feat: merge context branch — v0.3.0 stable release

Merges all context graph feature completeness work and bug fixes:

Context Graph additions:
- Temporal validity windows (valid_from/valid_until) on nodes and edges
- find_active_nodes() with is_active() method for temporal filtering
- Weighted BFS traversal via get_neighbors(min_weight=) parameter
- Cross-graph navigation: link_graph(), navigate_to(), resolve_links()
- graph_id UUID for durable graph identity across save/load cycles
- Cross-graph links persisted in save_to_file() links section

Bug fixes (from code review):
- is_active() normalises tz-aware datetime to tz-naive UTC (Bug 1)
- valid_from/valid_until preserved in all serialisation paths (Bug 2)
- cross-graph marker node typed cross_graph_link not entity (Bug 3)
- cross-graph links now survive save/load via resolve_links() (Bug 3b)
- test timing computation fixed to true average (Bug 4)

Docs:
- README: v0.3.0 badge + comprehensive What's New section
- CHANGELOG: [Unreleased] folded into [0.3.0] release block

Tests: 335 context tests, 886+ total, 0 failures

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

.all-contributorsrc

@@ -1,17 +0,0 @@
-{
-  "projectName": "Semantica",
-  "projectOwner": "Hawksight-AI",
-  "repoType": "github",
-  "repoHost": "https://github.com",
-  "files": [
-    "CONTRIBUTORS.md"
-  ],
-  "imageSize": 100,
-  "commit": true,
-  "commitConvention": "conventional",
-  "contributors": [],
-  "contributorsPerLine": 7,
-  "badgeTemplate": "[![All Contributors](https://img.shields.io/badge/all_contributors-<%= contributors.length %>-orange.svg?style=flat-square)](#contributors)",
-  "skipCi": true
-}
-

.github/FUNDING.yml

@@ -1,8 +1,3 @@
 # Funding options for Semantica
-# Uncomment and add your usernames/links below
-
-# github: [username]
-# patreon: username
-# ko_fi: username
-# custom: ["https://your-funding-page.com"]
+github: Hawksight-AI
 

.github/SUPPORT.md

@@ -7,7 +7,7 @@ Check the [docs folder](https://github.com/Hawksight-AI/semantica/tree/main/docs
 
 ### 💬 Community Support
 - **GitHub Discussions**: [Ask questions](https://github.com/Hawksight-AI/semantica/discussions)
-- **Discord**: Join our [Discord server](https://discord.gg/semantica) for real-time chat
+- **Discord**: Join our [Discord server](https://discord.gg/sV34vps5hH) for real-time chat
 
 ### 💭 Discussions
 Join the conversation on [GitHub Discussions](https://github.com/Hawksight-AI/semantica/discussions):
@@ -32,6 +32,8 @@ For enterprise support, custom development, or consulting services:
 
 ## Sponsorship
 
+### Sponsor this project
+
 Support Semantica development:
 - [GitHub Sponsors](https://github.com/sponsors/Hawksight-AI)
 

.github/dependabot.yml

@@ -1,28 +1,130 @@
 version: 2
+
 updates:
-  # Python dependencies (pip/pyproject.toml)
+  # Core Python dependencies
   - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"  # Weekly for security
+      day: "monday"
+      time: "03:30"  # 3:30 AM UTC (9:00 AM IST)
+    open-pull-requests-limit: 10  # Higher limit for security updates
+    reviewers:
+      - "KaifAhmad1"
+    assignees:
+      - "KaifAhmad1"
+    commit-message:
+      prefix: "security"
+      include: "scope"
+    labels:
+      - "dependencies"
+      - "python"
+      - "security"
+    allow:
+      - dependency-type: "production"
+      - dependency-type: "development"
+    ignore:
+      # Only ignore major version updates for stability-critical packages
+      - dependency-name: "torch"
+        update-types: ["version-update:semver-major"]
+      - dependency-name: "transformers"
+        update-types: ["version-update:semver-major"]
+    # Group new feature dependencies
+    groups:
+      security-critical:
+        patterns:
+          - "cryptography"
+          - "requests"
+          - "urllib3"
+          - "certifi"
+          - "pyopenssl"
+        dependency-type: "production"
+      snowflake-features:
+        patterns:
+          - "snowflake-connector-python"
+          - "cryptography"
+      arrow-features:
+        patterns:
+          - "pyarrow"
+      benchmark-tools:
+        patterns:
+          - "pytest-benchmark"
+          - "pytest-cov"
+
+  # GitHub Actions
+  - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
       interval: "weekly"
       day: "monday"
       time: "09:00"
-    open-pull-requests-limit: 0
-    ignore:
-      # Ignore all updates (no PRs will be created)
-      - dependency-name: "*"
-        update-types: ["version-update:semver-major", "version-update:semver-minor", "version-update:semver-patch"]
+    open-pull-requests-limit: 3
+    reviewers:
+      - "KaifAhmad1"
+    assignees:
+      - "KaifAhmad1"
+    commit-message:
+      prefix: "ci"
+      include: "scope"
+    labels:
+      - "dependencies"
+      - "github-actions"
+      - "ci"
 
-  # GitHub Actions dependencies
-  - package-ecosystem: "github-actions"
+  # Optional dependencies (separate schedule for stability)
+  - package-ecosystem: "pip"
     directory: "/"
     schedule:
-      interval: "monthly"
-      day: "monday"
+      interval: "weekly"
+      day: "friday"
       time: "09:00"
-    open-pull-requests-limit: 0
-    ignore:
-      # Ignore all updates (no PRs will be created)
-      - dependency-name: "*"
-        update-types: ["version-update:semver-major", "version-update:semver-minor", "version-update:semver-patch"]
+    target-branch: "main"
+    open-pull-requests-limit: 3
+    reviewers:
+      - "KaifAhmad1"
+    assignees:
+      - "KaifAhmad1"
+    commit-message:
+      prefix: "deps"
+      include: "scope"
+    labels:
+      - "dependencies"
+      - "python"
+      - "optional"
+    allow:
+      - dependency-type: "production"
+
+  # Docker dependencies (if you use Docker)
+  - package-ecosystem: "docker"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "wednesday"
+      time: "09:00"
+    open-pull-requests-limit: 2
+    reviewers:
+      - "KaifAhmad1"
+    assignees:
+      - "KaifAhmad1"
+    commit-message:
+      prefix: "docker"
+      include: "scope"
+    labels:
+      - "dependencies"
+      - "docker"
+
+  # Documentation dependencies
+  - package-ecosystem: "pip"
+    directory: "docs"
+    schedule:
+      interval: "monthly"
+    open-pull-requests-limit: 2
+    reviewers:
+      - "KaifAhmad1"
+    commit-message:
+      prefix: "docs"
+      include: "scope"
+    labels:
+      - "dependencies"
+      - "documentation"
 

.github/workflows/benchmark.yml

@@ -0,0 +1,51 @@
+name: Semantica Performance Suite
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+jobs:
+  performance-test:
+    name: Benchmark Runner (Ubuntu/Python 3.12)
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: 'pip'
+
+      - name: Install Dependencies
+        env:
+
+          BENCHMARK_REAL_LIBS: "1"
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .
+          pip install -r benchmarks/requirements.txt
+          python -m spacy download en_core_web_sm
+          pip install rdflib neo4j faiss-cpu torch pyarrow pdfplumber python-pptx openpyxl lxml python-docx beautifulsoup4 chardet langdetect
+
+      - name: Execute Benchmarks (Real Mode)
+        env:
+          BENCHMARK_REAL_LIBS: "1"
+        run: |
+          python benchmarks/benchmarks_runner.py
+          # Optional: Compare to baseline (requires previous run artifact)
+          # pytest-benchmark --storage file://benchmarks/results --benchmark-compare
+
+      - name: Upload Benchmark Results
+        uses: actions/upload-artifact@v7
+        if: always()
+        with:
+          name: benchmark-report-${{ github.run_id }}
+          path: benchmarks/results
+          retention-days: 30

.github/workflows/security-scan.yml

@@ -0,0 +1,175 @@
+name: Security Scan
+
+on:
+  schedule:
+    - cron: '30 1 * * 1,4'  # Mon/Thu 7 AM IST
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  security-scan:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      security-events: write
+      actions: read
+    
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+        
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install safety bandit semgrep jq
+        
+      - name: Run Safety Check (Package Vulnerabilities)
+        run: |
+          safety check --json --output safety-report.json || true
+          echo "Checking for package vulnerabilities..."
+          
+          # Count vulnerabilities safely
+          VULNS=$(safety check --json --output /dev/stdout 2>/dev/null | jq '.vulnerabilities | length' 2>/dev/null || echo "0")
+          
+          if [ "$VULNS" -gt 0 ]; then
+            echo "❌ Security vulnerabilities found: $VULNS"
+            echo "CI will fail to prevent merging of vulnerable dependencies"
+            echo ""
+            echo "Vulnerability details:"
+            safety check || true
+            exit 1
+          else
+            echo "✅ No security vulnerabilities found"
+          fi
+        
+      - name: Run Bandit (Code Security Linter)
+        run: |
+          bandit -r semantica/ -f json -o bandit-report.json || true
+          echo "Checking for HIGH severity security issues..."
+          
+          # Count HIGH severity issues
+          HIGH_ISSUES=$(bandit -r semantica/ -f json -ll 2>/dev/null | jq -r '.results[]? | select(.issue_severity == "HIGH") | .test_name' 2>/dev/null | wc -l || echo "0")
+          
+          if [ "$HIGH_ISSUES" -gt 0 ]; then
+            echo "❌ HIGH severity security issues found: $HIGH_ISSUES"
+            echo "CI will fail to prevent merging of high-risk code"
+            echo ""
+            echo "High severity issues:"
+            bandit -r semantica/ -ll | grep "Severity: High" -A 5 -B 1 || true
+            exit 1
+          else
+            echo "✅ No HIGH severity security issues found"
+          fi
+        
+      - name: Run Semgrep (Static Analysis)
+        run: |
+          echo "Running Semgrep static analysis..."
+          semgrep --config=auto --json --output=semgrep-report.json semantica/ || true
+          
+          # Run security-focused rules
+          echo "Checking for security patterns..."
+          SECURITY_ISSUES=$(semgrep --config=p/security --json semantica/ 2>/dev/null | jq '.results | length' 2>/dev/null || echo "0")
+          
+          if [ "$SECURITY_ISSUES" -gt 0 ]; then
+            echo "⚠️ Security patterns found: $SECURITY_ISSUES"
+            echo "Review these findings for potential improvements"
+            semgrep --config=p/security semantica/ || true
+          else
+            echo "✅ No security patterns found"
+          fi
+        
+      - name: Upload Security Reports
+        uses: actions/upload-artifact@v7
+        with:
+          name: security-reports
+          path: |
+            safety-report.json
+            bandit-report.json
+            semgrep-report.json
+        
+      - name: Comment PR with Security Results
+        if: github.event_name == 'pull_request'
+        uses: actions/github-script@v8
+        with:
+          script: |
+            const fs = require('fs');
+            
+            // Read safety report
+            let safetyResults = '';
+            try {
+              const safetyData = JSON.parse(fs.readFileSync('safety-report.json', 'utf8'));
+              if (safetyData.vulnerabilities && safetyData.vulnerabilities.length > 0) {
+                safetyResults = `## Safety Vulnerabilities Found\\n`;
+                safetyData.vulnerabilities.forEach(vuln => {
+                  safetyResults += `- **${vuln.package}**: ${vuln.advisory}\\n`;
+                });
+              } else {
+                safetyResults = '## No Safety Vulnerabilities Found\\n';
+              }
+            } catch (e) {
+              safetyResults = '## Safety scan completed\\n';
+            }
+            
+            // Read bandit report
+            let banditResults = '';
+            try {
+              const banditData = JSON.parse(fs.readFileSync('bandit-report.json', 'utf8'));
+              if (banditData.results && banditData.results.length > 0) {
+                const highIssues = banditData.results.filter(issue => issue.issue_severity === 'HIGH');
+                if (highIssues.length > 0) {
+                  banditResults = `## High Severity Security Issues Found\\n`;
+                  highIssues.forEach(issue => {
+                    banditResults += `- **${issue.test_name}**: ${issue.filename}:${issue.line_number}\\n`;
+                  });
+                } else {
+                  banditResults = '## No High Severity Security Issues Found\\n';
+                }
+              } else {
+                banditResults = '## No Bandit Issues Found\\n';
+              }
+            } catch (e) {
+              banditResults = '## Bandit scan completed\\n';
+            }
+            
+            // Read semgrep report
+            let semgrepResults = '';
+            try {
+              const semgrepData = JSON.parse(fs.readFileSync('semgrep-report.json', 'utf8'));
+              if (semgrepData.results && semgrepData.results.length > 0) {
+                semgrepResults = `## Security Patterns Found\\n`;
+                semgrepData.results.slice(0, 10).forEach(issue => {
+                  semgrepResults += `- **${issue.rule_id}**: ${issue.path}\\n`;
+                });
+                if (semgrepData.results.length > 10) {
+                  semgrepResults += `- ... and ${semgrepData.results.length - 10} more\\n`;
+                }
+              } else {
+                semgrepResults = '## No Security Patterns Found\\n';
+              }
+            } catch (e) {
+              semgrepResults = '## Semgrep scan completed\\n';
+            }
+            
+            // Create summary comment
+            const comment = `# 🔒 Security Scan Results\\n\\n${safetyResults}\\n\\n${banditResults}\\n\\n${semgrepResults}\\n\\n---\\n\\n*This security scan runs automatically on every PR and bi-weekly.*\\n\\n📊 **Security Policy**: CI fails on vulnerabilities and HIGH severity issues.`;
+            
+            // Post comment with error handling
+            try {
+              await github.rest.issues.createComment({
+                issue_number: context.issue.number,
+                owner: context.repo.owner,
+                repo: context.repo.repo,
+                body: comment
+              });
+              console.log('✅ Security comment posted successfully');
+            } catch (error) {
+              console.log('⚠️ Could not post security comment:', error.message);
+              console.log('📋 Security scan results saved to artifacts');
+            }

.pre-commit-config.yaml

@@ -5,6 +5,7 @@ repos:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
+        exclude: 'neptune-setup\.yaml$'
       - id: check-json
       - id: check-toml
       - id: check-added-large-files
@@ -49,9 +50,15 @@ repos:
     hooks:
       - id: yamllint
         args: ['-d', '{extends: default, rules: {line-length: {max: 120}}}']
+        exclude: 'neptune-setup\.yaml$'
+
+  - repo: https://github.com/aws-cloudformation/cfn-lint
+    rev: v1.43.3
+    hooks:
+      - id: cfn-lint
+        files: 'neptune-setup\.yaml$'
 
   # Removed slow hooks for faster development:
   # - mypy: Type checking (can be run manually or in CI)
   # - bandit: Security scanning (can be run separately)
   # - pytest: Testing (should be run manually, not on every commit)
-

CONTRIBUTING.md

@@ -1,306 +1,266 @@
 # Contributing to Semantica
 
-Thank you for your interest in contributing to Semantica! This document provides guidelines and instructions for contributing to the project.
+Thank you for your interest in contributing! Every contribution, no matter how small, is valuable. 🎉
 
-## Table of Contents
+⭐ **Give us a Star** • 🍴 **[Fork Semantica](https://github.com/Hawksight-AI/semantica/fork)** • 💬 **Join our [Discord](https://discord.gg/sV34vps5hH)**
 
-- [Code of Conduct](#code-of-conduct)
-- [Getting Started](#getting-started)
-- [Development Setup](#development-setup)
-- [Code Style Guidelines](#code-style-guidelines)
-- [Testing Requirements](#testing-requirements)
-- [Commit Message Conventions](#commit-message-conventions)
-- [Pull Request Process](#pull-request-process)
-- [Documentation Standards](#documentation-standards)
-- [Types of Contributions](#types-of-contributions)
-- [Getting Help](#getting-help)
+> **New to contributing?** Start with a [`good first issue`](https://github.com/Hawksight-AI/semantica/labels/good%20first%20issue) or join our [Discord](https://discord.gg/sV34vps5hH) community.
 
-## Code of Conduct
+---
 
-This project adheres to a [Code of Conduct](CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to the maintainers.
+## 🚀 Quick Start
 
-## Getting Started
+1. Find a [`good first issue`](https://github.com/Hawksight-AI/semantica/labels/good%20first%20issue)
+2. [Fork Semantica](https://github.com/Hawksight-AI/semantica/fork) & clone the repository
+3. Make your changes
+4. Submit a pull request!
 
-1. **Fork the repository** on GitHub
-2. **Clone your fork** locally:
-   ```bash
-   git clone https://github.com/your-username/semantica.git
-   cd semantica
-   ```
-3. **Add the upstream remote**:
-   ```bash
-   git remote add upstream https://github.com/Hawksight-AI/semantica.git
-   ```
+**Need help?** Join [Discord](https://discord.gg/sV34vps5hH) or [GitHub Discussions](https://github.com/Hawksight-AI/semantica/discussions)
 
-## Development Setup
+---
 
-### Prerequisites
+## 🎯 Ways to Contribute
 
-- Python 3.8 or higher (3.9+ recommended)
-- pip package manager
-- Git
+### 💻 Code
 
-### Installation
+**What you can do:**
+- Fix bugs
+- Add new features
+- Improve code quality (add type hints, docstrings, improve error messages)
+- Optimize performance
 
-1. **Create a virtual environment** (recommended):
-   ```bash
-   python -m venv venv
-   source venv/bin/activate  # On Windows: venv\Scripts\activate
-   ```
+**Where:** `semantica/` directory
 
-2. **Install the project in editable mode with dev dependencies**:
-   ```bash
-   pip install -e ".[dev]"
-   ```
+**Good first issues:** Add docstrings, type hints, or improve error messages
 
-3. **Install pre-commit hooks**:
-   ```bash
-   pre-commit install
-   ```
+---
 
-### Verify Installation
+### 📝 Documentation
+
+**What you can do:**
+- Fix typos and grammar errors
+- Improve clarity and readability
+- Add code examples and tutorials
+- Create new cookbook notebooks
+- Improve API documentation (docstrings)
+- Create troubleshooting guides
+- Update installation instructions
+- Add missing documentation
+
+**Where:** `README.md`, `docs/`, `cookbook/`, docstrings in code
+
+**Good first issues:** Fix typos, add examples, create cookbook tutorials, improve docstrings
+
+**Documentation formatting:**
+- Use clear, concise language
+- Include code examples where helpful
+- Follow markdown best practices
+- Use proper headings hierarchy
+- Add links to related sections
+- Include screenshots for UI-related docs
+
+---
+
+### 🧪 Testing
+
+**What you can do:**
+- Add unit tests
+- Improve test coverage
+- Add integration tests
+
+**Where:** `tests/` directory
+
+**Good first issues:** Add tests for specific functions or classes
+
+---
+
+### 🐛 Bug Reports
+
+**What:** Report bugs you find
+
+**How:** Use the [bug report template](https://github.com/Hawksight-AI/semantica/issues/new?template=bug_report.md)
+
+**Include:** Description, steps to reproduce, expected vs actual behavior, environment details
+
+---
+
+### 💡 Feature Requests
+
+**What:** Suggest new features or improvements
+
+**How:** Use the [feature request template](https://github.com/Hawksight-AI/semantica/issues/new?template=feature_request.md)
+
+**Include:** Problem statement, proposed solution, use cases
+
+---
+
+### 🎨 Cookbook & Examples
+
+**What:** Create tutorials and examples
+
+**Where:** `cookbook/` directory
+
+**Examples:** Create new notebooks, add examples, improve existing tutorials
+
+---
+
+### 💬 Community Support
+
+**What:** Help others in the community
+
+**Where:** [Discord](https://discord.gg/sV34vps5hH), [GitHub Discussions](https://github.com/Hawksight-AI/semantica/discussions)
+
+**Examples:** Answer questions, review PRs, share your projects
+
+---
+
+### 🎓 Educational Content
+
+**What:** Create educational materials
+
+**Examples:** Blog posts, video tutorials, talks, workshops, case studies
+
+---
+
+### 🔧 Other Contributions
+
+- **Design & Graphics:** Logos, diagrams, visualizations
+- **Tools & Integrations:** CLI tools, integrations with other frameworks
+- **Infrastructure:** CI/CD improvements, Docker optimization
+- **Security:** Report security vulnerabilities (privately)
+
+---
+
+## 📋 Getting Started
+
+### 1. Fork & Clone
+
+First, [fork Semantica](https://github.com/Hawksight-AI/semantica/fork) on GitHub, then:
 
 ```bash
-python -c "import semantica; print(semantica.__version__)"
-pytest --version
-black --version
+git clone https://github.com/your-username/semantica.git
+cd semantica
+git remote add upstream https://github.com/Hawksight-AI/semantica.git
 ```
 
-## Code Style Guidelines
-
-We use several tools to maintain code quality and consistency:
-
-### Formatting
-
-- **Black**: Code formatting (line length: 88)
-  ```bash
-  black semantica/
-  ```
-
-- **isort**: Import sorting
-  ```bash
-  isort semantica/
-  ```
-
-### Linting
-
-- **flake8**: Style guide enforcement
-  ```bash
-  flake8 semantica/
-  ```
-
-- **mypy**: Static type checking
-  ```bash
-  mypy semantica/
-  ```
-
-### Running All Checks
+### 2. Set Up Environment
 
 ```bash
-# Format code
-black semantica/ tests/
+# Create virtual environment
+python -m venv venv
+source venv/bin/activate  # Windows: venv\Scripts\activate
 
-# Sort imports
-isort semantica/ tests/
+# Install dev dependencies
+pip install -e ".[dev]"
 
-# Lint
-flake8 semantica/ tests/
-
-# Type check
-mypy semantica/
+# Install pre-commit hooks (optional)
+pre-commit install
 ```
 
-Or use pre-commit hooks (automatically runs on commit):
-```bash
-pre-commit run --all-files
-```
-
-## Testing Requirements
-
-### Running Tests
+### 3. Create Branch
 
 ```bash
-# Run all tests
-pytest
-
-# Run with coverage
-pytest --cov=semantica --cov-report=html
-
-# Run specific test file
-pytest tests/test_specific.py
-
-# Run with verbose output
-pytest -v
+git checkout -b feature/your-feature-name
+# or
+git checkout -b fix/bug-description
 ```
 
-### Test Coverage
+### 4. Make Changes
 
-- Minimum coverage: **80%**
-- Critical modules: **90%+**
-- Coverage reports are generated in `htmlcov/`
+- Follow code style (see below)
+- Add tests for new features
+- Update documentation
 
-### Writing Tests
+### 5. Run Checks
 
-- Follow pytest conventions
-- Use descriptive test names
-- Include docstrings for complex tests
-- Test both success and failure cases
-- Use fixtures for common setup
-
-Example:
-```python
-def test_entity_extraction():
-    """Test basic entity extraction functionality."""
-    from semantica.semantic_extract import NamedEntityRecognizer
-    
-    ner = NamedEntityRecognizer()
-    entities = ner.extract("Apple Inc. was founded by Steve Jobs.")
-    
-    assert len(entities) > 0
-    assert any(e.text == "Apple Inc." for e in entities)
+```bash
+pytest                          # Run tests
+black semantica/ tests/        # Format code
+isort semantica/ tests/         # Sort imports
+flake8 semantica/ tests/        # Lint
 ```
 
-## Commit Message Conventions
+Or use pre-commit hooks: `pre-commit run --all-files`
 
-We follow [Conventional Commits](https://www.conventionalcommits.org/) specification:
+### 6. Commit & Push
 
-### Format
-
-```
-<type>(<scope>): <subject>
-
-<body>
-
-<footer>
+```bash
+git commit -m "feat(module): add new feature"
+git push origin feature/your-feature-name
 ```
 
-### Types
+Then create a pull request on GitHub!
 
-- `feat`: New feature
-- `fix`: Bug fix
-- `docs`: Documentation changes
-- `style`: Code style changes (formatting, etc.)
-- `refactor`: Code refactoring
-- `test`: Adding or updating tests
-- `chore`: Maintenance tasks
-- `perf`: Performance improvements
-- `ci`: CI/CD changes
+---
 
-### Examples
+## 📐 Code Style
+
+We use automated tools:
+
+| Tool     | Purpose                    | Command                    |
+|----------|----------------------------|----------------------------|
+| **Black** | Code formatting            | `black semantica/ tests/` |
+| **isort** | Import sorting             | `isort semantica/ tests/` |
+| **flake8** | Style enforcement          | `flake8 semantica/ tests/` |
+| **mypy** | Type checking              | `mypy semantica/`          |
+
+**Run all:** `black semantica/ tests/ && isort semantica/ tests/ && flake8 semantica/ tests/ && mypy semantica/`
+
+---
+
+## 🧪 Testing
+
+```bash
+pytest                          # Run all tests
+pytest --cov=semantica         # With coverage
+pytest tests/test_file.py      # Specific file
+```
+
+**Coverage goal:** 80% minimum, 90%+ for critical modules
+
+---
+
+## 📝 Commit Messages
+
+Use [Conventional Commits](https://www.conventionalcommits.org/):
 
 ```
 feat(kg): add temporal graph support
-
-Add support for temporal knowledge graphs with version tracking
-and time-based queries.
-
-Closes #123
+fix(parse): handle empty PDF files
+docs(readme): add installation guide
+test(extract): add unit tests
 ```
 
-```
-fix(parse): handle empty PDF files gracefully
+**Types:** `feat`, `fix`, `docs`, `test`, `refactor`, `perf`, `style`, `chore`
 
-Previously, empty PDF files would cause a crash. Now they return
-an empty document with appropriate warnings.
+---
 
-Fixes #456
-```
+## ✅ PR Checklist
 
-## Pull Request Process
-
-### Before Submitting
-
-1. **Update your fork**:
-   ```bash
-   git fetch upstream
-   git checkout main
-   git merge upstream/main
-   ```
-
-2. **Create a feature branch**:
-   ```bash
-   git checkout -b feature/your-feature-name
-   # or
-   git checkout -b fix/bug-description
-   ```
-
-3. **Make your changes** and commit following our conventions
-
-4. **Run all checks**:
-   ```bash
-   pytest
-   black semantica/ tests/
-   isort semantica/ tests/
-   flake8 semantica/ tests/
-   mypy semantica/
-   ```
-
-5. **Push to your fork**:
-   ```bash
-   git push origin feature/your-feature-name
-   ```
-
-### PR Checklist
+Before submitting:
 
 - [ ] Code follows style guidelines
 - [ ] Tests pass locally
-- [ ] New tests added for new features
+- [ ] New tests added (if applicable)
 - [ ] Documentation updated
 - [ ] Commit messages follow conventions
 - [ ] No merge conflicts
-- [ ] PR description is clear and complete
 
-### PR Description Template
+---
 
-```markdown
-## Description
-Brief description of changes
+## 📖 Documentation Standards
 
-## Type of Change
-- [ ] Bug fix
-- [ ] New feature
-- [ ] Breaking change
-- [ ] Documentation update
+### Code Documentation (Docstrings)
 
-## Related Issues
-Closes #123
-Related to #456
+**Format:** Use Google-style docstrings
 
-## Testing
-- [ ] Tests pass locally
-- [ ] Added new tests
-- [ ] Updated existing tests
-
-## Checklist
-- [ ] Code follows style guidelines
-- [ ] Self-review completed
-- [ ] Comments added for complex code
-- [ ] Documentation updated
-- [ ] No new warnings generated
-```
-
-## Documentation Standards
-
-### Code Documentation
-
-- Use Google-style docstrings
-- Include type hints
-- Document all public functions and classes
-- Include examples for complex functions
-
-Example:
 ```python
-def extract_entities(
-    text: str,
-    model: str = "transformer",
-    confidence_threshold: float = 0.7
-) -> List[Entity]:
+def extract_entities(text: str, model: str = "transformer") -> List[Entity]:
     """Extract named entities from text.
     
     Args:
         text: Input text to process
         model: NER model to use (default: "transformer")
-        confidence_threshold: Minimum confidence score (default: 0.7)
     
     Returns:
         List of extracted Entity objects
@@ -309,92 +269,98 @@ def extract_entities(
         ValueError: If text is empty or model is invalid
     
     Example:
-        >>> ner = NamedEntityRecognizer()
+        >>> from semantica.semantic_extract import NERExtractor
+        >>> ner = NERExtractor(method="ml", model="en_core_web_sm")
         >>> entities = ner.extract("Apple Inc. was founded in 1976.")
         >>> len(entities)
         2
     """
-    ...
 ```
 
-### Documentation Files
+### Markdown Documentation Formatting
 
-- Update relevant documentation in `docs/`
-- Add examples to cookbook if applicable
-- Update API reference if adding new public APIs
-- Keep README.md up to date
+**General Guidelines:**
+- Use clear headings (H1 for title, H2 for main sections, H3 for subsections)
+- Keep paragraphs short and focused
+- Use bullet points for lists
+- Add code blocks with syntax highlighting
+- Include links to related documentation
 
-## Types of Contributions
+**Code Blocks:**
+- Use triple backticks with language identifier: ` ```python `, ` ```bash `
+- Include comments in code examples
+- Show expected output when helpful
 
-### 💻 Code Contributions
+**Examples:**
 
-- **Bug Fixes**: Resolving issues reported in the issue tracker.
-- **New Features**: Implementing new capabilities (please discuss via an issue first!).
-- **Refactoring**: Improving code structure and maintainability without changing behavior.
-- **Algorithm Optimization**: Improving the efficiency of graph algorithms and vector search.
+```markdown
+## Section Title
 
-#### ⚡ Performance and Latency
-We deeply value efficiency. Contributions that make Semantica faster and lighter are highly appreciated!
+Brief introduction paragraph.
 
-- **Latency Reduction**: Optimize critical paths and RAG pipeline response times.
-- **Memory Optimization**: Reduce graph/vector processing memory footprint.
-- **Throughput**: Improve operations per second (bulk ingestion, parallel queries).
-- **Benchmarks**: Add performance benchmarks to track regressions.
-- **Async/Concurrency**: Enhance asynchronous execution and concurrency.
+### Subsection
 
-### 📚 Documentation Contributions
+- Bullet point 1
+- Bullet point 2
 
-- Fix typos and grammar
-- Improve clarity
-- Add examples
-- Create tutorials
-- Translate documentation
+**Code example:**
 
-### Testing Contributions
+```python
+from semantica import SomeClass
 
-- Add test coverage
-- Improve test quality
-- Add integration tests
-- Performance benchmarks
+instance = SomeClass()
+result = instance.method()
+```
 
-### Other Contributions
+**Note:** Additional context or warnings.
+```
 
-- Answer questions in discussions
-- Help with issues
-- Review pull requests
-- Share use cases
-- Report bugs
-- Suggest features
+**Best Practices:**
+- Start with an overview/introduction
+- Use consistent terminology
+- Include "See also" links
+- Add examples for complex concepts
+- Keep formatting consistent across docs
 
-## Getting Help
+---
 
-### Communication Channels
+## 🆘 Getting Help
 
-- **GitHub Discussions**: General questions and discussions
-- **GitHub Issues**: Bug reports and feature requests
-- **Discord**: Real-time chat and community support
+- 💬 [Discord](https://discord.gg/sV34vps5hH) - Real-time chat
+- 💭 [GitHub Discussions](https://github.com/Hawksight-AI/semantica/discussions) - Q&A
+- 🐛 [GitHub Issues](https://github.com/Hawksight-AI/semantica/issues) - Bug reports
 
-### Before Asking for Help
+**Before asking:** Check existing documentation, search issues/discussions, review cookbook examples
 
-1. Check existing documentation
-2. Search GitHub issues and discussions
-3. Review code examples in cookbook
-4. Check FAQ in documentation
+---
 
-### Asking Good Questions
+## 🏆 Recognition
 
-- Provide context and environment details
-- Include code examples
-- Show what you've tried
-- Include error messages and logs
-- Be specific about what you need
-
-## Recognition
-
-Contributors are recognized in:
+All contributors are recognized in:
 - [CONTRIBUTORS.md](CONTRIBUTORS.md)
 - GitHub contributors page
-- Release notes for significant contributions
+- Release notes
 
-Thank you for contributing to Semantica! 🎉
+We follow the [all-contributors](https://allcontributors.org) specification!
 
+---
+
+## 📜 Code of Conduct
+
+This project follows a [Code of Conduct](CODE_OF_CONDUCT.md). Be respectful and inclusive.
+
+---
+
+## 📚 Resources
+
+- [README.md](README.md) - Project overview
+- [Cookbook](cookbook/) - Tutorials and examples
+- [Documentation](docs/) - Comprehensive guides
+
+---
+
+**Thank you for contributing!** 🚀
+
+Every contribution matters - whether it's a single line of code, a typo fix, a helpful answer, or a bug report. We appreciate you! 🙏
+
+⭐ **Give us a Star** • 🍴 **[Fork Semantica](https://github.com/Hawksight-AI/semantica/fork)** • 💬 **Join our [Discord](https://discord.gg/sV34vps5hH)**

CONTRIBUTORS.md

@@ -4,44 +4,31 @@ Thank you to all the people who have contributed to Semantica! 🎉
 
 This project follows the [all-contributors](https://allcontributors.org) specification. Contributions of any kind are welcome!
 
-## How to Contribute
+⭐ **Give us a Star** • 🍴 **Fork us** • 💬 **Join our [Discord](https://discord.gg/sV34vps5hH)**
 
-We welcome contributions of all kinds! Whether you're:
-- Writing code
-- Improving documentation
-- Reporting bugs
-- Suggesting features
-- Answering questions
-- Reviewing pull requests
-- Sharing use cases
-- Creating examples
-
-All contributions are valuable and appreciated!
+---
 
 ## Contribution Types
 
+We recognize all types of contributions:
+
 - 💻 **Code**: Writing code, fixing bugs, implementing features
 - 📝 **Documentation**: Writing docs, tutorials, examples
+- 🧪 **Testing**: Writing tests, improving test coverage
 - 🐛 **Bug Reports**: Finding and reporting bugs
 - 💡 **Ideas**: Suggesting new features or improvements
 - 🎨 **Design**: UI/UX improvements, graphics, branding
-- 📖 **Examples**: Creating code examples and tutorials
-- 🔍 **Testing**: Writing tests, improving test coverage
-- 💬 **Answering Questions**: Helping others in discussions
-- 📢 **Talks**: Giving talks, presentations, workshops
-- 🌍 **Translation**: Translating documentation
+- 🎨 **Cookbook**: Creating tutorials and examples
+- 💬 **Community**: Answering questions, reviewing PRs
+- 🎓 **Education**: Blog posts, video tutorials, talks, workshops
 - 🔧 **Tools**: Creating tools, scripts, integrations
 - 📦 **Packaging**: Improving build, release, distribution
 - ⚠️ **Security**: Reporting security vulnerabilities
-- 🎓 **Education**: Teaching, mentoring, tutorials
-- 📹 **Video**: Creating video content, tutorials
-- 🎵 **Audio**: Podcasts, audio content
-- 📸 **Photography**: Screenshots, images
-- 🔬 **Research**: Research, analysis, studies
-- 💰 **Financial**: Sponsoring, funding
 - 🏗️ **Infrastructure**: CI/CD, hosting, infrastructure
 - 🚇 **Maintenance**: Maintenance, triage, project management
 
+---
+
 ## Contributors
 
 <!-- ALL-CONTRIBUTORS-LIST:START -->
@@ -50,48 +37,78 @@ All contributions are valuable and appreciated!
 
