github-research

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, --output
find_implementations.py	Search cloned repo for specific code patterns	--repo-dir, --patterns, --output
repo_readme_fetch.py	Fetch README without cloning	--repos, --input, --output, --max-chars
compare_repos.py	Generate comparison matrix across repos	--input, --output
compile_github_report.py	Assemble final report from all phases	--topic-dir

---

Phase 1: Intake

Goal: Extract all relevant references, URLs, and keywords from the deep-research output.

Steps

1. Create output directory structure:

   SLUG=$(echo "$TOPIC" | tr '[:upper:]' '[:lower:]' | tr ' ' '-' | tr -cd 'a-z0-9-')
   mkdir -p github-research-output/$SLUG/{phase1_intake,phase2_discovery/search_results,phase3_filtering,phase4_deep_dive/{repos,analyses},phase5_analysis,phase6_blueprint}
   

2. Extract references from deep-research output:

   python ~/.claude/skills/github-research/scripts/extract_research_refs.py \
     --research-dir <deep-research-output-dir> \
     --output github-research-output/$SLUG/phase1_intake/extracted_refs.jsonl
   

3. Review extracted refs: Read the generated JSONL. Note:

   • GitHub URLs found directly in reports
   • Paper titles and arxiv IDs (for Papers With Code lookup)
   • Research keywords and themes (for GitHub search queries)

4. Write intake summary: Create phase1_intake/intake_summary.md with:

   • Number of direct GitHub URLs found
   • Number of papers with potential code links
   • Key research themes extracted
   • Planned search queries for Phase 2

Checkpoint

• extracted_refs.jsonl exists with entries
• intake_summary.md written
• Search strategy documented

---

Phase 2: Discovery

Goal: Cast a wide net to find 50-200 candidate repos from multiple sources.

Steps

1. Search by direct URLs: Any GitHub URLs from Phase 1 → fetch metadata:

   python ~/.claude/skills/github-research/scripts/repo_metadata.py \
     --repos owner1/name1 owner2/name2 ... \
     --output github-research-output/$SLUG/phase2_discovery/search_results/direct_urls.jsonl
   

2. Search Papers With Code: For each paper with an arxiv ID:

   python ~/.claude/skills/github-research/scripts/search_paperswithcode.py \
     --arxiv-id 2401.12345 \
     --output github-research-output/$SLUG/phase2_discovery/search_results/pwc_2401.12345.jsonl
   

3. Search GitHub by keywords (3-8 queries based on research themes):

   python ~/.claude/skills/github-research/scripts/search_github.py \
     --query "multi-agent LLM coordination" \
     --min-stars 10 --sort stars --max-results 50 \
     --output github-research-output/$SLUG/phase2_discovery/search_results/gh_query1.jsonl
   

4. Search GitHub code (for specific implementations):

   python ~/.claude/skills/github-research/scripts/search_github_code.py \
     --query "class MultiAgentOrchestrator" \
     --language python --max-results 30 \
     --output github-research-output/$SLUG/phase2_discovery/search_results/code_query1.jsonl
   

5. Fetch READMEs for repos that lack descriptions:

   python ~/.claude/skills/github-research/scripts/repo_readme_fetch.py \
     --input <repos.jsonl> \
     --output github-research-output/$SLUG/phase2_discovery/search_results/readmes.jsonl
   

6. Merge all results into master database:

   python ~/.claude/skills/github-research/scripts/repo_db.py merge \
     --inputs github-research-output/$SLUG/phase2_discovery/search_results/*.jsonl \
     --output github-research-output/$SLUG/repo_db.jsonl
   

7. Write discovery log: Create phase2_discovery/discovery_log.md with search queries used, results per source, total unique repos found.

Rate Limits

• GitHub search API: 30 requests/minute (authenticated)
• Papers With Code API: No strict limit but be respectful (1 req/sec)
• Add --delay 1.0 to batch operations when needed

Checkpoint

• repo_db.jsonl populated with 50-200 repos
• discovery_log.md with search details

---

Phase 3: Filtering

Goal: Score and rank repos, select top 15-30 for deeper analysis.

