syntropy-phi-c 0.1.0__tar.gz

syntropy_phi_c-0.1.0/LICENSE

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+Copyright (C) 2026 Syntropy Project (Alex Lopes da Silva) e Colaboradores.
+
+                    GNU AFFERO GENERAL PUBLIC LICENSE
+                       Version 3, 19 November 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
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syntropy_phi_c-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: syntropy-phi-c
+Version: 0.1.0
+Summary: A Fast Topological Heuristic for Connectome Pacemakers
+Author: Syntropy Project (Alex Lopes da Silva)
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+License-File: LICENSE
+Requires-Dist: numpy>=1.20.0
+Requires-Dist: networkx>=2.5
+Dynamic: author
+Dynamic: classifier
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: summary

syntropy_phi_c-0.1.0/README.md

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+# Phi-C ($\Phi_C$): Topological Connectome Pacemaker
+
+![Version](https://img.shields.io/badge/version-0.1.0-blue)
+![License: AGPL v3](https://img.shields.io/badge/License-AGPL%20v3-red)
+![Python](https://img.shields.io/badge/python-3.8%2B-green)
+
+**Phi-C** is a high-performance Python library designed to rapidly identify Central Pattern Generators (CPGs) and rhythmic pacemakers in massive biological connectomes using algebraic topology. 
+
+Developed by the **Syntropy Project** (Alex Lopes da Silva).
+
+---
+
+## 🧠 The Problem
+Finding autonomous oscillating regions in a brain (like the ones controlling breathing or locomotion) usually requires simulating the entire dynamic chemistry of the network, which becomes computationally intractable $O(2^N)$ in large mammalian brains.
+
+Furthermore, naive structural density metrics often fall into the **"Cerebellar Trap"**: flagging massive, dense, but purely feed-forward structures (like the cerebellum) as pacemakers.
+
+## ⚡ The Solution
+`phi-c` acts as a structural $O(N)$ pre-filter. We combine two mathematical concepts:
+1. **Simplicial Nerve Scaling**: A fast approximation of topological integration space using local clustering and eigenvector centrality.
+2. **Motif Discriminator**: A strict graph-theoretic filter that penalizes unidirectional cliques and actively seeks reciprocal feedback loops ($A \rightleftharpoons B$).
+
+By crossing these two metrics, the library instantly filters out false-positives and returns the absolute topological anatomical hotspots driving the network rhythm.
+
+---
+
+## 📦 Installation
+
+*(Pending PyPI release)*
+```bash
+git clone https://github.com/alexlopesdasilva/phi-c.git
+cd phi-c
+pip install .
+```
+
+---
+
+## 🚀 Quick Start
+
+The library takes any standard directed graph (like a connectome exported from Electron Microscopy data) and returns the top pacemaker nodes.
+
+```python
+import networkx as nx
+from phi_c.pacemaker import find_pacemaker
+
+# 1. Load a brain connectome (e.g., C. elegans)
+connectome = nx.read_graphml("worm_brain.graphml")
+
+# 2. Extract the top 5 Central Pattern Generators in milliseconds
+cpg_hotspots = find_pacemaker(connectome, top_k=5)
+
+# 3. View the results
+for rank, (neuron, score) in enumerate(cpg_hotspots, 1):
+    print(f"#{rank} - Neuron: {neuron} | Phi-C Score: {score:.2f}")
+```
+
+---
+
+## 📜 License
+This project is dual-licensed:
+1. **Open Source**: GNU AGPLv3 (Free for academic research and non-commercial public use).
+2. **Commercial License**: For enterprise usage in proprietary medical software or SaaS APIs without AGPL obligations, please contact the author.
+
+Copyright (C) 2026 Syntropy Project (Alex Lopes da Silva) and Contributors.

syntropy_phi_c-0.1.0/phi_c/__init__.py

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+from .topology import compute_simplicial_nerve
+from .motifs import compute_motif_discrimination
+from .pacemaker import find_pacemaker
+
+__all__ = [
+    'compute_simplicial_nerve',
+    'compute_motif_discrimination',
+    'find_pacemaker'
+]

syntropy_phi_c-0.1.0/phi_c/motifs.py

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+import networkx as nx
+
+def compute_motif_discrimination(G: nx.DiGraph) -> dict:
+    """
+    The 'Cerebellum Filter'.
+    Identifies strict rhythmic feedback loops (A <-> B) and penalizes 
+    nodes that only participate in dense feed-forward structures.
+    
+    Returns:
+        dict: Mapping of node to its Motif Reciprocity Multiplier (0.0 to 1.0+).
+    """
+    reciprocity_scores = {}
+    
+    for node in G.nodes():
+        out_edges = set(G.successors(node))
+        in_edges = set(G.predecessors(node))
+        
+        # Reciprocal edges: where A -> B and B -> A
+        reciprocal = out_edges.intersection(in_edges)
+        total_connections = len(out_edges.union(in_edges))
+        
+        if total_connections == 0:
+            reciprocity_scores[node] = 0.0
+        else:
+            # Ratio of purely bidirectional edges over all edges
+            # A true pacemaker has high bidirectionality (rhythmic feedback)
+            ratio = len(reciprocal) / total_connections
+            
+            # Penalize pure feed-forward (ratio near 0)
+            # Boost high feedback (ratio > 0.5)
+            reciprocity_scores[node] = ratio ** 2
+            
+    return reciprocity_scores