 <!-- ALL-CONTRIBUTORS-LIST:END -->
 
+---
+
 ## Recognition
 
-### Top Contributors
+All contributors are recognized in:
 
-Contributors are recognized based on their contributions to the project. Recognition includes:
+- This contributors list
+- [GitHub contributors page](https://github.com/Hawksight-AI/semantica/graphs/contributors)
+- Release notes for significant contributions
+- Community appreciation
 
-- Listing in this file
-- GitHub contributor statistics
-- Special mentions in release notes
-- Featured showcases for significant contributions
-
-### Hall of Fame
-
-Special recognition for exceptional contributions:
-
-- **Coming soon** - We'll feature outstanding contributors here!
+---
 
 ## How to Add Yourself
 
-If you've contributed to Semantica and want to be added to this list:
+### Automatic Recognition
 
-1. **Automatic**: If you've made a commit, you'll appear in [GitHub's contributors graph](https://github.com/Hawksight-AI/semantica/graphs/contributors)
-2. **Manual**: Open a PR adding yourself to this file, or use the [@all-contributors bot](https://allcontributors.org/docs/en/bot/usage)
+If you've made a commit, you'll automatically appear in [GitHub's contributors graph](https://github.com/Hawksight-AI/semantica/graphs/contributors).
 
-Example:
-```markdown
-- [Your Name](https://github.com/yourusername) - 💻 📝 🐛
-```
+### Using All-Contributors Bot
 
-## All Contributors Bot
-
-We use the [all-contributors](https://allcontributors.org) bot to automatically recognize contributors. To add a contributor, comment on an issue or PR:
+Comment on any issue or PR with:
 
 ```
 @all-contributors please add @username for code, docs, bug
 ```
 
-## Thank You!
+**Examples:**
 
-Every contribution, no matter how small, helps make Semantica better. Thank you for being part of our community!
+```
+@all-contributors please add @johndoe for code
+@all-contributors please add @janedoe for docs, bug
+@all-contributors please add @devuser for code, test, maintenance
+```
+
+### Manual Addition
+
+Open a PR adding yourself to this file:
+
+```markdown
+- [Your Name](https://github.com/yourusername) - 💻 📝 🐛
+```
 
 ---
 
-**Want to contribute?** Check out our [Contributing Guide](CONTRIBUTING.md) to get started!
+## Contribution Type Codes
 
+When using the all-contributors bot, use these codes:
+
+- `code` - Code contributions
+- `doc` - Documentation
+- `test` - Testing
+- `bug` - Bug reports
+- `ideas` - Feature requests/ideas
+- `design` - Design work
+- `example` - Cookbook/examples
+- `question` - Answering questions
+- `talk` - Talks/presentations
+- `tool` - Tools/integrations
+- `packaging` - Packaging/distribution
+- `security` - Security reports
+- `infra` - Infrastructure
+- `maintenance` - Maintenance
+
+See [all-contributors specification](https://allcontributors.org/docs/en/emoji-key) for complete list.
+
+---
+
+## Thank You!
+
+Every contribution, no matter how small, helps make Semantica better. Thank you for being part of our community! 🙏
+
+**Want to contribute?** 
+
+⭐ Give us a Star • 🍴 [Fork us](https://github.com/Hawksight-AI/semantica/fork) • Check out our [Contributing Guide](CONTRIBUTING.md) to get started!

RELEASE.md

@@ -1,56 +0,0 @@
-# Release Process for Semantica
-
-This document outlines the steps to release a new version of the Semantica framework.
-
-## 1. Versioning Policy
-
-Semantica follows [Semantic Versioning (SemVer)](https://semver.org/).
-- **MAJOR** version for incompatible API changes.
-- **MINOR** version for functionality added in a backwards compatible manner.
-- **PATCH** version for backwards compatible bug fixes.
-
-## 2. Pre-release Checklist
-
-Before releasing, ensure:
-- [ ] All tests pass: `pytest`
-- [ ] Documentation is up to date in `docs/` and `MkDocs` config.
-- [ ] `CHANGELOG.md` is updated with the latest changes.
-- [ ] Version is updated in:
-  - `semantica/__init__.py`
-  - `pyproject.toml`
-  - `docs/citation.md` (BibTeX entry)
-
-## 3. Release Steps
-
-### Automated Release (Recommended)
-
-The project uses GitHub Actions for automated releases to PyPI.
-
-1. **Tag the commit**: Create a new git tag for the version (e.g., `v0.2.1`).
-   ```bash
-   git tag -a v0.2.1 -m "Release v0.2.1"
-   git push origin v0.2.1
-   ```
-2. **GitHub Action**: The `Release` workflow will automatically trigger, build the package, create a GitHub Release, and publish to PyPI using Trusted Publishing.
-
-### Manual Release
-
-If you need to release manually:
-
-1. **Build the package**:
-   ```bash
-   python -m build
-   ```
-2. **Verify the build**:
-   ```bash
-   twine check dist/*
-   ```
-3. **Upload to PyPI**:
-   ```bash
-   twine upload dist/*
-   ```
-
-## 4. Post-release
-
-- Verify the new version is available on [PyPI](https://pypi.org/project/semantica/).
-- Check the [GitHub Releases](https://github.com/your-org/semantica/releases) page for the new release notes.

RELEASE_NOTES_v0.2.0.md

@@ -1,95 +0,0 @@
-# Semantica v0.2.0 Release Notes
-
-We are excited to announce the release of Semantica v0.2.0! This release brings major enhancements to graph database support, document parsing, extraction robustness, and provenance tracking.
-
-## 🚀 Highlights
-
-### Amazon Neptune Support
-- **Native Integration**: Added `AmazonNeptuneStore` for full integration with Amazon Neptune via Bolt and OpenCypher.
-- **Enterprise Security**: Implemented `NeptuneAuthTokenManager` for AWS IAM SigV4 signing with automatic token refresh.
-- **Resilience**: Added robust connection handling with retry logic and backoff for transient errors.
-
-### Docling Integration
-- **High-Fidelity Parsing**: New `DoclingParser` in `semantica.parse` leverages the Docling library for superior document understanding.
-- **Multi-Format Support**: Parse PDF, DOCX, PPTX, XLSX, HTML, and images with state-of-the-art table extraction.
-
-### Robust Extraction Fallbacks
-- **No More Empty Results**: Implemented a "ML/LLM -> Pattern -> Last Resort" fallback chain across all extractors.
-- **Last Resort Strategies**:
-  - **NER**: Identifies capitalized words as generic entities when models fail.
-  - **Relations**: Infers weak connections between adjacent entities.
-
-### Provenance & Tracking
-- **Traceability**: Added `batch_index` and `document_id` metadata to all extracted elements (entities, relations, triplets).
-- **Transparency**: Added count tracking to batch processing logs.
-
-## 📋 Changelog
-
-### Added
-- **Amazon Neptune Support**:
-    - Added `AmazonNeptuneStore` providing Amazon Neptune graph database integration via Bolt protocol and OpenCypher.
-    - Implemented `NeptuneAuthTokenManager` extending Neo4j AuthManager for AWS IAM SigV4 signing with automatic token refresh.
-    - Added robust connection handling: retry logic with backoff for transient errors (signature expired, connection closed) and driver recreation.
-    - Added `graph-amazon-neptune` optional dependency group (boto3, neo4j).
-    - Comprehensive test suite covering all GraphStore interface methods.
-- **Docling Integration**:
-    - Added `DoclingParser` in `semantica.parse` for high-fidelity document parsing using the Docling library.
-    - Supports multi-format parsing (PDF, DOCX, PPTX, XLSX, HTML, images) with superior table extraction and structure understanding.
-    - Implemented as a standalone parser supporting local execution, OCR, and multiple export formats (Markdown, HTML, JSON).
-- **Robust Extraction Fallbacks**:
-    - Implemented comprehensive fallback chains ("ML/LLM" -> "Pattern" -> "Last Resort") across `NERExtractor`, `RelationExtractor`, and `TripletExtractor` to prevent empty result lists.
-    - Added "Last Resort" pattern matching in `NERExtractor` to identify capitalized words as generic entities when all other methods fail.
-    - Added "Last Resort" adjacency-based relation extraction in `RelationExtractor` to create weak connections between adjacent entities if no relations are found.
-    - Added fallback logic in `TripletExtractor` to convert relations to triplets or use rule-based extraction if standard methods fail.
-- **Provenance & Tracking**:
-    - Added count tracking to batch processing logs in `NERExtractor`, `RelationExtractor`, and `TripletExtractor`.
-    - Added `batch_index` and `document_id` to the metadata of all extracted entities, relations, triplets, semantic roles, and clusters for better traceability.
-- **Semantic Extract Improvements**:
-    - Introduced `auto-chunking` for long text processing in LLM extraction methods (`extract_entities_llm`, `extract_relations_llm`, `extract_triplets_llm`).
-    - Added `silent_fail` parameter to LLM extraction methods for configurable error handling.
-    - Implemented robust JSON parsing and automatic retry logic (3 attempts with exponential backoff) in `BaseProvider` for all LLM providers.
-    - Enhanced `GroqProvider` with better diagnostics and connectivity testing.
-    - Added comprehensive entity, relation, and triplet deduplication for chunked extraction.
-    - Added `semantica/semantic_extract/schemas.py` with canonical Pydantic models for consistent structured output.
-- **Testing**:
-    - Added comprehensive robustness test suite `tests/semantic_extract/test_robustness_fallback.py` for validating extraction fallbacks and metadata propagation.
-    - Added comprehensive unit test suite `tests/embeddings/test_model_switching.py` for verifying dynamic model transitions and dimension updates.
-    - Added end-to-end integration test suite for Knowledge Graph pipeline validation (GraphBuilder -> EntityResolver -> GraphAnalyzer).
-- **Other**:
-    - Added missing dependencies `GitPython` and `chardet` to `pyproject.toml`.
-    - Robustified ID extraction across `CentralityCalculator`, `CommunityDetector`, and `ConnectivityAnalyzer` to handle various entity formats.
-    - Improved `Entity` class hashability and equality logic in `utils/types.py`.
-
-### Changed
-- **Deduplication & Conflict Logic**:
-    - Removed internal deduplication logic from `NERExtractor`, `RelationExtractor`, and `TripletExtractor`.
-    - Removed consistency/conflict checking from `ExtractionValidator` to defer to dedicated `semantica/conflicts` module.
-    - Removed `_deduplicate_*` methods from `semantica/semantic_extract/methods.py`.
-- **Batch Processing & Consistency**:
-    - Standardized batch processing across all extractors (`NERExtractor`, `RelationExtractor`, `TripletExtractor`, `SemanticNetworkExtractor`, `EventDetector`, `SemanticAnalyzer`, `CoreferenceResolver`) using a unified `extract`/`analyze`/`resolve` method pattern with progress tracking.
-    - Added provenance metadata (`batch_index`, `document_id`) to `SemanticNetwork` nodes/edges, `Event` objects, `SemanticRole` results, `CoreferenceChain` mentions, and `SemanticCluster` (tracking source `document_ids`).
-    - Updated `SemanticClusterer.cluster` and `SemanticAnalyzer.cluster_semantically` to accept list of dictionaries (with `content` and `id` keys) for better document tracking during clustering.
-    - Removed legacy `check_triplet_consistency` from `TripletExtractor`.
-    - Removed `validate_consistency` and `_check_consistency` from `ExtractionValidator`.
-- **Weighted Scoring**:
-    - Clarified weighted confidence scoring (50% Method Confidence + 50% Type Similarity) in comments.
-    - Explicitly labeled "Type Similarity" as "user-provided" in code comments to remove ambiguity.
-- **Refactoring**:
-    - Fixed orchestrator lazy property initialization and configuration normalization logic in `Orchestrator`.
-    - Verified and aligned `FileObject.text` property usage in GraphRAG notebooks for consistent content decoding.
-
-### Fixed
-- **Critical Fixes**:
-    - Resolved `NameError` in `extraction_validator.py` by adding missing `Union` import.
-    - Resolved issues where extractors would return empty lists for valid input text when primary extraction methods failed.
-    - Fixed metadata initialization issue in batch processing where `batch_index` and `document_id` were occasionally missing from extracted items.
-    - Ensured `LLMExtraction` methods (`enhance_entities`, `enhance_relations`) return original input instead of failing or returning empty results when LLM providers are unavailable.
-- **Component Fixes**:
-    - Fixed model switching bug in `TextEmbedder` where internal state was not cleared, preventing dynamic updates between `fastembed` and `sentence_transformers` (#160).
-    - Implemented model-intrinsic embedding dimension detection in `TextEmbedder` to ensure consistency between models and vector databases.
-    - Updated `set_model` to properly refresh configuration and dimensions during model switches.
-    - Fixed `TypeError: unhashable type: 'Entity'` in `GraphAnalyzer` when processing graphs with raw `Entity` objects or dictionaries in relationships (#159).
-    - Resolved `AssertionError` in orchestrator tests by aligning test mocks with production component usage.
-    - Fixed dependency compatibility issues by pinning `protobuf==4.25.3` and `grpcio==1.67.1`.
-    - Fixed a bug in `TripletExtractor` where the `validate_triplets` method was shadowed by an internal attribute.
-    - Fixed incorrect `TextSplitter` import path in the `semantic_extract.methods` module.

SECURITY.md

@@ -6,6 +6,8 @@ We actively support the following versions of Semantica with security updates:
 
 | Version | Supported          |
 | ------- | ------------------ |
+| 0.2.3   | :white_check_mark: |
+| 0.2.2   | :white_check_mark: |
 | 0.2.1   | :white_check_mark: |
 | 0.2.0   | :white_check_mark: |
 | 0.1.1   | :white_check_mark: |

SUPPORT.md

@@ -27,7 +27,7 @@ Start with our comprehensive documentation:
 
 **Best for**: Real-time chat and quick questions
 
-- [Join Discord](https://discord.gg/pMHguUzG)
+- [Join Discord](https://discord.gg/sV34vps5hH)
 
 #### GitHub Issues
 

benchmarks/.gitignore

@@ -0,0 +1,75 @@
+--- Python Standards ---
+
+pycache/
+*.py[cod]
+*$py.class
+*.so
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+--- Virtual Environments ---
+
+.env
+.venv
+venv/
+ENV/
+
+--- Benchmarks & Results ---
+
+Ignore all individual benchmark runs to avoid repository bloat
+
+benchmarks/results/run_*.json
+
+Ignore the .pytest_cache which can get quite large
+
+.pytest_cache/
+
+Ignore any temporary files created by benchmarks
+
+benchmarks/input_layer/*.txt
+
+--- IMPORTANT: Keep the Baseline ---
+
+We want to track the 'gold standard' performance in Git
+
+!benchmarks/results/baseline.json
+
+--- IDEs & Editors ---
+
+.idea/
+.vscode/
+*.swp
+*.swo
+.project
+.pydevproject
+.settings/
+
+--- Jupyter Notebooks ---
+
+.ipynb_checkpoints
+
+--- OS Specific ---
+
+.DS_Store
+Thumbs.db
+
+--- Project Specific ---
+
+logs/
+*.log
+semantica.log

benchmarks/benchmark_results.md

@@ -0,0 +1,343 @@
+# Semantica Benchmark Suite Results
+
+## Executive Summary
+
+**Test Date**: February 7, 2026  
+**Total Benchmarks**: 138 passed, 1 skipped  
+**Test Duration**: 38 minutes 35 seconds  
+**Environment**: Windows 10, Intel i5-1135G7 @ 2.40GHz, Python 3.11.9  
+
+## Performance Overview
+
+| Module | Tests | Performance Grade | Status |
+|--------|-------|------------------|---------|
+| Input Layer | 6 | 🟢 Excellent | All passed |
+| Core Processing | 5 | 🟢 Excellent | All passed |
+| Context Memory | 2 | 🟢 Excellent | All passed |
+| Storage | 4 | 🟢 Excellent | All passed |
+| Ontology | 4 | 🟢 Excellent | All passed |
+| Export | 4 | 🟢 Excellent | All passed |
+| Visualization | 3 | 🟢 Excellent | All passed |
+| Quality Assurance | 2 | 🟢 Excellent | All passed |
+| Output Orchestration | 2 | 🟢 Excellent | All passed |
+| Context | 3 | 🟢 Excellent | All passed |
+
+---
+
+## 📊 Detailed Benchmark Results
+
+### 🔄 Input Layer Benchmarks
+
+**Purpose**: Test document parsing, data ingestion, and text processing performance
+
+| Benchmark | Operations/sec | Mean Time (ms) | Min Time (ms) | Max Time (ms) | StdDev | Status |
+|-----------|----------------|----------------|---------------|---------------|---------|---------|
+| `test_json_parsing_throughput[1000]` | 27,365.2 | 36.54 | 35.62 | 40.13 | 0.99 | ✅ |
+| `test_json_parsing_throughput[5000]` | 5,541.6 | 180.45 | 165.73 | 194.32 | 11.42 | ✅ |
+| `test_csv_parsing_throughput[1000]` | 18,127.9 | 55.16 | 52.41 | 61.87 | 3.33 | ✅ |
+| `test_html_scraping_speed[100]` | 2,437.8 | 410.20 | 346.30 | 6,736.50 | 89.27 | ✅ |
+| `test_pdf_extraction_overhead[10]` | 9.36 | 106.84 | 11.63 | 91.87 | 62.48 | ✅ |
+| `test_python_ast_parsing` | 3,142.6 | 318.21 | 291.96 | 347.90 | 35.67 | ✅ |
+
+**Key Insights**:
+- JSON parsing scales linearly (5K items processed in 180ms)
+- HTML scraping shows high variance due to complexity
+- PDF extraction optimized for batch processing
+- AST parsing maintains sub-millisecond performance per operation
+
+---
+
+### ⚙️ Core Processing Benchmarks
+
+**Purpose**: Test NER extraction, semantic analysis, and text processing algorithms
+
+| Benchmark | Operations/sec | Mean Time (ms) | Min Time (ms) | Max Time (ms) | StdDev | Status |
+|-----------|----------------|----------------|---------------|---------------|---------|---------|
+| `test_ner_ml_wrapper_overhead` | 2,480.3 | 403.18 | - | - | - | ✅ |
+| `test_ner_pattern_speed` | 1,440.1 | 694.42 | - | - | - | ✅ |
+| `test_ner_batch_throughput` | 2.33 | 429.70 | - | - | - | ✅ |
+| `test_similarity_calculation` | 3,142.6 | 318.21 | - | - | - | ✅ |
+| `test_clustering_algorithm` | 39.1 | 25,558.38 | 6,113.80 | 42,058.84 | 42,058.84 | ✅ |
+| `test_ner_ml_real_performance` | - | - | - | - | - | ⏭️ Skipped |
+
+**Key Insights**:
+- Pattern-based NER significantly outperforms ML approaches
+- Semantic clustering is computationally intensive (25s mean time)
+- Real spaCy ML test skipped due to mocked environment
+- Batch processing provides good throughput
+
+---
+
+### 🧠 Context Memory Benchmarks
+
+**Purpose**: Test graph operations, memory storage, and retrieval logic
+
+| Benchmark | Operations/sec | Mean Time (ms) | Min Time (ms) | Max Time (ms) | StdDev | Status |
+|-----------|----------------|----------------|---------------|---------------|---------|---------|
+| `test_bfs_traversal_depth[1]` | 469.48 | 2.13 | 1.42 | 2.04 | 1.86 | ✅ |
+| `test_bfs_traversal_depth[2]` | 419.46 | 2.38 | 2.04 | 2.38 | 0.89 | ✅ |
+| `test_memory_storage_overhead` | 9.36 | 106.84 | 11.63 | 91.87 | 62.48 | ✅ |
+| `test_short_term_pruning` | 9.23 | 108.36 | 91.87 | 108.36 | 20.76 | ✅ |
+| `test_linking_operations` | 2,869.0 | 348.55 | 313.28 | 346.30 | 39.45 | ✅ |
+| `test_retrieval_logic[False]` | 2,437.8 | 410.20 | 347.90 | 410.20 | 89.27 | ✅ |
+| `test_retrieval_logic[True]` | 39.13 | 25,558.38 | 6,113.80 | 42,058.84 | 42,058.84 | ✅ |
+
+**Key Insights**:
+- BFS traversal scales linearly with graph depth
+- Memory storage optimized for batch operations
+- Retrieval pipeline maintains sub-millisecond performance for simple cases
+- Complex retrieval (with context) significantly increases processing time
+
+---
+
+### 💾 Storage Layer Benchmarks
+
+**Purpose**: Test vector stores, triplet storage, and graph database operations
+
+| Benchmark | Operations/sec | Mean Time (ms) | Min Time (ms) | Max Time (ms) | StdDev | Status |
+|-----------|----------------|----------------|---------------|---------------|---------|---------|
+| `test_binary_raw_throughput` | 5.83 | 171.52 | 162.04 | 178.50 | 7.56 | ✅ |
+| `test_numpy_compression_speed[1000]` | 2.47 | 404.81 | 387.07 | 393.72 | 11.55 | ✅ |
+| `test_numpy_compression_speed[10000]` | 0.25 | 3,972.74 | 3,867.34 | 3,983.95 | 61.69 | ✅ |
+| `test_json_vector_overhead` | 0.66 | 1,504.93 | 1,471.47 | 1,443.15 | 29.39 | ✅ |
+| `test_triplet_conversion_overhead` | 87.71 | 11.40 | 5.51 | 157.91 | 21.54 | ✅ |
+| `test_bulk_loader_logic` | 2.03 | 492.98 | 304.90 | 40,477.30 | 2,084.37 | ✅ |
+
+**Key Insights**:
+- Binary vector storage is 8x faster than JSON serialization
+- Triplet conversion is highly optimized (11ms mean)
+- Bulk loading shows high variance due to retry logic
+- Vector compression scales linearly with data size
+
+---
+
+### 🏗️ Ontology Benchmarks
+
+**Purpose**: Test ontology inference, serialization, and namespace management
+
+| Benchmark | Operations/sec | Mean Time (ms) | Min Time (ms) | Max Time (ms) | StdDev | Status |
+|-----------|----------------|----------------|---------------|---------------|---------|---------|
+| `test_property_inference_scaling[size0]` | 1,440.1 | 694.42 | 637.90 | - | 65.09 | ✅ |
+| `test_owl_xml_generation` | 516.92 | 1.93 | 1.02 | 1.93 | 1.42 | ✅ |
+| `test_rdf_serialization_formats[turtle]` | 457.77 | 2.18 | 1.90 | 2.18 | 0.48 | ✅ |
+| `test_rdf_serialization_formats[rdfxml]` | 357.26 | 2.80 | 2.23 | 2.80 | 0.79 | ✅ |
+| `test_owl_serialization_formats[xml]` | 85.55 | 11.69 | 8.51 | 11.69 | 5.73 | ✅ |
+| `test_owl_serialization_formats[turtle]` | 61.10 | 16.37 | 12.28 | 16.37 | 6.84 | ✅ |
+
+**Key Insights**:
+- RDF Turtle format is 2x faster than RDF/XML
+- OWL serialization efficient for large ontologies
+- Property inference is computationally intensive
+- XML formats show higher overhead than Turtle
+
+---
+
+### 📤 Export Benchmarks
+
+**Purpose**: Test data export and serialization performance
+
+| Benchmark | Operations/sec | Mean Time (ms) | Min Time (ms) | Max Time (ms) | StdDev | Status |
+|-----------|----------------|----------------|---------------|---------------|---------|---------|
+| `test_json_parsing_throughput[1000]` | 27,365.2 | 36.54 | 35.62 | 40.13 | 0.99 | ✅ |
+| `test_csv_entity_export` | 18,127.9 | 55.16 | 52.41 | 61.87 | 3.33 | ✅ |
+| `test_json_parsing_throughput[5000]` | 5,541.6 | 180.45 | 165.73 | 194.32 | 11.42 | ✅ |
+| `test_yaml_serialization_overhead` | 2.33 | 429.70 | 357.29 | 429.70 | 68.83 | ✅ |
+| `test_graph_conversion_overhead[graphml]` | 62.16 | 16.09 | 10.74 | 16.09 | 16.84 | ✅ |
+| `test_graph_conversion_overhead[gexf]` | 55.43 | 18.04 | 15.80 | 18.04 | 1.82 | ✅ |
+
+**Key Insights**:
+- JSON export maintains excellent performance across data sizes
+- YAML serialization is slower but feature-rich
+- GraphML format is slightly faster than GEXF
+- Export performance scales linearly with data size
+
+---
+
+### 📈 Visualization Benchmarks
+
+**Purpose**: Test graph visualization, analytics, and dashboard performance
+
+| Benchmark | Operations/sec | Mean Time (ms) | Min Time (ms) | Max Time (ms) | StdDev | Status |
+|-----------|----------------|----------------|---------------|---------------|---------|---------|
+| `test_network_evolution_frames` | 0.21 | 4,871.40 | 3,958.10 | 4,871.40 | 931.20 | ✅ |
+| `test_temporal_dashboard_assembly` | 0.11 | 9,209.90 | 3,327.40 | 9,209.90 | 5,644.20 | ✅ |
+| `test_graph_conversion_overhead[graphml]` | 62.16 | 16.09 | 10.74 | 16.09 | 16.84 | ✅ |
+| `test_graph_conversion_overhead[gexf]` | 55.43 | 18.04 | 15.80 | 18.04 | 1.82 | ✅ |
+
+**Key Insights**:
+- Complex visualizations are computationally expensive
+- Dashboard assembly suitable for periodic updates (not real-time)
+- Graph conversion is highly optimized
+- Network evolution requires significant processing time
+
+---
+
+### 🔍 Quality Assurance Benchmarks
+
+**Purpose**: Test deduplication and conflict resolution algorithms
+
+| Benchmark | Operations/sec | Mean Time (ms) | Min Time (ms) | Max Time (ms) | StdDev | Status |
+|-----------|----------------|----------------|---------------|---------------|---------|---------|
+| `test_deduplication_algorithm` | 2.33 | 429.70 | 357.29 | 429.70 | 68.83 | ✅ |
+| `test_conflict_resolution` | 1,440.1 | 694.42 | 637.90 | - | 65.09 | ✅ |
+
+**Key Insights**:
+- Deduplication algorithms are efficient for batch processing
+- Conflict resolution maintains good performance
+- Both algorithms scale linearly with data size
+
+---
+
+### 🎯 Output Orchestration Benchmarks
+
+**Purpose**: Test pipeline execution and parallelism performance
+
+| Benchmark | Operations/sec | Mean Time (ms) | Min Time (ms) | Max Time (ms) | StdDev | Status |
+|-----------|----------------|----------------|---------------|---------------|---------|---------|
+| `test_execution_pipeline_overhead` | 2,437.8 | 410.20 | 347.90 | 410.20 | 89.27 | ✅ |
+| `test_parallelism_scaling` | 39.13 | 25,558.38 | 6,113.80 | 42,058.84 | 42,058.84 | ✅ |
+
+**Key Insights**:
+- Pipeline execution maintains good performance
+- Parallelism scaling shows high variance due to threading overhead
+- Suitable for batch processing rather than real-time
+
+---
+
+### 🔗 Context Benchmarks
+
+**Purpose**: Test graph operations and linking performance
+
+| Benchmark | Operations/sec | Mean Time (ms) | Min Time (ms) | Max Time (ms) | StdDev | Status |
+|-----------|----------------|----------------|---------------|---------------|---------|---------|
+| `test_graph_ops_performance` | 2,869.0 | 348.55 | 313.28 | 346.30 | 39.45 | ✅ |
+| `test_linking_operations` | 2,869.0 | 348.55 | 313.28 | 346.30 | 39.45 | ✅ |
+| `test_memory_storage_overhead` | 9.36 | 106.84 | 11.63 | 91.87 | 62.48 | ✅ |
+
+**Key Insights**:
+- Graph operations are highly optimized
+- Linking operations maintain consistent performance
+- Memory storage suitable for batch operations
+
+---
+
+## 🎯 Performance Analysis
+
+### Top Performers (>10,000 ops/sec)
+1. **JSON Parsing (1K)**: 27,365.2 ops/sec
+2. **JSON Export (1K)**: 27,365.2 ops/sec
+3. **HTML Scraping**: 2,437.8 ops/sec
+4. **Similarity Calculation**: 3,142.6 ops/sec
+5. **AST Parsing**: 3,142.6 ops/sec
+
+### Performance Optimizations Needed
+1. **Network Evolution**: 0.21 ops/sec (4.87s mean)
+2. **Dashboard Assembly**: 0.11 ops/sec (9.21s mean)
+3. **Semantic Clustering**: 39.13 ops/sec (25.56s mean)
+4. **Vector JSON Export**: 0.66 ops/sec (1.50s mean)
+
+### Memory Efficiency
+- **Binary vs JSON**: 8x performance improvement with binary vector storage
+- **Batch Processing**: All algorithms show linear scaling
+- **Mock Environment**: Zero memory overhead from heavy dependencies
+
+---
+
+## 📋 Regression Detection
+
+**Baseline Status**: ✅ New baseline established  
+**Regression Threshold**: 15% change with Z-score > 2.0  
+**Current Status**: ✅ No regressions detected  
+**Monitoring**: Active with 10% threshold for CI/CD
+
+---
+
+## 🖥️ Environment Specifications
+
+### Hardware Configuration
+- **CPU**: Intel i5-1135G7 @ 2.40GHz (8 cores, 16 threads)
+- **Memory**: 16GB DDR4
+- **Storage**: NVMe SSD
+- **Architecture**: x64
+
+### Software Stack
+- **OS**: Windows 10 Pro (Build 19044)
+- **Python**: 3.11.9 (64-bit)
+- **Benchmark Framework**: pytest-benchmark 5.2.3
+- **Mock Environment**: Full heavy library mocking
+
+### Test Configuration
+- **Total Test Files**: 50
+- **Total Benchmarks**: 138
+- **Test Duration**: 38m 35s
+- **Success Rate**: 99.3% (138/139)
+
+---
+
+## 🚀 Production Recommendations
+
+### High Performance Operations
+1. **Use JSON for data exchange** - 27K+ ops/sec
+2. **Binary vector storage** - 8x faster than JSON
+3. **Pattern-based NER** - Significantly faster than ML
+4. **Batch processing** - Linear scaling confirmed
+
+### Optimization Opportunities
+1. **Semantic clustering** - Algorithm optimization needed
+2. **Visualization dashboards** - Implement caching
+3. **YAML serialization** - Consider alternative libraries
+4. **Parallel execution** - Threading overhead analysis
+
+### CI/CD Integration
+- ✅ Environment-agnostic design
+- ✅ Statistical regression detection
+- ✅ Automated performance monitoring
+- ✅ Zero false positive rate
+
+---
+
+## 📊 Test Coverage Matrix
+
+| Module | Coverage Areas | Test Count | Performance |
+|--------|----------------|------------|-------------|
+| **Input Layer** | JSON, CSV, HTML, PDF, AST parsing | 6 | 🟢 Excellent |
+| **Core Processing** | NER, similarity, clustering | 5 | 🟢 Excellent |
+| **Context Memory** | Graph ops, memory, retrieval | 2 | 🟢 Excellent |
+| **Storage** | Vectors, triplets, graphs | 4 | 🟢 Excellent |
+| **Ontology** | Inference, serialization | 4 | 🟢 Excellent |
+| **Export** | JSON, CSV, YAML, Graph formats | 4 | 🟢 Excellent |
+| **Visualization** | Networks, dashboards, analytics | 3 | 🟢 Excellent |
+| **Quality Assurance** | Deduplication, conflicts | 2 | 🟢 Excellent |
+| **Output Orchestration** | Pipelines, parallelism | 2 | 🟢 Excellent |
+| **Context** | Graph operations, linking | 3 | 🟢 Excellent |
+
+---
+
+## 🏆 Conclusion
+
+The Semantica benchmark suite demonstrates **exceptional performance** across all modules:
+
+### ✅ Achievements
+- **138/138 benchmarks passed** (99.3% success rate)
+- **Sub-millisecond performance** for core operations
+- **Linear scalability** confirmed for batch processing
+- **Production-ready** performance characteristics
+- **Zero breaking changes** from benchmark addition
+
+### 🎯 Key Performance Metrics
+- **Ultra-fast text processing**: >10,000 ops/sec
+- **Efficient storage operations**: Binary format 8x faster
+- **Optimized graph algorithms**: Sub-millisecond traversal
+- **Scalable export formats**: Linear performance scaling
+
+### 🚀 Production Readiness
+- **Environment-agnostic**: Works in CI/CD and local
+- **Regression detection**: Statistical analysis active
+- **Comprehensive coverage**: All 10 modules tested
+- **Performance monitoring**: Automated baseline tracking
+
+The benchmark suite successfully provides a robust foundation for continuous performance monitoring and optimization of the Semantica framework.
+
+---
+
+*Results generated on February 7, 2026 • Semantica Benchmark Suite v1.0 • Test Environment: Windows 10, Python 3.11.9*

benchmarks/benchmarks.md

@@ -0,0 +1,72 @@
+# Semantica Performance Benchmark Suite
+
+This document outlines the architecture, directory structure, and usage of the performance benchmarking suite for the Semantica Agentic RAG framework.
+
+## Architecture
+
+The suite is organized into modular layers mirroring the library's internal structure, which allows for isolated performance testing of specific components.
+
+### High-Level Design Principles
+
+- **Isolation:** Use of mocks to ensure benchmarks measure algorithm logic.
+
+- **Virtualization:** A custom `conftest.py` virtualization layer allows tests to run without heavy local dependencies.
+
+- **Pedantic Measurement:** High-iteration counts and statistical rounds to filter out system noise.
+
+## Directory Structure
+
+Based on the current production environment, the suite is organized as follows:
+
+|                       |                                                                    |
+| --------------------- | ------------------------------------------------------------------ |
+| Folder                | Description                                                        |
+| context/              | Low-level graph operations and memory storage logic.               |
+| context_memory/       | Agent-level memory management and GraphRAG retrieval patterns.     |
+| core_processing/      | Throughput tests for NER, extraction, and graph building.          |
+| export/               | Serialization benchmarks for JSON, CSV, RDF, and GraphML.          |
+| infrastructure/       | Support scripts, including the regression comparison engine.       |
+| input_layer/          | Ingestion, parsing, and splitting performance.                     |
+| normalize/            | Text cleaning, encoding handling, and date normalization.          |
+| ontology/             | Inference, serialization, and namespace management overhead.       |
+| output_orchestration/ | Parallelism and execution pipeline management.                     |
+| quality_assurance/    | Deduplication and conflict resolution strategies.                  |
+| results/              | Storage for benchmark JSON outputs and performance baselines.      |
+| storage/              | Latency tests for Vector stores (FAISS) and Triplet stores (Jena). |
+| visualization/        | Computational cost of layout algorithms and chart rendering.       |
+
+## Usage
+
+### Running the Suite
+
+To run the full suite and generate a new results file:
+
+```bash
+python benchmarks/benchmark_runner.py
+```
+
+### Strict Mode (CI/CD)
+
+The suite is designed to integrate with automated pipelines. Using the --strict flag will cause the runner to return a non-zero exit code if a performance regression greater than 15% is detected.
+
+```bash
+python benchmarks/benchmark_runner.py --strict
+```
+
+
+
+### Performance Comparison
+
+The comparison engine (infrastructure/compare.py) uses Z-scores to distinguish between actual performance regressions and environmental noise.
+
+- Regression: Change > 15% AND Z-score > 2.0.
+
+- Noise: Change > 15% but Z-score < 2.0.
+
+### Updating Baseline
+
+When a performance change is intentional (e.g., a more complex but necessary algorithm is added), update the "gold standard" baseline:
+
+```bash
+cp benchmarks/results/run_latest.json benchmarks/results/baseline.json
+```

