Agent-Skills.md

Agent Skills: gh-interactome - GitHub Author Interaction Network

GitHub author interaction network discovery. Maps cobordisms between

UncategorizedID: plurigrid/asi/gh-interactome

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Skill Metadata

Name
gh-interactome
Description
GitHub author interaction network discovery. Maps cobordisms between

gh-interactome - GitHub Author Interaction Network

Overview

Maps the interactome (interaction network) of GitHub contributors across discovered repos. Finds cobordisms - shared boundaries where different research communities meet.

┌─────────────────────────────────────────────────────────────────────────────┐
│                         INTERACTOME STRUCTURE                                │
├─────────────────────────────────────────────────────────────────────────────┤
│                                                                              │
│   BlockScience ◄────── olynch ──────► ToposInstitute                        │
│        │                  │                  │                               │
│        ▼                  ▼                  ▼                               │
│     cadCAD         AlgebraicJulia        poly                               │
│        │                  │                  │                               │
│        └──── jpfairbanks ─┴── epatters ─────┘                               │
│                                                                              │
│   HoTT/Coq-HoTT ◄─── abooij ───► mortberg/cubicaltt                         │
│        │                                     │                               │
│        └────── mikeshulman ──────────────────┘                               │
│                                                                              │
└─────────────────────────────────────────────────────────────────────────────┘

Discovered Cobordisms

Cobordism 1: AlgebraicJulia ↔ Topos Institute ↔ BlockScience

Shared contributors:

  • epatters (Evan Patterson) - Catlab.jl, ACSets.jl, Topos Institute
  • olynch (Owen Lynch) - poly, ACSets.jl, Catlab.jl, Topos Institute
  • jpfairbanks (James Fairbanks) - Catlab.jl, ACSets.jl, U Florida
  • kris-brown - Catlab.jl, ACSets.jl, Topos Institute
  • slibkind (Sophie Libkind) - Catlab.jl, Stanford/Topos

Bridge repos: | Repo | Stars | Role | |------|-------|------| | AlgebraicJulia/Catlab.jl | 681 | Applied category theory framework | | AlgebraicJulia/ACSets.jl | 25 | Algebraic databases | | AlgebraicJulia/AlgebraicPetri.jl | - | Compositional Petri nets | | ToposInstitute/poly | 113 | Polynomial functors |

Cobordism 2: HoTT ↔ Cubical Type Theory

Shared contributors:

  • abooij - HoTT/Coq-HoTT, mortberg/cubicaltt
  • mikeshulman (Mike Shulman) - HoTT, real cohesion
  • andrejbauer (Andrej Bauer) - HoTT, constructive math
  • DanGrayson - HoTT, cubicaltt, Agda

Bridge insight: HoTT contributors often work on multiple proof assistants.

Cobordism 3: DisCoPy ↔ Oxford Quantum Group

Key contributors:

  • toumix (1213 commits) - DisCoPy core
  • giodefelice (354 commits) - DisCoPy
  • y-richie-y (173 commits) - DisCoPy
  • oxford-quantum-group - Organizational account

Bridge insight: QNLP (Quantum NLP) research connects quantum computing to linguistics via categorical semantics.

Cobordism 4: GFlowNets ↔ Mila (Bengio's Lab)

Key contributors:

  • zdhNarsil (94 commits) - Awesome-GFlowNets curator
  • bengioe (Emmanuel Bengio) - GFlowNet contributor
  • Connection to Yoshua Bengio's lab at Mila

Bridge insight: GFlowNets for molecular design connects to chemistry/synthesis domains.

Author Profiles

Core AlgebraicJulia

| Author | Repos | Affiliation | |--------|-------|-------------| | epatters | Catlab.jl (2304), ACSets.jl (101) | Topos Institute | | olynch | poly (1), Catlab.jl (138), ACSets.jl (92) | Topos Institute | | jpfairbanks | Catlab.jl (79), ACSets.jl (19) | U Florida | | kris-brown | Catlab.jl (63) | Topos Institute |

Core HoTT

| Author | Repos | Affiliation | |--------|-------|-------------| | Alizter | Coq-HoTT (2191) | - | | jdchristensen | Coq-HoTT (1175) | UWO | | JasonGross | Coq-HoTT (930) | MIT | | mikeshulman | Coq-HoTT (888) | - | | andrejbauer | Coq-HoTT (396) | Ljubljana |

