cognigraph 0.4.0__tar.gz

cognigraph-0.4.0/.dockerignore

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+__pycache__
+*.pyc
+*.pyo
+.pytest_cache
+.mypy_cache
+.ruff_cache
+*.egg-info
+dist/
+build/
+.git
+.github
+tests/
+docs/
+*.md
+!README.md
+.env
+.env.*

cognigraph-0.4.0/.github/FUNDING.yml

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+github: quantamixsol
+custom: ["https://cognigraph.dev/pricing"]

cognigraph-0.4.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [master]
+    tags: ["v*"]
+  pull_request:
+    branches: [master]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev]"
+
+      - name: Lint with ruff
+        run: ruff check cognigraph/ tests/
+
+      - name: Run tests with coverage
+        run: pytest --cov=cognigraph --cov-report=xml --cov-report=term -q
+
+      - name: Upload coverage report
+        if: matrix.python-version == '3.12'
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-report
+          path: coverage.xml
+
+  publish:
+    needs: test
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/v')
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build tools
+        run: python -m pip install --upgrade pip build
+
+      - name: Build package
+        run: python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}

cognigraph-0.4.0/.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.egg-info/
+dist/
+build/
+*.egg
+
+# Virtual environments
+.venv/
+venv/
+env/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+.mypy_cache/
+.ruff_cache/
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Environment
+.env
+.env.local
+.env.*.local
+
+# Traces
+traces/
+
+# Benchmark data (large files)
+cognigraph/benchmarks/data/
+benchmarks/data/
+
+# Results (regeneratable)
+cognigraph/benchmarks/results/
+
+# Benchmark logs
+*.log

cognigraph-0.4.0/CONTRIBUTING.md

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+# Contributing to CogniGraph
+
+Thanks for your interest in contributing. Here's how to get started.
+
+## Development Setup
+
+```bash
+# Clone the repo
+git clone https://github.com/quantamixsol/cognigraph.git
+cd cognigraph
+
+# Create a virtual environment
+python -m venv .venv
+source .venv/bin/activate  # Windows: .venv\Scripts\activate
+
+# Install in development mode
+pip install -e ".[dev]"
+```
+
+## Running Tests
+
+```bash
+# Full test suite
+pytest tests/ -v
+
+# With coverage
+pytest tests/ --cov=cognigraph --cov-report=term-missing
+
+# Single test file
+pytest tests/test_activation.py -v
+```
+
+## Code Style
+
+We use **ruff** for linting and formatting:
+
+```bash
+# Check
+ruff check cognigraph/
+ruff format --check cognigraph/
+
+# Auto-fix
+ruff check --fix cognigraph/
+ruff format cognigraph/
+```
+
+All PRs must pass `ruff check` and `ruff format --check` with zero errors.
+
+## Pull Request Process
+
+1. **Fork** the repo and create a feature branch from `main`
+2. **Write tests** for any new functionality
+3. **Run the full test suite** — all 332 tests must pass
+4. **Run ruff** — zero lint errors, zero format issues
+5. **Write a clear PR description** — what changed and why
+6. Submit the PR and wait for review
+
+## What We're Looking For
+
+- Bug fixes with regression tests
+- New backend integrations
+- Performance improvements with benchmarks
+- Documentation improvements
+
+## What We Won't Accept
+
+- Changes that break existing tests
+- Features without tests
+- PRs that modify patent-protected innovation modules without prior discussion
+
+## Questions?
+
+Open an issue on GitHub. We'll respond within a few days.

cognigraph-0.4.0/Dockerfile

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+FROM python:3.11-slim AS base
+
+WORKDIR /app
+
+# Install system dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    build-essential \
+    && rm -rf /var/lib/apt/lists/*
+
+# Copy package files
+COPY pyproject.toml README.md LICENSE ./
+COPY cognigraph/ cognigraph/
+
+# Install cognigraph with server extras
+RUN pip install --no-cache-dir ".[server,api]"
+
+# Default config and graph placeholders
+COPY cognigraph.example.yaml /app/cognigraph.yaml
+
+EXPOSE 8000
+
+# Health check
+HEALTHCHECK --interval=30s --timeout=5s --retries=3 \
+    CMD python -c "import urllib.request; urllib.request.urlopen('http://localhost:8000/health')" || exit 1
+
+CMD ["kogni", "serve", "--host", "0.0.0.0", "--port", "8000"]