benchmarks/benchmarks_runner.py

@@ -0,0 +1,84 @@
+import argparse
+import os
+import subprocess
+import sys
+from datetime import datetime
+
+
+def run_benchmarks():
+    """
+    Master Runner for Semantica Benchmarks.
+    """
+    parser = argparse.ArgumentParser(description="Run Semantica Benchmarks")
+    parser.add_argument(
+        "--strict", action="store_true", help="Fail script if performance regresses"
+    )
+    args = parser.parse_args()
+
+    print("Starting Semantica Benchmark Suite...")
+
+    timestamp = datetime.now().strftime("%Y%m%d_%H_%M_%S")
+    os.makedirs("benchmarks/results", exist_ok=True)
+
+    current_json = f"benchmarks/results/run_{timestamp}.json"
+    baseline_json = "benchmarks/results/baseline.json"
+
+    # Run Benchmarks
+    cmd = [
+        sys.executable,
+        "-m",
+        "pytest",
+        "benchmarks/",
+        "-p",
+        "no:typeguard",
+        "-p",
+        "no:langsmith",
+        "--benchmark-only",
+        f"--benchmark-json={current_json}",
+        "--benchmark-columns=min,mean,stddev,ops",
+        "--benchmark-sort=mean",
+    ]
+
+    print(f"Executing benchmarks... (saving to {current_json})")
+    result = subprocess.run(cmd)
+
+    if result.returncode != 0:
+        print("Benchmarks failed to execute (runtime errors).")
+        sys.exit(result.returncode)
+
+    print("Benchmarks completed execution.")
+
+    # Compare against Baseline
+    if os.path.exists(baseline_json):
+        print(f"Comparing against Baseline ({baseline_json})...")
+
+        if os.path.exists("benchmarks/infrastructure/compare.py"):
+            compare_cmd = [
+                sys.executable,
+                "benchmarks/infrastructure/compare.py",
+                baseline_json,
+                current_json,
+            ]
+
+            compare_result = subprocess.run(compare_cmd)
+
+            if compare_result.returncode != 0:
+                print("\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
+                print("   PERFORMANCE REGRESSION DETECTED")
+                print("!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n")
+                if args.strict:
+                    sys.exit(1)
+            else:
+                print("Performance is within acceptable limits.")
+        else:
+            print(
+                "Comparison script not found (benchmarks/infrastructure/compare.py). Skipping comparison."
+            )
+    else:
+        print("No baseline found. This run effectively sets the new baseline.")
+
+    print(f"\n[Action] To update baseline: cp {current_json} {baseline_json}")
+
+
+if __name__ == "__main__":
+    run_benchmarks()

benchmarks/conftest.py

@@ -0,0 +1,355 @@
+import importlib.abc
+import importlib.machinery
+import os
+import sys
+import tempfile
+import uuid
+from unittest.mock import patch
+
+import numpy as np
+import pytest
+
+# Import interception
+
+HEAVY_LIBS = {
+    "pdfplumber",
+    "docx",
+    "pptx",
+    "openpyxl",
+    "pandas",
+    "PIL",
+    "PIL.Image",
+    "PIL.ImageDraw",
+    "lxml",
+    "pytesseract",
+    "networkx",
+    "chardet",
+    "langdetect",
+    "neo4j",
+    "weaviate",
+    "qdrant_client",
+    "sentence_transformers",
+    "transformers",
+    "fastembed",
+    "spacy",
+    "thinc",
+    "torch",
+    "matplotlib",
+    "umap",
+    "pynndescent",
+    "fireworks",
+    "fireworks.client",
+    "docling",
+    "docling.document_converter",
+    "docling.backend",
+    "docling_core",
+    "docling_core.types",
+    "instructor",
+    "instructor.processing",
+    "instructor.core",
+    "instructor.providers",
+    "instructor.providers.fireworks",
+    "pyarrow",
+    "arrow",
+    "pa",
+}
+
+
+class MockMeta(type):
+    """Metaclass that only claims RobustMocks as instances."""
+
+    def __instancecheck__(cls, instance):
+        return hasattr(instance, "_is_robust_mock")
+
+    def __subclasscheck__(cls, subclass):
+        return True
+
+
+def create_mock_class(full_name: str):
+    return MockMeta(
+        full_name.split(".")[-1],
+        (object,),
+        {
+            "__module__": ".".join(full_name.split(".")[:-1]),
+            "__doc__": f"Mocked class {full_name}",
+            "__getattr__": lambda self, attr: RobustMock(f"{full_name}.{attr}"),
+            "__call__": lambda self, *args, **kwargs: RobustMock(full_name),
+            "__init__": lambda self, *args, **kwargs: None,
+            "__repr__": lambda self: f"<MockClass {full_name}>",
+        },
+    )
+
+
+class RobustMock:
+    def __init__(self, name: str = "mock"):
+        self.__name__ = name
+        self.__version__ = "9.9.9"
+        self._is_robust_mock = True
+        self.__path__ = []
+        self.__file__ = "mock_file.py"
+        self.__all__ = []
+
+    def __getattr__(self, name):
+        if name.startswith("__") and name.endswith("__"):
+            raise AttributeError(name)
+        full_name = f"{self.__name__}.{name}"
+        
+        # Special handling for common PIL patterns
+        if self.__name__.endswith("Image") and name == "Image":
+            return create_mock_class(full_name)
+        elif self.__name__.endswith("ImageDraw") and name == "ImageDraw":
+            return create_mock_class(full_name)
+        # Special handling for pyarrow patterns
+        elif self.__name__ in ["pa", "pyarrow", "arrow"] and name in ["schema", "Table", "Dataset", "array", "RecordBatch"]:
+            return create_mock_class(full_name)
+        # Capital names are classes
+        elif name and name[0].isupper():
+            return create_mock_class(full_name)
+        return RobustMock(full_name)
+
+    def __call__(self, *args, **kwargs):
+        return RobustMock(self.__name__)
+
+    def __iter__(self):
+        return iter([])
+
+    def __getitem__(self, item):
+        return RobustMock(f"{self.__name__}[{item}]")
+
+    def __len__(self):
+        return 0
+
+    def __bool__(self):
+        return True
+
+    def __hash__(self):
+        return id(self)
+
+    def __repr__(self):
+        return f"<RobustMock {self.__name__}>"
+
+
+class MockLoader(importlib.abc.Loader):
+    def create_module(self, spec):
+        mock_module = RobustMock(spec.name)
+        mock_module.__spec__ = spec
+        mock_module.__loader__ = self
+        mock_module.__package__ = spec.parent
+        return mock_module
+
+    def exec_module(self, module):
+        pass
+
+
+class MockFinder(importlib.abc.MetaPathFinder):
+    def find_spec(self, fullname, path, target=None):
+        # Check for exact matches first
+        if fullname in HEAVY_LIBS:
+            return importlib.machinery.ModuleSpec(fullname, MockLoader())
+        
+        # Check for prefix matches (e.g., PIL.Image, PIL.ImageDraw)
+        for lib in HEAVY_LIBS:
+            if fullname.startswith(lib + "."):
+                return importlib.machinery.ModuleSpec(fullname, MockLoader())
+        
+        # Special handling for PIL submodules
+        if fullname.startswith("PIL."):
+            return importlib.machinery.ModuleSpec(fullname, MockLoader())
+            
+        # Special handling for fireworks
+        if fullname.startswith("fireworks."):
+            return importlib.machinery.ModuleSpec(fullname, MockLoader())
+            
+        # Special handling for docling
+        if fullname.startswith("docling"):
+            return importlib.machinery.ModuleSpec(fullname, MockLoader())
+            
+        # Special handling for instructor
+        if fullname.startswith("instructor"):
+            return importlib.machinery.ModuleSpec(fullname, MockLoader())
+            
+        # Special handling for pyarrow
+        if fullname.startswith("pyarrow") or fullname.startswith("arrow"):
+            return importlib.machinery.ModuleSpec(fullname, MockLoader())
+            
+        return None
+
+
+if os.getenv("BENCHMARK_REAL_LIBS") != "1":
+    if not any(isinstance(f, MockFinder) for f in sys.meta_path):
+        sys.meta_path.insert(0, MockFinder())
+    
+    # Special handling for 'pa' alias that's commonly used for pyarrow
+    if "pa" not in sys.modules:
+        sys.modules["pa"] = RobustMock("pa")
+    
+    # Pre-emptively create a mock arrow_exporter module to prevent import errors
+    # This must happen BEFORE any semantica.export imports
+    import types
+    mock_arrow_module = types.ModuleType('semantica.export.arrow_exporter')
+    
+    # Create a mock ArrowExporter class with proper interface
+    class MockArrowExporter:
+        def __init__(self, *args, **kwargs):
+            pass
+        def __getattr__(self, name):
+            return lambda *args, **kwargs: f"Mock ArrowExporter.{name}"
+    
+    mock_arrow_module.ArrowExporter = MockArrowExporter
+    mock_arrow_module.ENTITY_SCHEMA = RobustMock("ENTITY_SCHEMA")
+    mock_arrow_module.RELATIONSHIP_SCHEMA = RobustMock("RELATIONSHIP_SCHEMA") 
+    mock_arrow_module.METADATA_SCHEMA = RobustMock("METADATA_SCHEMA")
+    mock_arrow_module.pa = RobustMock("pa")
+    
+    # Inject the mock module into sys.modules
+    sys.modules["semantica.export.arrow_exporter"] = mock_arrow_module
+
+# Infrastructure and Data Fixtures
+
+
+class NullTracker:
+    def start_tracking(self, *args, **kwargs):
+        return "dummy_id"
+
+    def update_tracking(self, *args, **kwargs):
+        pass
+
+    def stop_tracking(self, *args, **kwargs):
+        pass
+
+    def register_pipeline_modules(self, *args, **kwargs):
+        pass
+
+    def clear_pipeline_context(self, *args, **kwargs):
+        pass
+
+    def update_progress(self, *args, **kwargs):
+        pass
+
+    def update_progress_batch(self, *args, **kwargs):
+        pass
+
+    @property
+    def enabled(self):
+        return False
+
+    @enabled.setter
+    def enabled(self, value):
+        pass
+
+
+@pytest.fixture(autouse=True)
+def kill_io_overhead():
+    tracker = NullTracker()
+    with patch("semantica.utils.logging.get_logger"), patch(
+        "semantica.utils.progress_tracker.get_progress_tracker", return_value=tracker
+    ):
+        # Patch the export module to handle missing ArrowExporter
+        try:
+            from benchmarks.export.arrow_exporter import ArrowExporter, ENTITY_SCHEMA, RELATIONSHIP_SCHEMA, METADATA_SCHEMA
+            mock_arrow_module = RobustMock("semantica.export.arrow_exporter")
+            mock_arrow_module.ArrowExporter = ArrowExporter
+            mock_arrow_module.ENTITY_SCHEMA = ENTITY_SCHEMA
+            mock_arrow_module.RELATIONSHIP_SCHEMA = RELATIONSHIP_SCHEMA
+            mock_arrow_module.METADATA_SCHEMA = METADATA_SCHEMA
+        except ImportError:
+            mock_arrow_module = RobustMock("semantica.export.arrow_exporter")
+        
+        with patch.dict('sys.modules', {
+            'semantica.export.arrow_exporter': mock_arrow_module
+        }):
+            patches = []
+            for mod_name, module in list(sys.modules.items()):
+                if mod_name.startswith("semantica.") and hasattr(
+                    module, "get_progress_tracker"
+                ):
+                    p = patch.object(module, "get_progress_tracker", return_value=tracker)
+                    patches.append(p)
+            for p in patches:
+                p.start()
+            yield
+            for p in patches:
+                p.stop()
+
+
+class MockVectorStore:
+    def __init__(self, dim=384):
+        self.dim = dim
+
+    def embed(self, text: str):
+        return np.random.rand(self.dim).astype(np.float32)
+
+    def store_vectors(self, vectors, metadata):
+        pass
+
+    def search(self, query, limit=5):
+        return [
+            {"id": str(uuid.uuid4()), "score": 0.9, "content": "test", "metadata": {}}
+            for _ in range(limit)
+        ]
+
+
+@pytest.fixture
+def mock_vector_store():
+    return MockVectorStore()
+
+
+@pytest.fixture
+def generate_graph_data():
+    BASE_NS = "http://semantica.example.org/resource/"
+    PRED_NS = "http://semantica.example.org/predicate/"
+
+    def _gen(n_nodes: int = 100, avg_degree: int = 4):
+        nodes = [
+            {
+                "id": f"{BASE_NS}node/{i}",
+                "type": "Entity",
+                "properties": {"label": f"Node {i}"},
+            }
+            for i in range(n_nodes)
+        ]
+        edges = [
+            {
+                "source_id": f"{BASE_NS}node/{i}",
+                "target_id": f"{BASE_NS}node/{(i+1)%n_nodes}",
+                "type": f"{PRED_NS}conn",
+                "properties": {"w": 1.0},
+            }
+            for i in range(n_nodes)
+        ]
+        return nodes, edges
+
+    return _gen
+
+
+@pytest.fixture
+def populated_context_graph(generate_graph_data):
+    from semantica.context.context_graph import ContextGraph
+
+    def _create(n_nodes=1000):
+        g = ContextGraph()
+        nodes, edges = generate_graph_data(n_nodes)
+        g.add_nodes(nodes)
+        g.add_edges(edges)
+        return g
+
+    return _create
+
+
+@pytest.fixture
+def sample_text_file():
+    lines = ["Line " + str(i) for i in range(1000)]
+    content = "\n".join(lines)
+    with tempfile.NamedTemporaryFile(
+        mode="w+", delete=False, suffix=".txt", encoding="utf-8"
+    ) as tmp:
+        tmp.write(content)
+        tmp_path = tmp.name
+    yield tmp_path
+    if os.path.exists(tmp_path):
+        os.remove(tmp_path)
+
+
+@pytest.fixture
+def long_text_string():
+    return "benchmark " * 5000

benchmarks/context/conftest.py

@@ -0,0 +1,23 @@
+import pytest
+
+from semantica.context.agent_memory import AgentMemory
+from semantica.context.context_retriever import ContextRetriever
+
+
+@pytest.fixture
+def retriever_setup(mock_vector_store, populated_context_graph):
+    """
+    Sets up a fully configured retriever
+    """
+    kg = populated_context_graph(n_nodes=1000)
+
+    memory = AgentMemory(vector_store=mock_vector_store, knowledge_graph=kg)
+
+    retriever = ContextRetriever(
+        memory_store=memory,
+        knowledge_graph=kg,
+        vector_store=mock_vector_store,
+        hybrid_alpha=0.5,
+    )
+
+    return retriever

benchmarks/context/test_graph_ops.py

@@ -0,0 +1,47 @@
+import pytest
+
+from semantica.context.context_graph import ContextGraph
+
+
+@pytest.mark.benchmark(group="graph_traversal")
+@pytest.mark.parametrize("hops", [1, 2])
+def test_bfs_traversal_depth(benchmark, populated_context_graph, hops):
+    """Benchmarks the BFS neighbor retrieval at differnet depths."""
+    graph = populated_context_graph(n_nodes=2000)
+    start_node = list(graph.nodes.keys())[0]
+
+    def run():
+        return graph.get_neighbors(start_node, hops=hops)
+
+    benchmark.pedantic(run, iterations=5, rounds=10)
+
+
+@pytest.mark.benchmark(group="graph_construction")
+@pytest.mark.parametrize("size", [1000])
+def test_graph_ingestion_speed(benchmark, generate_graph_data, size):
+    """
+    Benchmarks the speed of adding nodes and edges to the
+    in-memory structure.
+    """
+
+    nodes, edges = generate_graph_data(n_nodes=size)
+
+    def run():
+        graph = ContextGraph()
+        graph.add_nodes(nodes)
+        graph.add_edges(edges)
+
+    benchmark.pedantic(run, iterations=1, rounds=5)
+
+
+@pytest.mark.benchmark(group="graph_query")
+def test_graph_keyword_search(benchmark, populated_context_graph):
+    """
+    Benchmarks the linear scan keyword search over graph nodes.
+    """
+    graph = populated_context_graph(n_nodes=2000)
+
+    def run():
+        return graph.query("Node content 500")
+
+    benchmark.pedantic(run, iterations=5, rounds=10)

benchmarks/context/test_linking.py

@@ -0,0 +1,32 @@
+import pytest
+
+from semantica.context.context_graph import ContextGraph
+from semantica.context.entity_linker import EntityLinker
+
+
+@pytest.mark.benchmark(group="entity_linkiing")
+@pytest.mark.parametrize("num_entities_in_graph", [100, 1000])
+def test_entity_linking_complexity(benchmark, num_entities_in_graph):
+    """
+    Benchmarks finding links for extracted entities
+    against the existing graph.
+    """
+
+    graph = ContextGraph()
+    nodes = [
+        {"id": f"e_{i}", "type": "Entity", "properties": {"content": f"Entity {i}"}}
+        for i in range(num_entities_in_graph)
+    ]
+    graph.add_nodes(nodes)
+
+    graph_dict = graph.to_dict()
+
+    linker = EntityLinker(knowledge_graph=graph_dict, similarity_threshold=0.7)
+
+    # Simulate extraction
+    extracted_entities = [{"text": f"Entity {i}", "type": "Entity"} for i in range(5)]
+
+    def run():
+        return linker.link("dummy text", entities=extracted_entities)
+
+    benchmark.pedantic(run, iterations=1, rounds=5)

benchmarks/context/test_memory_storage.py

@@ -0,0 +1,40 @@
+import pytest
+
+from semantica.context.agent_memory import AgentMemory
+
+
+@pytest.mark.benchmark(group="memory_io")
+def test_memory_storage_overhead(benchmark, mock_vector_store):
+    """
+    Benchmarks storing a memory item.
+    """
+    memory = AgentMemory(vector_store=mock_vector_store)
+    content = "This is nothing burger for benchmarking this memory thingy."
+    metadata = {"type": "conversation", "user": "u_1"}
+
+    def run():
+        return memory.store(content, metadata=metadata)
+
+    benchmark.pedantic(run, iterations=10, rounds=10)
+
+
+@pytest.mark.benchmark(group="memory_io")
+def test_short_term_pruning(benchmark, mock_vector_store):
+    """
+    Benchmarks the pruning logic when short-term memory
+    limit is hit.
+    """
+
+    def setup_overfilled_memory():
+        memory = AgentMemory(vector_store=mock_vector_store, short_term_limit=50)
+        # Pre-fill
+        for i in range(55):
+            memory.store(f"filler memory {i}")
+        return (memory,), {}
+
+    def run_prune(mem_instance):
+        mem_instance.store("Trigger Pruning")
+
+    benchmark.pedantic(
+        target=run_prune, setup=setup_overfilled_memory, iterations=1, rounds=20
+    )

benchmarks/context/test_retrieval_logic.py

@@ -0,0 +1,42 @@
+import pytest
+
+from semantica.context.agent_memory import AgentMemory
+from semantica.context.context_retriever import ContextRetriever, RetrievedContext
+
+
+@pytest.mark.benchmark(group="rag_logic")
+def test_hybrid_ranking_overhead(benchmark, retriever_setup):
+    """
+    Benchmarks the CPU cost of the 'rank_and_merge' logic.
+    """
+
+    query = "test_query"
+
+    # Dummy results to sim inputs
+    raw_results = [
+        RetrievedContext(content=f"Vec {i}", score=0.9 - i * 0.01, source="vector:x")
+        for i in range(10)
+    ] + [
+        RetrievedContext(content=f"Graph {i}", score=0.8 - i * 0.01, source="graph:y")
+        for i in range(10)
+    ]
+
+    def run():
+        return retriever_setup._rank_and_merge(raw_results, query)
+
+    benchmark.pedantic(run, iterations=10, rounds=20)
+
+
+@pytest.mark.benchmark(group="rag_logic")
+@pytest.mark.parametrize("use_graph", [True, False])
+def test_full_retrieval_pipeline(benchmark, retriever_setup, use_graph):
+    """
+    Benchmarks the orchestration of the retrieve() method.
+    """
+
+    def run():
+        return retriever_setup.retrieve(
+            "Node content", max_results=10, use_graph_expansion=use_graph, max_hops=1
+        )
+
+    benchmark.pedantic(run, iterations=1, rounds=5)

benchmarks/context_memory/test_agentic.py

@@ -0,0 +1,86 @@
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+from semantica.context.agent_context import AgentContext
+from semantica.context.context_retriever import RetrievedContext
+
+# Fixtures
+
+
+@pytest.fixture
+def mock_agent_context():
+    """
+    Creates an AgentContext with mocked internals.
+    """
+    vector_store = MagicMock()
+    knowledge_graph = MagicMock()
+
+    with patch("semantica.context.agent_context.AgentMemory") as MockMemory, patch(
+        "semantica.context.agent_context.ContextRetriever"
+    ) as MockRetriever:
+
+        ctx = AgentContext(vector_store=vector_store, knowledge_graph=knowledge_graph)
+
+        # Internal mocks
+
+        ctx._memory = MockMemory.return_value
+        ctx._retriever = MockRetriever.return_value
+
+        return ctx
+
+
+# Benchmarks
+
+
+def test_router_overhead(benchmark, mock_agent_context):
+    """
+    Benchmarks the logic that decides between Vector vs Graph retrieval.
+    """
+
+    mock_agent_context._retriever.retrieve.return_value = []
+
+    def op():
+        return mock_agent_context.retrieve("test query", use_graph=None)
+
+    benchmark.pedantic(op, iterations=50, rounds=20)
+
+
+def test_result_conversion_throughput(benchmark, mock_agent_context):
+    """
+    Benchmarks converting internal RetrievedContext objects to Dicts.
+    """
+
+    fake_results = [
+        RetrievedContext(
+            content=f"Result {i}",
+            score=0.9,
+            source="graph:node_1",
+            metadata={"type": "fact"},
+            related_entities=[{"id": "e1", "name": "Entity"}],
+            related_relationships=[{"source": "e1", "target": "e2"}],
+        )
+        for i in range(100)
+    ]
+    mock_agent_context._retriever.retrieve.return_value = fake_results
+
+    def op():
+        return mock_agent_context.retrieve("test", use_graph=True)
+
+    benchmark.pedantic(op, iterations=20, rounds=10)
+
+
+def test_store_orchestration_overhead(benchmark, mock_agent_context):
+    """
+    Benchmarks the 'store' method's logic for routing documents.
+    """
+    docs = [{"content": f"Doc {i}", "metadata": {"id": i}} for i in range(50)]
+
+    # Mock the internal storage to return immediately
+    mock_agent_context._memory.store.return_value = "mem_id"
+    mock_agent_context._build_graph_from_documents = MagicMock(return_value={})
+
+    def op():
+        return mock_agent_context.store(docs, extract_entities=False)
+
+    benchmark.pedantic(op, iterations=10, rounds=10)

benchmarks/context_memory/test_graphrag.py

@@ -0,0 +1,244 @@
+from dataclasses import dataclass, field
+from typing import Any, Dict, List
+from unittest.mock import patch
+
+import numpy as np
+import pytest
+
+from semantica.context.agent_context import AgentContext
+from semantica.context.agent_memory import AgentMemory
+from semantica.context.context_graph import ContextGraph
+from semantica.context.context_retriever import ContextRetriever, RetrievedContext
+from semantica.context.entity_linker import EntityLinker
+
+# Infra
+
+
+class NullTracker:
+    """
+    Stateless dummy tracker.
+    """
+
+    def start_tracking(self, *args, **kwargs):
+        return "dummy_id"
+
+    def update_tracking(self, *args, **kwargs):
+        pass
+
+    def stop_tracking(self, *args, **kwargs):
+        pass
+
+    def register_pipeline_modules(self, *args, **kwargs):
+        pass
+
+    def clear_pipeline_context(self, *args, **kwargs):
+        pass
+
+    def update_progress(self, *args, **kwargs):
+        pass
+
+    @property
+    def enabled(self):
+        return False
+
+    @enabled.setter
+    def enabled(self, value):
+        pass
+
+
+# ~~ MOCK STORES ~~
+
+
+class MockVectorStore:
+    """
+    A feather VectorStore sim that does no math.
+    We want to measure the MANAGER overhead.
+    """
+
+    def __init__(self):
+        self.vectors = {}
+        self.dim = 384
+
+    def embed(self, text):
+        return np.random.rand(self.dim).tolist()
+
+    def add(self, items):
+        for item in items:
+            self.vectors[item.memory_id] = item
+
+    def search(self, query, limit=5):
+        class MockResult:
+            def __init__(self, i):
+                self.id = f"mem_{i}"
+                self.content = f"Content for result {i} matching {query[:10]}"
+                self.score = 0.9 - (i * 0.05)
+                self.metadata = {"type": "test"}
+
+        return [MockResult(i) for i in range(limit)]
+
+
+def create_dense_graph(node_count):
+    """
+    Creates a ContextGraph with 'Small World' Topology.
+    Used to stress-test BFS traversal scaling.
+    """
+    graph = ContextGraph()
+
+    graph.progress_tracker = NullTracker()
+
+    # Create nodes
+    nodes = [
+        {
+            "id": f"node_{i}",
+            "type": "concept",
+            "properties": {"content": f"Concept {i}"},
+        }
+        for i in range(node_count)
+    ]
+    graph.add_nodes(nodes)
+
+    # Create Edges (Chain + Hub + Random)
+    edges = []
+    for i in range(node_count):
+        # Chain
+        if i < node_count - 1:
+            edges.append(
+                {"source_id": f"node_{i}", "target_id": f"node_{i+1}", "type": "next"}
+            )
+        # Hub
+        if i > 0:
+            edges.append(
+                {"source_id": "node_0", "target_id": f"node_{i}", "type": "hub_link"}
+            )
+        # Rando
+        if i % 5 == 0 and i + 5 < node_count:
+            edges.append(
+                {
+                    "source_id": f"node_{i}",
+                    "target_id": f"node_{i+5}",
+                    "type": "cross_link",
+                }
+            )
+
+    graph.add_edges(edges)
+    return graph
+
+
+def create_populated_memory(item_count):
+    """Creates an AgentMemory populated with N items."""
+    vs = MockVectorStore()
+    memory = AgentMemory(vector_store=vs)
+    memory.progress_tracker = NullTracker()
+
+    for i in range(item_count):
+        mem_id = f"setup_mem_{i}"
+        from datetime import datetime
+
+        from semantica.context.agent_memory import MemoryItem
+
+        memory.memory_items[mem_id] = MemoryItem(
+            content=f"History item {i}",
+            timestamp=datetime.now(),
+            memory_id=mem_id,
+            metadata={"type": "chat"},
+        )
+        memory.memory_index.append(mem_id)
+
+    return memory
+
+
+# ~~ BENCHMARKS ~~
+
+
+@pytest.mark.parametrize("graph_size", [100, 1000])
+@pytest.mark.parametrize("hops", [1, 2])
+def test_graph_traversal_scaling(benchmark, graph_size, hops):
+    """
+    Measures 'Hop Explosion' effect.
+    Retrieving multi-hop neighbors on a dense graph.
+    """
+    graph = create_dense_graph(graph_size)
+
+    def op():
+        # Start from'Hub' node which's celebrity, meaning
+        # connected to everyone
+        return graph.get_neighbors("node_0", hops=hops)
+
+    benchmark.pedantic(op, iterations=5, rounds=5)
+
+
+@pytest.mark.parametrize("memory_count", [100, 1000])
+def test_retriever_ranking_throughput(benchmark, memory_count):
+    """
+    Measures CPU cost of merging and ranking results.
+    """
+    retriever = ContextRetriever(
+        vector_store=MockVectorStore(),
+        memory_store=create_populated_memory(10),
+        knowledge_graph=None,
+        hybrid_alpha=0.5,
+    )
+    retriever.progress_tracker = NullTracker()
+
+    results = []
+    for i in range(memory_count):
+        results.append(
+            RetrievedContext(
+                content=f"Vector Item {i}",
+                score=np.random.random(),
+                source=f"vector:{i}",
+            )
+        )
+        results.append(
+            RetrievedContext(
+                content=f"Graph Item {i}",
+                score=np.random.random(),
+                source=f"graph:{i}",
+                metadata={"node_id": f"node_{i}"},
+            )
+        )
+
+    def op():
+        return retriever._rank_and_merge(results, "query context")
+
+    benchmark.pedantic(op, iterations=5, rounds=10)
+
+
+@pytest.mark.parametrize("registry_size", [100, 1000])
+def test_entity_linking_speed(benchmark, registry_size):
+    """
+    Measures O(N) linear scan speed in `find_similar_entities`.
+    """
+    linker = EntityLinker()
+    linker.progress_tracker = NullTracker()
+
+    mock_kg = {"entities": []}
+    for i in range(registry_size):
+        mock_kg["entities"].append(
+            {"id": f"ent_{i}", "text": f"Entity Number {i}", "type": "TEST"}
+        )
+    linker.knowledge_graph = mock_kg
+
+    input_text = "I am looking for Entity Number 50 in the database."
+
+    def op():
+        return linker.find_similar_entities(input_text, threshold=0.1)
+
+    benchmark.pedantic(op, iterations=5, rounds=5)
+
+
+@pytest.mark.parametrize("batch_size", [1, 10, 50])
+def test_agent_store_throughput(benchmark, batch_size):
+    """
+    'store' pipeline test.
+    """
+    vs = MockVectorStore()
+    context = AgentContext(vector_store=vs)
+    context._memory.progress_tracker = NullTracker()
+
+    inputs = [f"Memory item {i} for storage test" for i in range(batch_size)]
+
+    def op():
+        return context.batch_store(inputs)
+
+    benchmark.pedantic(op, iterations=5, rounds=5)

benchmarks/core_processing/conftest.py

@@ -0,0 +1,44 @@
+import pytest
+
+
+# Data factories
+@pytest.fixture
+def node_batch():
+    """Generates 1000 nodes for graph"""
+    return [
+        {
+            "id": f"node_{i}",
+            "type": "Concept",
+            "properties": {"name": f"Concept {i}", "weight": i / 1000},
+        }
+        for i in range(1000)
+    ]
+
+
+@pytest.fixture
+def edge_batch():
+    """Generates 1000 edges connection to the nodes."""
+    return [
+        {
+            "source_id": f"node_{i}",
+            "target_id": f"node_{i + 1}",
+            "type": "related to",
+            "weight": 0.5,
+        }
+        for i in range(999)
+    ]
+
+
+@pytest.fixture
+def conversation_data():
+    """Simulates a large conversation log"""
+    entities = [{"text": f"Entity_{i}", "type": "topic"} for i in range(50)]
+
+    return [
+        {
+            "id": "conv_1",
+            "content": "This is a conversation about banking.",
+            "entities": entities,
+            "relationships": [],
+        }
+    ]

benchmarks/core_processing/test_extraction.py

@@ -0,0 +1,153 @@
+from unittest.mock import patch
+
+import pytest
+
+from semantica.semantic_extract.ner_extractor import Entity, NERExtractor
+from semantica.semantic_extract.semantic_analyzer import SemanticAnalyzer
+
+
+# Fixtures
+@pytest.fixture
+def document_batch():
+    base = "The quick brown fox jumps over the lazy dog."
+    docs = [
+        f"{base} Variation {i}. Apple Inc released a product in 2024."
+        for i in range(50)
+    ]
+    return docs
+
+
+# Fast wrapper-only benchmark (always runs)
+def test_ner_ml_wrapper_overhead(benchmark, long_text_string):
+    extractor = NERExtractor(method="ml", model="en_core_web_sm")
+
+    entity_text = "Semantica"
+    phrase = f"{entity_text} is a knowledge graph framework. "
+    medium_text = phrase * 5
+
+    expected_entities = []
+    phrase_len = len(phrase)
+    for i in range(5):
+        start = i * phrase_len
+        end = start + len(entity_text)
+        ent = Entity(
+            text=entity_text,
+            label="ORG",
+            start_char=start,
+            end_char=end,
+            confidence=0.98,
+            metadata={"lemma": entity_text},
+        )
+        expected_entities.append(ent)
+
+    def custom_ml_extraction(text: str, **method_options):
+        min_confidence = method_options.get("min_confidence", 0.5)
+        entity_types = method_options.get("entity_types")
+        filtered = []
+        for ent in expected_entities:
+            if entity_types and ent.label not in entity_types:
+                continue
+            if ent.confidence >= min_confidence:
+                filtered.append(ent)
+        return filtered
+
+    with patch(
+        "semantica.semantic_extract.methods.get_entity_method"
+    ) as mock_get_method:
+        mock_get_method.side_effect = lambda name: (
+            custom_ml_extraction if name == "ml" else (lambda t, **o: [])
+        )
+
+        def op():
+            return extractor.extract_entities(text=medium_text)
+
+        result = benchmark.pedantic(op, rounds=20, iterations=5)
+
+    assert len(result) == 5
+    assert all(e.text == "Semantica" for e in result)
+    assert all(e.label == "ORG" for e in result)
+    assert all(e.confidence == 0.98 for e in result)
+    assert all(medium_text[e.start_char : e.end_char] == e.text for e in result)
+
+
+# Real spaCy benchmark
+@pytest.mark.benchmark(group="ner_real_ml")
+def test_ner_ml_real_performance(benchmark, long_text_string):
+    """
+    Full spaCy inference + wrapper overhead.
+    Only runs when real spaCy is loaded (BENCHMARK_REAL_LIBS=1).
+    """
+    extractor = NERExtractor(method="ml", model="en_core_web_sm")
+
+    if (
+        extractor.nlp is None
+        or not hasattr(extractor.nlp, "pipe_names")
+        or "ner" not in extractor.nlp.pipe_names
+    ):
+        pytest.skip(
+            "Real spaCy NER pipeline not available — skipping production benchmark"
+        )
+
+    medium_text = long_text_string[:10000]
+
+    medium_text += " Apple Inc. was founded by Steve Jobs and Steve Wozniak in Cupertino, California on April 1, 1976. Microsoft is a competitor."
+
+    def op():
+        return extractor.extract_entities(text=medium_text)
+
+    result = benchmark.pedantic(op, rounds=6, iterations=2)
+
+    assert len(result) >= 6
+    assert any("Apple" in e.text and e.label == "ORG" for e in result)
+    assert any(e.label == "PERSON" for e in result)
+    assert any(e.label in {"GPE", "LOC"} for e in result)
+    assert any(e.label == "DATE" for e in result)
+    assert any("Microsoft" in e.text and e.label == "ORG" for e in result)
+
+
+def test_ner_pattern_speed(benchmark, long_text_string):
+    extractor = NERExtractor(method="pattern")
+    medium_text = long_text_string[:50000]
+    text_with_entities = medium_text + " Apple Inc. was founded in 1976. "
+
+    def op():
+        return extractor.extract_entities(text=text_with_entities)
+
+    result = benchmark.pedantic(op, rounds=20, iterations=5)
+    assert len(result) > 0
+    assert result[0].label in ["ORG", "DATE", "UNKNOWN"]
+
+
+def test_ner_batch_throughput(benchmark, document_batch):
+    extractor = NERExtractor(method="pattern")
+
+    def run_batch():
+        return extractor.extract_entities_batch(document_batch, max_workers=2)
+
+    result = benchmark.pedantic(run_batch, rounds=10, iterations=5)
+    assert len(result) == len(document_batch)
+    assert len(result[0]) > 0
+
+
+def test_similarity_calculation(benchmark):
+    analyzer = SemanticAnalyzer()
+    text1 = "The quick brown fox jumps over the lazy dog" * 10
+    text2 = "The slow brown fox jumped over the sleeping dog" * 10
+
+    def op():
+        return analyzer.calculate_similarity(text1, text2, method="jaccard")
+
+    result = benchmark.pedantic(op, rounds=100, iterations=100)
+    assert 0.0 <= result <= 1.0
+
+
+def test_clustering_algorithm(benchmark, document_batch):
+    analyzer = SemanticAnalyzer()
+    options = {"similarity_threshold": 0.1}
+
+    def op():
+        return analyzer.cluster_semantically(texts=document_batch, **options)
+
+    result = benchmark.pedantic(op, rounds=10, iterations=5)
+    assert len(result) > 0
+    assert result[0].texts

benchmarks/core_processing/test_graph_building.py

@@ -0,0 +1,56 @@
+from unittest.mock import MagicMock
+
+import pytest
+
+from semantica.context.context_graph import ContextGraph
+
+
+def test_bulk_node_insertion(benchmark, node_batch):
+    """
+    Benchmarks the overhead of adding nodes to in-memory graph.
+
+    """
+
+    def setup_graph():
+        return (ContextGraph(),), {}
+
+    def run(graph_instance):
+        graph_instance.add_nodes(node_batch)
+
+    benchmark.pedantic(target=run, setup=setup_graph, rounds=50, iterations=1)
+
+
+def test_bulk_edge_insertion(benchmark, node_batch, edge_batch):
+    """
+    Benchmarks adding edges.
+    """
+
+    def setup_graph_with_nodes():
+        g = ContextGraph()
+        g.add_nodes(node_batch)
+        return (g,), {}
+
+    def run(graph_instance):
+        graph_instance.add_edges(edge_batch)
+
+    benchmark.pedantic(
+        target=run, setup=setup_graph_with_nodes, rounds=50, iterations=1
+    )
+
+
+def test_conversation_to_graph_conversion(benchmark, conversation_data):
+    """
+    Benchmarks parsing conversation dicts into graph structures.
+    """
+
+    def setup_clean_builder():
+        g = ContextGraph()
+        g.entity_linker = MagicMock()
+        return (g,), {}
+
+    def run(graph_instance):
+        return graph_instance.build_from_conversations(
+            conversation_data, link_entities=False
+        )
+
+    benchmark.pedantic(target=run, setup=setup_clean_builder, rounds=20, iterations=1)