Core BlockScience

| Author | Repos | Affiliation | |--------|-------|-------------| | JEJodesty | cadCAD (731), cats (107) | BlockScience | | mzargham | cadCAD (3) | BlockScience founder | | markusbkoch | cadCAD (74) | - | | danlessa | cadCAD (37) | - |

Core DisCoPy

| Author | Repos | Affiliation | |--------|-------|-------------| | toumix | discopy (1213) | Oxford | | giodefelice | discopy (354) | - | | y-richie-y | discopy (173) | - |

Key Bridge Authors

| Author | Connects | Via | |--------|----------|-----| | olynch | Topos ↔ AlgebraicJulia | poly, Catlab, ACSets | | abooij | HoTT ↔ Cubical | Coq-HoTT, cubicaltt | | dspivak | Topos ↔ Poly | poly (186 commits) |

Network Metrics

Centrality (Bridge Authors)

# Authors who connect multiple communities
BRIDGE_AUTHORS = {
    "olynch": ["ToposInstitute/poly", "AlgebraicJulia/Catlab.jl", "AlgebraicJulia/ACSets.jl"],
    "epatters": ["AlgebraicJulia/Catlab.jl", "AlgebraicJulia/ACSets.jl", "ToposInstitute/*"],
    "abooij": ["HoTT/Coq-HoTT", "mortberg/cubicaltt"],
    "jpfairbanks": ["AlgebraicJulia/Catlab.jl", "AlgebraicJulia/ACSets.jl"],
    "mikeshulman": ["HoTT/Coq-HoTT", "HoTT/book"],
}

Community Clusters

Cluster 1: Applied Category Theory
  - AlgebraicJulia (epatters, olynch, jpfairbanks, kris-brown)
  - Topos Institute (dspivak, olynch, epatters)
  - DisCoPy (toumix, giodefelice)

Cluster 2: Type Theory / Foundations
  - HoTT (Alizter, jdchristensen, mikeshulman)
  - Cubical (mortberg, simhu, coquand)
  - Rzk (fizruk)

Cluster 3: Complex Systems / Token Engineering
  - BlockScience (mzargham, JEJodesty)
  - cadCAD ecosystem

Cluster 4: Haskell Categorical
  - connections (cmk)
  - lattices (phadej)
  - haskerwaul (sellout)

Implementation

#!/usr/bin/env python3
"""
GitHub Interactome: Map author interactions across repos.
"""
# /// script
# requires-python = ">=3.11"
# dependencies = ["rich", "networkx"]
# ///

import subprocess
import json
from collections import defaultdict

def get_contributors(repo: str) -> list[dict]:
    """Get contributors for a repo via gh CLI."""
    cmd = f"gh api repos/{repo}/contributors --jq '.[] | {{login, contributions}}'"
    result = subprocess.run(cmd, shell=True, capture_output=True, text=True)
    contributors = []
    for line in result.stdout.strip().split('\n'):
        if line:
            contributors.append(json.loads(line))
    return contributors

def build_interactome(repos: list[str]) -> dict:
    """Build author-repo bipartite graph."""
    author_repos = defaultdict(list)
    repo_authors = defaultdict(list)
    
    for repo in repos:
        contributors = get_contributors(repo)
        for c in contributors:
            author = c['login']
            author_repos[author].append({
                'repo': repo,
                'contributions': c['contributions']
            })
            repo_authors[repo].append(author)
    
    return {
        'author_repos': dict(author_repos),
        'repo_authors': dict(repo_authors),
    }

def find_bridges(interactome: dict, min_repos: int = 2) -> list[dict]:
    """Find authors who contribute to multiple repos (bridges)."""
    bridges = []
    for author, repos in interactome['author_repos'].items():
        if len(repos) >= min_repos:
            bridges.append({
                'author': author,
                'repos': [r['repo'] for r in repos],
                'total_contributions': sum(r['contributions'] for r in repos),
            })
    return sorted(bridges, key=lambda x: len(x['repos']), reverse=True)

def find_cobordisms(interactome: dict) -> list[dict]:
    """Find shared boundaries between repo communities."""
    cobordisms = []
    repos = list(interactome['repo_authors'].keys())
    
    for i, repo_a in enumerate(repos):
        for repo_b in repos[i+1:]:
            shared = set(interactome['repo_authors'][repo_a]) & \
                     set(interactome['repo_authors'][repo_b])
            if shared:
                cobordisms.append({
                    'repos': (repo_a, repo_b),
                    'shared_authors': list(shared),
                    'strength': len(shared),
                })
    
    return sorted(cobordisms, key=lambda x: x['strength'], reverse=True)