cognigraph-0.4.0/LICENSE

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+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   Copyright 2026 Quantamix Solutions B.V.
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

cognigraph-0.4.0/NOTICE

@@ -0,0 +1,48 @@
+CogniGraph — Governed Intelligence through Graph-of-Agents Reasoning
+Copyright 2026 Quantamix Solutions B.V.
+
+INTELLECTUAL PROPERTY NOTICE
+============================
+
+This software implements methods described in:
+
+  European Patent Application EP26162901.8
+  "Method and system for trust-aware multi-signal document retrieval
+   with graph-based compliance scoring and gap attribution for
+   regulatory AI systems"
+  Filed: 6 March 2026
+  Applicant: Quantamix Solutions B.V.
+  Inventor: Harish Kumar
+
+The following components are covered by the patent claims:
+
+  - Prize-Collecting Steiner Tree (PCST) activation for subgraph selection
+  - TRACE score computation (Trust, Relevance, Accuracy, Completeness, Evidence)
+  - Gap attribution scoring for regulatory compliance
+  - TAMRConnector integration pipeline (TRACE priors -> PCST activation)
+
+OPEN SOURCE LICENSE
+===================
+
+The CogniGraph SDK source code is licensed under the Apache License 2.0.
+You may use, modify, and distribute this software in accordance with the
+Apache 2.0 license terms.
+
+The patent rights are separately held. Use of the patented methods in
+commercial products or services may require a separate patent license
+from Quantamix Solutions B.V. Contact: harish.kumar@quantamixsolutions.com
+
+ACADEMIC AND RESEARCH USE
+=========================
+
+Academic and non-commercial research use of all components, including
+patented methods, is permitted without additional licensing.
+
+CITATION
+========
+
+If you use CogniGraph in academic work, please cite:
+
+  H. Kumar, "CogniGraph: Governed Intelligence through Graph-of-Agents
+  Reasoning over Knowledge Graph Topologies with Semantic SHACL Validation,"
+  arXiv preprint, March 2026. Quantamix Solutions B.V.

