived from MODEL OUTPUTS?
83
+ 3. If derived: is it explicitly labeled as proxy evaluation?
84
+ 4. Are official eval scripts used when available for this benchmark?
85
+ FAIL if: GT is derived from model outputs without explicit proxy labeling.
86
+
87
+ ### B. Score Normalization
88
+ For each metric computation:
89
+ 1. Is any metric divided by max/min/mean of the model's OWN output?
90
+ 2. Are raw scores reported alongside any normalized scores?
91
+ 3. Are any scores suspiciously close to 1.0 or 100%?
92
+ FAIL if: Normalization denominator comes from prediction statistics.
93
+
94
+ ### C. Result File Existence
95
+ For each claim in the paper/narrative:
96
+ 1. Does the referenced result file actually exist?
97
+ 2. Does the claimed metric key exist in that file?
98
+ 3. Does the claimed NUMBER match what's in the file?
99
+ 4. Is the experiment tracker status DONE (not TODO/IN_PROGRESS)?
100
+ FAIL if: Claimed results reference nonexistent files or mismatched numbers.
101
+
102
+ ### D. Dead Code Detection
103
+ For each metric function defined in eval scripts:
104
+ 1. Is it actually CALLED in any evaluation pipeline?
105
+ 2. Does its output appear in any result file?
106
+ WARN if: Metric functions exist but are never called.
107
+
108
+ ### E. Scope Assessment
109
+ 1. How many scenes/datasets/configurations were actually tested?
110
+ 2. How many seeds/runs per configuration?
111
+ 3. Does the paper use words like "comprehensive", "extensive", "robust"?
112
+ 4. Is the actual scope sufficient for those claims?
113
+ WARN if: Scope language exceeds actual evidence.
114
+
115
+ ### F. Evaluation Type Classification
116
+ Classify each evaluation as:
117
+ - real_gt: uses dataset-provided ground truth
118
+ - synthetic_proxy: uses model-generated reference
119
+ - self_supervised_proxy: no GT by design
120
+ - simulation_only: simulated environment
121
+ - human_eval: human judges
122
+
123
+ ## Output Format
124
+
125
+ For each check (A-F), report:
126
+ - Status: PASS | WARN | FAIL
127
+ - Evidence: exact file:line references
128
+ - Details: what specifically was found
129
+
130
+ Overall verdict: PASS | WARN | FAIL
131
+
132
+ Be thorough. Read every eval script line by line.
133
+ ```
134
+
135
+ ### Step 3: Parse and Write Report (Executor โ€” Codex)
136
+
137
+ Parse the reviewer's response and write `EXPERIMENT_AUDIT.md`:
138
+
139
+ ```markdown
140
+ # Experiment Audit Report
141
+
142
+ **Date**: [today]
143
+ **Auditor**: GPT-5.6-Sol ultra (fresh same-family agent, read-only, provisional)
144
+ **Project**: [project name]
145
+
146
+ ## Overall Verdict: [PASS | WARN | FAIL]
147
+
148
+ ## Integrity Status: [pass | warn | fail]
149
+
150
+ ## Checks
151
+
152
+ ### A. Ground Truth Provenance: [PASS|WARN|FAIL]
153
+ [details + file:line evidence]
154
+
155
+ ### B. Score Normalization: [PASS|WARN|FAIL]
156
+ [details]
157
+
158
+ ### C. Result File Existence: [PASS|WARN|FAIL]
159
+ [details]
160
+
161
+ ### D. Dead Code Detection: [PASS|WARN|FAIL]
162
+ [details]
163
+
164
+ ### E. Scope Assessment: [PASS|WARN|FAIL]
165
+ [details]
166
+
167
+ ### F. Evaluation Type: [real_gt | synthetic_proxy | ...]
168
+ [classification + evidence]
169
+
170
+ ## Action Items
171
+ - [specific fixes if WARN or FAIL]
172
+
173
+ ## Claim Impact
174
+ - Claim 1: [supported | needs qualifier | unsupported]
175
+ - Claim 2: ...
