/inno-code-survey

id: inno-code-survey
name: inno-code-survey
version: 1.0.0
description: |-
  Acquires missing code repositories for the selected idea (Phase A) and conducts comprehensive code survey mapping academic concepts to implementations (Phase B).
stages: ["ideation", "experiment"]
tools: ["read_file", "search_project", "write_file", "run_terminal"]
summary: |-
  Acquires missing code repositories for the selected idea (Phase A) and conducts comprehensive code survey mapping academic concepts to implementations (Phase B). Outputs acquired_code_repos, updated_prepare_res, and model_survey for downst...
primaryIntent: research
intents: ["research"]
capabilities: ["search-retrieval"]
domains: ["general"]
keywords: ["inno-code-survey", "survey", "search-retrieval", "inno", "code", "acquires", "missing", "repositories", "selected", "idea", "phase", "conducts"]
source: builtin
status: verified
upstream:
  repo: dr-claw
  path: skills/inno-code-survey
  revision: 8322dc4ef575affaa374aa7922c0a0971c6db7d7
resourceFlags:
  hasReferences: true
  hasScripts: true
  hasTemplates: false
  hasAssets: false
  referenceCount: 2
  scriptCount: 1
  templateCount: 0
  assetCount: 0
  optionalScripts: true

inno-code-survey

Canonical Summary

Acquires missing code repositories for the selected idea (Phase A) and conducts comprehensive code survey mapping academic concepts to implementations (Phase B). Outputs acquired_code_repos, updated_prepare_res, and model_survey for downst...

Trigger Rules

Use this skill when the user request matches its research workflow scope. Prefer the bundled resources instead of recreating templates or reference material. Keep outputs traceable to project files, citations, scripts, or upstream evidence.

Resource Use Rules

• Read from `references/` only when the current task needs the extra detail.
• Treat `scripts/` as optional helpers. Run them only when their dependencies are available, keep outputs in the project workspace, and explain a manual fallback if execution is blocked.

Execution Contract

• Resolve every relative path from this skill directory first.
• Prefer inspection before mutation when invoking bundled scripts.
• If a required runtime, CLI, credential, or API is unavailable, explain the blocker and continue with the best manual fallback instead of silently skipping the step.
• Do not write generated artifacts back into the skill directory; save them inside the active project workspace.

Upstream Instructions

Inno Code Survey (Repo Acquisition + Code Survey)

Merges `_acquire_missing_repos`, `_update_prepare_res_with_new_repos`, and `_conduct_code_survey` from [run_infer_idea_ours.py](workspace/medical/Medical_ai_scientist_idea/research_agent/run_infer_idea_ours.py) (lines 639–828, 1038–1052) into a single two-phase skill.

Directory structure

skills/inno-code-survey/
├── SKILL.md                                          ← this file
├── prompts/
│   ├── build_repo_acquisition_query.md               ← Phase A query template
│   └── build_code_survey_query.md                    ← Phase B query template
├── references/
│   ├── repo_acquisition_agent.md                     ← Phase A agent system prompt & tools
│   └── code_survey_agent.md                          ← Phase B agent system prompt & tools
└── scripts/
    └── github_search_clone.py                        ← GitHub search + clone helper

Path conventions

All file paths use semantic directory names under the project root:

| Path | Contents | |------|----------| | `Ideation/references/papers/` | Downloaded arXiv LaTeX sources (`.tex`, `.txt`, `.md`) | | `Experiment/code_references/<repo_name>/` | Cloned GitHub repositories | | `Experiment/code_references/model_survey.md` | Code survey implementation report | | `Experiment/code_references/logs/` | Phase A & B agent cache files |

Inputs

These are aligned with outputs from **inno-idea-generation** and **inno-prepare-resources**:

| Input | Source | Description | |-------|--------|-------------| | `selected_idea` | `Ideation/ideas/selected_idea.txt` or `final_selected_idea_data` | The finalized selected idea (full markdown) | | `download_res` | `inno-prepare-resources` output | Result log from downloading arXiv paper sources | | `prepare_res` | `inno-prepare-resources` output (JSON) | Contains `reference_codebases` and `reference_paths` | | `context_variables` | Shared context dict | Accumulated pipeline context | | `instance.json` | `<project_path>/instance.json` | Paths are **absolute** when created by Dr. Claw (`Experiment.code_references`, `Ideation.references`); use as-is or resolve with `path.join(project_path, value)` if relative. Also `date_limit` from context. |

Outputs

| Output | Description | Consumer | |--------|-------------|----------| | `acquired_code_repos` | Dict of `{name: path}` for newly cloned repos | Phase B, cache | | `updated_prepare_res` | `prepare_res` JSON with new repos merged into `reference_codebases` / `reference_paths` | Downstream pipeline | | `extra_repo_info` | Formatted string listing acquired repos | Phase B query | | `model_survey` | Comprehensive code survey implementation report | `inno-experiment-dev` |

---

Phase A — Repo Acquisition

> Full template & parameter docs: [prompts/build_repo_acquisition_query.md](prompts/build_repo_acquisition_query.md) > Agent system prompt & tools: [references/repo_acquisition_agent.md](references/repo_acquisition_agent.md)

Maps to `_acquire_missing_repos` (lines 745–792) + `_update_prepare_res_with_new_repos` (lines 639–686).

Step A1: Analyze the selected idea and identify gaps

Read `selected_idea` and identify 2–3 **missing technical components** — novel or specialized parts that are likely NOT in the standard repos already present in `Experiment/code_references/`.

Step A2: Search GitHub using the "Cascade" strategy

For each missing component, perform **6 distinct queries** using progressive decomposition:

1. **Level 1 (S