syntropy_phi_c-0.1.0/phi_c/pacemaker.py

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+import networkx as nx
+from .topology import compute_simplicial_nerve
+from .motifs import compute_motif_discrimination
+
+def find_pacemaker(G: nx.DiGraph, top_k: int = 5) -> list:
+    """
+    The main Phi_C algorithm.
+    Crosses raw structural density (Simplicial Nerve) with the 
+    directional feedback filter (Motif Discriminator) to output
+    the absolute Central Pattern Generator (CPG) hot-spots.
+    
+    Args:
+        G (nx.DiGraph): The connectome graph.
+        top_k (int): Number of top pacemaker candidate nodes to return.
+        
+    Returns:
+        list: Top K nodes sorted by final Phi_C pacemaker score.
+    """
+    raw_density = compute_simplicial_nerve(G)
+    motif_multiplier = compute_motif_discrimination(G)
+    
+    final_scores = {}
+    for node in G.nodes():
+        # The Final Phi_C metric: 
+        # High Density * High Reciprocity = True Pacemaker
+        # High Density * Low Reciprocity (Cerebellum trap) = Dropped to 0
+        final_scores[node] = raw_density[node] * motif_multiplier[node]
+        
+    # Sort by score descending
+    ranked_nodes = sorted(final_scores.items(), key=lambda item: item[1], reverse=True)
+    return ranked_nodes[:top_k]

syntropy_phi_c-0.1.0/phi_c/topology.py

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+import networkx as nx
+import numpy as np
+
+def compute_simplicial_nerve(G: nx.DiGraph) -> dict:
+    """
+    Computes the fast O(N) structural simplicial nerve density (Phi_C proxy) 
+    for each node in a Directed Graph.
+    
+    Instead of calculating exact O(2^N) Integration Information (Phi), 
+    we measure the local graph density (clique-like structures) and 
+    eigenvector centrality to act as a topological pre-filter.
+    
+    Returns:
+        dict: Mapping of node to its raw structural density score.
+    """
+    # Use undirected version for pure structural density
+    G_undirected = G.to_undirected()
+    
+    # 1. Local Clustering Coefficient (measure of local simplices/triangles)
+    clustering = nx.clustering(G_undirected)
+    
+    # 2. Eigenvector Centrality (measure of global network influence)
+    try:
+        centrality = nx.eigenvector_centrality_numpy(G)
+    except Exception:
+        # Fallback if matrix is perfectly un-diagonalizable
+        centrality = nx.degree_centrality(G)
+        
+    scores = {}
+    for node in G.nodes():
+        # The topological heuristic Phi_C raw
+        scores[node] = clustering[node] * centrality[node] * 1000
+        
+    return scores

syntropy_phi_c-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

syntropy_phi_c-0.1.0/setup.py

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+from setuptools import setup, find_packages
+
+setup(
+    name='syntropy-phi-c',
+    version='0.1.0',
+    description='A Fast Topological Heuristic for Connectome Pacemakers',
+    author='Syntropy Project (Alex Lopes da Silva)',
+    packages=find_packages(),
+    install_requires=[
+        'numpy>=1.20.0',
+        'networkx>=2.5',
+    ],
+    classifiers=[
+        'Development Status :: 3 - Alpha',
+        'Intended Audience :: Science/Research',
+        'Intended Audience :: Healthcare Industry',
+        'License :: OSI Approved :: MIT License',
+        'Programming Language :: Python :: 3',
+        'Topic :: Scientific/Engineering :: Medical Science Apps.',
+    ],
+)

syntropy_phi_c-0.1.0/syntropy_phi_c.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: syntropy-phi-c
+Version: 0.1.0
+Summary: A Fast Topological Heuristic for Connectome Pacemakers
+Author: Syntropy Project (Alex Lopes da Silva)
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+License-File: LICENSE
+Requires-Dist: numpy>=1.20.0
+Requires-Dist: networkx>=2.5
+Dynamic: author
+Dynamic: classifier
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: summary

syntropy_phi_c-0.1.0/syntropy_phi_c.egg-info/SOURCES.txt

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+LICENSE
+README.md
+setup.py
+phi_c/__init__.py
+phi_c/motifs.py
+phi_c/pacemaker.py
+phi_c/topology.py
+syntropy_phi_c.egg-info/PKG-INFO
+syntropy_phi_c.egg-info/SOURCES.txt
+syntropy_phi_c.egg-info/dependency_links.txt
+syntropy_phi_c.egg-info/requires.txt
+syntropy_phi_c.egg-info/top_level.txt

syntropy_phi_c-0.1.0/syntropy_phi_c.egg-info/dependency_links.txt

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+

syntropy_phi_c-0.1.0/syntropy_phi_c.egg-info/requires.txt

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+numpy>=1.20.0
+networkx>=2.5

syntropy_phi_c-0.1.0/syntropy_phi_c.egg-info/top_level.txt

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+phi_c