cognigraph-0.4.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: cognigraph
+Version: 0.4.0
+Summary: Self-governing development for Claude Code — graph-of-agents reasoning with 13 innovations, GCC/GSD/Ralph protocols, and MCP integration
+Project-URL: Homepage, https://cognigraph.dev
+Project-URL: Documentation, https://github.com/quantamixsol/cognigraph#readme
+Project-URL: Repository, https://github.com/quantamixsol/cognigraph
+Project-URL: Changelog, https://github.com/quantamixsol/cognigraph/releases
+Project-URL: Bug Tracker, https://github.com/quantamixsol/cognigraph/issues
+Author-email: Harish Kumar <harish.kumar@quantamixsolutions.com>
+License-Expression: Apache-2.0
+License-File: LICENSE
+License-File: NOTICE
+Keywords: adaptive-activation,bayesian-learning,claude-code,development-tools,distributed-reasoning,gcc,governance,graph-of-agents,gsd,knowledge-graph,lora,mcp,multi-agent,ontology,owl,pcst,reasoning,regulatory-ai,self-governing,shacl,slm
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Requires-Python: >=3.10
+Requires-Dist: networkx>=3.0
+Requires-Dist: numpy>=1.24
+Requires-Dist: pydantic-settings>=2.0
+Requires-Dist: pydantic>=2.0
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: rich>=13.0
+Requires-Dist: typer[all]>=0.9
+Provides-Extra: all
+Requires-Dist: anthropic>=0.18; extra == 'all'
+Requires-Dist: boto3>=1.28; extra == 'all'
+Requires-Dist: fastapi>=0.100; extra == 'all'
+Requires-Dist: httpx>=0.25; extra == 'all'
+Requires-Dist: neo4j>=5.0; extra == 'all'
+Requires-Dist: openai>=1.0; extra == 'all'
+Requires-Dist: peft>=0.7; extra == 'all'
+Requires-Dist: sentence-transformers>=2.2; extra == 'all'
+Requires-Dist: torch>=2.0; extra == 'all'
+Requires-Dist: transformers>=4.35; extra == 'all'
+Requires-Dist: uvicorn[standard]>=0.20; extra == 'all'
+Requires-Dist: vllm>=0.3; extra == 'all'
+Provides-Extra: api
+Requires-Dist: anthropic>=0.18; extra == 'api'
+Requires-Dist: boto3>=1.28; extra == 'api'
+Requires-Dist: httpx>=0.25; extra == 'api'
+Requires-Dist: openai>=1.0; extra == 'api'
+Provides-Extra: cpu
+Requires-Dist: llama-cpp-python>=0.2; extra == 'cpu'
+Requires-Dist: sentence-transformers>=2.2; extra == 'cpu'
+Provides-Extra: dev
+Requires-Dist: coverage>=7.0; extra == 'dev'
+Requires-Dist: mypy>=1.0; extra == 'dev'
+Requires-Dist: pytest-asyncio>=0.21; extra == 'dev'
+Requires-Dist: pytest-cov>=4.0; extra == 'dev'
+Requires-Dist: pytest-env>=1.0; extra == 'dev'
+Requires-Dist: pytest-mock>=3.10; extra == 'dev'
+Requires-Dist: pytest>=7.0; extra == 'dev'
+Requires-Dist: ruff>=0.1; extra == 'dev'
+Provides-Extra: gpu
+Requires-Dist: peft>=0.7; extra == 'gpu'
+Requires-Dist: sentence-transformers>=2.2; extra == 'gpu'
+Requires-Dist: torch>=2.0; extra == 'gpu'
+Requires-Dist: transformers>=4.35; extra == 'gpu'
+Requires-Dist: vllm>=0.3; extra == 'gpu'
+Provides-Extra: neo4j
+Requires-Dist: neo4j>=5.0; extra == 'neo4j'
+Provides-Extra: server
+Requires-Dist: fastapi>=0.100; extra == 'server'
+Requires-Dist: uvicorn[standard]>=0.20; extra == 'server'
+Description-Content-Type: text/markdown
+
+<div align="center">
+
+# CogniGraph
+
+### Graphs That Think — Self-Governing Development for Claude Code
+
+Turn any codebase into a governed, self-improving reasoning network.<br/>
+One command. Full governance. Zero cloud infrastructure.
+
+[![PyPI version](https://badge.fury.io/py/cognigraph.svg)](https://pypi.org/project/cognigraph/)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+[![License: Apache 2.0](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](LICENSE)
+[![Tests: 332 passing](https://img.shields.io/badge/tests-332%20passing-brightgreen.svg)]()
+[![MCP Compatible](https://img.shields.io/badge/MCP-compatible-8A2BE2.svg)]()
+[![Patent: EP26162901.8](https://img.shields.io/badge/patent-EP26162901.8-orange.svg)](NOTICE)
+
+</div>
+
+---
+
+> **What if your development environment learned from every mistake and never repeated one?**
+>
+> CogniGraph is the first self-governing development tool. It transforms any knowledge graph into a reasoning network where each node is an autonomous LLM agent — then wraps your Claude Code sessions in structured protocols that enforce spec-before-code, atomic commits, and autonomous fix-test-fix loops. Install it, run `kogni init`, and your dev environment starts getting smarter every session.