Justfile Recipes

# Build interactome
gh-interactome-build:
    @echo "🕸️ Building GitHub Interactome..."
    python3 interactome.py build

# Find bridge authors
gh-interactome-bridges:
    @echo "🌉 Finding bridge authors..."
    python3 interactome.py bridges

# Find cobordisms
gh-interactome-cobordisms:
    @echo "🔗 Finding cobordisms..."
    python3 interactome.py cobordisms

# Author lookup
gh-interactome-author login:
    @echo "👤 Author: {{login}}"
    gh api users/{{login}} --jq '{name, company, blog, bio}'
    gh api users/{{login}}/repos --jq '.[].name' | head -10

Key Cobordism: AlgebraicJulia → BlockScience

The compositional systems approach connects:

┌─────────────────────────────────────────────────────────────────────────────┐
│                    COMPOSITIONAL SYSTEMS COBORDISM                           │
├─────────────────────────────────────────────────────────────────────────────┤
│                                                                              │
│   UC Riverside ──── John Baez ────► AlgebraicJulia ◄─── Topos Institute     │
│       │                │                   │                  │              │
│       │                ▼                   ▼                  ▼              │
│       │         Stock & Flow        Catlab.jl, ACSets      poly            │
│       │         Diagrams                   │               (Spivak)         │
│       │                │                   │                  │              │
│       └────────────────┼───────────────────┼──────────────────┘              │
│                        │                   │                                 │
│                        ▼                   ▼                                 │
│                 Compositional      AlgebraicPetri.jl                        │
│                   Epidemiology     AlgebraicDynamics.jl                     │
│                        │                   │                                 │
│                        └─────────┬─────────┘                                │
│                                  │                                          │
│                                  ▼                                          │
│                           BlockScience                                      │
│                           (cadCAD, Token Engineering)                       │
│                                                                              │
└─────────────────────────────────────────────────────────────────────────────┘

Key Papers Bridging Communities

  1. "Compositional Scientific Computing with Catlab and SemanticModels" (2020)

    • Halter, Patterson, Baas, Fairbanks
    • ArXiv: 2005.04831

  2. "Compositional Modeling with Stock and Flow Diagrams" (2022)

    • Baez, Li, Libkind, Osgood
    • ArXiv: 2205.08373 (COVID epidemiology application)

  3. "AlgebraicRL.jl: Compositional Reinforcement Learning"

    • Uses Catlab.jl for MDP composition

Shared Methodology

| Concept | AlgebraicJulia | BlockScience | |---------|---------------|--------------| | Compositionality | Operad algebras | cadCAD nested configs | | Open systems | Undirected wiring diagrams | State variables + policies | | Semantics | Functors to dynamical systems | Simulation runs | | Visualization | String diagrams | System dynamics diagrams |

Bridge Authors

| Author | AlgebraicJulia | BlockScience | Academic | |--------|---------------|--------------|----------| | John Baez | Advisor/papers | - | UC Riverside | | Sophie Libkind | AlgebraicDynamics | - | Stanford/Topos | | James Fairbanks | Catlab core | - | U Florida | | Evan Patterson | Catlab lead | - | Topos | | Michael Zargham | - | cadCAD lead | BlockScience |

Conceptual Bridge: Both communities use category theory for compositional modeling of complex systems - AlgebraicJulia in scientific computing, BlockScience in cryptoeconomics/token engineering.

See Also

  • gh-skill-explorer - Discovery skill that feeds into this
  • galois-connections - Adjunctions between domains
  • acsets-algebraic-databases - ACSets patterns
  • discopy - String diagrams

End-of-Skill Interface

r2con Speaker Resources

Target organizations for interactome mapping:

| Speaker | Handle | Organization | Interactome Target | |---------|--------|--------------|-------------------| | pancake | trufae | radareorg | Core r2 ecosystem (75+ repos) | | thestr4ng3r | thestr4ng3r | rizinorg | Rizin/Cutter fork community | | oleavr | oleavr | frida | Dynamic instrumentation ecosystem | | xvilka | XVilka | radareorg | UEFI, radeco, decompilation | | cryptax | cryptax | rednaga | Android security tooling |

Commands

# Build interactome for discovered repos
just gh-interactome build

# Find bridge authors
just gh-interactome bridges

# Find cobordisms between communities
just gh-interactome cobordisms

# Show author profile
just gh-interactome author olynch

# Visualize network
just gh-interactome viz

# NEW: Map r2con speaker orgs
just gh-interactome orgs radareorg rizinorg frida