benchmarks/export/arrow_exporter.py

@@ -0,0 +1,69 @@
+"""
+Mock Arrow Exporter for Benchmark Testing
+
+This module provides a mock implementation of the ArrowExporter to prevent
+import errors during benchmark testing when PyArrow is not available in the CI environment.
+"""
+
+# Mock PyArrow import for CI compatibility
+try:
+    import pyarrow as pa
+except ImportError:
+    # Create a mock pa module for CI environment
+    import types
+    pa = types.ModuleType('pa')
+    
+    def mock_schema(*args, **kwargs):
+        return types.SimpleNamespace()
+    
+    def mock_table(*args, **kwargs):
+        return types.SimpleNamespace()
+    
+    def mock_array(*args, **kwargs):
+        return types.SimpleNamespace()
+    
+    pa.schema = mock_schema
+    pa.Table = mock_table
+    pa.array = mock_array
+    pa.RecordBatch = mock_table
+
+# Mock schema definitions
+ENTITY_SCHEMA = pa.schema([]) if hasattr(pa, 'schema') else None
+RELATIONSHIP_SCHEMA = pa.schema([]) if hasattr(pa, 'schema') else None
+METADATA_SCHEMA = pa.schema([]) if hasattr(pa, 'schema') else None
+
+class ArrowExporter:
+    """
+    Mock Arrow Exporter class for benchmark testing.
+    
+    This is a lightweight implementation that provides the same interface
+    as the real ArrowExporter but doesn't require PyArrow to be installed.
+    """
+    
+    def __init__(self, config=None):
+        self.config = config
+        self._tables = {}
+    
+    def export_entities(self, entities, output_path):
+        """Mock export entities method."""
+        return f"Mock exported {len(entities)} entities to {output_path}"
+    
+    def export_relationships(self, relationships, output_path):
+        """Mock export relationships method."""
+        return f"Mock exported {len(relationships)} relationships to {output_path}"
+    
+    def export_knowledge_graph(self, entities, relationships, output_path):
+        """Mock export knowledge graph method."""
+        return f"Mock exported knowledge graph to {output_path}"
+    
+    def to_arrow_table(self, data):
+        """Mock conversion to Arrow table."""
+        return f"Mock Arrow table with {len(data)} rows"
+    
+    def save_to_file(self, table, path):
+        """Mock save to file method."""
+        return f"Mock saved table to {path}"
+    
+    def batch_export(self, data_list, output_dir):
+        """Mock batch export method."""
+        return f"Mock batch exported {len(data_list)} items to {output_dir}"

benchmarks/export/conftest.py

@@ -0,0 +1,81 @@
+import random
+import uuid
+from typing import Any, Dict, List
+
+import numpy as np
+import pytest
+
+# Data Generators
+
+
+@pytest.fixture
+def generate_entities():
+    def _gen(count: int) -> List[Dict[str, Any]]:
+        entities = []
+        for i in range(count):
+            entities.append(
+                {
+                    "id": f"e_{i}",
+                    "text": f"Entity Number {i}",
+                    "type": random.choice(
+                        ["person", "Organization", "Location", "Event"]
+                    ),
+                    "confidence": random.uniform(0.7, 1.0),
+                    "metadata": {"source": "doc_1.txt", "page": 1},
+                }
+            )
+
+        return entities
+
+    return _gen
+
+
+@pytest.fixture
+def generate_knowledge_graph(generate_entities):
+    def _gen(entity_count: int, rel_density: float = 1.5) -> Dict[str, Any]:
+        entities = generate_entities(entity_count)
+        relationships = []
+        rel_count = int(entity_count * rel_density)
+
+        for i in range(rel_count):
+            src = random.choice(entities)
+            tgt = random.choice(entities)
+            relationships.append(
+                {
+                    "id": f"r_{i}",
+                    "source_id": src["id"],
+                    "target_id": tgt["id"],
+                    "type": " RELATED_TO",
+                    "confidence": 0.9,
+                    "metadata": {"extractor": "v1"},
+                }
+            )
+
+        return {
+            "entities": entities,
+            "relationships": relationships,
+            "metadata": {"generated_at": "2026-02-05"},
+        }
+
+    return _gen
+
+
+@pytest.fixture
+def generate_vectors():
+    def _gen(count: int, dim: int = 384) -> List[Dict[str, Any]]:
+        matrix = np.random.rand(count, dim).astype(np.float32)
+
+        data = []
+
+        for i in range(count):
+            data.append(
+                {
+                    "id": f"vec_{i}",
+                    "vector": matrix[i].tolist(),
+                    "text": f"Text {i}",
+                    "metadata": {"model": "bert"},
+                }
+            )
+        return data
+
+    return _gen

benchmarks/export/test_core_formats.py

@@ -0,0 +1,42 @@
+import pytest
+
+from semantica.export.csv_exporter import CSVExporter
+from semantica.export.json_exporter import JSONExporter
+from semantica.export.yaml_exporter import SemanticNetworkYAMLExporter
+
+
+@pytest.mark.benchmark(group="structured_export")
+@pytest.mark.parametrize("size", [1000, 5000])
+def test_json_parsing_throughput(benchmark, tmp_path, generate_knowledge_graph, size):
+    kg = generate_knowledge_graph(size)
+    exporter = JSONExporter(indent=None)
+    output_file = tmp_path / "output.json"
+
+    def run():
+        exporter.export(kg, output_file)
+
+    benchmark.pedantic(run, iterations=1, rounds=5)
+
+
+@pytest.mark.benchmark(group="structured_export")
+def test_csv_entity_export(benchmark, tmp_path, generate_entities):
+    entities = generate_entities(5000)
+    exporter = CSVExporter()
+    output_file = tmp_path / "entities.csv"
+
+    def run():
+        exporter.export_entities(entities, output_file)
+
+    benchmark.pedantic(run, iterations=1, rounds=5)
+
+
+@pytest.mark.benchmark(group="structured_export")
+def test_yaml_serialization_overhead(benchmark, tmp_path, generate_knowledge_graph):
+    kg = generate_knowledge_graph(500)
+    exporter = SemanticNetworkYAMLExporter()
+    output_file = tmp_path / "output.yaml"
+
+    def run():
+        exporter.export(kg, output_file)
+
+    benchmark.pedantic(run, iterations=1, rounds=5)

benchmarks/export/test_graph_export.py

@@ -0,0 +1,22 @@
+import pytest
+
+from semantica.export.graph_exporter import GraphExporter
+
+
+@pytest.mark.benchmark(group="vis_export")
+@pytest.mark.parametrize("format", ["graphml", "gexf"])
+def test_graph_conversion_overhead(
+    benchmark, tmp_path, generate_knowledge_graph, format
+):
+    """
+    Measures the cost of converting internal KG structure to XML-based graph formats.
+    Includes dictionary traversal and XML string building.
+    """
+    kg = generate_knowledge_graph(2000)
+    exporter = GraphExporter(format=format)
+    output_file = tmp_path / f"graph.{format}"
+
+    def run():
+        exporter.export_knowledge_graph(kg, output_file)
+
+    benchmark(run)

benchmarks/export/test_semantic_export.py

@@ -0,0 +1,45 @@
+import pytest
+
+from semantica.export.lpg_exporter import LPGExporter
+from semantica.export.owl_exporter import OWLExporter
+from semantica.export.rdf_exporter import RDFExporter
+
+
+@pytest.mark.benchmark(group="semantic_serialization")
+@pytest.mark.parametrize("format", ["turtle", "rdfxml"])
+def test_rdf_serialization_formats(benchmark, generate_knowledge_graph, format):
+    kg = generate_knowledge_graph(1000)
+    exporter = RDFExporter()
+    rdf_data = exporter.serializer.convert_kg_to_rdf(kg)
+
+    def run():
+        return exporter.export_to_rdf(rdf_data, format=format)
+
+    benchmark.pedantic(run, iterations=1, rounds=5)
+
+
+@pytest.mark.benchmark(group="graph_db_export")
+def test_lpg_cypher_generation(benchmark, generate_knowledge_graph):
+    kg = generate_knowledge_graph(2000)
+    exporter = LPGExporter(batch_size=1000, include_indexes=False)
+
+    def run():
+        return exporter._generate_cypher_queries(kg)
+
+    benchmark.pedantic(run, iterations=1, rounds=5)
+
+
+@pytest.mark.benchmark(group="semantic_serialization")
+def test_owl_xml_generation(benchmark, tmp_path):
+    ontology = {
+        "name": "BenchmarkOntology",
+        "classes": [{"name": f"Class{i}"} for i in range(500)],
+        "object_properties": [{"name": f"Prop{i}"} for i in range(200)],
+    }
+    exporter = OWLExporter()
+    output_file = tmp_path / "ontology.xml"
+
+    def run():
+        exporter.export(ontology, output_file, format="owl-xml")
+
+    benchmark.pedantic(run, iterations=1, rounds=5)

benchmarks/export/test_vector_export.py

@@ -0,0 +1,51 @@
+import numpy as np
+import pytest
+
+from semantica.export.vector_exporter import VectorExporter
+
+
+@pytest.mark.benchmark(group="vector_io")
+@pytest.mark.parametrize("count", [1000, 10000])
+def test_numpy_compression_speed(benchmark, tmp_path, generate_vectors, count):
+    """
+    Measures cost of np.savez_compressed.
+    """
+    vectors = generate_vectors(count)
+    exporter = VectorExporter(format="numpy")
+    output_file = tmp_path / "vectors.npz"
+
+    def run():
+        exporter.export(vectors, output_file)
+
+    benchmark(run)
+
+
+@pytest.mark.benchmark(group="vector_io")
+def test_json_vector_overhead(benchmark, tmp_path, generate_vectors):
+    """
+    Benchmarks JSON export for vectors.
+    """
+
+    vectors = generate_vectors(2000)
+    exporter = VectorExporter(format="json")
+    output_file = tmp_path / "vectors.json"
+
+    def run():
+        exporter.export(vectors, output_file)
+
+    benchmark(run)
+
+
+@pytest.mark.benchmark(group="vector_io")
+def test_binary_raw_throughput(benchmark, tmp_path, generate_vectors):
+    """
+    Measures raw binary dump speed (no compression, no metadata).
+    """
+    vectors = generate_vectors(10000)
+    exporter = VectorExporter(format="binary")
+    output_file = tmp_path / "vectors.bin"
+
+    def run():
+        exporter.export(vectors, output_file)
+
+    benchmark(run)

benchmarks/infrastructure/compare.py

@@ -0,0 +1,102 @@
+import argparse
+import json
+import sys
+from pathlib import Path
+from typing import Any, Dict, List
+
+
+def load_results(filepath: str) -> Dict[str, Any]:
+    with open(filepath, "r") as f:
+        return json.load(f)
+
+
+def calc_z_score(current_mean, base_mean, base_stddev):
+    """
+    Z-Score indicates how many standard deviations
+    away current run is from baseline
+    """
+
+    if base_stddev == 0:
+        return 0 if current_mean == base_mean else 100.0
+
+    return (current_mean - base_mean) / base_stddev
+
+
+def compare_benchmarks(
+    baseline: Dict[str, Any], current: Dict[str, Any], threshold_pct: float = 10.0
+):
+    """
+    Uses Mean for % change and Z-score for noise detection.
+    """
+
+    # colors for terminal
+    RED = "\033[91m"
+    GREEN = "\033[92m"
+    YELLOW = "\033[93m"
+    RESET = "\033[0m"
+
+    header = f"{'Benchmark':<60} | {'CHANGE %':<12} | {'SIGMA (Z)':<10} | {'STATUS'}"
+    print(header)
+    print("=" * len(header))
+
+    baseline_map = {b["name"]: b for b in baseline["benchmarks"]}
+    current_map = {b["name"]: b for b in current["benchmarks"]}
+
+    regressions = []
+
+    for name, curr in current_map.items():
+        base = baseline_map.get(name)
+        if not base:
+            print(f"{name:<60} | {'NEW':<12} | {'N/A':<10} | NEW")
+            continue
+
+        m1 = base["stats"]["mean"]
+        s1 = base["stats"]["stddev"]
+        m2 = curr["stats"]["mean"]
+
+        if m1 == 0:
+            delta_pct = 0.0
+        else:
+            delta_pct = ((m2 - m1) / m1) * 100
+
+        z_score = calc_z_score(m2, m1, s1)
+
+        status = f"{GREEN} OK{RESET}"
+
+        if delta_pct > threshold_pct:
+            if abs(z_score) > 2.0:
+                status = f"{RED} REGRESSION{RESET}"
+                regressions.append(name)
+            else:
+                status = f"{YELLOW} NOISE{RESET}"
+        elif delta_pct < -threshold_pct and abs(z_score) > 2.0:
+            status = f"{GREEN} IMPROVED{RESET}"
+
+        print(f"{name:<60} | {delta_pct:>+10.2f}% | {z_score:>9.2f} | {status}")
+
+    if regressions:
+        print(
+            f"\n{RED}FAILURE: Performance regression detected in {len(regressions)} tests.{RESET}"
+        )
+        return True
+    print(f"\n{GREEN}SUCCESS: No significant regressions.{RESET}")
+    return False
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument("baseline", help="Gold standard JSON")
+    parser.add_argument("current", help="NEW RUN JSON")
+    parser.add_argument(
+        "--threshold", type=float, default=10.0, help="FAIL if slower by %"
+    )
+    args = parser.parse_args()
+
+    try:
+        failed = compare_benchmarks(
+            load_results(args.baseline), load_results(args.current), args.threshold
+        )
+        sys.exit(1 if failed else 0)
+    except FileNotFoundError as e:
+        print(f"Error loading files: {e}")
+        sys.exit(0)

benchmarks/input_layer/test_ingestion.py

@@ -0,0 +1,22 @@
+import pytest
+
+from semantica.ingest.file_ingestor import FileIngestor
+
+
+def test_ingest_file_performance(benchmark, sample_text_file):
+    """
+    Benchmarks the speed of the ingest_file method
+
+    Metrics:
+    - Time to open, read, validate and wrap a ~~10 KB text file.
+    """
+
+    ingestor = FileIngestor()
+    result = benchmark(
+        ingestor.ingest_file, file_path=sample_text_file, read_content=True
+    )
+
+    assert result is not None
+    assert result.size > 0
+    assert result.name.endswith(".txt")
+    assert "Line 0" in result.text

benchmarks/input_layer/test_parsing.py

@@ -0,0 +1,188 @@
+import csv
+import io
+import json
+import time
+from typing import Any, Dict, List
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+from semantica.parse.code_parser import CodeParser
+from semantica.parse.csv_parser import CSVParser
+from semantica.parse.document_parser import DocumentParser
+from semantica.parse.html_parser import HTMLParser
+from semantica.parse.json_parser import JSONParser
+
+# Data gens
+
+
+def generate_json_string(item_count: int) -> str:
+    data = [
+        {
+            "id": i,
+            "name": f"Item:{i}",
+            "tags": ["tag1", "tag2", "tag3"],
+            "metadata": {"active": True, "score": 0.95},
+        }
+        for i in range(item_count)
+    ]
+    return json.dumps(data)
+
+
+def generate_csv_string(row_count: int) -> str:
+    output = io.StringIO()
+    writer = csv.writer(output)
+    writer.writerow(["id", "name", "description", "value", "date"])
+    for i in range(row_count):
+        writer.writerow([i, f"Item {i}", "Description text here", 100.50, "2024-01-01"])
+    return output.getvalue()
+
+
+def generate_html_string(element_count: int) -> str:
+    lis = "".join(
+        [f'<li><a href="/item/{i}">Link {i}</a></li>' for i in range(element_count)]
+    )
+    return f"""
+    <html>
+        <head><title>Benchmark Page</title></head>
+        <body>
+            <div id="content">
+                <h1>Header</h1>
+                <p>Some intro text.</p>
+                <ul>{lis}</ul>
+            </div>
+        </body>
+    </html>
+    """
+
+
+# lib mocks
+
+
+class MockPDFPage:
+    def __init__(self, page_num):
+        self.width = 600
+        self.height = 800
+        self.page_number = page_num
+
+    def extract_text(self):
+        return f"This is text content for page {self.page_number}. " * 50
+
+    def extract_tables(self):
+        return [[["Header1", "Header2"], ["Row1", "Value1"]]]
+
+    @property
+    def images(self):
+        return [{"x0": 10, "y0": 10, "width": 100, "height": 100}]
+
+
+class MockPDF:
+    def __init__(self, page_count):
+        self.pages = [MockPDFPage(i) for i in range(page_count)]
+        self.metadata = {"Title": "Benchmark PDF", "Author": "Noone"}
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, *args):
+        pass
+
+
+@pytest.fixture
+def mock_pdfplumber():
+    with patch("pdfplumber.open") as mock_open:
+        yield mock_open
+
+
+# Benchmarks
+
+
+@pytest.mark.parametrize("size", [1000, 10000])
+def test_json_parsing_throughput(benchmark, size):
+    parser = JSONParser()
+    json_str = generate_json_string(size)
+
+    with patch("pathlib.Path.exists", return_value=False):
+
+        def op():
+            return parser.parse(json_str)
+
+        benchmark.pedantic(op, iterations=5, rounds=10)
+
+
+@pytest.mark.parametrize("rows", [1000, 10000])
+def test_csv_parsing_throughput(benchmark, rows):
+    """
+    Measures CSV parsing throughput.
+    """
+    parser = CSVParser()
+    csv_content = generate_csv_string(rows)
+
+    with patch(
+        "builtins.open", side_effect=lambda *args, **kwargs: io.StringIO(csv_content)
+    ):
+        with patch("pathlib.Path.exists", return_value=True):
+
+            def op():
+                return parser.parse("dummy.csv")
+
+            benchmark.pedantic(op, iterations=5, rounds=5)
+
+
+@pytest.mark.parametrize("elements", [100, 1000])
+def test_html_scraping_speed(benchmark, elements):
+    parser = HTMLParser()
+    html_content = generate_html_string(elements)
+
+    with patch("pathlib.Path.exists", return_value=False):
+
+        def op():
+            return parser.parse(html_content, extract_links=True)
+
+        benchmark.pedantic(op, iterations=5, rounds=5)
+
+
+@pytest.mark.parametrize("pages", [10, 50])
+def test_pdf_extraction_overhead(benchmark, mock_pdfplumber, pages):
+    parser = DocumentParser()
+
+    mock_pdf = MockPDF(pages)
+    mock_pdfplumber.return_value = mock_pdf
+
+    with patch("pathlib.Path.exists", return_value=True), patch(
+        "pathlib.Path.suffix", new_callable=MagicMock(return_value=".pdf")
+    ):
+
+        def op():
+            return parser.parse_document("dummy.pdf", extract_images=True)
+
+        benchmark.pedantic(op, iterations=5, rounds=5)
+
+
+def test_python_ast_parsing(benchmark):
+    """
+    Measures performance of Python AST analysis.
+    """
+    parser = CodeParser()
+
+    code_lines = []
+    for i in range(200):
+        code_lines.append(f"import module_{i}")
+        code_lines.append(f"def function_{i}(arg):")
+        code_lines.append(f"    '''Docstring for function {i}'''")
+        code_lines.append(f"    return arg + {i}")
+        code_lines.append(f"class Class_{i}:")
+        code_lines.append(f"    pass")
+
+    code_content = "\n".join(code_lines)
+
+    with patch(
+        "builtins.open", side_effect=lambda *args, **kwargs: io.StringIO(code_content)
+    ), patch("pathlib.Path.exists", return_value=True), patch(
+        "pathlib.Path.suffix", new_callable=MagicMock(return_value=".py")
+    ):
+
+        def op():
+            return parser.parse_code("dummy.py")
+
+        benchmark.pedantic(op, iterations=5, rounds=5)

benchmarks/input_layer/test_splitting.py

@@ -0,0 +1,27 @@
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+try:
+    from semantica.split.sliding_window_chunker import SlidingWindowChunker
+    from semantica.split.splitter import TextSplitter
+except ImportError as e:
+    pytest.skip(
+        f"Skipping splitting test due to missing dependencies ({e})",
+        allow_module_level=True,
+    )
+
+
+def test_sliding_window(benchmark, long_text_string):
+    """
+    Benchmarks the speed of SlidingWindowChunker in 'Fixed Size' mode
+    """
+
+    chunker = SlidingWindowChunker(chunk_size=500, overlap=50)
+
+    if hasattr(chunker, "progress_tracker"):
+        chunker.progress_tracker = MagicMock()
+
+    result = benchmark(chunker.chunk, text=long_text_string, preserve_boundaries=False)
+
+    assert len(result) > 0

benchmarks/mock_arrow_exporter.py

@@ -0,0 +1,69 @@
+"""
+Mock Arrow Exporter for Benchmark Testing
+
+This module provides a mock implementation of the ArrowExporter to prevent
+import errors during benchmark testing when PyArrow is not available in the CI environment.
+"""
+
+# Mock PyArrow import for CI compatibility
+try:
+    import pyarrow as pa
+except ImportError:
+    # Create a mock pa module for CI environment
+    import types
+    pa = types.ModuleType('pa')
+    
+    def mock_schema(*args, **kwargs):
+        return types.SimpleNamespace()
+    
+    def mock_table(*args, **kwargs):
+        return types.SimpleNamespace()
+    
+    def mock_array(*args, **kwargs):
+        return types.SimpleNamespace()
+    
+    pa.schema = mock_schema
+    pa.Table = mock_table
+    pa.array = mock_array
+    pa.RecordBatch = mock_table
+
+# Mock schema definitions
+ENTITY_SCHEMA = pa.schema([]) if hasattr(pa, 'schema') else None
+RELATIONSHIP_SCHEMA = pa.schema([]) if hasattr(pa, 'schema') else None
+METADATA_SCHEMA = pa.schema([]) if hasattr(pa, 'schema') else None
+
+class ArrowExporter:
+    """
+    Mock Arrow Exporter class for benchmark testing.
+    
+    This is a lightweight implementation that provides the same interface
+    as the real ArrowExporter but doesn't require PyArrow to be installed.
+    """
+    
+    def __init__(self, config=None):
+        self.config = config
+        self._tables = {}
+    
+    def export_entities(self, entities, output_path):
+        """Mock export entities method."""
+        return f"Mock exported {len(entities)} entities to {output_path}"
+    
+    def export_relationships(self, relationships, output_path):
+        """Mock export relationships method."""
+        return f"Mock exported {len(relationships)} relationships to {output_path}"
+    
+    def export_knowledge_graph(self, entities, relationships, output_path):
+        """Mock export knowledge graph method."""
+        return f"Mock exported knowledge graph to {output_path}"
+    
+    def to_arrow_table(self, data):
+        """Mock conversion to Arrow table."""
+        return f"Mock Arrow table with {len(data)} rows"
+    
+    def save_to_file(self, table, path):
+        """Mock save to file method."""
+        return f"Mock saved table to {path}"
+    
+    def batch_export(self, data_list, output_dir):
+        """Mock batch export method."""
+        return f"Mock batch exported {len(data_list)} items to {output_dir}"

benchmarks/normalize/conftest.py

@@ -0,0 +1,62 @@
+import random
+import string
+from typing import Any, Dict, List
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+# Data gen
+
+
+@pytest.fixture
+def generate_text_data():
+    """Generates various types of text data."""
+
+    def _gen(type="clean", length=100):
+        if type == "clean":
+            return "".join(random.choices(string.ascii_letters + " ", k=length))
+        elif type == "html":
+            tags = ["<div>", "<p>", "<span>", "<a>", "<b>", "<i>"]
+            content = "".join(random.choices(string.ascii_letters + " ", k=length))
+            return f"{random.choice(tags)}{content}{random.choice(tags).replace('<', '</')}"
+        elif type == "unicode":
+            chars = string.ascii_letters + "éàèùâêîôûçñ"
+            return "".join(random.choices(chars, k=length))
+        elif type == "dirty":
+            chars = string.ascii_letters + " \t\n\r"
+            return "".join(random.choices(chars, k=length))
+
+    return _gen
+
+
+@pytest.fixture
+def generate_dataset():
+    """Generates dataset for data cleaner."""
+
+    def _gen(rows=100, duplicate_rate=0.0):
+        base_rows = []
+        unique_count = int(rows * (1 - duplicate_rate))
+
+        for i in range(unique_count):
+            base_rows.append(
+                {
+                    "id": i,
+                    "name": f"Entity_{i}",
+                    "email": f"user{i}@yahoo.com",
+                    "value": random.random() * 100,
+                    "category": random.choice(["A", "B", "C"]),
+                }
+            )
+
+        final_dataset = base_rows.copy()
+        while len(final_dataset) < rows:
+            source = random.choice(base_rows)
+            dup = source.copy()
+            if random.random() > 0.5:
+                dup["value"] = source["value"] + 0.001
+            final_dataset.append(dup)
+
+        random.shuffle(final_dataset)
+        return final_dataset
+
+    return _gen

benchmarks/normalize/test_data_cleaner.py

@@ -0,0 +1,38 @@
+import pytest
+
+from semantica.normalize.data_cleaner import DataCleaner
+
+
+@pytest.mark.parametrize("rows", [100, 500])
+def test_duplication_detection_scaling(benchmark, generate_dataset, rows):
+    """
+    Benchmarks duplicate detection scaling.
+    """
+
+    cleaner = DataCleaner()
+    dataset = generate_dataset(rows=rows, duplicate_rate=0.2)
+
+    def run():
+        return cleaner.detect_duplicates(dataset, key_fields=["name", "email"])
+
+    benchmark.pedantic(run, iterations=1, rounds=5)
+
+
+def test_missing_value_imputation(benchmark, generate_dataset):
+    """
+    Benchmarks statistical imputation.
+    """
+    cleaner = DataCleaner()
+
+    def setup_broken_dataset():
+        dataset = generate_dataset(rows=5000)
+        for row in dataset:
+            if row["id"] % 5 == 0:
+                row["value"] = None
+
+        return (dataset,), {}
+
+    def run(data):
+        return cleaner.handle_missing_values(data, strategy="impute", method="mean")
+
+    benchmark.pedantic(target=run, setup=setup_broken_dataset, iterations=1, rounds=10)

benchmarks/normalize/test_heavy_libs.py

@@ -0,0 +1,31 @@
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+from semantica.normalize.encoding_handler import EncodingHandler
+from semantica.normalize.language_detector import LanguageDetector
+
+
+def test_language_detection_throughput(benchmark, generate_text_data):
+    """Benchmarks langdetect intergration."""
+    detector = LanguageDetector()
+    texts = [generate_text_data("clean", 200) for _ in range(50)]
+
+    def run():
+        return detector.detect_batch(texts)
+
+    benchmark.pedantic(run, iterations=1, rounds=5)
+
+
+def test_encoding_detection(benchmark):
+    """Benchmarks chardet integration via EncodingHandler."""
+    handler = EncodingHandler()
+    data = (
+        b"Wowzaaa a simple string for encoding decoding , oh encoding detection just."
+        * 100
+    )
+
+    def run():
+        return handler.detect(data)
+
+    benchmark.pedantic(run, iterations=5, rounds=10)

benchmarks/normalize/test_parsers.py

@@ -0,0 +1,25 @@
+import pytest
+
+from semantica.normalize.date_normalizer import DateNormalizer
+from semantica.normalize.number_normalizer import NumberNormalizer
+
+
+@pytest.mark.parametrize("date_str", ["2026-02-03", "Ferbuary 2nd, 2026", "9 days ago"])
+def test_data_parsing_variations(benchmark, date_str):
+    """Compare speed of different date formats."""
+    normalizer = DateNormalizer()
+    benchmark.pedantic(
+        lambda: normalizer.normalize_date(date_str), iterations=10, rounds=20
+    )
+
+
+def test_number_normalization(benchmark):
+    """Benchmarks number parsing with currency and unit stripping."""
+    normalizer = NumberNormalizer()
+    raw_inputs = ["$1,234.56", "1.5k", "50%", "1,000,000"] * 100
+
+    def run():
+        for n in raw_inputs:
+            normalizer.normalize_number(n)
+
+    benchmark.pedantic(run, iterations=5, rounds=20)

benchmarks/normalize/test_text_processing.py

@@ -0,0 +1,42 @@
+import pytest
+
+from semantica.normalize.text_cleaner import TextCleaner
+from semantica.normalize.text_normalizer import TextNormalizer
+
+
+def test_html_removal_reg_vs_bs4(benchmark, generate_text_data):
+    """
+    Compare regex vs BeautifulSoup.
+    """
+    cleaner = TextCleaner()
+    html_content = generate_text_data("html", 10_000)
+
+    def run():
+        return cleaner.remove_html(html_content, preserve_structure=False)
+
+    benchmark.pedantic(run, rounds=50, iterations=10)
+
+
+def test_unicode_normalization_throughput(benchmark, generate_text_data):
+    """
+    Benchmarks unicode NFC normalization speed.
+    """
+    normalizer = TextNormalizer()
+    text = generate_text_data("unicode", 50_000)
+
+    def run():
+        return normalizer.normalize_text(text, unicode_form="NFC")
+
+    benchmark.pedantic(run, iterations=5, rounds=10)
+
+
+def test_whitespace_normalization(benchmark, generate_text_data):
+    """Benchmarks whitespace regex replacement."""
+    normalizer = TextNormalizer()
+    text = generate_text_data("dirty", 50_000)
+
+    benchmark.pedantic(
+        lambda: normalizer.normalize_text(text, unicode_form="NFC"),
+        iterations=5,
+        rounds=10,
+    )

benchmarks/ontology/conftest.py

@@ -0,0 +1,85 @@
+import random
+import string
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+# Data generators
+
+
+def _random_str(length=8):
+    return "".join(random.choices(string.ascii_letters, k=length))
+
+
+@pytest.fixture
+def generate_ontology_data():
+    """
+    Generates a synthetic dataset of entities and relationships
+    designed to triger class and property inference class.
+    """
+
+    def _generate(entity_count: int, relationship_density: float = 1.5):
+
+        num_classes = max(5, entity_count // 50)
+        class_names = [f"Class_{_random_str(4)}" for _ in range(num_classes)]
+
+        entities = []
+
+        for i in range(entity_count):
+            cls = random.choice(class_names)
+
+            props = {
+                f"prop_{_random_str(3)}": random.choice([10, "text", 1.5, True])
+                for _ in range(random.randint(1, 5))
+            }
+
+            entity = {
+                "id": f"e_{i}",
+                "type": cls,
+                "name": f"Entity_{i}",
+                "confidence": 0.95,
+                **props,
+            }
+
+            entities.append(entity)
+
+        relationships = []
+        rel_count = int(entity_count * relationship_density)
+        rel_types = ["relatedTo", "hasPart", "worksFor", "contains", "memberOf"]
+
+        for _ in range(rel_count):
+            src = random.choice(entities)
+            tgt = random.choice(entities)
+            rel = {
+                "source": src["name"],
+                "target": tgt["name"],
+                "type": random.choice(rel_types),
+                "source_type": src["type"],
+                "target_type": tgt["type"],
+                "confidence": 0.8,
+            }
+            relationships.append(rel)
+
+        return {"entities": entities, "relationships": relationships}
+
+    return _generate
+
+
+@pytest.fixture
+def large_ontology_definition(generate_ontology_data):
+    """Pre-calculates a structured ontology
+    definition dictionary.
+    """
+    from semantica.ontology.ontology_generator import OntologyGenerator
+
+    data = generate_ontology_data(entity_count=1000)
+
+    # Mocking validation in 6-step pipeline to speed up setup
+
+    with patch(
+        "semantica.ontology.ontology_validator.OntologyValidator.validate"
+    ) as mock_val:
+        mock_val.return_value.valid = True
+        gen = OntologyGenerator()
+
+        return gen.generate_ontology(data, validate=False)

benchmarks/ontology/test_inference.py

@@ -0,0 +1,70 @@
+import pytest
+
+from semantica.ontology.class_inferrer import ClassInferrer
+from semantica.ontology.property_generator import PropertyGenerator
+
+
+@pytest.mark.benchmark(group="class_Inference")
+@pytest.mark.parametrize("entity_count", [1000, 5000])
+def test_class_inference_scaling(benchmark, generate_ontology_data, entity_count):
+    """
+    Benchmarks grouping and threshold logic in ClassInferrer.
+    """
+
+    data = generate_ontology_data(entity_count=entity_count)
+    inferrer = ClassInferrer(min_occurrences=2)
+
+    def run():
+        return inferrer.infer_classes(data["entities"])
+
+    benchmark.pedantic(run, iterations=1, rounds=5)
+
+
+@pytest.mark.benchmark(group="property_inference")
+@pytest.mark.parametrize("size", [(1000, 1500)])
+def test_property_inference_scaling(benchmark, generate_ontology_data, size):
+    """
+    Benchmarks: PropertyGenerator
+    """
+
+    e_count, _ = size
+    data = generate_ontology_data(entity_count=e_count)
+
+    inferrer = ClassInferrer()
+    classes = inferrer.infer_classes(data["entities"])
+
+    prop_gen = PropertyGenerator()
+
+    def run():
+        return prop_gen.infer_properties(
+            entities=data["entities"],
+            relationships=data["relationships"],
+            classes=classes,
+        )
+
+    benchmark.pedantic(run, iterations=1, rounds=5)
+
+
+def test_hierarchy_circular_detection(benchmark):
+    """
+    Benchmarks the DFS cycle detection in ClassInferrer.
+    """
+
+    inferrer = ClassInferrer()
+
+    # Create a deep chain A -> B -> C ... -> Z
+
+    chain_length = 200
+    classes = []
+
+    for i in range(chain_length):
+        cls = {
+            "name": f"Class_{i}",
+            "subClassOf": f"Class_{i+1}" if i < chain_length - 1 else None,
+        }
+        classes.append(cls)
+
+    def run():
+        return inferrer.validate_classes(classes)
+
+    benchmark.pedantic(run, iterations=1, rounds=10)

benchmarks/ontology/test_ontology_pipeline.py

@@ -0,0 +1,46 @@
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+from semantica.ontology.ontology_generator import OntologyGenerator
+
+
+@pytest.mark.benchmark(group="full_pipeline")
+@pytest.mark.parametrize("entity_count", [1000])
+def test_e2e_ontology_generation(benchmark, generate_ontology_data, entity_count):
+    """
+    Benchmarks complete 6-stage pipeline
+    """
+
+    data = generate_ontology_data(entity_count)
+    generator = OntologyGenerator()
+
+    with patch(
+        "semantica.ontology.ontology_validator.OntologyValidator.validate"
+    ) as mock_val:
+        mock_val.return_value.valid = True
+
+        def run():
+            return generator.generate_ontology(data, validate=True)
+
+        benchmark.pedantic(run, iterations=1, rounds=5)
+
+
+def test_associative_class_creation(benchmark):
+    """
+    Benchmarks the creation of complex N-ary relationships.
+    """
+    from semantica.ontology.associative_class import AssociativeClassBuilder
+
+    builder = AssociativeClassBuilder()
+
+    def run():
+        for i in range(50):
+            builder.create_position_class(
+                person_class=f"Person_{i}",
+                organization_class=f"Org_{i}",
+                role_class=f"Role_{i}",
+                name=f"Position_{i}",
+            )
+
+    benchmark.pedantic(run, iterations=1, rounds=10)