+
+---
+
+## Quick Start
+
+```bash
+pip install cognigraph[api]
+cd your-project
+kogni init
+```
+
+That's it. CogniGraph scans your repo, builds a knowledge graph, creates a governed `CLAUDE.md`, and registers an MCP server. Open Claude Code and you're running with:
+
+- **GCC** — session continuity, branch management, auto-commits
+- **GSD** — structured DISCUSS → PLAN → EXECUTE → VERIFY workflow
+- **Ralph Loop** — autonomous fix-test-fix iteration with safety guards
+- **MCP tools** — governed graph reasoning inside Claude Code
+
+No cloud account. No infrastructure. Your machine, your API keys, your data.
+
+---
+
+## What You Get
+
+| Tool | What it does |
+|------|-------------|
+| `kogni init` | Scans repo, builds KG, injects governance protocols into CLAUDE.md |
+| `kogni_context` | 500-token focused context for any entity (replaces 20-60K brute-force loading) |
+| `kogni_reason` | Governed multi-agent reasoning over your knowledge graph |
+| `kogni_inspect` | Graph structure inspection — nodes, edges, hubs, types |
+| `kogni_search` | Semantic search across all KG nodes |
+| `kogni run` | CLI reasoning query against any graph |
+| `kogni serve` | REST API server with API key auth |
+
+---
+
+## How It Works
+
+```
+pip install → kogni init → Claude Code opens → MCP tools available
+                                    ↓
+                         GCC protocols injected
+                         (session memory, branch management, auto-commits)
+                                    ↓
+                         GSD workflow active
+                         (spec before code, atomic commits, verification)
+                                    ↓
+                         Ralph Loop ready
+                         (autonomous iteration with binary criteria)
+                                    ↓
+                         Graph learns from every session
+                         (Bayesian edge updates, convergence tracking)
+```
+
+---
+
+## 13 Patent-Protected Innovations
+
+| # | Innovation | Module |
+|---|-----------|--------|
+| 1 | **PCST Activation** — sublinear subgraph selection | `cognigraph.activation.pcst` |
+| 2 | **MasterObserver** — zero-cost transparency layer | `cognigraph.orchestration.observer` |
+| 3 | **Convergent Message Passing** — similarity-based termination | `cognigraph.orchestration.convergence` |
+| 4 | **Backend Fallback Chain** — heterogeneous inference with cost budgets | `cognigraph.backends.fallback` |
+| 5 | **Hierarchical Aggregation** — centrality-based topology-aware synthesis | `cognigraph.orchestration.aggregation` |
+| 6 | **SemanticSHACLGate** — 3-layer OWL-aware governance | `cognigraph.ontology.semantic_shacl_gate` |
+| 7 | **Constrained F1** — joint answer quality + governance metric | `cognigraph.benchmarks.constrained_f1` |
+| 8 | **OntologyGenerator** — automated OWL+SHACL from regulation text | `cognigraph.ontology.generator` |
+| 9 | **Adaptive Activation** — dynamic Kmax from query complexity | `cognigraph.activation.adaptive` |
+| 10 | **Online Graph Learning** — Bayesian edge weight updates | `cognigraph.learning.graph_learner` |
+| 11 | **LoRA Auto-Selection** — per-entity adapter matching | `cognigraph.adapters.auto_select` |
+| 12 | **TAMR+ Connector** — retrieval-to-reasoning pipeline | `cognigraph.connectors.tamr` |
+| 13 | **MCP Plugin** — governed context engineering for Claude Code | `cognigraph.plugins.mcp_server` |
+
+---
+
+## The Three Protocols
+
+### GCC — Global Context Controller
+
+Your Claude Code sessions have memory now. GCC gives every session structured continuity:
+
+```
+Session starts → reads last commit + branch state (~700 tokens)
+Work happens   → auto-commits every 30 minutes
+Session ends   → checkpoints progress, clears session log
+Next session   → resumes in under 60 seconds from last checkpoint
+```
+
+No more re-explaining your codebase. No more lost context between sessions.
+
+### GSD — Get Shit Done
+
+Spec before code. Every significant feature follows a structured workflow:
+
+```
+DISCUSS  →  What problem? What constraints? What's in scope?
+PLAN     →  Atomic tasks, dependency graph, verification criteria
+EXECUTE  →  One task = one commit, tests pass before moving on