176
+ ```
177
+
178
+ Also write `EXPERIMENT_AUDIT.json` for machine consumption:
179
+
180
+ ```json
181
+ {
182
+ "audit_skill": "experiment-audit",
183
+ "verdict": "WARN",
184
+ "reason_code": "scope_exceeds_evidence",
185
+ "summary": "Two-scene evaluation supports a qualified claim only.",
186
+ "audited_input_hashes": {"results/eval.json": "sha256:<hash>"},
187
+ "trace_path": ".aris/traces/experiment-audit/2026-04-10_run01/",
188
+ "agent_id": "agent_019f...",
189
+ "verdict_id": "agent_019f...",
190
+ "executor_model": "codex-gpt-5.6-sol",
191
+ "executor_family": "openai",
192
+ "reviewer_model": "gpt-5.6-sol",
193
+ "reviewer_family": "openai",
194
+ "reviewer_reasoning": "ultra",
195
+ "review_independence": "same-family",
196
+ "acceptance_status": "provisional",
197
+ "generated_at": "2026-04-10T00:00:00Z",
198
+ "date": "2026-04-10",
199
+ "auditor": "gpt-5.6-sol-ultra",
200
+ "overall_verdict": "warn",
201
+ "integrity_status": "warn",
202
+ "checks": {
203
+ "gt_provenance": {"status": "pass", "details": "..."},
204
+ "score_normalization": {"status": "warn", "details": "..."},
205
+ "result_existence": {"status": "pass", "details": "..."},
206
+ "dead_code": {"status": "pass", "details": "..."},
207
+ "scope": {"status": "warn", "details": "..."},
208
+ "eval_type": "real_gt"
209
+ },
210
+ "claims": [
211
+ {"id": "C1", "impact": "supported"},
212
+ {"id": "C2", "impact": "needs_qualifier"}
213
+ ]
214
+ }
215
+ ```
216
+
217
+ ### Step 4: Print Summary
218
+
219
+ ```
220
+ ๐Ÿ”ฌ Experiment Audit Complete
221
+
222
+ GT Provenance: โœ… PASS โ€” real dataset GT used
223
+ Score Normalization: โš ๏ธ WARN โ€” boundary metric uses self-reference
224
+ Result Existence: โœ… PASS โ€” all files exist, numbers match
225
+ Dead Code: โœ… PASS โ€” all metric functions called
226
+ Scope: โš ๏ธ WARN โ€” 2 scenes, paper says "comprehensive"
227
+
228
+ Overall: โš ๏ธ WARN
229
+
230
+ See EXPERIMENT_AUDIT.md for details.
231
+ ```
232
+
233
+ ## Integration with Other Skills
234
+
235
+ ### Automatic in /research-pipeline (advisory, never blocks)
236
+
237
+ When integrated into the pipeline, this skill runs automatically after `/experiment-bridge` and before `/auto-review-loop`:
238
+
239
+ ```
240
+ /experiment-bridge โ†’ results ready
241
+ โ†“
242
+ /experiment-audit (automatic, advisory)
243
+ โ”œโ”€โ”€ PASS โ†’ continue normally
244
+ โ”œโ”€โ”€ WARN โ†’ print โš ๏ธ warning, continue, tag claims as [INTEGRITY: WARN]
245
+ โ””โ”€โ”€ FAIL โ†’ print ๐Ÿ”ด alert, continue, tag claims as [INTEGRITY CONCERN]
246
+ โ†“
247
+ /auto-review-loop โ†’ proceeds with integrity tags visible to reviewer
248
+ ```
249
+
250
+ **Never blocks the pipeline.** Even on FAIL, the pipeline continues โ€” but claims carry visible integrity tags.
251
+
252
+ ### Read by /result-to-claim (if exists)
253
+
254
+ ```
255
+ if EXPERIMENT_AUDIT.json exists:
256
+ read integrity_status
257
+ attach to verdict: {claim_supported: "yes", integrity_status: "warn"}
258
+ if integrity_status == "fail":
259
+ downgrade verdict display: "yes [INTEGRITY CONCERN]"
260
+ else:
261
+ verdict as normal, integrity_status = "unavailable"
262
+ mark as "provisional โ€” no integrity audit"
263
+ ```
264
+
265
+ ### Read by /paper-write (if exists)
266
+
267
+ ```
268
+ if EXPERIMENT_AUDIT.json exists AND integrity_status == "fail":
269
+ add footnote to affected claims: "Note: integrity audit flagged concerns with this evaluation"
270
+ ```
271
+
272
+ ## Key Rules
273
+
274
+ - **Reviewer independence**: executor collects paths, reviewer judges. Period.
275
+ - **Never block**: warn loudly, never halt the pipeline.
276
+ - **File-as-switch**: no EXPERIMENT_AUDIT.md = skill was never run = zero impact on existing behavior.
277
+ - **Review class**: base Codex is same-family provisional; only an overlay may claim cross-family accepted.
278
+ - **Honest about limits**: the audit catches common patterns, not all possible fraud. It is a safety net, not a guarantee.
279
+
280
+ ## Acknowledgements
281
+
282
+ Motivated by community-reported integrity issues (#57, #131) where executor agents created fake ground truth and self-normalized scores.
283
+
284
+ ## Review Tracing
285
+
286
+ After each reviewer agent call, save the trace following `shared-references/review-tracing.md` (Policy C โ€” forensic; never silently skip). Use `save_trace.sh` (resolved per the chain in `shared-references/integration-contract.md` ยง2) or write files directly to `.aris/traces/<skill>/<date>_run<NN>/`. Respect the `--- trace:` parameter (default: `full`).