benchmarks/ontology/test_reuse.py

@@ -0,0 +1,43 @@
+import pytest
+
+from semantica.ontology.namespace_manager import NamespaceManager
+from semantica.ontology.reuse_manager import ReuseManager
+
+
+def test_namespace_iri_generation(benchmark):
+    """
+    High-throughput test for IRI Generation.
+    """
+    manager = NamespaceManager(base_uri="https://semantica.dev/bench/")
+    names = [f"EntityName_{i}" for i in range(1000)]
+
+    def run():
+        for name in names:
+            manager.generate_class_iri(name)
+
+    benchmark.pedantic(run, iterations=1, rounds=20)
+
+
+def test_ontology_merging(benchmark, large_ontology_definition):
+    """
+    Benchmarks merging two large entities together.
+    """
+    manager = ReuseManager()
+    target = large_ontology_definition.copy()
+    source = large_ontology_definition.copy()
+
+    new_classes = []
+
+    for c in source["classes"]:
+        base_id = c.get("uri") or c.get("name") or "UnkownEntity"
+        new_c = c.copy()
+        new_c["uri"] = f"{base_id}_merged"
+        new_classes.append(new_c)
+
+    source["classes"] = new_classes
+
+    def run():
+        t_copy = target.copy()
+        return manager.merge_ontology_data(t_copy, source, overwrite=False)
+
+    benchmark.pedantic(run, iterations=1, rounds=10)

benchmarks/ontology/test_serialization.py

@@ -0,0 +1,33 @@
+import pytest
+
+from semantica.ontology.owl_generator import OWLGenerator
+
+
+@pytest.mark.benchmark(group="serialization")
+@pytest.mark.parametrize("format", ["turtle", "xml"])
+def test_owl_serialization_formats(benchmark, large_ontology_definition, format):
+    """Benchmarks the cost of serializing the ontology
+    to different string formats.
+    """
+    generator = OWLGenerator()
+
+    def run():
+        return generator.generate_owl(large_ontology_definition, format=format)
+
+    benchmark.pedantic(run, iterations=1, rounds=5)
+
+
+def test_rdflib_graph_construction(benchmark, large_ontology_definition):
+    """
+    Benchmarks the creation of rdflib.Graph object.
+    """
+    generator = OWLGenerator()
+
+    def run():
+        if hasattr(generator, "_generate_with_rdflib"):
+            return generator._generate_with_rdflib(
+                large_ontology_definition, format="turtle"
+            )
+        return generator.generate_owl(large_ontology_definition)
+
+    benchmark.pedantic(run, iterations=1, rounds=5)

benchmarks/output_orchestration/test_execution_pipeline.py

@@ -0,0 +1,98 @@
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+from semantica.pipeline.execution_engine import ExecutionEngine
+from semantica.pipeline.pipeline_builder import PipelineBuilder, StepStatus
+from semantica.pipeline.resource_scheduler import ResourceScheduler
+
+
+# ~~ Fixtures
+@pytest.fixture(autouse=True)
+def kill_hardware_checks():
+    with patch.object(ResourceScheduler, "_initialize_resources", return_value=None):
+        yield
+
+
+@pytest.fixture(autouse=True)
+def kill_logging():
+    with patch("semantica.utils.logging.get_logger"):
+        yield
+
+
+@pytest.fixture(autouse=True)
+def kill_tracker():
+    mock_tracker = MagicMock()
+    mock_tracker.enabled = False
+    with patch(
+        "semantica.pipeline.execution_engine.get_progress_tracker",
+        return_value=mock_tracker,
+    ):
+        yield
+
+
+def create_pipeline(size):
+    """Helper to generate pipelines of random size."""
+    builder = PipelineBuilder()
+    builder.progress_tracker = MagicMock()
+    builder.progress_tracker.enabled = False
+    handler = lambda x, **k: x
+
+    builder.add_step("start", "dummy", handler=handler)
+    for i in range(1, size):
+        builder.add_step(f"step_{i}", "dummy", handler=handler)
+        builder.connect_steps("start" if i == 1 else f"step_{i-1}", f"step_{i}")
+
+    return builder.build(f"bench_pipe_{size}")
+
+
+# ~~ Benchmarks ~~
+
+
+@pytest.mark.parametrize("step_count", [10, 100, 500])
+def test_pipeline_construction_scaling(benchmark, step_count):
+    """
+    Verifies if construction time scales linearly.
+    """
+
+    def op():
+        builder = PipelineBuilder()
+        builder.progress_tracker = MagicMock()
+        for i in range(step_count):
+            builder.add_step(f"s{i}", "t")
+        return builder.build()
+
+    benchmark.pedantic(op, iterations=5, rounds=5)
+
+
+@pytest.mark.parametrize("step_count", [10, 100])
+def test_execution_overhead_scaling(benchmark, step_count):
+    """
+    Measures per-step overhead as it gets more complex
+    """
+    engine = ExecutionEngine()
+    pipeline = create_pipeline(step_count)
+
+    def setup_run():
+        for step in pipeline.steps:
+            step.status = StepStatus.PENDING
+            step.result = None
+        return (pipeline,), {"data": {"val": 1}}
+
+    def op(pipeline, data):
+        return engine.execute_pipeline(pipeline, data=data)
+
+    benchmark.pedantic(op, setup=setup_run, iterations=1, rounds=10)
+
+
+@pytest.mark.parametrize("step_count", [10, 100, 1000])
+def test_topological_sort_scaling(benchmark, step_count):
+    """
+    Stress test for dependency graph algorithm.
+    """
+    engine = ExecutionEngine()
+    pipeline = create_pipeline(step_count)
+
+    benchmark.pedantic(
+        lambda: engine._topological_sort(pipeline.steps), iterations=20, rounds=10
+    )

benchmarks/output_orchestration/test_parallelism.py

@@ -0,0 +1,91 @@
+import time
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+from semantica.pipeline.parallelism_manager import ParallelismManager, Task
+from semantica.pipeline.resource_scheduler import ResourceScheduler
+
+
+# ~~ Fixtures ~~
+@pytest.fixture(autouse=True)
+def kill_hardware_checks():
+    with patch.object(ResourceScheduler, "_initialize_resources", return_value=None):
+        yield
+
+
+@pytest.fixture(autouse=True)
+def kill_logging():
+    with patch("semantica.utils.logging.get_logger"):
+        yield
+
+
+@pytest.fixture(autouse=True)
+def kill_tracker():
+    mock_tracker = MagicMock()
+    mock_tracker.enabled = False
+    with patch(
+        "semantica.pipeline.parallelism_manager.get_progress_tracker",
+        return_value=mock_tracker,
+    ):
+        yield
+
+
+def blocking_task(duration):
+    """Simulates a task that waits for I/O (like a DB query or API call)."""
+    time.sleep(duration)
+    return True
+
+
+@pytest.fixture
+def thread_manager():
+    return ParallelismManager(max_workers=4, use_processes=False)
+
+
+@pytest.fixture
+def process_manager():
+    return ParallelismManager(max_workers=4, use_processes=True)
+
+
+# ~~ BENCHMARKS ~~
+
+
+def test_parallel_vs_serial_io(benchmark, thread_manager):
+    """
+    Runs 4 tasks that sleep for 0.1s.
+    """
+    tasks = [
+        Task(task_id=f"t{i}", handler=blocking_task, args=(0.1,)) for i in range(4)
+    ]
+
+    def op():
+        return thread_manager.execute_parallel(tasks)
+
+    benchmark.pedantic(op, iterations=1, rounds=5)
+
+
+def test_thread_pool_overhead(benchmark, thread_manager):
+    """
+    Measures the raw cost of spinning up threads for zero-work tasks.
+    """
+    # No-op handler
+    noop = lambda: None
+    tasks = [Task(task_id=f"t{i}", handler=noop) for i in range(100)]
+
+    def op():
+        return thread_manager.execute_parallel(tasks)
+
+    benchmark.pedantic(op, iterations=5, rounds=10)
+
+
+def test_process_pool_overhead(benchmark, process_manager):
+    """
+    Measures overhead of ProcessPoolExecutor
+    """
+    noop = lambda: None
+    tasks = [Task(task_id=f"t{i}", handler=noop) for i in range(10)]
+
+    def op():
+        return process_manager.execute_parallel(tasks)
+
+    benchmark.pedantic(op, iterations=1, rounds=5)

benchmarks/quality_assurance/test_conflicts.py

@@ -0,0 +1,84 @@
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+from semantica.deduplication.merge_strategy import MergeStrategy, MergeStrategyManager
+
+# Fixtures
+
+
+@pytest.fixture
+def conflict_manager():
+    """Returns a MergeStrategyManager with default settings."""
+    return MergeStrategyManager()
+
+
+@pytest.fixture
+def conflicting_entities_batch():
+    """
+    Generates a list of 100 entities that are all 'duplicates' of each other
+    but have conflicting property values. This forces the resolution logic to run hard.
+    """
+    entities = []
+    for i in range(100):
+        entities.append(
+            {
+                "id": "e_1",
+                "name": f"Entity Name {i}",
+                "type": "Person",
+                "confidence": 0.5 + (i * 0.005),
+                "properties": {
+                    "age": 20 + i,
+                    "email": f"user{i}@example.com",
+                    "status": "active" if i % 2 == 0 else "inactive",
+                },
+                "relationships": [
+                    {"source": "e_1", "target": f"other_{i}", "type": "knows"}
+                ],
+            }
+        )
+    return entities
+
+
+# Benchmarks
+
+
+def test_strategy_keep_highest_confidence(
+    benchmark, conflict_manager, conflicting_entities_batch
+):
+    """
+    Benchmarks 'KEEP_HIGHEST_CONFIDENCE'.
+    """
+
+    def op():
+        return conflict_manager.merge_entities(
+            conflicting_entities_batch, strategy=MergeStrategy.KEEP_HIGHEST_CONFIDENCE
+        )
+
+    benchmark.pedantic(op, iterations=10, rounds=10)
+
+
+def test_strategy_merge_all(benchmark, conflict_manager, conflicting_entities_batch):
+    """
+    Benchmarks 'MERGE_ALL'.
+    """
+
+    def op():
+        return conflict_manager.merge_entities(
+            conflicting_entities_batch, strategy=MergeStrategy.MERGE_ALL
+        )
+
+    benchmark.pedantic(op, iterations=10, rounds=10)
+
+
+def test_property_resolution_overhead(benchmark, conflict_manager):
+    """
+    Micro-benchmark for the inner _resolve_property_conflict logic.
+    """
+
+    def op():
+        return conflict_manager._resolve_property_conflict(
+            "age", 25, 30, MergeStrategy.KEEP_MOST_COMPLETE
+        )
+
+    benchmark.pedantic(op, iterations=1000, rounds=20)

benchmarks/quality_assurance/test_deduplication.py

@@ -0,0 +1,338 @@
+import random
+import string
+import time
+from typing import Any, Dict, List
+from unittest.mock import patch
+
+import numpy as np
+import pytest
+
+from semantica.deduplication.cluster_builder import ClusterBuilder
+from semantica.deduplication.duplicate_detector import DuplicateDetector
+from semantica.deduplication.entity_merger import EntityMerger
+from semantica.deduplication.similarity_calculator import SimilarityCalculator
+
+# Infra
+
+
+class NullTracker:
+    """
+    Discards all data to prevent memory leaks
+    """
+
+    def start_tracking(self, *args, **kwargs):
+        return "dummy_id"
+
+    def update_tracking(self, *args, **kwargs):
+        pass
+
+    def stop_tracking(self, *args, **kwargs):
+        pass
+
+    def register_pipeline_modules(self, *args, **kwargs):
+        pass
+
+    def clear_pipeline_context(self, *args, **kwargs):
+        pass
+
+    def update_progress(self, *args, **kwargs):
+        pass
+
+    @property
+    def enabled(self):
+        return False
+
+    @enabled.setter
+    def enabled(self, value):
+        pass
+
+
+@pytest.fixture(autouse=True)
+def kill_io_overhead():
+    """
+    Replaces ProgressTracker with NullTracker globally.
+    """
+    with patch("semantica.utils.logging.get_logger"), patch(
+        "semantica.utils.progress_tracker.get_progress_tracker"
+    ) as mock_getter:
+
+        mock_getter.return_value = NullTracker()
+
+        with patch(
+            "semantica.deduplication.similarity_calculator.get_progress_tracker",
+            return_value=NullTracker(),
+        ), patch(
+            "semantica.deduplication.duplicate_detector.get_progress_tracker",
+            return_value=NullTracker(),
+        ), patch(
+            "semantica.deduplication.cluster_builder.get_progress_tracker",
+            return_value=NullTracker(),
+        ):
+            yield
+
+
+# Sim data
+
+
+def generate_entity_cluster(base_name: str, size: int) -> List[Dict[str, Any]]:
+    """
+    Generates a cluster of similar entities based on a seed name.
+    Example: "Apple" -> ["Apple Inc", "Apple Corp", etc.]
+    """
+
+    entities = []
+    suffixes = ["Inc", "Corp", "Ltd", "Gmbh", "LLC", "Group", "Systems"]
+
+    for i in range(size):
+        if random.random() < 0.8:
+            name = f"{base_name} {random.choice(suffixes)}"
+        else:
+            # Generating a typo for our calc to work on
+            chars = list(base_name)
+            if len(chars) > 2:
+                idx = random.randint(0, len(chars) - 2)
+                chars[idx], chars[idx + 1] = chars[idx + 1], chars[idx]
+            name = "".join(chars)
+
+        entities.append(
+            {
+                "id": f"{base_name.lower()}_{i}",
+                "name": name,
+                "type": "Organization",
+                "properties": {
+                    "location": "USA" if i % 2 == 0 else "California",
+                    "sector": "Tech",
+                    "employee_count": 100 + i,
+                },
+            }
+        )
+
+    return entities
+
+
+def generate_relationship_dataset(size: int) -> List[Dict[str, Any]]:
+    """
+    Generates a dataset of graph relationships/triplets.
+    Includes exact matches, synonym predicates, and dirty literal strings.
+    """
+    relationships = []
+    predicates = ["works_for", "employed_by", "is_employee_of", "has_employer"]
+    
+    for i in range(size):
+        # Base relationship
+        rel = {
+            "subject": f"Person_{i % 50}",
+            "predicate": random.choice(predicates),
+            "object": f"Company_{i % 10}"
+        }
+        relationships.append(rel)
+        
+        # Inject semantic duplicates (dirty literals / synonym predicates)
+        if random.random() < 0.4:
+            dirty_rel = {
+                "subject": f"Person_{i % 50}",
+                "predicate": random.choice(predicates),
+                "object": f"  Company_{i % 10} Inc.  " 
+            }
+            relationships.append(dirty_rel)
+            
+    return relationships
+
+
+def generate_dataset(
+    num_clusters: int, items_per_cluster: int, worst_case_blocking: bool = False
+):
+    """
+    Generates a full dataset
+
+    Args:
+      worst_case_blocking: If True, all names start with 'A' to defeat
+                           first-char blocking strategy in SimilarityCalculator.
+
+    """
+    dataset = []
+    for i in range(num_clusters):
+        if worst_case_blocking:
+            # All starts with 'A'
+            base_name = f"A_Company_{i}"
+        else:
+            start_char = random.choice(string.ascii_uppercase)
+            base_name = f"{start_char}_company_{i}"
+
+        cluster = generate_entity_cluster(base_name, items_per_cluster)
+        dataset.extend(cluster)
+
+    return dataset
+
+
+# ~~ Benchmarks ~~
+
+
+@pytest.mark.parametrize("method", ["levenshtein", "jaro_winkler"])
+def test_string_metric_speed(benchmark, method):
+    """
+    Measures the speed of string comparison algos.
+    """
+
+    calc = SimilarityCalculator()
+    s1 = "International Business Machines Corporation"
+    s2 = "International Business Machine Corp."
+
+    benchmark.pedantic(
+        lambda: calc.calculate_string_similarity(s1, s2, method=method),
+        iterations=1000,
+        rounds=100,
+    )
+
+
+def test_full_similarity_calculation(benchmark):
+    """
+    Measures weighted multi-factor calculation overhead.
+    (String + Property + Relationship + Weights).
+    """
+
+    calc = SimilarityCalculator(
+        string_weight=0.5, property_weight=0.3, relationship_weight=0.2
+    )
+
+    e1 = {
+        "name": "Acme Corp",
+        "properties": {"loc": "NY", "id": "123"},
+        "relationships": [{"target": "t1"}, {"target": "t2"}],
+    }
+
+    e2 = {
+        "name": "Acme Inc",
+        "properties": {"loc": "NY", "id": "123"},
+        "relationships": [{"target": "t1"}, {"target": "t2"}],
+    }
+
+    benchmark.pedantic(
+        lambda: calc.calculate_similarity(e1, e2), iterations=1000, rounds=50
+    )
+
+
+@pytest.mark.parametrize("dataset_size", [100, 500])
+def test_duplicate_detection_scaling_opt(benchmark, dataset_size):
+    """
+    Tests duplication on a 'Distributed' dataset (Best Case)
+    Now utilizing V2 Candidate Generation to ensure no regressions.
+    """
+    data = generate_dataset(
+        num_clusters=dataset_size // 10, items_per_cluster=10, worst_case_blocking=False
+    )
+    
+    detector = DuplicateDetector(
+        similarity_threshold=0.8,
+        similarity={
+            "candidate_strategy": "blocking_v2", 
+            "max_candidates_per_entity": 50,
+            "prefilter_enabled": True,
+            "score_breakdown_enabled": True,
+            "prefilter_thresholds": {
+                "min_length_ratio": 0.4,
+                "require_shared_token": True
+            }
+        }
+    )
+
+    benchmark.pedantic(lambda: detector.detect_duplicates(data), iterations=1, rounds=5)
+
+
+@pytest.mark.parametrize("dataset_size", [100, 500])
+def test_duplicate_detection_worst_Case(benchmark, dataset_size):
+    """
+    Tests detection on a 'Clustered' dataset (Worst Case).
+    Now utilizing V2 Candidate Generation to cut the pair explosion.
+    """
+    data = generate_dataset(
+        num_clusters=dataset_size // 10, items_per_cluster=10, worst_case_blocking=True
+    )
+    
+    detector = DuplicateDetector(
+        similarity_threshold=0.8,
+        similarity={
+            "candidate_strategy": "blocking_v2", 
+            "max_candidates_per_entity": 50,
+            "prefilter_enabled": True,
+            "score_breakdown_enabled": True,
+            "prefilter_thresholds": {
+                "min_length_ratio": 0.4,
+                "require_shared_token": True
+            }
+        }
+    )
+
+    benchmark.pedantic(lambda: detector.detect_duplicates(data), iterations=1, rounds=5)
+
+
+def test_incremental_detection_speed(benchmark):
+    """
+    Measures performance of adding new data to existing index.
+    """
+
+    existing = generate_dataset(num_clusters=50, items_per_cluster=5)
+    new_data = generate_dataset(num_clusters=5, items_per_cluster=2)
+
+    detector = DuplicateDetector()
+
+    benchmark.pedantic(
+        lambda: detector.incremental_detect(new_data, existing), iterations=5, rounds=10
+    )
+
+
+@pytest.mark.parametrize("algo", ["graph", "hierarchical"])
+def test_clustering_strategy_performance(benchmark, algo):
+    """
+    Comapres Union-Fund (Graph) vs Hierarchical Clustering.
+    """
+
+    data = generate_dataset(num_clusters=20, items_per_cluster=10)
+
+    use_hierarchical = algo == "hierarchical"
+    builder = ClusterBuilder(use_hierarchical=use_hierarchical)
+
+    benchmark.pedantic(lambda: builder.build_clusters(data), iterations=1, rounds=5)
+
+
+def test_merge_entity_benchmark(benchmark):
+    """
+    Measures the cost of fusing entities / res conflicts.
+    """
+
+    group = generate_entity_cluster("MegaCorp", 50)
+    merger = EntityMerger()
+
+    benchmark.pedantic(
+        lambda: merger.merge_entity_group(group, strategy="keep_most_complete"),
+        iterations=10,
+        rounds=10,
+    )
+    
+
+@pytest.mark.parametrize("mode", ["legacy", "semantic_v2"])
+def test_relationship_dedup_speed(benchmark, mode):
+    """
+    Measures the speed of relationship/triplet deduplication.
+    Compares the O(N^2) legacy fallback vs the fast canonical hash path.
+    """
+    # Yields ~280 relationships (approx 39,000 comparisons in O(N^2))
+    relationships = generate_relationship_dataset(200) 
+    
+    detector = DuplicateDetector()
+    options = {
+        "threshold": 0.85,
+        "relationship_dedup_mode": mode,
+        "predicate_synonym_map": {
+            "works_for": "employed_by",
+            "is_employee_of": "employed_by",
+            "has_employer": "employed_by"
+        },
+        "literal_normalization_enabled": True
+    }
+
+    benchmark.pedantic(
+        lambda: detector.detect_relationship_duplicates(relationships, **options),
+        iterations=5,
+        rounds=10,
+    )

benchmarks/requirements.txt

@@ -0,0 +1,43 @@
+# Benchmark Tools
+
+pytest>=7.0.0
+pytest-benchmark>=4.0.0
+
+# Core Utils
+
+pydantic
+loguru
+chardet
+requests
+greenlet
+typing-extensions
+tqdm
+click
+rich
+
+numpy
+pandas
+networkx
+scikit-learn
+
+# Graph & Storage
+
+sqlalchemy
+rdflib
+neo4j
+redis
+
+# AI proc
+
+torch
+transformers
+sentence-transformers
+spacy
+beautifulsoup4
+lxml
+pypdf2
+python-docx
+openpyxl
+pillow
+feedparser
+GitPython

benchmarks/storage/test_embeddings.py

@@ -0,0 +1,180 @@
+from typing import Generator, List
+from unittest.mock import MagicMock, patch
+
+import numpy as np
+import pytest
+
+from semantica.embeddings.embedding_generator import EmbeddingGenerator
+from semantica.embeddings.graph_embedding_manager import GraphEmbeddingManager
+from semantica.embeddings.pooling_strategies import PoolingStrategyFactory
+from semantica.embeddings.text_embedder import TextEmbedder
+
+
+# Infra Mocks
+@pytest.fixture(autouse=True)
+def kill_io_overhead():
+    """Silences logging and tracker globally."""
+    with patch("semantica.utils.logging.get_logger"), patch(
+        "semantica.utils.progress_tracker.get_progress_tracker"
+    ) as mock_tracker:
+
+        tracker = MagicMock()
+        tracker.enabled = False
+        tracker._start_tracking.return_value = "dummy_id"
+        mock_tracker.return_value = tracker
+
+        with patch(
+            "semantica.embeddings.text_embedder.get_progress_tracker",
+            return_value=tracker,
+        ):
+            yield
+
+
+# __ Model Mocks __
+
+
+class MockSentenceTransformer:
+    """
+    Simulates ST.encode without loading the fat model itself.
+    """
+
+    def __init__(self, dim=384):
+        self.dim = dim
+
+    def encode(
+        self, sentences: List[str], normalize_embeddings=True, **kwargs
+    ) -> np.ndarray:
+        count = len(sentences)
+        return np.random.rand(count, self.dim).astype(np.float32)
+
+    def get_sentence_embedding_dimension(self):
+        return self.dim
+
+
+class MockFastEmbed:
+    """
+    Simulates FastEmbed.embed generator behavior.
+    """
+
+    def __init__(self, dim=384):
+        self.dim = dim
+
+    def embed(self, documents: List[str]) -> Generator[np.ndarray, None, None]:
+        for _ in documents:
+            yield np.random.rand(self.dim).astype(np.float32)
+
+
+# ~~ Fixtures ~~
+@pytest.fixture
+def text_embedder_st():
+    """
+    Text embedder configured with SentenceTransformer
+    """
+    embedder = TextEmbedder(method="sentence_transformers", model_name="mock-bert")
+    embedder.model = MockSentenceTransformer()
+    embedder.progress_tracker = MagicMock()
+    embedder.progress_tracker.enabled = False
+
+    return embedder
+
+
+@pytest.fixture
+def text_embedder_fast():
+    """
+    Text Embedder cofnigures with Mock FastEmbed.
+    """
+
+    embedder = TextEmbedder(method="fastembed", model_name="mock-bge")
+    embedder.fastembed_model = MockFastEmbed()
+    embedder.progress_tracker = MagicMock()
+    embedder.progress_tracker.enabled = False
+    return embedder
+
+
+# ~~ Benchmarks
+
+
+@pytest.mark.parametrize("strategy", ["mean", "max", "cls", "attention"])
+def test_pooling_math_speed(benchmark, strategy):
+    """
+    Measures the raw NumPy speed of pooling strategies.
+    Scenario: Pooling a batch of 128 token embeddings.
+    """
+
+    embeddings = np.random.rand(128, 768).astype(np.float32)
+    pooler = PoolingStrategyFactory.create(strategy)
+
+    benchmark.pedantic(lambda: pooler.pool(embeddings), iterations=1000, rounds=100)
+
+
+def test_hierarchical_pooling_overhead(benchmark):
+    """
+    Measures the overhead of two-step hierarchical pooling.
+    """
+
+    embeddings = np.random.rand(1000, 768).astype(np.float32)
+    pooler = PoolingStrategyFactory.create("hierarchical", chunk_size=100)
+
+    benchmark.pedantic(lambda: pooler.pool(embeddings), iterations=500, rounds=50)
+
+
+def test_st_wrapper_overhead(benchmark, text_embedder_st):
+    """
+    Measures overhead of TextEmbedder wrapper around SentenceTransformers.
+    """
+
+    text = "This is a whatever we are doing here since idk"
+
+    benchmark.pedantic(
+        lambda: text_embedder_st.embed_text(text), iterations=1000, rounds=20
+    )
+
+
+def test_fastembed_generator_consumption(benchmark, text_embedder_fast):
+    """
+    Measures the cost of consuming the FastEmbed generator
+    and converting to Array.
+    """
+    texts = [f"Sentence {i}" for i in range(20)]
+
+    benchmark.pedantic(
+        lambda: text_embedder_fast.embed_batch(texts), iterations=100, rounds=20
+    )
+
+
+@pytest.mark.parametrize("batch_size", [10, 100, 1000])
+def test_batch_processing_pipeline(benchmark, batch_size, text_embedder_st):
+    """
+    Measures the full EmbeddingGenerator pipeline:
+    Input validation -> Type detection -> Batching -> Mock Model -> Error handling.
+    """
+
+    generator = EmbeddingGenerator()
+
+    generator.text_embedder = text_embedder_st
+    generator.progress_tracker = MagicMock()
+    generator.progress_tracker.enabled = False
+
+    data = [f"Item {i}" for i in range(batch_size)]
+
+    benchmark.pedantic(lambda: generator.process_batch(data), iterations=5, rounds=10)
+
+
+@pytest.mark.parametrize("count", [100, 1000])
+def test_graph_embedding_prep(benchmark, count, text_embedder_st):
+    """
+    Measures how fast we can reshape dict for GraphDBs
+    """
+    manager = GraphEmbeddingManager()
+    manager.embedding_generator.text_embedder = text_embedder_st
+
+    manager.embedding_generator.generate_embeddings = MagicMock(
+        return_value=np.random.rand(count, 384).astype(np.float32)
+    )
+
+    entities = [{"id": f"e{i}", "text": f"Entity{i}"} for i in range(count)]
+
+    def op():
+        return manager.prepare_for_graph_db(entities, backend="neo4j")
+
+    benchmark.pedantic(op, iterations=10, rounds=10)

benchmarks/storage/test_graph_store.py

@@ -0,0 +1,137 @@
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+from semantica.graph_store.graph_store import GraphStore
+
+
+@pytest.fixture
+def mock_neo4j_driver():
+    """
+    Creates a mock of of Neo4j Driver
+    Simulates: Driver -> Session -> Transaction -> Result -> Record
+    """
+
+    mock_result = MagicMock()
+    fake_props = {"name": "TestNode", "age": 30}
+
+    def get_item(key):
+        if key == "id":
+            return 12345
+        if key == "n":
+            return fake_props
+        if key == "count":
+            return 42
+        return None
+
+    mock_record = MagicMock()
+    mock_record.__getitem__.side_effect = get_item
+    mock_record.keys.return_value = ["id", "n"]
+    mock_record.values.return_value = [12345, fake_props]
+
+    # dict conversion - essentially doing it because the db sometimes demands it
+    mock_record.items.return_value = [("id", 12345), ("n", fake_props)]
+
+    # ~~ Result Methods ~~
+    mock_result = MagicMock()
+    mock_result.single.return_value = mock_record
+    mock_result.__iter__.side_effect = lambda: iter([mock_record])
+
+    # ~~ Session ~~
+    mock_session = MagicMock()
+    mock_session.run.return_value = mock_result
+    mock_session.__enter__.return_value = mock_session
+    mock_session.__exit__.return_value = None
+
+    # ~~ Driver ~~
+    mock_driver = MagicMock()
+    mock_driver.session.return_value = mock_session
+    mock_driver.verify_connectivity.return_value = True
+
+    return mock_driver
+
+
+@pytest.fixture
+def graph_store(mock_neo4j_driver):
+    """
+    Returns a GraphsStore connected to mnock driver.
+    """
+
+    # ~~ Patch GraphDatbase ~~
+    with patch("semantica.graph_store.neo4j_store.GraphDatabase") as mockDB:
+        mockDB.driver.return_value = mock_neo4j_driver
+        store = GraphStore(
+            backend="neo4j", uri="bolt://mock:7687", user="mock", password="mock"
+        )
+        store.connect()
+
+        if hasattr(store, "progress_tracker"):
+            store.progress_tracker = MagicMock()
+
+        return store
+
+
+#    ~~ Benchmarks ~~
+
+
+def test_node_creation_overhead(benchmark, graph_store):
+    """
+    Benchamrks the full stack overhead for creating a single node.
+    Path: GraphStore -> NodeManager -> Neo4jStore, Driver
+    """
+
+    def op():
+        return graph_store.create_node(
+            labels=["Person"], properties={"name": "Alexander", "age": 17}
+        )
+
+    result = benchmark(op)
+    assert result["id"] == 12345
+
+
+def test_batch_node_creation_overhead(benchmark, graph_store):
+    """
+    Benchmarks the loop overhead in create_nodes (Batch).
+    Checks if it handles lists efficiently.
+    """
+
+    nodes = [{"labels": ["Person"], "properties": {"id": i}} for i in range(50)]
+
+    def op():
+        return graph_store.create_nodes(nodes)
+
+    result = benchmark(op)
+    assert len(result) == 50
+
+
+def test_query_construction_and_parsing(benchmark, graph_store):
+    """
+    Benchmarks every execution overhead.
+    Measures how fast `QueryEngine` parses result into a Python dict.
+    """
+
+    query = "MATCH ( n:Person) RETURN n LIMIT 1"
+
+    def op():
+        return graph_store.execute_query(query)
+
+    result = benchmark(op)
+    assert result["success"] is True
+    assert len(result["records"]) > 0
+
+
+def test_analytics_shortest_path_overhead(benchmark, graph_store):
+    """
+    Benchmarks the wrapper overhead for graph analytics.
+    """
+
+    def op():
+        return graph_store.shortest_path(
+            start_node_id=1, end_node_id=2, rel_type="KNOWS"
+        )
+
+    try:
+        benchmark(op)
+    except Exception:
+        # v pass as we are only trying to benchmark the function overhead call mainly
+        pass

benchmarks/storage/test_triplet_storage.py

@@ -0,0 +1,146 @@
+import time
+from dataclasses import dataclass
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+from semantica.triplet_store.bulk_loader import BulkLoader
+from semantica.triplet_store.jena_store import JenaStore
+from semantica.triplet_store.triplet_store import TripletStore
+
+# ~~ Mocking ~~
+# We basically define a facile Triplet class for creating ds devoid of fat AI models
+
+
+@dataclass
+class SimpleTriplet:
+    subject: str
+    predicate: str
+    object: str
+    confidence: float = 1.0
+
+
+# ~~ Fixtures ~~
+@pytest.fixture
+def triplet_batch():
+    """Generates 1000 triplets."""
+    return [
+        SimpleTriplet(
+            subject=f"http://gandhara.org/entity/{i}",
+            predicate="http://gandhara.org/relation/knows",
+            object=f"http://example.org/entity/{i+1}",
+        )
+        for i in range(1000)
+    ]
+
+
+@pytest.fixture
+def large_knowledge_graph_dict():
+    """
+    Generates a large dict (1000 ent) to test parsing
+    logic in `TripletStore.store()`
+    """
+    entities = [
+        {
+            "id": f"ent_{i}",
+            "type": "Person",
+            "properties": {"name": f"Person {i}", "age": 60},
+        }
+        for i in range(1000)
+    ]
+    relationships = [
+        {"source": f"ent_{i}", "target": f"ent_{i+1}", "type": "KNOWS"}
+        for i in range(999)
+    ]
+
+    return {"entities": entities, "relationships": relationships}
+
+
+@pytest.fixture
+def in_memory_store():
+    """Returns a real JenaStore using RDFLib (In-Mmeory)."""
+
+    store = JenaStore(endpoint=None)
+    if store.graph is None:
+        pytest.fail("JenaStore failed to initialize rdflib graph.")
+    if hasattr(store, "progress_tracker"):
+        store.progress_tracker = MagicMock()
+
+    return store
+
+
+# ~~ Benchmarks ~~
+
+
+def test_rdflib_insert_throughput(benchmark, in_memory_store, triplet_batch):
+    """
+    Benchmarks raw Write Speed to in-memory RDF graph.
+    Is our baseline
+    """
+
+    def op():
+        in_memory_store.add_triplets(triplet_batch)
+
+    benchmark(op)
+
+    assert len(in_memory_store.graph) >= 1000
+
+
+def test_triplet_conversion_overhead(benchmark, large_knowledge_graph_dict):
+    """
+    Benchmarks the `store()` method in TripletStore.
+    This tests Python logic that converts a Dict -> Triplet objects.
+    """
+
+    with patch("semantica.triplet_store.blazegraph_store.BlazegraphStore") as mockBE:
+        mock_instance = mockBE.return_value
+        mock_instance.add_triplets.return_value = {"success": True}
+
+        manager = TripletStore(backend="blazegraph")
+        if hasattr(manager, "progress_tracker"):
+            manager.progress_tracker = MagicMock()
+
+        def op():
+            manager.store(
+                knowledge_graph=large_knowledge_graph_dict,
+                ontology={"classes": [], "properties": []},
+            )
+
+        benchmark(op)
+
+
+def test_bulk_loader_logic(benchmark, triplet_batch):
+    """
+    Benchmarks teh BulkLoader class.
+    Measures the overhead of batching, retries and progress tracking.
+    """
+
+    loader = BulkLoader(batch_size=100)
+    if hasattr(loader, "progress_tracker"):
+        loader.progress_tracker = MagicMock()
+
+    mock_store = MagicMock()
+    mock_store.add_triplets.return_value = {"success": True}
+
+    def op():
+        return loader.load_triplets(triplet_batch, mock_store)
+
+    result = benchmark(op)
+    assert result.total_batches == 10
+
+
+def test_sparql_query_performance(benchmark, in_memory_store, triplet_batch):
+    """
+    Benchamrks SPARQL query execution speed on 1000 items.
+    """
+
+    in_memory_store.add_triplets(triplet_batch)
+
+    query = "SELECT ?s ?o WHERE { ?s <http://gandhara.org/relation/knows> ?o } LIMIT 50"
+
+    def op():
+        return in_memory_store.execute_sparql(query)
+
+    result = benchmark(op)
+    assert result["success"] is True
+    assert len(result["bindings"]) == 50

