github-research

The saved excerpt is a snapshot from review. The external source remains the complete and most current version.

---
name: github-research
description: Explore and analyze GitHub repositories related to a research topic. Reads deep-research output, discovers repos from multiple sources, deeply analyzes code, and produces integration blueprints.
argument-hint: [deep-research-output-dir]
---

# GitHub Research Skill

## Trigger

Activate this skill when the user wants to:
- "Find repos for [topic]", "GitHub research on [topic]"
- "Analyze open-source code for [topic]"
- "Find implementations of [paper/technique]"
- "Which repos implement [algorithm]?"
- Uses `/github-research <deep-research-output-dir>` slash command

## Overview

This skill systematically discovers, evaluates, and deeply analyzes GitHub repositories related to a research topic. It reads **deep-research** output (paper database, phase reports, code references) and produces an actionable integration blueprint for reusing open-source code.

**Installation**: `~/.claude/skills/github-research/` — scripts, references, and this skill definition.
**Output**: `./github-research-output/{slug}/` relative to the current working directory.
**Input**: A deep-research output directory (containing `paper_db.jsonl`, phase reports, `code_repos.md`, etc.)

## 6-Phase Pipeline

```
Phase 1: Intake     → Extract refs, URLs, keywords from deep-research output
Phase 2: Discovery  → Multi-source broad GitHub search (50-200 repos)
Phase 3: Filtering  → Score & rank → select top 15-30 repos
Phase 4: Deep Dive  → Clone & deeply analyze top 8-15 repos (code reading)
Phase 5: Analysis   → Per-repo reports + cross-repo comparison
Phase 6: Blueprint  → Integration/reuse plan for research topic
```

## Output Directory Structure

```
github-research-output/{slug}/
├── repo_db.jsonl                     # Master repo database
├── phase1_intake/
│   ├── extracted_refs.jsonl          # URLs, keywords, paper-repo links
│   └── intake_summary.md
├── phase2_discovery/
│   ├── search_results/               # Raw JSONL from each search
│   └── discovery_log.md
├── phase3_filtering/
│   ├── ranked_repos.jsonl            # Scored & ranked subset
│   └── filtering_report.md
├── phase4_deep_dive/
│   ├── repos/                        # Cloned repos (shallow)
│   ├── analyses/                     # Per-repo analysis .md files
│   └── deep_dive_summary.md
├── phase5_analysis/
│   ├── comparison_matrix.md          # Cross-repo comparison
│   ├── technique_map.md              # Paper concept → code mapping
│   └── analysis_report.md
└── phase6_blueprint/
    ├── integration_plan.md           # How to combine repos
    ├── reuse_catalog.md              # Reusable components catalog
    ├── final_report.md               # Complete compiled report
    └── blueprint_summary.md
```

## Scripts Reference

All scripts are Python 3, stdlib-only, located in `~/.claude/skills/github-research/scripts/`.

| Script | Purpose | Key Flags |
|--------|---------|-----------|
| `extract_research_refs.py` | Parse deep-research output for GitHub URLs, paper refs, keywords | `--research-dir`, `--output` |
| `search_github.py` | Search GitHub repos via `gh api` | `--query`, `--language`, `--min-stars`, `--sort`, `--max-results`, `--topic`, `--output` |
| `search_github_code.py` | Search GitHub code for implementations | `--query`, `--language`, `--filename`, `--max-results`, `--output` |
| `search_paperswithcode.py` | Search Papers With Code for paper→repo mappings | `--paper-title`, `--arxiv-id`, `--query`, `--output` |
| `repo_db.py` | JSONL repo database management | subcommands: `merge`, `filter`, `score`, `search`, `tag`, `stats`, `export`, `rank` |
| `repo_metadata.py` | Fetch detailed metadata via `gh api` | `--repos`, `--input`, `--output`, `--delay` |
| `clone_repo.py` | Shallow-clone repos for analysis | `--repo`, `--output-dir`, `--depth`, `--branch` |
| `analyze_repo_structure.py` | Map file tree, key files, LOC stats | `--repo-dir`, `--output` |
| `extract_dependencies.py` | Extract and parse dependency files | `--repo-dir`, `-