Github Research

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

• 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}

• 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

• 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)

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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"

• 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

• 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

• 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

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

• 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/

• 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

• 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

• 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

• 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)

• 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

• 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

• 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

• 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

• 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

• 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

• 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)

• Compile final report:

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

• 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

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