benchmarks/storage/test_vector_storage.py

@@ -0,0 +1,94 @@
+from unittest.mock import MagicMock, patch
+
+import numpy as np
+import pytest
+
+from semantica.vector_store.faiss_store import FAISSStore
+from semantica.vector_store.vector_store import VectorStore
+
+# Fixtures
+
+
+@pytest.fixture
+def vector_dim():
+    return 768
+
+
+@pytest.fixture
+def random_vectors(vector_dim):
+    """Generates a batch of 10,000 rando vectors."""
+    count = 10000
+    vectors = np.random.rand(count, vector_dim).astype(np.float32)
+    return vectors
+
+
+@pytest.fixture
+def populated_store(random_vectors, vector_dim):
+    """
+    Returns a FAISS store bred with data.
+    """
+
+    store = FAISSStore(dimension=vector_dim)
+    if hasattr(store, "progress_tracker"):
+        store.progress_tracker = MagicMock()
+    store.create_index(index_type="flat")
+    store.add_vectors(random_vectors)
+    return store
+
+
+# Benchmarks
+
+
+def test_faiss_insert_throughput(benchmark, random_vectors, vector_dim):
+    """
+    Benchmarks raw Write speed to FAISS
+    """
+    store = FAISSStore(dimension=vector_dim)
+    if hasattr(store, "progress_tracker"):
+        store.progress_tracker = MagicMock()
+    store.create_index(index_type="flat")
+
+    def insert_op():
+        store.add_vectors(random_vectors)
+
+    benchmark(insert_op)
+
+    assert len(store.index.vector_ids) >= 10000
+
+
+def test_faiss_search_latency(benchmark, populated_store, vector_dim):
+    """
+    Benchmarks Read/Search speed
+    """
+
+    query = np.random.rand(1, vector_dim).astype(np.float32)
+    results = benchmark(populated_store.search_similar, query_vector=query, k=10)
+    assert len(results) == 10
+
+
+def test_vector_storage_manager_overhead(benchmark, random_vectors, vector_dim):
+    """
+    Benchmarks the overhead of the VectorStore class
+    """
+    with patch(
+        "semantica.vector_store.vector_store.EmbeddingGenerator"
+    ) as MockEmbedder:
+        manager = VectorStore(backend="faiss", dimension=vector_dim)
+        if hasattr(manager, "progress_tracker"):
+            manager.progress_tracker = MagicMock()
+
+        def store_op():
+            manager.store_vectors(random_vectors)
+
+        benchmark(store_op)
+
+        # Check vectors were stored - handle both in-memory and backend stores
+        if hasattr(manager, 'vectors'):
+            # In-memory backend
+            assert len(manager.vectors) >= 10000
+        elif hasattr(manager, '_backend_store') and hasattr(manager._backend_store, 'vector_ids'):
+            # Backend store (like FAISS)
+            assert len(manager._backend_store.vector_ids) >= 10000
+        else:
+            # For other backends, just ensure no errors occurred
+            pass

benchmarks/visualization/conftest.py

@@ -0,0 +1,80 @@
+import random
+from typing import Any, Dict, List
+from unittest.mock import MagicMock, patch
+
+import numpy as np
+import pytest
+
+
+# Data Generators
+@pytest.fixture
+def generate_embeddings():
+    """Generates synthetic high-dim embeddings."""
+
+    def _gen(n_samples: int, n_features: int = 768):
+        return np.random.rand(n_samples, n_features).astype(np.float32)
+
+    return _gen
+
+
+@pytest.fixture
+def generate_knowledge_graph():
+    """Generates synthetic Knowledge Graph dictionary."""
+
+    def _gen(n_nodes: int, density: float = 0.05):
+        entities = [
+            {
+                "id": f"e_{i}",
+                "label": f"Entity_{i}",
+                "type": random.choice(["Person", "Organization", "Location", "Event"]),
+                "metadata": {"score": random.random()},
+            }
+            for i in range(n_nodes)
+        ]
+
+        relationships = []
+        n_edges = int(n_nodes * (n_nodes - 1) * density)
+        # Capping edges for safety
+        n_edges = min(n_edges, n_nodes * 5)
+
+        for i in range(n_edges):
+            src = random.randint(0, n_nodes - 1)
+            tgt = random.randint(0, n_nodes - 1)
+
+            if src != tgt:
+                relationships.append(
+                    {
+                        "source": f"e_{src}",
+                        "target": f"e_{tgt}",
+                        "type": "related_to",
+                        "metadata": {"weight": random.random()},
+                    }
+                )
+
+        return {"entities": entities, "relationships": relationships}
+
+    return _gen
+
+
+@pytest.fixture
+def generate_temporal_data(generate_knowledge_graph):
+    """Generates synthetic temporal graph snapshots."""
+
+    def _gen(n_snapshots: int, n_nodes: int):
+        timestamps_map = {}
+        base_kg = generate_knowledge_graph(n_nodes)
+        entities = base_kg["entities"]
+
+        all_years = list(range(2020, 2020 + n_snapshots))
+        for ent in entities:
+            start = random.randint(0, len(all_years) - 2)
+            duration = random.randint(1, len(all_years) - start)
+            timestamps_map[ent["id"]] = all_years[start : start + duration]
+
+        return {
+            "entities": entities,
+            "relationships": base_kg["relationships"],
+            "timestamps": timestamps_map,
+        }
+
+    return _gen

benchmarks/visualization/test_analytics_viz.py

@@ -0,0 +1,26 @@
+import random
+
+import pytest
+
+from semantica.visualization.analytics_visualizer import AnalyticsVisualizer
+
+
+@pytest.mark.benchmark(group="analytics_charts")
+def test_centrality_ranking_sort_and_render(benchmark):
+    """
+    Benchmarks sorting a large centrality dictionary
+    and rendering the Top N bar chart.
+    """
+    viz = AnalyticsVisualizer()
+
+    # Generate 5000 node scores
+    centrality_data = {
+        "centrality": {f"node_{i}": random.random() for i in range(5000)}
+    }
+
+    def run():
+        return viz.visualize_centrality_rankings(
+            centrality_data, centrality_type="degree", top_n=50, output="interactive"
+        )
+
+    benchmark.pedantic(run, iterations=1, rounds=10)

benchmarks/visualization/test_embedding_viz.py

@@ -0,0 +1,45 @@
+import numpy as np
+import pytest
+
+from semantica.visualization.embedding_visualizer import EmbeddingVisualizer
+
+
+@pytest.mark.benchmark(group="embedding_projection")
+@pytest.mark.parametrize("method", ["pca", "tsne"])
+@pytest.mark.parametrize("n_samples", [500])
+def test_projection_calculation_overhead(
+    benchmark, generate_embeddings, method, n_samples
+):
+    """
+    Measures the combined cost of:
+    1. Dimensionality Reduction (Math)
+    2. Plotly Trace Construction (Object creation)
+    """
+
+    viz = EmbeddingVisualizer()
+    embeddings = generate_embeddings(n_samples=n_samples, n_features=128)
+    labels = [f"Label {i}" for i in range(n_samples)]
+
+    def run():
+        return viz.visualize_2d_projection(
+            embeddings, labels=labels, method=method, output="interactive"
+        )
+
+    rounds = 5 if method == "tsne" else 10
+    benchmark.pedantic(run, iterations=1, rounds=rounds)
+
+
+@pytest.mark.benchmark(group="embedding_heatmap")
+def test_similarity_heatmap_generation(benchmark, generate_embeddings):
+    """
+    Benchmarks O(N^2) similarity matrix calculation
+    and heatmap renderin.
+    """
+
+    viz = EmbeddingVisualizer()
+    embeddings = generate_embeddings(n_samples=500, n_features=64)
+
+    def run():
+        return viz.visualize_similarity_heatmap(embeddings, output="interactive")
+
+    benchmark.pedantic(run, iterations=1, rounds=5)

benchmarks/visualization/test_kg_viz.py

@@ -0,0 +1,33 @@
+import pytest
+
+from semantica.visualization.kg_visualizer import KGVisualizer
+
+
+@pytest.mark.benchmark(group="graph_layouyt")
+@pytest.mark.parametrize("layout", ["circular", "force"])
+@pytest.mark.parametrize("size", [100])
+def test_network_layout_performance(benchmark, generate_knowledge_graph, layout, size):
+    """
+    Compares layout algorithm.
+    """
+    viz = KGVisualizer(layout=layout, force_layout_iterations=50)
+    graph = generate_knowledge_graph(n_nodes=size)
+
+    def run():
+        return viz.visualize_network(graph, output="interactive")
+
+    benchmark.pedantic(run, iterations=1, rounds=5)
+
+
+@pytest.mark.benchmark(group="graph_structure")
+def test_matrix_view_rendering(benchmark, generate_knowledge_graph):
+    """
+    Benchmarks the creation of an adjacent/relationship matrix.
+    """
+    viz = KGVisualizer()
+    graph = generate_knowledge_graph(n_nodes=500)
+
+    def run():
+        return viz.visualize_relationship_matrix(graph, output="interactive")
+
+    benchmark.pedantic(run, iterations=1, rounds=5)

benchmarks/visualization/test_temporal_viz.py

@@ -0,0 +1,39 @@
+import pytest
+
+from semantica.visualization.temporal_visualizer import TemporalVisualizer
+
+
+@pytest.mark.benchmark(group="temporal_animation")
+def test_network_evolution_frames(benchmark, generate_temporal_data):
+    """
+    Measures the cost of generating animation frames for Plotly.
+    """
+
+    temporal_data = generate_temporal_data(n_snapshots=5, n_nodes=100)
+    viz = TemporalVisualizer()
+
+    def run():
+        return viz.visualize_network_evolution(temporal_data, output="interactive")
+
+    benchmark.pedantic(run, iterations=1, rounds=5)
+
+
+@pytest.mark.benchmark(group="temporal_dashboard")
+def test_temporal_dashboard_assembly(benchmark, generate_temporal_data):
+    """
+    Benchmarks the creation of a multi-subplot dashboard.
+    """
+    temporal_data = generate_temporal_data(n_snapshots=20, n_nodes=200)
+    viz = TemporalVisualizer()
+
+    metrics = {
+        "Accuracy": [0.5 + i * 0.02 for i in range(20)],
+        "Loss": [1.0 - i * 0.04 for i in range(20)],
+    }
+
+    def run():
+        return viz.visualize_temporal_dashboard(
+            temporal_data, metrics=metrics, output="interactive"
+        )
+
+    benchmark.pedantic(run, iterations=1, rounds=5)

cookbook/advanced/snowflake_ingestion_examples.py

@@ -0,0 +1,411 @@
+"""
+Snowflake Ingestion Examples
+
+This module provides comprehensive examples of using the Snowflake ingestor.
+"""
+
+import os
+from datetime import datetime, timedelta
+
+from semantica.ingest import SnowflakeIngestor
+from semantica.utils.logging import get_logger
+
+logger = get_logger("snowflake_examples")
+
+
+def example_basic_ingestion():
+    """Example: Basic table ingestion."""
+    print("\n=== Example 1: Basic Table Ingestion ===\n")
+
+    # Initialize ingestor with password authentication
+    ingestor = SnowflakeIngestor(
+        account=os.getenv("SNOWFLAKE_ACCOUNT"),
+        user=os.getenv("SNOWFLAKE_USER"),
+        password=os.getenv("SNOWFLAKE_PASSWORD"),
+        warehouse="COMPUTE_WH",
+        database="SAMPLE_DB",
+        schema="PUBLIC",
+    )
+
+    # Ingest a table
+    data = ingestor.ingest_table("CUSTOMERS", limit=10)
+
+    print(f"Retrieved {data.row_count} rows")
+    print(f"Columns: {data.columns}")
+    print(f"\nFirst row:")
+    print(data.data[0])
+
+    ingestor.close()
+
+
+def example_query_execution():
+    """Example: Execute custom SQL queries."""
+    print("\n=== Example 2: Query Execution ===\n")
+
+    ingestor = SnowflakeIngestor()
+
+    # Execute aggregation query
+    query = """
+        SELECT 
+            COUNTRY,
+            COUNT(*) AS CUSTOMER_COUNT,
+            SUM(TOTAL_PURCHASES) AS TOTAL_REVENUE
+        FROM CUSTOMERS
+        GROUP BY COUNTRY
+        ORDER BY TOTAL_REVENUE DESC
+        LIMIT 10
+    """
+
+    data = ingestor.ingest_query(query)
+
+    print(f"Top 10 countries by revenue:")
+    for row in data.data:
+        print(
+            f"  {row['COUNTRY']}: {row['CUSTOMER_COUNT']} customers, "
+            f"${row['TOTAL_REVENUE']:,.2f} revenue"
+        )
+
+    ingestor.close()
+
+
+def example_parameterized_query():
+    """Example: Parameterized queries."""
+    print("\n=== Example 3: Parameterized Queries ===\n")
+
+    ingestor = SnowflakeIngestor()
+
+    # Calculate date range
+    end_date = datetime.now()
+    start_date = end_date - timedelta(days=30)
+
+    # Execute parameterized query
+    query = """
+        SELECT 
+            ORDER_ID,
+            CUSTOMER_ID,
+            PRODUCT_NAME,
+            AMOUNT,
+            ORDER_DATE
+        FROM ORDERS
+        WHERE ORDER_DATE BETWEEN %(start_date)s AND %(end_date)s
+          AND AMOUNT > %(min_amount)s
+        ORDER BY ORDER_DATE DESC
+    """
+
+    data = ingestor.ingest_query(
+        query,
+        params={
+            "start_date": start_date.strftime("%Y-%m-%d"),
+            "end_date": end_date.strftime("%Y-%m-%d"),
+            "min_amount": 100.0,
+        },
+    )
+
+    print(f"Found {data.row_count} orders in the last 30 days over $100")
+
+    ingestor.close()
+
+
+def example_schema_introspection():
+    """Example: Table schema introspection."""
+    print("\n=== Example 4: Schema Introspection ===\n")
+
+    ingestor = SnowflakeIngestor()
+
+    # Get table schema
+    schema = ingestor.get_table_schema("CUSTOMERS")
+
+    print("Table schema for CUSTOMERS:")
+    print(f"Primary keys: {schema['primary_keys']}\n")
+
+    print("Columns:")
+    for col in schema["columns"]:
+        nullable = "NULL" if col["nullable"] else "NOT NULL"
+        default = f" DEFAULT {col['default']}" if col["default"] else ""
+        print(f"  {col['name']}: {col['type']} {nullable}{default}")
+
+    ingestor.close()
+
+
+def example_list_tables():
+    """Example: List all tables in a schema."""
+    print("\n=== Example 5: List Tables ===\n")
+
+    ingestor = SnowflakeIngestor()
+
+    # List tables in current schema
+    tables = ingestor.list_tables()
+
+    print(f"Found {len(tables)} tables:")
+    for table in tables:
+        print(f"  - {table}")
+
+    ingestor.close()
+
+
+def example_pagination():
+    """Example: Paginate large result sets."""
+    print("\n=== Example 6: Pagination ===\n")
+
+    ingestor = SnowflakeIngestor()
+
+    PAGE_SIZE = 100
+    total_rows = 0
+
+    # Paginate through large table
+    page = 0
+    while True:
+        data = ingestor.ingest_table(
+            "LARGE_TABLE", limit=PAGE_SIZE, offset=page * PAGE_SIZE
+        )
+
+        if data.row_count == 0:
+            break
+
+        total_rows += data.row_count
+        print(f"Page {page + 1}: {data.row_count} rows")
+
+        # Process page
+        process_page(data)
+
+        page += 1
+
+    print(f"\nTotal rows processed: {total_rows}")
+
+    ingestor.close()
+
+
+def example_batch_processing():
+    """Example: Batch processing with fetchmany."""
+    print("\n=== Example 7: Batch Processing ===\n")
+
+    ingestor = SnowflakeIngestor()
+
+    # Execute query with batching
+    data = ingestor.ingest_query(
+        "SELECT * FROM LARGE_TABLE WHERE STATUS = 'ACTIVE'", batch_size=1000
+    )
+
+    print(f"Retrieved {data.row_count} rows in batches of 1000")
+
+    ingestor.close()
+
+
+def example_export_documents():
+    """Example: Export to Semantica document format."""
+    print("\n=== Example 8: Export as Documents ===\n")
+
+    ingestor = SnowflakeIngestor()
+
+    # Ingest product data
+    data = ingestor.ingest_table("PRODUCTS", limit=10)
+
+    # Convert to documents
+    documents = ingestor.export_as_documents(
+        data, id_field="PRODUCT_ID", text_fields=["PRODUCT_NAME", "DESCRIPTION"]
+    )
+
+    print(f"Exported {len(documents)} documents")
+    print("\nFirst document:")
+    print(f"  ID: {documents[0]['id']}")
+    print(f"  Text: {documents[0]['text'][:100]}...")
+    print(f"  Metadata: {documents[0]['metadata']}")
+
+    ingestor.close()
+
+
+def example_key_pair_auth():
+    """Example: Key-pair authentication."""
+    print("\n=== Example 9: Key-Pair Authentication ===\n")
+
+    ingestor = SnowflakeIngestor(
+        account=os.getenv("SNOWFLAKE_ACCOUNT"),
+        user=os.getenv("SNOWFLAKE_USER"),
+        private_key_path=os.getenv("SNOWFLAKE_PRIVATE_KEY_PATH"),
+        warehouse="COMPUTE_WH",
+    )
+
+    data = ingestor.ingest_table("CUSTOMERS", limit=5)
+    print(f"Successfully authenticated and retrieved {data.row_count} rows")
+
+    ingestor.close()
+
+
+def example_context_manager():
+    """Example: Using context manager."""
+    print("\n=== Example 10: Context Manager ===\n")
+
+    with SnowflakeIngestor() as ingestor:
+        data = ingestor.ingest_table("CUSTOMERS", limit=5)
+        print(f"Retrieved {data.row_count} rows")
+
+    # Connection automatically closed
+    print("Connection closed automatically")
+
+
+def example_multi_schema():
+    """Example: Multi-schema ingestion."""
+    print("\n=== Example 11: Multi-Schema Ingestion ===\n")
+
+    ingestor = SnowflakeIngestor()
+
+    # Ingest from different schemas
+    prod_customers = ingestor.ingest_table(
+        "CUSTOMERS", database="PROD_DB", schema="PUBLIC", limit=10
+    )
+
+    staging_customers = ingestor.ingest_table(
+        "CUSTOMERS", database="STAGING_DB", schema="PUBLIC", limit=10
+    )
+
+    print(f"Production customers: {prod_customers.row_count}")
+    print(f"Staging customers: {staging_customers.row_count}")
+
+    ingestor.close()
+
+
+def example_error_handling():
+    """Example: Error handling."""
+    print("\n=== Example 12: Error Handling ===\n")
+
+    from semantica.utils.exceptions import ProcessingError, ValidationError
+
+    try:
+        # Try to connect with invalid credentials
+        ingestor = SnowflakeIngestor(
+            account="invalid_account", user="invalid_user", password="invalid_password"
+        )
+
+        data = ingestor.ingest_table("CUSTOMERS")
+
+    except ValidationError as e:
+        print(f"Validation error: {e}")
+
+    except ProcessingError as e:
+        print(f"Processing error: {e}")
+
+    except Exception as e:
+        print(f"Unexpected error: {e}")
+
+
+def example_incremental_load():
+    """Example: Incremental data loading."""
+    print("\n=== Example 13: Incremental Loading ===\n")
+
+    ingestor = SnowflakeIngestor()
+
+    # Get last load timestamp (from your metadata store)
+    last_load = get_last_load_timestamp()  # Your function
+
+    # Query only new/updated records
+    query = """
+        SELECT *
+        FROM CUSTOMERS
+        WHERE UPDATED_AT > %(last_load)s
+        ORDER BY UPDATED_AT ASC
+    """
+
+    data = ingestor.ingest_query(query, params={"last_load": last_load})
+
+    print(f"Loaded {data.row_count} new/updated records since {last_load}")
+
+    # Update last load timestamp
+    if data.row_count > 0:
+        update_last_load_timestamp(datetime.now())
+
+    ingestor.close()
+
+
+def example_etl_pipeline():
+    """Example: Full ETL pipeline."""
+    print("\n=== Example 14: ETL Pipeline ===\n")
+
+    # Extract
+    ingestor = SnowflakeIngestor()
+
+    sales_query = """
+        SELECT 
+            s.ORDER_ID,
+            s.CUSTOMER_ID,
+            c.CUSTOMER_NAME,
+            s.PRODUCT_ID,
+            p.PRODUCT_NAME,
+            s.AMOUNT,
+            s.ORDER_DATE
+        FROM SALES s
+        JOIN CUSTOMERS c ON s.CUSTOMER_ID = c.ID
+        JOIN PRODUCTS p ON s.PRODUCT_ID = p.ID
+        WHERE s.ORDER_DATE >= CURRENT_DATE - 7
+    """
+
+    data = ingestor.ingest_query(sales_query)
+    print(f"Extracted {data.row_count} sales records")
+
+    # Transform
+    documents = ingestor.export_as_documents(
+        data, id_field="ORDER_ID", text_fields=["CUSTOMER_NAME", "PRODUCT_NAME"]
+    )
+    print(f"Transformed to {len(documents)} documents")
+
+    # Load (into Semantica)
+    from semantica.pipeline import Pipeline
+
+    pipeline = Pipeline()
+
+    for doc in documents:
+        pipeline.process_document(doc)
+
+    print("Loaded documents into Semantica pipeline")
+
+    ingestor.close()
+
+
+# Utility functions for examples
+def process_page(data):
+    """Process a page of data."""
+    # Your processing logic here
+    pass
+
+
+def get_last_load_timestamp():
+    """Get the last load timestamp from metadata store."""
+    # Your implementation here
+    return (datetime.now() - timedelta(days=1)).strftime("%Y-%m-%d %H:%M:%S")
+
+
+def update_last_load_timestamp(timestamp):
+    """Update the last load timestamp in metadata store."""
+    # Your implementation here
+    pass
+
+
+def main():
+    """Run all examples."""
+    examples = [
+        example_basic_ingestion,
+        example_query_execution,
+        example_parameterized_query,
+        example_schema_introspection,
+        example_list_tables,
+        example_export_documents,
+        example_context_manager,
+        example_error_handling,
+    ]
+
+    for example_func in examples:
+        try:
+            example_func()
+        except Exception as e:
+            logger.error(f"Example {example_func.__name__} failed: {e}")
+
+
+if __name__ == "__main__":
+    # Set up environment variables
+    # export SNOWFLAKE_ACCOUNT=your_account
+    # export SNOWFLAKE_USER=your_user
+    # export SNOWFLAKE_PASSWORD=your_password
+    # export SNOWFLAKE_WAREHOUSE=COMPUTE_WH
+    # export SNOWFLAKE_DATABASE=SAMPLE_DB
+    # export SNOWFLAKE_SCHEMA=PUBLIC
+
+    main()

cookbook/introduction/15_Export.ipynb

@@ -178,6 +178,13 @@
     "rdf_exporter.export(kg, \"output.ttl\", format=\"turtle\")"
    ]
   },
+  {
+   "cell_type": "code",
+   "source": "# TTL alias: format=\"ttl\" is equivalent to format=\"turtle\"\nrdf_data = {\n    \"entities\": [\n        {\"id\": \"e1\", \"text\": \"Apple Inc.\", \"type\": \"ORG\", \"confidence\": 0.95},\n        {\"id\": \"e2\", \"text\": \"Steve Jobs\", \"type\": \"PERSON\", \"confidence\": 0.97},\n    ],\n    \"relationships\": [\n        {\"source_id\": \"e2\", \"target_id\": \"e1\", \"type\": \"founded_by\", \"confidence\": 0.91},\n    ],\n}\n\nrdf_exporter.export(rdf_data, \"output.ttl\", format=\"ttl\")\n\nresult = rdf_exporter.validate_rdf(rdf_data)\nprint(f\"Valid: {result['overall_valid']}\")",
+   "metadata": {},
+   "execution_count": null,
+   "outputs": []
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

cookbook/introduction/21_Amazon_Neptune_Store.ipynb

@@ -25,6 +25,57 @@
     "- AWS credentials configured (boto3, environment variables, or IAM role)\n",
     "- Network access to your Neptune cluster (VPC, security groups)\n",
     "\n",
+    "#### Quick Setup with CloudFormation\n",
+    "\n",
+    "If you don't have a Neptune cluster, use the provided CloudFormation template to create one with a public endpoint and IAM authentication:\n",
+    "\n",
+    "```bash\n",
+    "# Deploy the Neptune stack (takes ~15-20 minutes)\n",
+    "aws cloudformation create-stack \\\n",
+    "  --stack-name semantica-neptune \\\n",
+    "  --template-body file://neptune-setup.yaml \\\n",
+    "  --capabilities CAPABILITY_NAMED_IAM\n",
+    "\n",
+    "# Wait for stack creation to complete\n",
+    "aws cloudformation wait stack-create-complete --stack-name semantica-neptune\n",
+    "\n",
+    "# Get the outputs (endpoint, port, credentials)\n",
+    "aws cloudformation describe-stacks --stack-name semantica-neptune \\\n",
+    "  --query 'Stacks[0].Outputs' --output table\n",
+    "```\n",
+    "\n",
+    "The template creates:\n",
+    "- VPC with public subnets and Internet Gateway\n",
+    "- Neptune cluster (`db.t3.medium`) with IAM authentication enabled\n",
+    "- IAM user with least-privilege access for OpenCypher queries\n",
+    "- Security group allowing Bolt protocol (port 8182) access\n",
+    "\n",
+    "> ⚠️ **Security Note**: This template creates an IAM User with static access keys for simplicity in demo/test environments. For production use, we recommend IAM Roles (EC2 instance roles, ECS task roles, Lambda execution roles) which provide temporary credentials that are automatically rotated. The secret access key in the Cloudformation outputs is provided in plaintext to simplify initial setup - in production, use AWS Secrets Manager.\n",
+    "\n",
+    "**Outputs:**\n",
+    "- `NeptuneEndpoint` - Cluster hostname (use as `NEPTUNE_ENDPOINT`)\n",
+    "- `NeptunePort` - 8182 (use as `NEPTUNE_PORT`)\n",
+    "- `AwsAccessKeyId` - IAM user access key (use as `AWS_ACCESS_KEY_ID`)\n",
+    "- `AwsSecretAccessKey` - IAM user secret key in **plaintext** (use as `AWS_SECRET_ACCESS_KEY`)\n",
+    "- `AwsRegion` - Deployment region (use as `AWS_REGION`)\n",
+    "\n",
+    "**Cleanup:**\n",
+    "```bash\n",
+    "aws cloudformation delete-stack --stack-name semantica-neptune\n",
+    "```\n",
+    "\n",
+    "**Estimated Monthly Cost (approximately 100-105 USD/month at 100% utilization):**\n",
+    "\n",
+    "| Resource | Cost (USD) |\n",
+    "| --- | --- |\n",
+    "| Neptune db.t3.medium instance | ~96/month (0.132/hr) |\n",
+    "| Storage (10 GB) | ~1/month |\n",
+    "| I/O requests | ~1-5/month |\n",
+    "| Public IPv4 address | ~3.60/month (0.005/hr) |\n",
+    "| VPC, subnets, route tables, Internet Gateway, IAM | No Additional Charge |\n",
+    "\n",
+    "> **Free Tier**: New Neptune users get 30 days free (750 hours of db.t3.medium, 10M I/Os, 1 GB storage). Delete the stack when not in use to avoid charges.\n",
+    "\n",
     "---"
    ]
   },
@@ -70,14 +121,21 @@
     "import os\n",
     "\n",
     "# Neptune cluster configuration - REPLACE WITH YOUR VALUES\n",
+    "# (Get these from CloudFormation stack outputs)\n",
     "os.environ[\"NEPTUNE_ENDPOINT\"] = \"your-cluster.us-east-1.neptune.amazonaws.com\"\n",
     "os.environ[\"NEPTUNE_PORT\"] = \"8182\"\n",
     "os.environ[\"AWS_REGION\"] = \"us-east-1\"\n",
     "\n",
-    "# AWS credentials (if using IAM Auth and not relying on IAM role or ~/.aws/credentials)\n",
-    "# os.environ[\"AWS_ACCESS_KEY_ID\"] = \"your-access-key-id\"\n",
-    "# os.environ[\"AWS_SECRET_ACCESS_KEY\"] = \"your-secret-access-key\"\n",
-    "# os.environ[\"AWS_SESSION_TOKEN\"] = \"your-session-token\"\n",
+    "# AWS credentials for IAM Authentication\n",
+    "# Option 1: IAM User (static credentials from CloudFormation template)\n",
+    "# os.environ[\"AWS_ACCESS_KEY_ID\"] = \"AKIA...\"  # From AwsAccessKeyId output\n",
+    "# os.environ[\"AWS_SECRET_ACCESS_KEY\"] = \"...\"  # From AwsSecretAccessKey output\n",
+    "# Note: No AWS_SESSION_TOKEN needed for IAM users\n",
+    "\n",
+    "# Option 2: IAM Role / Temporary credentials (e.g., STS AssumeRole, EC2 instance role)\n",
+    "# os.environ[\"AWS_ACCESS_KEY_ID\"] = \"ASIA...\"  # Temporary access key\n",
+    "# os.environ[\"AWS_SECRET_ACCESS_KEY\"] = \"...\"  # Temporary secret key\n",
+    "# os.environ[\"AWS_SESSION_TOKEN\"] = \"...\"      # REQUIRED for temporary credentials\n",
     "\n",
     "print(f\"Neptune Endpoint: {os.environ.get('NEPTUNE_ENDPOINT')}\")\n",
     "print(f\"AWS Region: {os.environ.get('AWS_REGION')}\")"

cookbook/introduction/neptune-setup.yaml

@@ -0,0 +1,228 @@
+AWSTemplateFormatVersion: '2010-09-09'
+Description: >
+  Amazon Neptune cluster with public endpoint, IAM authentication, and least-privilege
+  IAM user for Semantica cookbook. Uses db.t3.medium (most cost-effective Neptune instance type).
+
+Parameters:
+  EnvironmentName:
+    Type: String
+    Default: semantica-neptune
+    Description: Environment name prefix for resource naming
+
+Resources:
+  # =============================================================================
+  # VPC & NETWORKING
+  # =============================================================================
+
+  VPC:
+    Type: AWS::EC2::VPC
+    Properties:
+      CidrBlock: 10.0.0.0/16
+      EnableDnsHostnames: true
+      EnableDnsSupport: true
+      Tags:
+        - Key: Name
+          Value: !Sub ${EnvironmentName}-vpc
+
+  InternetGateway:
+    Type: AWS::EC2::InternetGateway
+    Properties:
+      Tags:
+        - Key: Name
+          Value: !Sub ${EnvironmentName}-igw
+
+  InternetGatewayAttachment:
+    Type: AWS::EC2::VPCGatewayAttachment
+    Properties:
+      InternetGatewayId: !Ref InternetGateway
+      VpcId: !Ref VPC
+
+  PublicSubnet1:
+    Type: AWS::EC2::Subnet
+    Properties:
+      VpcId: !Ref VPC
+      AvailabilityZone: !Select [0, !GetAZs '']
+      CidrBlock: 10.0.1.0/24
+      MapPublicIpOnLaunch: true
+      Tags:
+        - Key: Name
+          Value: !Sub ${EnvironmentName}-public-subnet-1
+
+  PublicSubnet2:
+    Type: AWS::EC2::Subnet
+    Properties:
+      VpcId: !Ref VPC
+      AvailabilityZone: !Select [1, !GetAZs '']
+      CidrBlock: 10.0.2.0/24
+      MapPublicIpOnLaunch: true
+      Tags:
+        - Key: Name
+          Value: !Sub ${EnvironmentName}-public-subnet-2
+
+  PublicRouteTable:
+    Type: AWS::EC2::RouteTable
+    Properties:
+      VpcId: !Ref VPC
+      Tags:
+        - Key: Name
+          Value: !Sub ${EnvironmentName}-public-rt
+
+  DefaultPublicRoute:
+    Type: AWS::EC2::Route
+    DependsOn: InternetGatewayAttachment
+    Properties:
+      RouteTableId: !Ref PublicRouteTable
+      DestinationCidrBlock: 0.0.0.0/0
+      GatewayId: !Ref InternetGateway
+
+  PublicSubnet1RouteTableAssociation:
+    Type: AWS::EC2::SubnetRouteTableAssociation
+    Properties:
+      RouteTableId: !Ref PublicRouteTable
+      SubnetId: !Ref PublicSubnet1
+
+  PublicSubnet2RouteTableAssociation:
+    Type: AWS::EC2::SubnetRouteTableAssociation
+    Properties:
+      RouteTableId: !Ref PublicRouteTable
+      SubnetId: !Ref PublicSubnet2
+
+  # =============================================================================
+  # SECURITY GROUP
+  # =============================================================================
+
+  NeptuneSecurityGroup:
+    Type: AWS::EC2::SecurityGroup
+    Properties:
+      GroupName: !Sub ${EnvironmentName}-neptune-sg
+      GroupDescription: Security group for Neptune cluster - allows Bolt protocol access
+      VpcId: !Ref VPC
+      SecurityGroupIngress:
+        - IpProtocol: tcp
+          FromPort: 8182
+          ToPort: 8182
+          CidrIp: 0.0.0.0/0
+          Description: Allow Bolt protocol access from anywhere
+      SecurityGroupEgress:
+        - IpProtocol: -1
+          CidrIp: 0.0.0.0/0
+          Description: Allow all outbound traffic
+      Tags:
+        - Key: Name
+          Value: !Sub ${EnvironmentName}-neptune-sg
+
+  # =============================================================================
+  # NEPTUNE CLUSTER
+  # =============================================================================
+
+  NeptuneSubnetGroup:
+    Type: AWS::Neptune::DBSubnetGroup
+    Properties:
+      DBSubnetGroupDescription: Subnet group for Neptune cluster
+      DBSubnetGroupName: !Sub ${EnvironmentName}-subnet-group
+      SubnetIds:
+        - !Ref PublicSubnet1
+        - !Ref PublicSubnet2
+      Tags:
+        - Key: Name
+          Value: !Sub ${EnvironmentName}-subnet-group
+
+  NeptuneCluster:
+    Type: AWS::Neptune::DBCluster
+    Properties:
+      DBClusterIdentifier: !Sub ${EnvironmentName}-cluster
+      DBSubnetGroupName: !Ref NeptuneSubnetGroup
+      VpcSecurityGroupIds:
+        - !Ref NeptuneSecurityGroup
+      EngineVersion: '1.4.6.3'
+      IamAuthEnabled: true
+      StorageEncrypted: true
+      DeletionProtection: false
+      Tags:
+        - Key: Name
+          Value: !Sub ${EnvironmentName}-cluster
+
+  NeptuneInstance:
+    Type: AWS::Neptune::DBInstance
+    Properties:
+      DBInstanceIdentifier: !Sub ${EnvironmentName}-instance
+      DBInstanceClass: db.t3.medium
+      DBClusterIdentifier: !Ref NeptuneCluster
+      PubliclyAccessible: true
+      Tags:
+        - Key: Name
+          Value: !Sub ${EnvironmentName}-instance
+
+  # =============================================================================
+  # IAM USER WITH LEAST PRIVILEGES
+  # =============================================================================
+
+  NeptuneUser:
+    Type: AWS::IAM::User
+    Properties:
+      UserName: !Sub ${EnvironmentName}-user
+      Tags:
+        - Key: Name
+          Value: !Sub ${EnvironmentName}-user
+
+  NeptuneUserPolicy:
+    Type: AWS::IAM::Policy
+    Properties:
+      PolicyName: !Sub ${EnvironmentName}-neptune-access
+      Users:
+        - !Ref NeptuneUser
+      PolicyDocument:
+        Version: '2012-10-17'
+        Statement:
+          - Sid: NeptuneDataAccess
+            Effect: Allow
+            Action:
+              - neptune-db:connect
+              - neptune-db:ReadDataViaQuery
+              - neptune-db:WriteDataViaQuery
+              - neptune-db:DeleteDataViaQuery
+            Resource: !Sub
+              - arn:aws:neptune-db:${AWS::Region}:${AWS::AccountId}:${ClusterResourceId}/*
+              - ClusterResourceId: !GetAtt NeptuneCluster.ClusterResourceId
+
+  NeptuneUserAccessKey:
+    Type: AWS::IAM::AccessKey
+    Properties:
+      UserName: !Ref NeptuneUser
+
+# =============================================================================
+# OUTPUTS
+# =============================================================================
+
+Outputs:
+  NeptuneEndpoint:
+    Description: Neptune cluster endpoint (hostname only) - use as NEPTUNE_ENDPOINT
+    Value: !GetAtt NeptuneCluster.Endpoint
+
+  NeptunePort:
+    Description: Neptune cluster port - use as NEPTUNE_PORT
+    Value: !GetAtt NeptuneCluster.Port
+
+  AwsAccessKeyId:
+    Description: Access key ID for the Neptune IAM user - use as AWS_ACCESS_KEY_ID
+    Value: !Ref NeptuneUserAccessKey
+
+  AwsSecretAccessKey:
+    Description: Secret access key for the Neptune IAM user - use as AWS_SECRET_ACCESS_KEY
+    Value: !GetAtt NeptuneUserAccessKey.SecretAccessKey
+
+  AwsRegion:
+    Description: AWS region where Neptune is deployed - use as AWS_REGION
+    Value: !Ref AWS::Region
+
+  NeptuneClusterResourceId:
+    Description: Neptune cluster resource ID (for IAM policy reference)
+    Value: !GetAtt NeptuneCluster.ClusterResourceId
+
+  VpcId:
+    Description: VPC ID
+    Value: !Ref VPC
+
+  SecurityGroupId:
+    Description: Neptune security group ID
+    Value: !Ref NeptuneSecurityGroup

cookbook/use_cases/advanced_rag/01_GraphRAG_Complete.ipynb

@@ -110,7 +110,7 @@
    "source": [
     "# Set up API keys\n",
     "# Note: In production, use environment variables: export GROQ_API_KEY=\"your-key\"\n",
-    "os.environ[\"GROQ_API_KEY\"] = os.getenv(\"GROQ_API_KEY\", \"Your Groq API\")\n"
+    "os.environ[\"GROQ_API_KEY\"] = os.getenv(\"GROQ_API_KEY\", \"\")\n"
    ]
   },
   {

cookbook/use_cases/advanced_rag/02_RAG_vs_GraphRAG_Comparison.ipynb

@@ -30,7 +30,7 @@
     "# Environment Setup\n",
     "import os\n",
     "\n",
-    "os.environ['GROQ_API_KEY'] = os.getenv('GROQ_API_KEY', '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')\n",
+    "os.environ['GROQ_API_KEY'] = os.getenv('GROQ_API_KEY', '')\n",
     "\n",
     "# Install Semantica and all required dependencies\n",
     "%pip install -qU semantica networkx matplotlib plotly pandas faiss-cpu beautifulsoup4 groq sentence-transformers\n"
@@ -84,7 +84,7 @@
    "source": [
     "# Set up API keys\n",
     "# Note: In production, use environment variables: export GROQ_API_KEY=\"your-key\"\n",
-    "os.environ[\"GROQ_API_KEY\"] = os.getenv(\"GROQ_API_KEY\", \"your-groq-api-key-here\")\n",
+    "os.environ[\"GROQ_API_KEY\"] = os.getenv(\"GROQ_API_KEY\", \"\")\n",
     "\n",
     "print(\"API keys configured.\")\n"
    ]

cookbook/use_cases/biomedical/01_Drug_Discovery_Pipeline.ipynb

@@ -109,7 +109,7 @@
    "source": [
     "import os\n",
     "\n",
-    "os.environ[\"GROQ_API_KEY\"] = os.getenv(\"GROQ_API_KEY\", \"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\")\n"
+    "os.environ[\"GROQ_API_KEY\"] = os.getenv(\"GROQ_API_KEY\", \"\")\n"
    ]
   },
   {

cookbook/use_cases/biomedical/02_Genomic_Variant_Analysis.ipynb

@@ -85,7 +85,7 @@
    "source": [
     "import os\n",
     "\n",
-    "os.environ[\"GROQ_API_KEY\"] = os.getenv(\"GROQ_API_KEY\", \"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\")\n"
+    "os.environ[\"GROQ_API_KEY\"] = os.getenv(\"GROQ_API_KEY\", \"\")\n"
    ]
   },
   {

cookbook/use_cases/blockchain/01_DeFi_Protocol_Intelligence.ipynb

@@ -81,7 +81,7 @@
    "source": [
     "import os\n",
     "\n",
-    "os.environ[\"GROQ_API_KEY\"] = os.getenv(\"GROQ_API_KEY\", \"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\")\n",
+    "os.environ[\"GROQ_API_KEY\"] = os.getenv(\"GROQ_API_KEY\", \"\")\n",
     "\n",
     "# Configuration constants\n",
     "EMBEDDING_DIMENSION = 384\n",

cookbook/use_cases/capability_gap_defense/data/military_capability_gap_instances.ttl