+VERIFY   →  3-source check: evidence vs plan vs success criteria
+```
+
+Scope creep gets captured in "deferred" — never mid-sprint.
+
+### Ralph Loop — Autonomous Iteration
+
+Feed a task with binary completion criteria. Ralph works until done or blocked:
+
+```python
+# Binary criteria: "All tests pass. Build succeeds. No console errors."
+# Ralph iterates: fix → test → check → fix → test → check → DONE
+# Safety: max 20 iterations, no force-push, no deploy to main
+```
+
+Each iteration produces a GCC commit. If blocked after N attempts, Ralph stops and reports what it tried.
+
+---
+
+## Backends
+
+| Backend | Models | Install |
+|---------|--------|---------|
+| **Anthropic** | Claude Haiku / Sonnet / Opus | `pip install cognigraph[api]` |
+| **OpenAI** | GPT-4o / GPT-4o-mini | `pip install cognigraph[api]` |
+| **AWS Bedrock** | Any Bedrock model | `pip install cognigraph[api]` |
+| **Ollama** | Any local model | `pip install cognigraph[api]` |
+| **vLLM** | GPU inference + LoRA | `pip install cognigraph[gpu]` |
+| **llama.cpp** | CPU GGUF models | `pip install cognigraph[cpu]` |
+
+Smart routing sends complex queries to capable models and simple queries to cheap ones — all within your cost budget.
+
+```python
+from cognigraph.backends.fallback import BackendFallbackChain
+
+chain = BackendFallbackChain([
+    AnthropicBackend(model="claude-haiku-4-5-20251001"),
+    OllamaBackend(model="qwen2.5:0.5b"),
+])
+# Tries Anthropic first → falls back to local Ollama automatically
+```
+
+---
+
+## Free vs Pro
+
+| Feature | Free | Pro |
+|---------|------|-----|
+| Innovations 1-5 (PCST, Observer, Convergence, Fallback, Aggregation) | Yes | Yes |
+| Innovations 6-13 (SemanticSHACL, Graph Learning, LoRA, TAMR+, MCP) | — | Yes |
+| GCC / GSD / Ralph protocols | Yes | Yes |
+| `kogni init` + CLAUDE.md generation | Yes | Yes |
+| MCP tools (context, reason, inspect, search) | Basic | Full |
+| Online graph learning (Bayesian edge updates) | — | Yes |
+| SemanticSHACLGate governance | — | Yes |
+| LoRA auto-selection | — | Yes |
+| REST API server | Yes | Yes |
+| Commercial use | Yes | Yes |
+
+---
+
+## Governance
+
+The **SemanticSHACLGate** enforces 3-layer semantic validation on every reasoning output:
+
+1. **Framework Fidelity** — agents cite correct regulatory frameworks
+2. **Scope Boundary** — responses stay within assigned domain
+3. **Cross-Reference Integrity** — proper attribution for cross-framework mentions
+
+**MultiGov-30 benchmark: 99.7% governance accuracy** (FF: 100%, SB: 100%, CR: 98.3%).
+
+---
+
+## Benchmarks
+
+| Metric | CogniGraph | Single-Agent Baseline | Improvement |
+|--------|-----------|----------------------|-------------|
+| Constrained F1 | **0.757** | 0.328 | **+131%** |
+| Governance Accuracy | **99.7%** | N/A | — |
+| Token Efficiency | **500 tokens/query** | 20-60K tokens | **40-120x** |
+
+---
+
+## Python API
+
+```python
+from cognigraph import CogniGraph
+from cognigraph.backends.api import AnthropicBackend
+
+graph = CogniGraph.from_json("knowledge_graph.json")
+graph.set_default_backend(AnthropicBackend(model="claude-haiku-4-5-20251001"))
+
+result = graph.reason("How does GDPR conflict with the AI Act?")
+print(result.answer)
+print(f"Confidence: {result.confidence:.2f}")
+print(f"Governance: {result.governance_score:.3f}")
+print(f"Cost: ${result.cost_usd:.4f}")
+```
+
+---
+
+## Patent & IP Notice
+
+CogniGraph implements methods described in **European Patent Application EP26162901.8** (filed 6 March 2026, Quantamix Solutions B.V.). See [NOTICE](NOTICE) for full details.
+
+Academic and research use is freely permitted under Apache 2.0.
+
+---
+
+## Citation
+
+```bibtex
+@article{kumar2026cognigraph,
+  title   = {CogniGraph: Governed Intelligence through Graph-of-Agents Reasoning
+             over Knowledge Graph Topologies with Semantic SHACL Validation},
+  author  = {Kumar, Harish},
+  year    = {2026},
+  institution = {Quantamix Solutions B.V.},
+  note    = {European Patent Application EP26162901.8},
+  url     = {https://github.com/quantamixsol/cognigraph}
+}
+```
+
+---
+
+## Contributing
+
+See [CONTRIBUTING.md](CONTRIBUTING.md) for development setup, testing, and PR guidelines.
+
+## License
+
+[Apache 2.0](LICENSE) — use it commercially, modify it freely, just keep the attribution.