Steps

1. Enrich metadata for all repos:

   python ~/.claude/skills/github-research/scripts/repo_metadata.py \
     --input github-research-output/$SLUG/repo_db.jsonl \
     --output github-research-output/$SLUG/repo_db.jsonl \
     --delay 0.5
   

2. Score repos (quality + activity scores):

   python ~/.claude/skills/github-research/scripts/repo_db.py score \
     --input github-research-output/$SLUG/repo_db.jsonl \
     --output github-research-output/$SLUG/repo_db.jsonl
   

3. LLM relevance scoring: Read through the top ~50 repos (by quality_score) and assign relevance_score (0.0-1.0) based on:

   • Direct relevance to research topic
   • Implementation completeness
   • Code quality signals (from README, description)
   • Update the relevance scores:

   python ~/.claude/skills/github-research/scripts/repo_db.py tag \
     --input github-research-output/$SLUG/repo_db.jsonl \
     --ids owner/name --tags "relevance:0.85"
   

4. Compute composite scores and rank:

   python ~/.claude/skills/github-research/scripts/repo_db.py score \
     --input github-research-output/$SLUG/repo_db.jsonl \
     --output github-research-output/$SLUG/repo_db.jsonl
   python ~/.claude/skills/github-research/scripts/repo_db.py rank \
     --input github-research-output/$SLUG/repo_db.jsonl \
     --output github-research-output/$SLUG/phase3_filtering/ranked_repos.jsonl \
     --by composite_score
   

5. Select top repos: Filter to top 15-30:

   python ~/.claude/skills/github-research/scripts/repo_db.py filter \
     --input github-research-output/$SLUG/phase3_filtering/ranked_repos.jsonl \
     --output github-research-output/$SLUG/phase3_filtering/ranked_repos.jsonl \
     --max-repos 30 --not-archived
   

6. Write filtering report: Create phase3_filtering/filtering_report.md:

   • Stats before/after filtering
   • Score distributions
   • Top 30 repos with scores and rationale

Scoring Formula

activity_score = sigmoid((days_since_push < 90) * 0.4 + has_recent_commits * 0.3 + open_issues_ratio * 0.3)
quality_score  = normalize(log(stars+1) * 0.3 + log(forks+1) * 0.2 + has_license * 0.15 + has_readme * 0.15 + not_archived * 0.2)
composite_score = relevance * 0.4 + quality * 0.35 + activity * 0.25

Checkpoint

• ranked_repos.jsonl with 15-30 repos
• filtering_report.md with scoring details

---

Phase 4: Deep Dive

Goal: Clone and deeply analyze the top 8-15 repos.

Steps

1. Select repos for deep dive: Take top 8-15 from ranked list.

2. Clone each repo (shallow):

   python ~/.claude/skills/github-research/scripts/clone_repo.py \
     --repo owner/name \
     --output-dir github-research-output/$SLUG/phase4_deep_dive/repos/
   

3. Analyze structure for each cloned repo:

   python ~/.claude/skills/github-research/scripts/analyze_repo_structure.py \
     --repo-dir github-research-output/$SLUG/phase4_deep_dive/repos/name/ \
     --output github-research-output/$SLUG/phase4_deep_dive/analyses/name_structure.json
   

4. Extract dependencies:

   python ~/.claude/skills/github-research/scripts/extract_dependencies.py \
     --repo-dir github-research-output/$SLUG/phase4_deep_dive/repos/name/ \
     --output github-research-output/$SLUG/phase4_deep_dive/analyses/name_deps.json
   

5. Find implementations: Search for key algorithms/concepts from research:

   python ~/.claude/skills/github-research/scripts/find_implementations.py \
     --repo-dir github-research-output/$SLUG/phase4_deep_dive/repos/name/ \
     --patterns "class Transformer" "def forward" "attention" \
     --output github-research-output/$SLUG/phase4_deep_dive/analyses/name_impls.jsonl
   

6. Deep code reading: For each repo, READ the key source files identified by structure analysis. Write a per-repo analysis in phase4_deep_dive/analyses/{name}_analysis.md:

   • Architecture overview
   • Key algorithms implemented
   • Code quality assessment
   • API / interface design
   • Dependencies and requirements
   • Strengths and limitations
   • Reusability assessment (how easy to extract components)

7. Write deep dive summary: phase4_deep_dive/deep_dive_summary.md

IMPORTANT: Actually Read Code

Do NOT just summarize READMEs. You must:

• Read the main source files (entry points, core modules)
• Understand the actual implementation approach
• Identify specific functions/classes that implement research concepts
• Note code patterns, design decisions, and trade-offs

Checkpoint

• Repos cloned in repos/
• Per-repo analysis files in analyses/
• deep_dive_summary.md written

---

Phase 5: Analysis

Goal: Cross-repo comparison and technique-to-code mapping.

Steps

1. Generate comparison matrix:

   python ~/.claude/skills/github-research/scripts/compare_repos.py \
     --input github-research-output/$SLUG/phase4_deep_dive/analyses/ \
     --output github-research-output/$SLUG/phase5_analysis/comparison.json
   

2. Write comparison matrix: Create phase5_analysis/comparison_matrix.md:

   • Table comparing repos across dimensions (language, LOC, stars, framework, license, tests)
   • Dependency overlap analysis
   • Strengths/weaknesses per repo

3. Write technique map: Create phase5_analysis/technique_map.md:

   • Map each paper concept / research technique → specific repo + file + function
   • Identify gaps (techniques with no implementation found)
   • Note alternative implementations of the same concept

4. Write analysis report: phase5_analysis/analysis_report.md:

   • Executive summary of findings
   • Key insights from code analysis
   • Recommendations for which repos to use for which purposes

Checkpoint

• comparison_matrix.md with repo comparison table
• technique_map.md mapping concepts to code
• analysis_report.md with findings

---

Phase 6: Blueprint

Goal: Produce an actionable integration and reuse plan.

Steps

1. Write integration plan: phase6_blueprint/integration_plan.md:

   • Recommended architecture for combining repos
   • Step-by-step integration approach
   • Dependency resolution strategy
   • Potential conflicts and how to resolve them

2. Write reuse catalog: phase6_blueprint/reuse_catalog.md:

   • For each reusable component: source repo, file path, function/class, what it does, how to extract it
   • License compatibility matrix
   • Effort estimates (easy/medium/hard to integrate)

3. Compile final report:

   python ~/.claude/skills/github-research/scripts/compile_github_report.py \
     --topic-dir github-research-output/$SLUG/
   

4. Write blueprint summary: phase6_blueprint/blueprint_summary.md:

   • One-page executive summary
   • Top 5 repos and why
   • Recommended next steps

Checkpoint

• integration_plan.md complete
• reuse_catalog.md with component catalog
• final_report.md compiled
• blueprint_summary.md as executive summary

---

Quality Conventions

1. Repos are ranked by composite score: relevance × 0.4 + quality × 0.35 + activity × 0.25
2. Deep dive requires reading actual code, not just READMEs
3. Integration blueprint must map paper concepts → specific code files/functions
4. Incremental saves: Each phase writes to disk immediately
5. Checkpoint recovery: Can resume from any phase by checking what outputs exist
6. All scripts are stdlib-only Python — no pip installs needed
7. gh CLI is required for GitHub API access (must be authenticated)
8. Deduplication by repo_id (owner/name) across all searches
9. Rate limit awareness: Respect GitHub search API limits (30 req/min)

Error Handling

• If gh is not installed: warn user and provide installation instructions
• If a repo is archived/deleted: skip gracefully, note in log
• If clone fails: skip, note in log, continue with remaining repos
• If Papers With Code API is down: skip, rely on GitHub search only
• Always write partial progress to disk so work is not lost

References

• See references/phase-guide.md for detailed phase execution guidance
• Deep-research skill: ~/.claude/skills/deep-research/SKILL.md
• Paper database pattern: ~/.claude/skills/deep-research/scripts/paper_db.py