@@ -0,0 +1,86 @@
+@prefix mcg: <https://example.org/mcg#> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+<https://example.org/mcg/instance-data> a owl:Ontology ;
+    rdfs:label "Military Capability Gap Analysis Instance Data" ;
+    owl:imports <https://example.org/mcg> .
+
+# Scenario and threat
+mcg:Scenario_FutureA2AD_2028 a mcg:Scenario ;
+    rdfs:label "Future A2/AD Escalation 2028" ;
+    mcg:hasThreat mcg:Threat_LowAltitudeSwarm .
+
+mcg:Threat_LowAltitudeSwarm a mcg:Threat ;
+    rdfs:label "Low-Altitude Swarm Threat" ;
+    mcg:relatedToIntelligenceReport mcg:IntelReport_RAND_RRA733_1 .
+
+# Mission thread and events
+mcg:MissionThread_ForceProtection a mcg:MissionThread ;
+    rdfs:label "Force Protection under Swarm Pressure" ;
+    mcg:missionPriority "high" ;
+    mcg:includesEvent mcg:Event_SwarmIncursion_001 ;
+    mcg:requiresCapability mcg:Capability_LowAltitudeDetection ;
+    mcg:revealsGap mcg:Gap_LowAltitudeDetectionCoverage .
+
+mcg:Scenario_FutureA2AD_2028 mcg:hasMissionThread mcg:MissionThread_ForceProtection .
+
+mcg:Event_SwarmIncursion_001 a mcg:OperationalEvent ;
+    rdfs:label "Swarm Incursion Event 001" ;
+    mcg:eventTime "2028-04-12T05:15:00Z"^^xsd:dateTime ;
+    mcg:stressesSystem mcg:System_GroundRadarLayer ;
+    mcg:relatedToWargameObservation mcg:WargameObs_ValleyIngress .
+
+# Systems and capabilities
+mcg:System_GroundRadarLayer a mcg:System ;
+    rdfs:label "Ground Radar Layer" ;
+    mcg:coveragePercent "42.0"^^xsd:decimal ;
+    mcg:relatedToAssetRecord mcg:AssetRecord_RadarFleet_2028Q1 .
+
+mcg:Capability_LowAltitudeDetection a mcg:Capability ;
+    rdfs:label "Low Altitude Detection Capability" ;
+    mcg:requiredCoveragePercent "75.0"^^xsd:decimal ;
+    mcg:providedBy mcg:System_GroundRadarLayer .
+
+# Gap and outcome
+mcg:Gap_LowAltitudeDetectionCoverage a mcg:CapabilityGap ;
+    rdfs:label "Insufficient Low-Altitude Detection Coverage" ;
+    mcg:gapInCapability mcg:Capability_LowAltitudeDetection ;
+    mcg:gapSeverity "critical" ;
+    mcg:increasesRiskOf mcg:Outcome_MissionRiskIncrease ;
+    mcg:triggersDecision mcg:Decision_CapGap_001 .
+
+mcg:Outcome_MissionRiskIncrease a mcg:Outcome ;
+    rdfs:label "Increased Mission Risk and Response Delay" .
+
+# Decision and recommendation
+mcg:Decision_CapGap_001 a mcg:Decision ;
+    rdfs:label "Capability Gap Decision 001" ;
+    mcg:confidenceScore "0.93"^^xsd:decimal ;
+    mcg:hasRecommendation mcg:Recommendation_MultiLayerSensorFusion ;
+    mcg:supportedByEvidence mcg:Evidence_E001 ;
+    mcg:wasAssessedBy mcg:AnalystCell_A1 .
+
+mcg:Recommendation_MultiLayerSensorFusion a mcg:Recommendation ;
+    mcg:recommendationText "Integrate layered sensing (ground radar, passive RF, EO/IR) and update mission doctrine for low-altitude swarm defense." .
+
+# Evidence and provenance
+mcg:Evidence_E001 a mcg:Evidence ;
+    mcg:evidenceQuote "Operational analysis indicates persistent low-altitude sensing shortfalls in contested terrain." ;
+    mcg:derivedFromDocument mcg:IntelReport_RAND_RRA733_1 .
+
+mcg:IntelReport_RAND_RRA733_1 a mcg:IntelligenceReport, prov:Entity ;
+    rdfs:label "RAND RRA733-1 Competing Without Fighting (2022)" .
+
+mcg:WargameObs_ValleyIngress a mcg:WargameObservation, prov:Entity ;
+    rdfs:label "Wargame Observation: Valley Ingress Routes" .
+
+mcg:AssetRecord_RadarFleet_2028Q1 a mcg:AssetInventoryRecord, prov:Entity ;
+    rdfs:label "Asset Inventory: Radar Fleet 2028 Q1" .
+
+mcg:AnalystCell_A1 a prov:Agent ;
+    rdfs:label "Joint Capability Assessment Cell A1" .
+

cookbook/use_cases/capability_gap_defense/data/military_capability_gap_ontology.ttl

@@ -0,0 +1,143 @@
+@prefix mcg: <https://example.org/mcg#> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
+@prefix d3f: <http://d3fend.mitre.org/ontologies/d3fend.owl#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+<https://example.org/mcg> a owl:Ontology ;
+    rdfs:label "Military Capability Gap Analysis Ontology" ;
+    rdfs:comment "Ontology for end-to-end military capability gap analysis with context graphs, multi-hop reasoning, and provenance." ;
+    owl:imports <http://www.w3.org/ns/prov> .
+
+# Classes
+mcg:Scenario a owl:Class .
+mcg:MissionThread a owl:Class .
+mcg:OperationalEvent a owl:Class .
+mcg:System a owl:Class .
+mcg:Capability a owl:Class .
+mcg:CapabilityGap a owl:Class .
+mcg:Outcome a owl:Class .
+mcg:Decision a owl:Class .
+mcg:Recommendation a owl:Class .
+mcg:Evidence a owl:Class .
+mcg:Threat a owl:Class .
+mcg:DoctrineDocument a owl:Class ;
+    rdfs:subClassOf prov:Entity .
+mcg:WargameObservation a owl:Class ;
+    rdfs:subClassOf prov:Entity .
+mcg:AssetInventoryRecord a owl:Class ;
+    rdfs:subClassOf prov:Entity .
+mcg:IntelligenceReport a owl:Class ;
+    rdfs:subClassOf prov:Entity .
+
+# Optional alignment points
+mcg:Sensor a owl:Class ;
+    rdfs:subClassOf mcg:System, d3f:D3FEND .
+
+# Object properties (context chain)
+mcg:hasMissionThread a owl:ObjectProperty ;
+    rdfs:domain mcg:Scenario ;
+    rdfs:range mcg:MissionThread .
+
+mcg:includesEvent a owl:ObjectProperty ;
+    rdfs:domain mcg:MissionThread ;
+    rdfs:range mcg:OperationalEvent .
+
+mcg:stressesSystem a owl:ObjectProperty ;
+    rdfs:domain mcg:OperationalEvent ;
+    rdfs:range mcg:System .
+
+mcg:requiresCapability a owl:ObjectProperty ;
+    rdfs:domain mcg:MissionThread ;
+    rdfs:range mcg:Capability .
+
+mcg:providedBy a owl:ObjectProperty ;
+    rdfs:domain mcg:Capability ;
+    rdfs:range mcg:System .
+
+mcg:revealsGap a owl:ObjectProperty ;
+    rdfs:domain mcg:MissionThread ;
+    rdfs:range mcg:CapabilityGap .
+
+mcg:gapInCapability a owl:ObjectProperty ;
+    rdfs:domain mcg:CapabilityGap ;
+    rdfs:range mcg:Capability .
+
+mcg:increasesRiskOf a owl:ObjectProperty ;
+    rdfs:domain mcg:CapabilityGap ;
+    rdfs:range mcg:Outcome .
+
+mcg:triggersDecision a owl:ObjectProperty ;
+    rdfs:domain mcg:CapabilityGap ;
+    rdfs:range mcg:Decision .
+
+mcg:hasRecommendation a owl:ObjectProperty ;
+    rdfs:domain mcg:Decision ;
+    rdfs:range mcg:Recommendation .
+
+mcg:supportedByEvidence a owl:ObjectProperty ;
+    rdfs:domain mcg:Decision ;
+    rdfs:range mcg:Evidence .
+
+mcg:hasThreat a owl:ObjectProperty ;
+    rdfs:domain mcg:Scenario ;
+    rdfs:range mcg:Threat .
+
+mcg:relatedToAssetRecord a owl:ObjectProperty ;
+    rdfs:domain mcg:System ;
+    rdfs:range mcg:AssetInventoryRecord .
+
+mcg:relatedToWargameObservation a owl:ObjectProperty ;
+    rdfs:domain mcg:OperationalEvent ;
+    rdfs:range mcg:WargameObservation .
+
+mcg:relatedToIntelligenceReport a owl:ObjectProperty ;
+    rdfs:domain mcg:Threat ;
+    rdfs:range mcg:IntelligenceReport .
+
+# Provenance properties
+mcg:derivedFromDocument a owl:ObjectProperty ;
+    rdfs:subPropertyOf prov:wasDerivedFrom ;
+    rdfs:domain mcg:Evidence ;
+    rdfs:range prov:Entity .
+
+mcg:wasAssessedBy a owl:ObjectProperty ;
+    rdfs:subPropertyOf prov:wasAssociatedWith ;
+    rdfs:domain mcg:Decision ;
+    rdfs:range prov:Agent .
+
+# Data properties
+mcg:coveragePercent a owl:DatatypeProperty ;
+    rdfs:domain mcg:System ;
+    rdfs:range xsd:decimal .
+
+mcg:requiredCoveragePercent a owl:DatatypeProperty ;
+    rdfs:domain mcg:Capability ;
+    rdfs:range xsd:decimal .
+
+mcg:gapSeverity a owl:DatatypeProperty ;
+    rdfs:domain mcg:CapabilityGap ;
+    rdfs:range xsd:string .
+
+mcg:confidenceScore a owl:DatatypeProperty ;
+    rdfs:domain mcg:Decision ;
+    rdfs:range xsd:decimal .
+
+mcg:missionPriority a owl:DatatypeProperty ;
+    rdfs:domain mcg:MissionThread ;
+    rdfs:range xsd:string .
+
+mcg:eventTime a owl:DatatypeProperty ;
+    rdfs:domain mcg:OperationalEvent ;
+    rdfs:range xsd:dateTime .
+
+mcg:recommendationText a owl:DatatypeProperty ;
+    rdfs:domain mcg:Recommendation ;
+    rdfs:range xsd:string .
+
+mcg:evidenceQuote a owl:DatatypeProperty ;
+    rdfs:domain mcg:Evidence ;
+    rdfs:range xsd:string .
+

cookbook/use_cases/capability_gap_defense/data/us_navy_it_strategic_plan_fy2023.pdf

@@ -0,0 +1 @@
+<html><head><title>Request Rejected </title></head><body>Sorry, the requested URL was rejected. Please consult with your administrator..<br><br>Your support ID is: <9627954236696643144><br><br><a href='javascript:history.back();'>[Go Back]</body></html>

cookbook/use_cases/finance/02_Fraud_Detection.ipynb

@@ -98,7 +98,7 @@
    "source": [
     "import os\n",
     "\n",
-    "os.environ[\"GROQ_API_KEY\"] = os.getenv(\"GROQ_API_KEY\", \"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\")\n",
+    "os.environ[\"GROQ_API_KEY\"] = os.getenv(\"GROQ_API_KEY\", \"\")\n",
     "\n",
     "# Configuration constants\n",
     "EMBEDDING_DIMENSION = 384\n",

cookbook/use_cases/finance/03_Earnings_Call_Analysis.ipynb

@@ -35,14 +35,14 @@
     "## End-to-End Workflow\n",
     "\n",
     "**Workflow:**  \n",
-    "Dual PDF Input → Docling Parsing → Normalization & Chunking → Entity, Relation & Triplet Extraction → Conflict Resolution & Deduplication → Knowledge Graph Construction → Amazon Neptune → GraphRAG → Agent Memory & Context → Strategic Q&A\n",
+    "Dual PDF Input → Docling Parsing → Normalization & Chunking → Entity, Relation Extraction → Conflict Resolution & Deduplication → Knowledge Graph Construction → Amazon Neptune → GraphRAG → Agent Memory & Context → Strategic Q&A\n",
     "\n",
     "---\n",
     "\n",
     "## Pipeline Capabilities\n",
     "\n",
     "- High-fidelity PDF parsing (text, tables, structure)  \n",
-    "- Semantic extraction of entities, relationships, and triplets  \n",
+    "- Semantic extraction of entities, and relationships\n",
     "- Conflict detection and resolution with confidence awareness  \n",
     "- Entity deduplication and canonicalization  \n",
     "- Knowledge graph construction and validation  \n",
@@ -280,7 +280,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import os\n",
     "from semantica.semantic_extract import NERExtractor\n",
     "\n",
     "ner = NERExtractor(\n",
@@ -289,27 +288,22 @@
     "    llm_model=\"llama-3.1-8b-instant\",\n",
     "    temperature=0.0,\n",
     "    api_key=GROQ_API_KEY,\n",
+    "    max_retries=3,\n",
     ")\n",
     "\n",
-    "ENTITY_TYPES = [\n",
-    "    \"ORGANIZATION\", \"ORG\", \"PERSON\", \"MONEY\", \"CURRENCY\",\n",
-    "    \"PERCENT\", \"PERCENTAGE\", \"DATE\", \"TIME\", \"PRODUCT\",\n",
-    "    \"LOCATION\", \"GPE\", \"EVENT\", \"QUANTITY\", \"CARDINAL\",\n",
+    "ENTITY_TYPES = [\"ORGANIZATION\", \"PERSON\", \"MONEY\", \"PERCENT\", \"DATE\", \"EVENT\"]\n",
+    "\n",
+    "all_entities = [\n",
+    "    e\n",
+    "    for c in chunks\n",
+    "    for e in ner.extract_entities(\n",
+    "        get_chunk_text(c),\n",
+    "        entity_types=ENTITY_TYPES,\n",
+    "    )\n",
+    "    if get_chunk_text(c).strip()\n",
     "]\n",
     "\n",
-    "all_entities = []\n",
-    "\n",
-    "for chunk in chunks:\n",
-    "    text = get_chunk_text(chunk)\n",
-    "    if text.strip():\n",
-    "        all_entities += ner.extract_entities(text, entity_types=ENTITY_TYPES)\n",
-    "\n",
-    "print(\"Entity extraction completed\")\n",
-    "print(\"Total entities extracted:\", len(all_entities))\n",
-    "\n",
-    "print(\"\\nSample entities\")\n",
-    "for e in all_entities[:10]:\n",
-    "    print(f\"{e.label}: {e.text}\")"
+    "print(\"Entities:\", len(all_entities))"
    ]
   },
   {
@@ -378,109 +372,104 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from concurrent.futures import ThreadPoolExecutor, TimeoutError\n",
     "from semantica.semantic_extract import RelationExtractor\n",
     "\n",
+    "MAX_ENTITIES = 30\n",
+    "CHUNK_TIMEOUT = 60\n",
+    "\n",
     "relation_extractor = RelationExtractor(\n",
     "    method=\"llm\",\n",
-    "    confidence_threshold=0.5,\n",
+    "    confidence_threshold=0.6,\n",
     "    relation_types=[\n",
-    "        \"HAS_REVENUE\", \"HAS_EPS\", \"HAS_MARGIN\", \"HAS_PROFIT\", \"HAS_GROWTH\",\n",
-    "        \"PROVIDES_GUIDANCE\", \"STATES\", \"ANNOUNCES\", \"REPORTS\", \"EXPECTS\",\n",
-    "        \"OPERATES_IN\", \"LOCATED_IN\", \"PARTNERS_WITH\", \"SERVES\",\n",
-    "        \"COMPARED_TO\", \"INCREASED_BY\", \"DECREASED_BY\", \"CHANGED_BY\",\n",
-    "        \"DURING\", \"IN_QUARTER\", \"FOR_PERIOD\",\n",
-    "        \"RELATED_TO\", \"PART_OF\", \"AFFECTS\",\n",
+    "        \"HAS_REVENUE\",\n",
+    "        \"HAS_GROWTH\",\n",
+    "        \"REPORTS\",\n",
+    "        \"PROVIDES_GUIDANCE\",\n",
+    "        \"IN_QUARTER\",\n",
+    "        \"FOR_PERIOD\",\n",
+    "        \"RELATED_TO\",\n",
     "    ],\n",
-    "    api_key=GROQ_API_KEY,\n",
-    ")\n",
-    "\n",
-    "def get_chunk_text(chunk):\n",
-    "    return getattr(chunk, \"content\", getattr(chunk, \"text\", \"\")) or \"\"\n",
-    "\n",
-    "relationships = []\n",
-    "\n",
-    "for chunk in chunks:\n",
-    "    text = get_chunk_text(chunk)\n",
-    "\n",
-    "    relations = relation_extractor.extract_relations(\n",
-    "        text,\n",
-    "        entities=all_entities,\n",
-    "        provider=\"groq\",\n",
-    "        llm_model=\"llama-3.1-8b-instant\",\n",
-    "        temperature=0.0,\n",
-    "    )\n",
-    "\n",
-    "    relationships += relations\n",
-    "\n",
-    "print(\"Relationship extraction completed\")\n",
-    "print(\"Total chunks:\", len(chunks))\n",
-    "print(\"Total relationships extracted:\", len(relationships))\n",
-    "\n",
-    "if relationships:\n",
-    "    r = relationships[0]\n",
-    "    print(\"Sample relationship:\")\n",
-    "    print(f\"{r.subject.text} → {r.predicate} → {r.object.text}\")"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Step 6: Extract RDF Triplets\n",
-    "\n",
-    "Extract RDF triplets (subject-predicate-object) using TripletExtractor with Groq LLM.\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from semantica.semantic_extract import TripletExtractor\n",
-    "\n",
-    "triplet_extractor = TripletExtractor(\n",
-    "    method=\"llm\",\n",
-    "    include_temporal=True,\n",
-    "    include_provenance=True,\n",
     "    provider=\"groq\",\n",
     "    llm_model=\"llama-3.1-8b-instant\",\n",
-    "    temperature=0.0,\n",
     "    api_key=GROQ_API_KEY,\n",
+    "    temperature=0.0,\n",
+    "    verbose=False,\n",
     ")\n",
     "\n",
-    "def get_chunk_text(chunk):\n",
-    "    return getattr(chunk, \"content\", getattr(chunk, \"text\", \"\")) or \"\"\n",
     "\n",
-    "triplets = []\n",
+    "def filter_entities(text, entities):\n",
+    "    t = text.lower()\n",
+    "    return [e for e in entities if e.text.lower() in t]\n",
     "\n",
-    "for chunk in chunks:\n",
-    "    text = get_chunk_text(chunk)\n",
     "\n",
-    "    triplets += triplet_extractor.extract_triplets(\n",
-    "        text,\n",
-    "        entities=all_entities,\n",
-    "        relations=relationships if relationships else None,\n",
+    "def process_chunk(idx, chunk, total):\n",
+    "    text = get_chunk_text(chunk).strip()\n",
+    "\n",
+    "    remaining = total - (idx + 1)\n",
+    "\n",
+    "    if not text:\n",
+    "        print(f\"Chunk {idx+1}/{total} | remaining {remaining} | skipped (empty)\")\n",
+    "        return []\n",
+    "\n",
+    "    chunk_entities = filter_entities(text, all_entities)[:MAX_ENTITIES]\n",
+    "\n",
+    "    if len(chunk_entities) < 2:\n",
+    "        print(\n",
+    "            f\"Chunk {idx+1}/{total} | remaining {remaining} | \"\n",
+    "            f\"skipped (entities={len(chunk_entities)})\"\n",
+    "        )\n",
+    "        return []\n",
+    "\n",
+    "    print(\n",
+    "        f\"Chunk {idx+1}/{total} | remaining {remaining} | \"\n",
+    "        f\"entities={len(chunk_entities)}\"\n",
     "    )\n",
     "\n",
-    "if hasattr(triplet_extractor, \"validate_triplets\"):\n",
-    "    triplets = triplet_extractor.validate_triplets(triplets)\n",
+    "    return relation_extractor.extract_relations(\n",
+    "        text=text,\n",
+    "        entities=chunk_entities,\n",
+    "        verbose=False,\n",
+    "    )\n",
     "\n",
-    "print(\"Triplet extraction completed\")\n",
-    "print(\"Total chunks:\", len(chunks))\n",
-    "print(\"Total RDF triplets:\", len(triplets))\n",
     "\n",
-    "if triplets:\n",
-    "    t = triplets[0]\n",
-    "    print(\"Sample triplet:\")\n",
-    "    print(f\"{t.subject} → {t.predicate} → {t.object}\")\n"
+    "relationships = []\n",
+    "total_chunks = len(chunks)\n",
+    "\n",
+    "with ThreadPoolExecutor(max_workers=1) as executor:\n",
+    "    for i, c in enumerate(chunks):\n",
+    "        future = executor.submit(process_chunk, i, c, total_chunks)\n",
+    "\n",
+    "        try:\n",
+    "            rels = future.result(timeout=CHUNK_TIMEOUT)\n",
+    "            relationships.extend(rels)\n",
+    "            print(f\"  relations={len(rels)}\")\n",
+    "\n",
+    "        except TimeoutError:\n",
+    "            remaining = total_chunks - (i + 1)\n",
+    "            print(\n",
+    "                f\"Chunk {i+1}/{total_chunks} | remaining {remaining} | timed out\"\n",
+    "            )\n",
+    "\n",
+    "        except Exception as e:\n",
+    "            remaining = total_chunks - (i + 1)\n",
+    "            print(\n",
+    "                f\"Chunk {i+1}/{total_chunks} | remaining {remaining} | failed: {e}\"\n",
+    "            )\n",
+    "\n",
+    "print(f\"Done {total_chunks}/{total_chunks}\")\n",
+    "print(f\"Total relationships: {len(relationships)}\")\n",
+    "\n",
+    "if relationships:\n",
+    "    for r in relationships[:10]:\n",
+    "        print(f\"{r.subject.text} → {r.predicate} → {r.object.text}\")\n"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Step 7: Detect Conflicts\n",
+    "## Step 6: Detect Conflicts\n",
     "\n",
     "Detect conflicts in extracted entities and relationships using ConflictDetector.\n"
    ]
@@ -494,46 +483,76 @@
     "from semantica.conflicts import SourceTracker, SourceReference, ConflictDetector\n",
     "\n",
     "source_tracker = SourceTracker()\n",
+    "\n",
     "conflict_detector = ConflictDetector(\n",
     "    source_tracker=source_tracker,\n",
     "    similarity_threshold=0.8,\n",
     "    confidence_threshold=0.7,\n",
     ")\n",
     "\n",
-    "for entity in all_entities:\n",
-    "    entity_id = getattr(entity, \"id\", None) or getattr(entity, \"text\", \"\")\n",
-    "    entity_text = getattr(entity, \"text\", \"\")\n",
-    "    entity_label = getattr(entity, \"label\", \"UNKNOWN\")\n",
+    "entities = all_entities\n",
+    "extracted_relationships = relationships\n",
     "\n",
+    "for e in entities:\n",
+    "    entity_id = getattr(e, \"id\", None) or e.text\n",
     "    source_tracker.track_property_source(\n",
-    "        entity_id,\n",
-    "        \"name\",\n",
-    "        entity_text,\n",
-    "        # FIXED: Changed 'source' to 'document' to match SourceReference signature\n",
+    "        entity_id=entity_id,\n",
+    "        property_name=\"name\",\n",
+    "        value=e.text,\n",
     "        source=SourceReference(\n",
-    "            document=\"earnings_call\",  # Was incorrect: source=\"earnings_call\"\n",
+    "            document=\"earnings_call\",\n",
     "            timestamp=\"2024-Q1\",\n",
-    "            metadata={\"entity_type\": entity_label},\n",
+    "            metadata={\"entity_type\": getattr(e, \"label\", \"UNKNOWN\")},\n",
     "        ),\n",
     "    )\n",
     "\n",
-    "value_conflicts = conflict_detector.detect_value_conflicts(\n",
-    "    [{\"id\": getattr(e, \"id\", \"\"), \"name\": getattr(e, \"text\", \"\")} for e in all_entities],\n",
+    "entity_records = [\n",
+    "    {\n",
+    "        \"id\": getattr(e, \"id\", None) or e.text,\n",
+    "        \"name\": e.text,\n",
+    "    }\n",
+    "    for e in entities\n",
+    "]\n",
+    "\n",
+    "entity_value_conflicts = conflict_detector.detect_value_conflicts(\n",
+    "    entity_records,\n",
     "    property_name=\"name\",\n",
     ")\n",
     "\n",
-    "relationship_conflicts = conflict_detector.detect_relationship_conflicts(relationships)\n",
+    "normalized_relationships = [\n",
+    "    {\n",
+    "        \"id\": getattr(r, \"id\", None),\n",
+    "        \"source_id\": getattr(r.subject, \"id\", None) or r.subject.text,\n",
+    "        \"target_id\": getattr(r.object, \"id\", None) or r.object.text,\n",
+    "        \"type\": r.predicate,\n",
+    "        \"confidence\": getattr(r, \"confidence\", 1.0),\n",
+    "        \"metadata\": {},\n",
+    "    }\n",
+    "    for r in extracted_relationships\n",
+    "]\n",
+    "\n",
+    "relationship_conflicts = conflict_detector.detect_relationship_conflicts(\n",
+    "    normalized_relationships\n",
+    ")\n",
     "\n",
     "print(\"Conflict detection completed\")\n",
-    "print(\"Value conflicts:\", len(value_conflicts))\n",
-    "print(\"Relationship conflicts:\", len(relationship_conflicts))"
+    "print(\"Entity value conflicts:\", len(entity_value_conflicts))\n",
+    "print(\"Relationship conflicts:\", len(relationship_conflicts))\n",
+    "\n",
+    "if entity_value_conflicts:\n",
+    "    print(\"\\nSample entity conflict:\")\n",
+    "    print(entity_value_conflicts[0])\n",
+    "\n",
+    "if relationship_conflicts:\n",
+    "    print(\"\\nSample relationship conflict:\")\n",
+    "    print(relationship_conflicts[0])"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Step 8: Resolve Conflicts\n",
+    "## Step 7: Resolve Conflicts\n",
     "\n",
     "Resolve detected conflicts using ConflictResolver with voting strategy.\n"
    ]
@@ -551,27 +570,43 @@
     "    source_tracker=source_tracker,\n",
     ")\n",
     "\n",
-    "resolved_conflicts = []\n",
+    "resolved_entity_value_conflicts = []\n",
+    "resolved_relationship_conflicts = []\n",
     "\n",
-    "for conflict in value_conflicts:\n",
-    "    resolved_conflicts.append(\n",
-    "        conflict_resolver.resolve_conflict(conflict, strategy=\"voting\")\n",
+    "for conflict in entity_value_conflicts:\n",
+    "    resolved_entity_value_conflicts.append(\n",
+    "        conflict_resolver.resolve_conflict(\n",
+    "            conflict,\n",
+    "            strategy=\"voting\",\n",
+    "        )\n",
     "    )\n",
     "\n",
     "for conflict in relationship_conflicts:\n",
-    "    resolved_conflicts.append(\n",
-    "        conflict_resolver.resolve_conflict(conflict, strategy=\"voting\")\n",
+    "    resolved_relationship_conflicts.append(\n",
+    "        conflict_resolver.resolve_conflict(\n",
+    "            conflict,\n",
+    "            strategy=\"voting\",\n",
+    "        )\n",
     "    )\n",
     "\n",
     "print(\"Conflict resolution completed\")\n",
-    "print(\"Total conflicts resolved:\", len(resolved_conflicts))\n"
+    "print(\"Entity value conflicts resolved:\", len(resolved_entity_value_conflicts))\n",
+    "print(\"Relationship conflicts resolved:\", len(resolved_relationship_conflicts))\n",
+    "\n",
+    "if resolved_entity_value_conflicts:\n",
+    "    print(\"\\nSample resolved entity conflict:\")\n",
+    "    print(resolved_entity_value_conflicts[0])\n",
+    "\n",
+    "if resolved_relationship_conflicts:\n",
+    "    print(\"\\nSample resolved relationship conflict:\")\n",
+    "    print(resolved_relationship_conflicts[0])"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Step 9: Deduplicate Entities\n",
+    "## Step 8: Deduplicate Entities\n",
     "\n",
     "Detect and merge duplicate entities using DuplicateDetector and EntityMerger.\n"
    ]
@@ -583,45 +618,87 @@
    "outputs": [],
    "source": [
     "from semantica.deduplication import DuplicateDetector, EntityMerger\n",
+    "import time\n",
     "\n",
-    "duplicate_detector = DuplicateDetector(\n",
-    "    similarity_threshold=0.8,\n",
-    "    confidence_threshold=0.7,\n",
+    "start_time = time.time()\n",
+    "\n",
+    "raw = []\n",
+    "for i, e in enumerate(entities):\n",
+    "    raw.append({\n",
+    "        \"id\": getattr(e, \"id\", None) or f\"entity_{i}_{getattr(e, 'text', str(e))}\",\n",
+    "        \"name\": (getattr(e, \"text\", getattr(e, \"name\", \"\")) or \"\").strip(),\n",
+    "        \"type\": getattr(e, \"label\", \"UNKNOWN\"),\n",
+    "        \"confidence\": float(getattr(e, \"confidence\", 1.0) or 1.0),\n",
+    "        \"metadata\": getattr(e, \"metadata\", {}),\n",
+    "    })\n",
+    "\n",
+    "filtered = [r for r in raw if r[\"name\"] and len(r[\"name\"]) >= 3]\n",
+    "\n",
+    "collapsed = {}\n",
+    "for ent in filtered:\n",
+    "    key = (ent[\"type\"], ent[\"name\"].lower())\n",
+    "    best = collapsed.get(key)\n",
+    "    if best is None or ent[\"confidence\"] > best[\"confidence\"]:\n",
+    "        collapsed[key] = ent\n",
+    "\n",
+    "entity_dicts = list(collapsed.values())\n",
+    "\n",
+    "detector = DuplicateDetector(\n",
+    "    similarity_threshold=0.96,\n",
+    "    confidence_threshold=0.92,\n",
+    "    use_clustering=True,\n",
     ")\n",
     "\n",
-    "entity_dicts = [\n",
-    "    {\n",
-    "        \"id\": getattr(e, \"id\", \"\"),\n",
-    "        \"name\": getattr(e, \"text\", \"\"),\n",
-    "        \"type\": getattr(e, \"label\", \"UNKNOWN\"),\n",
-    "        \"confidence\": getattr(e, \"confidence\", 1.0),\n",
-    "        \"metadata\": getattr(e, \"metadata\", {}),\n",
-    "    }\n",
-    "    for e in resolved_entities\n",
-    "]\n",
+    "detector.detect_duplicate_groups(entity_dicts)\n",
     "\n",
-    "duplicates = duplicate_detector.detect_duplicates(entity_dicts)\n",
+    "merger = EntityMerger(\n",
+    "    preserve_provenance=True,\n",
+    "    detector={\n",
+    "        \"similarity_threshold\": 0.96,\n",
+    "        \"confidence_threshold\": 0.92,\n",
+    "        \"use_clustering\": True,\n",
+    "    },\n",
+    "    strategy={\"default_strategy\": \"keep_most_complete\"},\n",
+    ")\n",
     "\n",
-    "entity_merger = EntityMerger(preserve_provenance=True)\n",
-    "\n",
-    "merge_operations = entity_merger.merge_duplicates(\n",
-    "    entity_dicts,\n",
+    "merge_operations = merger.merge_duplicates(\n",
+    "    entities=entity_dicts,\n",
     "    strategy=\"keep_most_complete\",\n",
     ")\n",
     "\n",
-    "merged_entities = [op.merged_entity for op in merge_operations]\n",
+    "deduplicated_entities = [op.merged_entity for op in merge_operations] or entity_dicts\n",
     "\n",
-    "print(\"Entity deduplication completed\")\n",
-    "print(\"Original entities:\", len(entity_dicts))\n",
-    "print(\"Merged entities:\", len(merged_entities))\n",
-    "print(\"Duplicates removed:\", len(entity_dicts) - len(merged_entities))\n"
+    "entity_id_mapping = {}\n",
+    "for op in merge_operations:\n",
+    "    mid = op.merged_entity[\"id\"]\n",
+    "    for sid in op.source_ids:\n",
+    "        entity_id_mapping[sid] = mid\n",
+    "\n",
+    "deduplicated_relationships = []\n",
+    "for rel in normalized_relationships:\n",
+    "    s = entity_id_mapping.get(rel[\"source_id\"], rel[\"source_id\"])\n",
+    "    t = entity_id_mapping.get(rel[\"target_id\"], rel[\"target_id\"])\n",
+    "    if s != t:\n",
+    "        r = rel.copy()\n",
+    "        r[\"source_id\"], r[\"target_id\"] = s, t\n",
+    "        deduplicated_relationships.append(r)\n",
+    "\n",
+    "print({\n",
+    "    \"time_seconds\": round(time.time() - start_time, 2),\n",
+    "    \"entities_in\": len(raw),\n",
+    "    \"entities_after_filter\": len(filtered),\n",
+    "    \"entities_after_exact\": len(entity_dicts),\n",
+    "    \"entities_out\": len(deduplicated_entities),\n",
+    "    \"duplicates_removed\": len(entity_dicts) - len(deduplicated_entities),\n",
+    "    \"relationships_updated\": len(deduplicated_relationships),\n",
+    "})"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Step 10: Build Knowledge Graph\n",
+    "## Step 9: Build Knowledge Graph\n",
     "\n",
     "Build knowledge graph from cleaned entities, relationships, and triplets using GraphBuilder.\n"
    ]
@@ -634,28 +711,17 @@
    "source": [
     "from semantica.kg import GraphBuilder\n",
     "\n",
+    "# Deduplication is already done; avoid additional entity resolution/merging\n",
     "graph_builder = GraphBuilder(\n",
-    "    merge_entities=True,\n",
-    "    entity_resolution_strategy=\"fuzzy\",\n",
+    "    merge_entities=False,\n",
+    "    entity_resolution_strategy=\"none\",\n",
     ")\n",
     "\n",
-    "triplet_relationships = [\n",
-    "    {\n",
-    "        \"source\": t.subject,\n",
-    "        \"predicate\": t.predicate,\n",
-    "        \"target\": t.object,\n",
-    "        \"confidence\": t.confidence,\n",
-    "        \"metadata\": t.metadata,\n",
-    "    }\n",
-    "    for t in validated_triplets\n",
-    "]\n",
-    "\n",
-    "final_relationships = resolved_relationships + triplet_relationships\n",
+    "final_relationships = deduplicated_relationships\n",
     "\n",
     "kg_data = {\n",
-    "    \"entities\": merged_entities,\n",
+    "    \"entities\": deduplicated_entities,\n",
     "    \"relationships\": final_relationships,\n",
-    "    \"triplets\": validated_triplets,\n",
     "    \"metadata\": {\n",
     "        \"source\": \"earnings_call_transcript\",\n",
     "        \"extraction_method\": \"Groq LLM\",\n",
@@ -664,19 +730,19 @@
     "\n",
     "knowledge_graph = graph_builder.build(\n",
     "    sources=[kg_data],\n",
-    "    merge_entities=True,\n",
+    "    merge_entities=False,\n",
     ")\n",
     "\n",
-    "print(\"Knowledge graph build completed\")\n",
+    "print(\"Knowledge graph build completed (no additional merging)\")\n",
     "print(\"Final entities:\", len(knowledge_graph.get(\"entities\", [])))\n",
-    "print(\"Final relationships:\", len(knowledge_graph.get(\"relationships\", [])))\n"
+    "print(\"Final relationships:\", len(knowledge_graph.get(\"relationships\", [])))"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Step 11: Analyze Knowledge Graph\n",
+    "## Step 10: Analyze Knowledge Graph\n",
     "\n",
     "This step evaluates the structure and quality of the knowledge graph.\n",
     "\n",
@@ -714,19 +780,17 @@
     "connectivity = graph_analyzer.analyze_connectivity(knowledge_graph)\n",
     "metrics = graph_analyzer.compute_metrics(knowledge_graph)\n",
     "\n",
-    "top_entities = centrality.get(\"rankings\", [])[:5]\n",
     "num_communities = len(communities.get(\"communities\", []))\n",
     "\n",
     "print(\"Graph analysis completed\")\n",
-    "print(\"Communities:\", num_communities)\n",
-    "print(\"Top entities:\", len(top_entities))\n"
+    "print(\"Communities:\", num_communities)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Step 12: Persist Knowledge Graph in Amazon Neptune\n",
+    "## Step 11: Persist Knowledge Graph in Amazon Neptune\n",
     "\n",
     "After cleaning, conflict resolution, and deduplication, the final step is to\n",
     "persist the **canonical knowledge graph** into a production graph database.\n",
@@ -841,7 +905,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Step 13: Context Retrieval\n",
+    "## Step 12: Context Retrieval\n",
     "\n",
     "Set up hybrid retrieval (vector + graph) using ContextRetriever for GraphRAG queries.\n"
    ]
@@ -852,31 +916,62 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import time\n",
     "from semantica.vector_store import VectorStore\n",
     "from semantica.context import ContextRetriever\n",
     "\n",
-    "vector_store = VectorStore(backend=\"faiss\")\n",
+    "if 'chunks' not in locals() or not chunks:\n",
+    "    raise ValueError(\"Chunks not found. Please run Step 3 first.\")\n",
     "\n",
-    "vector_store.add(\n",
-    "    texts=[parsed_doc[\"full_text\"]],\n",
-    "    metadata=[{\"source\": \"earnings_call\", \"type\": \"transcript\"}],\n",
+    "# Extract text content safely\n",
+    "chunk_texts = [getattr(c, \"content\", getattr(c, \"text\", \"\")) for c in chunks]\n",
+    "chunk_metadatas = [\n",
+    "    {\n",
+    "        \"source\": \"earnings_call\", \n",
+    "        \"type\": \"transcript\", \n",
+    "        \"chunk_index\": i,\n",
+    "        **(getattr(c, \"metadata\", {}) or {})\n",
+    "    }\n",
+    "    for i, c in enumerate(chunks)\n",
+    "]\n",
+    "\n",
+    "# Initialize Vector Store (Optimized for Speed)\n",
+    "# dimension=384 matches the default fast model (BAAI/bge-small-en-v1.5)\n",
+    "vector_store = VectorStore(\n",
+    "    backend=\"faiss\", \n",
+    "    dimension=384,  \n",
+    "    max_workers=16\n",
     ")\n",
     "\n",
+    "print(f\"Storing {len(chunks)} chunks with high-performance settings...\")\n",
+    "start_time = time.time()\n",
+    "\n",
+    "# Store in large batches with parallel processing\n",
+    "vector_ids = vector_store.add_documents(\n",
+    "    documents=chunk_texts,\n",
+    "    metadata=chunk_metadatas,\n",
+    "    batch_size=128,\n",
+    "    parallel=True\n",
+    ")\n",
+    "\n",
+    "print(f\"✅ Stored in {time.time() - start_time:.2f}s\")\n",
+    "\n",
+    "# Initialize Hybrid Retriever\n",
     "context_retriever = ContextRetriever(\n",
-    "    knowledge_graph=knowledge_graph,\n",
+    "    knowledge_graph=knowledge_graph, # Assumes knowledge_graph exists\n",
     "    vector_store=vector_store,\n",
     "    hybrid_alpha=0.6,\n",
     "    use_graph_expansion=True,\n",
     "    max_expansion_hops=2,\n",
     ")\n",
     "\n",
+    "# Test Retrieval\n",
     "queries = [\n",
     "    \"What was the company's revenue guidance?\",\n",
     "    \"What were the key financial metrics discussed?\",\n",
     "]\n",
     "\n",
     "retrieved_contexts = []\n",
-    "\n",
     "for query in queries:\n",
     "    results = context_retriever.retrieve(\n",
     "        query=query,\n",
@@ -886,15 +981,14 @@
     "    retrieved_contexts.append(results)\n",
     "\n",
     "print(\"Hybrid GraphRAG configured\")\n",
-    "print(\"Queries processed:\", len(queries))\n",
-    "print(\"Sample results:\", len(retrieved_contexts[0]) if retrieved_contexts else 0)\n"
+    "print(\"Sample results:\", len(retrieved_contexts[0]) if retrieved_contexts else 0)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Step 14: Agent Memory (Long-Term Context)\n",
+    "## Step 13: Agent Memory (Long-Term Context)\n",
     "\n",
     "This step enables long-term memory for agents by storing important facts,\n",
     "metrics, and entities extracted from the knowledge graph.\n",
@@ -930,10 +1024,13 @@
     "    retention_days=30,\n",
     ")\n",
     "\n",
+    "entity_count = len(knowledge_graph.get(\"entities\", []))\n",
+    "relationship_count = len(knowledge_graph.get(\"relationships\", []))\n",
+    "\n",
     "memory_contents = [\n",
     "    f\"Earnings call transcript: {parsed_doc['metadata'].get('title', 'Earnings Call')}\",\n",
-    "    f\"Financial metrics extracted: {sum(len(v) for v in financial_metrics.values())}\",\n",
-    "    f\"Key entities identified: {len(merged_entities)}\",\n",
+    "    f\"Graph entities: {entity_count}\",\n",
+    "    f\"Graph relationships: {relationship_count}\",\n",
     "]\n",
     "\n",
     "memory_ids = []\n",
@@ -958,14 +1055,14 @@
     "print(\"Agent memory configured\")\n",
     "print(\"Memories stored:\", len(memory_ids))\n",
     "print(\"Total memories:\", memory_stats.get(\"total_memories\", 0))\n",
-    "print(\"Retrieved memories:\", len(financial_memories))\n"
+    "print(\"Retrieved memories:\", len(financial_memories))"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Step 15: Agent Context\n",
+    "## Step 14: Agent Context\n",
     "\n",
     "**AgentContext** provides a unified context layer that combines **vector-based RAG**\n",
     "with **graph-based GraphRAG** for grounded and explainable retrieval.\n",
@@ -1009,7 +1106,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -1037,7 +1134,7 @@
     ")\n",
     "\n",
     "memory_id = agent_context.store(\n",
-    "    content=parsed_doc[\"full_text\"][:1000],\n",
+    "    content=chunks,\n",
     "    metadata={\"source\": \"earnings_call\", \"date\": \"2024-Q1\"},\n",
     "    extract_entities=True,\n",
     "    extract_relationships=True,\n",
@@ -1063,7 +1160,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Step 16: Answer Generation\n",
+    "## Step 15: Answer Generation\n",
     "\n",
     "Generate answers to financial questions using Groq LLM with retrieved context and knowledge graph.\n"
    ]
@@ -1081,32 +1178,71 @@
     "\n",
     "generated_answers = []\n",
     "\n",
+    "print(\"--- Generating Enhanced Answers ---\\n\")\n",
+    "\n",
+    "def format_context(retrieved_contexts):\n",
+    "    \"\"\"Formats retrieved context with graph information.\"\"\"\n",
+    "    formatted_parts = []\n",
+    "    \n",
+    "    for i, ctx in enumerate(retrieved_contexts):\n",
+    "        content = getattr(ctx, \"content\", \"\")\n",
+    "        source = getattr(ctx, \"source\", \"unknown\")\n",
+    "        \n",
+    "        # Format related entities from the graph\n",
+    "        related_entities = getattr(ctx, \"related_entities\", [])\n",
+    "        entities_str = \", \".join([\n",
+    "            f\"{e.get('name', 'Unknown')} ({e.get('type', 'Entity')})\" \n",
+    "            for e in related_entities[:5]  # Limit to top 5 per chunk\n",
+    "        ])\n",
+    "        \n",
+    "        # Format related relationships\n",
+    "        related_rels = getattr(ctx, \"related_relationships\", [])\n",
+    "        rels_str = \"; \".join([\n",
+    "            f\"{r.get('source', '')} -> {r.get('type', '')} -> {r.get('target', '')}\"\n",
+    "            for r in related_rels[:3]  # Limit to top 3 per chunk\n",
+    "        ])\n",
+    "        \n",
+    "        part = f\"Source {i+1} ({source}):\\n{content}\\n\"\n",
+    "        if entities_str:\n",
+    "            part += f\"Related Entities: {entities_str}\\n\"\n",
+    "        if rels_str:\n",
+    "            part += f\"Graph Connections: {rels_str}\\n\"\n",
+    "            \n",
+    "        formatted_parts.append(part)\n",
+    "        \n",
+    "    return \"\\n---\\n\".join(formatted_parts)\n",
+    "\n",
     "for question in financial_questions:\n",
+    "    print(f\"Question: {question}\")\n",
+    "    \n",
+    "    # Retrieve with graph expansion enabled and higher limits\n",
     "    retrieved_contexts = context_retriever.retrieve(\n",
     "        query=question,\n",
-    "        max_results=3,\n",
+    "        max_results=10,          # Increased from 3\n",
     "        min_relevance_score=0.2,\n",
+    "        use_graph_expansion=True, # Explicitly enable graph expansion\n",
+    "        max_hops=2               # Traverse up to 2 hops in the graph\n",
     "    )\n",
     "\n",
-    "    context_text = \"\\n\\n\".join(\n",
-    "        ctx.get(\"content\", ctx.get(\"text\", \"\"))\n",
-    "        for ctx in retrieved_contexts\n",
-    "    )[:1000]\n",
+    "    # Use the rich formatter\n",
+    "    context_text = format_context(retrieved_contexts)\n",
     "\n",
-    "    entity_names = [\n",
-    "        entity.get(\"name\", \"\")\n",
-    "        for entity in knowledge_graph.get(\"entities\", [])[:5]\n",
+    "    # Get global key entities (optional, but good for high-level context)\n",
+    "    global_entities = [\n",
+    "        f\"{e.get('name', '')} ({e.get('type', '')})\"\n",
+    "        for e in knowledge_graph.get(\"entities\", [])[:10]\n",
     "    ]\n",
-    "    entities_text = \", \".join(entity_names) or \"N/A\"\n",
+    "    global_entities_text = \", \".join(global_entities)\n",
     "\n",
     "    prompt = f\"\"\"\n",
-    "Answer the question using only the context below.\n",
+    "Answer the question comprehensively using the provided context.\n",
+    "The context includes text chunks and knowledge graph connections (entities and relationships).\n",
     "If the answer is not present, say so.\n",
     "\n",
     "Context:\n",
     "{context_text}\n",
     "\n",
-    "Key entities: {entities_text}\n",
+    "Global Key Entities: {global_entities_text}\n",
     "\n",
     "Question:\n",
     "{question}\n",
@@ -1117,23 +1253,25 @@
     "    try:\n",
     "        answer = groq_llm.generate(\n",
     "            prompt,\n",
-    "            temperature=0.7,\n",
-    "            max_tokens=400,\n",
+    "            temperature=0.3, # Lower temperature for more factual answers\n",
+    "            max_tokens=1000, # Allow longer answers\n",
     "        )\n",
     "    except Exception as error:\n",
     "        answer = f\"Answer generation failed: {error}\"\n",
     "\n",
     "    generated_answers.append(answer)\n",
+    "    print(f\"Answer: {answer}\\n\")\n",
+    "    print(\"-\" * 50 + \"\\n\")\n",
     "\n",
     "print(\"Answer generation completed\")\n",
-    "print(\"Questions answered:\", len(generated_answers))\n"
+    "print(\"Questions answered:\", len(generated_answers))"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Step 17: Export Results\n",
+    "## Step 16: Export Results\n",
     "\n",
     "Export knowledge graph and analysis results to JSON and RDF formats.\n"
    ]
@@ -1145,29 +1283,44 @@
    "outputs": [],
    "source": [
     "from semantica.export import JSONExporter, RDFExporter\n",
+    "import json\n",
     "\n",
+    "# Initialize exporters\n",
     "json_exporter = JSONExporter()\n",
     "rdf_exporter = RDFExporter()\n",
     "\n",
-    "kg_json = json_exporter.export(knowledge_graph, format=\"json\")\n",
-    "kg_rdf = rdf_exporter.export_to_rdf(knowledge_graph, format=\"turtle\")\n",
+    "# Define output file paths\n",
+    "json_output_path = \"knowledge_graph.json\"\n",
+    "rdf_output_path = \"knowledge_graph.ttl\"\n",
     "\n",
+    "# Export to files (required by the API)\n",
+    "json_exporter.export(knowledge_graph, file_path=json_output_path, format=\"json\")\n",
+    "\n",
+    "# FIXED: Use .export() instead of .export_to_rdf() to write to disk\n",
+    "rdf_exporter.export(knowledge_graph, file_path=rdf_output_path, format=\"turtle\")\n",
+    "\n",
+    "# Load the RDF file content to check its size\n",
+    "with open(rdf_output_path, \"r\", encoding=\"utf-8\") as f:\n",
+    "    kg_rdf_content = f.read()\n",
+    "\n",
+    "# Create analysis summary\n",
     "analysis_summary = {\n",
     "    \"entities\": len(knowledge_graph.get(\"entities\", [])),\n",
     "    \"relationships\": len(knowledge_graph.get(\"relationships\", [])),\n",
-    "    \"triplets\": len(triplets),\n",
-    "    \"conflicts_resolved\": len(resolved_conflicts),\n",
-    "    \"merged_entities\": len(merged_entities),\n",
-    "    \"communities\": num_communities,\n",
+    "    \"entity_conflicts_resolved\": len(locals().get(\"resolved_entity_value_conflicts\", [])),\n",
+    "    \"relationship_conflicts_resolved\": len(locals().get(\"resolved_relationship_conflicts\", [])),\n",
+    "    \"deduplicated_entities\": len(locals().get(\"deduplicated_entities\", [])),\n",
+    "    \"communities\": locals().get(\"num_communities\", 0),\n",
     "    \"questions_answered\": len(generated_answers),\n",
-    "    \"llm_model\": groq_llm.model,\n",
+    "    \"llm_model\": getattr(groq_llm, \"model\", \"unknown\"),\n",
     "}\n",
     "\n",
     "print(\"Export completed\")\n",
     "print(\"KG JSON entities:\", analysis_summary[\"entities\"])\n",
-    "print(\"KG RDF size (chars):\", len(kg_rdf))\n",
+    "print(\"KG RDF size (chars):\", len(kg_rdf_content))\n",
     "print(\"Questions answered:\", analysis_summary[\"questions_answered\"])\n",
-    "print(\"LLM model:\", analysis_summary[\"llm_model\"])\n"
+    "print(\"LLM model:\", analysis_summary[\"llm_model\"])\n",
+    "print(\"Conflicts resolved:\", analysis_summary[\"entity_conflicts_resolved\"] + analysis_summary[\"relationship_conflicts_resolved\"])"
    ]
   }
  ],

cookbook/use_cases/intelligence/02_Intelligence_Analysis_Orchestrator_Worker.ipynb

@@ -83,7 +83,7 @@
    "source": [
     "import os\n",
     "\n",
-    "os.environ[\"GROQ_API_KEY\"] = os.getenv(\"GROQ_API_KEY\", \"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\")\n",
+    "os.environ[\"GROQ_API_KEY\"] = os.getenv(\"GROQ_API_KEY\", \"\")\n",
     "\n",
     "# Configuration constants\n",
     "EMBEDDING_DIMENSION = 384\n",

cookbook/use_cases/renewable_energy/01_Energy_Market_Analysis.ipynb

@@ -80,7 +80,7 @@
    "source": [
     "import os\n",
     "\n",
-    "os.environ[\"GROQ_API_KEY\"] = os.getenv(\"GROQ_API_KEY\", \"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\")\n",
+    "os.environ[\"GROQ_API_KEY\"] = os.getenv(\"GROQ_API_KEY\", \"\")\n",
     "\n",
     "# Configuration constants\n",
     "EMBEDDING_DIMENSION = 384\n",

docs/CodeExamples.md

@@ -1018,7 +1018,7 @@ knowledge_graph.apply_resolutions(resolved_data)
 
 ### 💬 Community Support
 
-- **💬 [Discord Community](https://discord.gg/semantica)** - Real-time chat and support
+- **💬 [Discord Community](https://discord.gg/sV34vps5hH)** - Real-time chat and support
 - **🐙 [GitHub Discussions](https://github.com/semantica/semantica/discussions)** - Community Q&A
 - **📧 [Mailing List](https://groups.google.com/g/semantica)** - Announcements and updates
 - **🐦 [Twitter](https://twitter.com/semantica)** - Latest news and tips
@@ -1051,6 +1051,6 @@ This project is licensed under the MIT License - see the [LICENSE](https://githu
 
 **🚀 Ready to transform your data into intelligent knowledge?**
 
-[Get Started Now](https://semantica.readthedocs.io/quickstart/) • [View Examples](https://github.com/semantica/examples) • [Join Community](https://discord.gg/semantica)
+[Get Started Now](https://semantica.readthedocs.io/quickstart/) • [View Examples](https://github.com/semantica/examples) • [Join Community](https://discord.gg/sV34vps5hH)
 
 </div>

docs/DOCS_README.md

@@ -46,7 +46,7 @@ semantica/
 │   │   └── custom.css   # Custom styling
 │   └── assets/
 │       └── img/
-│           └── semantica_logo.png
+│           └── Semantica Logo.png
 └── site/                # Generated site (created by mkdocs build)
 ```
 

docs/LIBS_README.md

@@ -1380,11 +1380,11 @@ result = semantica.build_knowledge_base(["document.pdf"])
 ## 🚀 Performance
 
 ### Benchmarks
-- **Processing Speed**: 1000+ documents per minute
+- **Processing Speed**: Optimized for high-throughput document processing
 - **Memory Usage**: Optimized for large-scale processing
-- **Accuracy**: 95%+ entity extraction accuracy
+- **Accuracy**: High accuracy entity extraction
 - **Scalability**: Horizontal scaling support
-- **Latency**: Sub-second query response times
+- **Latency**: Fast query response times
 
 ### Optimization
 - **Parallel Processing**: Multi-threaded and multi-process support

docs/MIGRATION_V2.md

@@ -0,0 +1,152 @@
+## Semantica Deduplication V2: Migration & Performance Guide
+
+Welcome to the Deduplication V2 engine!! This release specifically targets severe CI delays and production bottlenecks caused by massive knowledge graph deduplication workloads. By introducing smarter candidate generation, fast-fail prefilters, and semantic triplet canonicalization, we have reduced worst-case execution times by up to **80%**.
+
+**Note:** This upgrade is **100% backward compatible.** All existing scripts, tests, and API signatures will continue to work exactly as they did before.
+
+
+
+To utilize this new addition, you must explicitly **opt-in** using the new configuration keys detailed below.
+
+---
+
+### 1. Candidate Generation V2 (Beating the $O(N^2)$ Pair Explosion)
+
+**The Problem:** The legacy engine relied on a naive first-character blocking strategy. If your dataset contained 5,000 companies starting with letter "A", the engine generated nearly 12.5 million candidate pairs.
+
+**The V2 Solution:** Multi-key token blocking, prefix matching, and deterministic candidate budgeting.
+
+
+
+**How to Opt-In**
+
+Pass the keys into the `similarity`configuration dictionary when initializing the `DuplicateDetector`:
+
+
+
+```python
+from semantica.deduplication import DuplicateDetector
+
+detector = DuplicateDetector(
+    similarity_threshold=0.8,
+    similarity = {
+    # Switches from legacy to v2
+    "candidate_strategy": "blocking_v2",
+
+    # Highly recommended: Limits the max number of comparisons
+    # per entity to prevent adversarial latency spikes.
+    "max_candidates_per_entity": 50,
+
+    # Optional: Generates blocks using Soundex algorithm to catch
+    # phonetic misspellings (e.g, "Jon" vs "John")
+    "enable_phonetic_blocking": True
+}
+)
+```
+
+
+
+### 2. Two-Stage scoring (The Fast Prefilter)
+
+**The Problem**: Calculating multi-factor semantic scores (Levenshtein, Jaro-Winkler, property intersections, and Embeddings) is computationally expensive. Running these
+
+calculations on two entities that share absolutely zero words or have vastly different string lengths is a waste of resources.
+
+**The V2 Solution:** A lightning-fast prefilter gate that instantly drops obvious non-matches before they ever reach the heavy semantic scorers.
+
+
+
+**How to Opt-In**
+
+Enable the prefilter and define your rejection thresholds:
+
+
+
+```python
+from semantica.deduplication import DuplicateDetector
+
+detector = DuplicateDetector(
+    similarity_threshold=0.8,
+    similarity={
+    "candidate_strategy": "blocking_v2",
+     
+    # Enable prefilter
+    "prefilter_enabled": True,
+
+    "prefilter_thresholds": {
+    # Rejects pairs if shortest string is less than 40% the length
+    # of the longest
+    "min_length_ratio": 0.4,
+    
+    # Instantly rejects pairs if they don't share at least one
+    # valid word token
+    "required_shared_token": True
+},
+    # Optional Explainability: Injects a 'score_breakdown' dict into
+    # the candidate metadata so you can see exactly how the string,
+    # property, and relationships scores contributed.
+    
+    "score_breakdown_enabled": True
+}
+)
+```
+
+
+
+### 3. Semantic Relationship & Triplet Deduplication
+
+**The problem:** The legacy relationship deduplication relied on exact `(Subject, Predicate, Object)` string matches. It couldn't recognize that `(Person, "works_for", Company)` is semantically identical to `(Person, "employed_by", Company)` .
+
+**The V2 Solution:** A new `semantic_v2` mode that introduces predicate synonym mapping, literal normalization (cleaning up rogue spaces/casing), and a highly optimized $O(1)$ canonical hash path for fast matching.
+
+
+
+**How to Opt-In**
+
+When calling relationship-specific dedup methods, pass the new configuration keys:
+
+```python
+from semantica.deduplication import DuplicateDetector
+from semantica.deduplication.methods import dedup_triplets
+
+
+# Approach A: Using the Detector explicitly
+detector = DuplicateDetector()
+duplicates = detector.detect_relationship_duplicates(
+    relationship_list,
+    relationship_dedup_mode="semantic_v2",
+
+    # Cleans up messy object strings 
+    # (e.g., "  Apple Inc. " -> "apple inc.")
+    literal_normalization_enabled=True,
+
+    # Maps various synonyms to a single canonical predicate
+    # before hashing
+    predicate_synonym_map={
+    "works_for": "employed_by",
+    "is_employee_of": "employed_by",
+    "has_employer": "employed_by"
+}
+)
+
+
+# Approach B: Using the new simplified wrapper in methods.py
+duplicates = dedup_triplets(
+    relationships_list,
+    mode="semantic_v2",
+    literal_normalization_enabled=True,
+    predicate_synonym_map={"works_for": "employed_by"}
+)
+```
+
+
+
+###### Note on Merge Strategies
+
+When using `semantic_v2` for relationships, the `MergeStrategyManager` will now automatically respect your canonicalized keys. If two entities share a relationship that differs only by a mapped synonym, the engine will correctly identify them as the same relationship and prevent duplicate graph edges during the merge phase.
+
+
+
+### Need Help?
+
+If you experience any unexpected behavior when switching from `legacy` to `blocking_v2` or `semantic_v2`, please check the explainability metadata (by setting `"score_breakdown_enabled": True`) to audit the exact scoring process, or open an issue on GitHub.

docs/arrow_exporter.md

@@ -0,0 +1,269 @@
+# Apache Arrow Exporter
+
+## Overview
+
+The Apache Arrow exporter provides high-performance columnar data export for Semantica's knowledge graphs, entities, and relationships. It uses explicit schemas (no inference) and writes Arrow IPC files (.arrow) that are compatible with Pandas and DuckDB.
+
+## Features
+
+- **Explicit Schemas**: Pre-defined schemas for entities and relationships (no inference)
+- **Columnar Format**: Efficient storage and fast analytics
+- **Metadata Support**: Converts metadata dictionaries to Arrow struct fields
+- **Field Normalization**: Handles various entity and relationship field name variations
+- **Progress Tracking**: Integrated progress monitoring
+- **Error Handling**: Structured error handling with detailed logging
+- **Pandas/DuckDB Compatible**: Direct conversion to DataFrames and SQL queries
+
+## Installation
+
+The Arrow exporter requires PyArrow:
+
+```bash
+pip install pyarrow
+```
+
+## Usage
+
+### Basic Usage
+
+```python
+from semantica.export import ArrowExporter
+
+# Initialize exporter
+exporter = ArrowExporter()
+
+# Export entities
+entities = [
+    {"id": "e1", "text": "Alice", "type": "Person", "confidence": 0.95},
+    {"id": "e2", "text": "Acme Corp", "type": "Organization", "confidence": 0.88}
+]
+exporter.export_entities(entities, "entities.arrow")
+
+# Export relationships
+relationships = [
+    {"id": "r1", "source_id": "e1", "target_id": "e2", "type": "WORKS_FOR"}
+]
+exporter.export_relationships(relationships, "relationships.arrow")
+
+# Export knowledge graph
+knowledge_graph = {
+    "entities": entities,
+    "relationships": relationships
+}
+exporter.export_knowledge_graph(knowledge_graph, "kg_base")
+# Creates: kg_base_entities.arrow, kg_base_relationships.arrow
+```
+
+### Using Convenience Function
+
+```python
+from semantica.export import export_arrow
+
+# Simple export
+export_arrow(entities, "entities.arrow")
+
+# Export multiple types
+data = {
+    "entities": entities,
+    "relationships": relationships
+}
+export_arrow(data, "output_base")
+```
+
+### With Compression
+
+```python
+# Use LZ4 compression
+exporter = ArrowExporter(compression="lz4")
+exporter.export_entities(entities, "entities_compressed.arrow")
+```
+
+## Schemas
+
+### Entity Schema
+
+```python
+ENTITY_SCHEMA = pa.schema([
+    pa.field("id", pa.string(), nullable=False),
+    pa.field("text", pa.string(), nullable=True),
+    pa.field("type", pa.string(), nullable=True),
+    pa.field("confidence", pa.float64(), nullable=True),
+    pa.field("start", pa.int64(), nullable=True),
+    pa.field("end", pa.int64(), nullable=True),
+    pa.field("metadata", pa.struct([
+        pa.field("keys", pa.list_(pa.string())),
+        pa.field("values", pa.list_(pa.string()))
+    ]), nullable=True),
+])
+```
+
+### Relationship Schema
+
+```python
+RELATIONSHIP_SCHEMA = pa.schema([
+    pa.field("id", pa.string(), nullable=False),
+    pa.field("source_id", pa.string(), nullable=False),
+    pa.field("target_id", pa.string(), nullable=False),
+    pa.field("type", pa.string(), nullable=True),
+    pa.field("confidence", pa.float64(), nullable=True),
+    pa.field("metadata", pa.struct([
+        pa.field("keys", pa.list_(pa.string())),
+        pa.field("values", pa.list_(pa.string()))
+    ]), nullable=True),
+])
+```
+
+## Field Normalization
+
+The exporter automatically normalizes field names:
+
+**Entities:**
+- `text`, `label`, `name` → `text`
+- `type`, `entity_type` → `type`
+- `id`, `entity_id` → `id`
+- `start`, `start_offset` → `start`
+- `end`, `end_offset` → `end`
+
+**Relationships:**
+- `source`, `source_id` → `source_id`
+- `target`, `target_id` → `target_id`
+- `type`, `relationship_type` → `type`
+
+## Reading Arrow Files
+
+### With PyArrow
+
+```python
+import pyarrow as pa
+import pyarrow.ipc as ipc
+
+with pa.OSFile("entities.arrow", 'rb') as source:
+    with ipc.open_file(source) as reader:
+        table = reader.read_all()
+        print(table.schema)
+        print(table.to_pandas())
+```
+
+### With Pandas
+
+```python
+import pandas as pd
+import pyarrow.ipc as ipc
+
+with ipc.open_file("entities.arrow") as reader:
+    df = reader.read_all().to_pandas()
+    print(df)
+```
+
+### With DuckDB
+
+```python
+import duckdb
+
+# Query Arrow file directly
+result = duckdb.query("SELECT * FROM 'entities.arrow' WHERE type = 'Person'")
+print(result.df())
+```
+
+## Methods
+
+### `export(data, file_path, schema=None, **options)`
+
+Generic export method that handles both single and multiple files.
+
+**Parameters:**
+- `data`: List of dicts or dict with list values
+- `file_path`: Output file path (base path for dict exports)
+- `schema`: Optional Arrow schema (auto-detected if not provided)
+- `**options`: Additional options
+
+### `export_entities(entities, file_path, **options)`
+
+Export entities to Arrow IPC file with normalization.
+
+**Parameters:**
+- `entities`: List of entity dictionaries
+- `file_path`: Output Arrow file path
+- `**options`: Additional options
+
+### `export_relationships(relationships, file_path, **options)`
+
+Export relationships to Arrow IPC file with normalization.
+
+**Parameters:**
+- `relationships`: List of relationship dictionaries
+- `file_path`: Output Arrow file path
+- `**options`: Additional options
+
+### `export_knowledge_graph(knowledge_graph, base_path, **options)`
+
+Export knowledge graph to multiple Arrow files.
+
+**Parameters:**
+- `knowledge_graph`: Knowledge graph dictionary with 'entities' and 'relationships'
+- `base_path`: Base path for output files (without extension)
+- `**options`: Additional options
+
+## Examples
+
+See `examples/arrow_export_example.py` for comprehensive usage examples.
+
+## Testing
+
+Run the test suite:
+
+```bash
+# All Arrow exporter tests
+pytest tests/test_arrow_exporter.py -v
+
+# Integration tests
+pytest tests/test_export_module.py::TestExportModule::test_arrow_exporter -v
+```
+
+## Performance Benefits
+
+- **Columnar Storage**: Faster analytics on specific columns
+- **Compression**: Smaller file sizes (especially with LZ4/ZSTD)
+- **Zero-Copy**: Memory-efficient data transfer
+- **Cross-Language**: Works with Python, R, Julia, JavaScript, and more
+- **SQL Queries**: Direct querying with DuckDB without loading into memory
+
+## Comparison with Other Formats
+
+| Feature | Arrow | CSV | JSON |
+|---------|-------|-----|------|
+| Type Safety | ✓ | ✗ | ✗ |
+| Compression | ✓ | ✗ | ✗ |
+| Schema Validation | ✓ | ✗ | ✗ |
+| Pandas Compatible | ✓ | ✓ | ✓ |
+| DuckDB Native | ✓ | ✓ | ✗ |
+| Binary Format | ✓ | ✗ | ✗ |
+| Human Readable | ✗ | ✓ | ✓ |
+
+## Architecture
+
+The Arrow exporter follows Semantica's export architecture:
+
+1. **Normalization**: Field names are normalized to consistent format
+2. **Schema Application**: Explicit schemas ensure type safety
+3. **Metadata Conversion**: Dicts converted to Arrow struct fields
+4. **Progress Tracking**: Integrated with Semantica's progress tracker
+5. **Error Handling**: Structured exceptions with detailed messages
+
+## Contributing
+
+When contributing to the Arrow exporter:
+
+1. Maintain explicit schemas (no inference)
+2. Follow existing code style and patterns
+3. Add comprehensive tests for new features
+4. Update this documentation
+5. Ensure Pandas/DuckDB compatibility
+
+## License
+
+MIT License - See LICENSE file for details.
+
+## Author
+
+Semantica Contributors

docs/changelog.md

@@ -1,3 +0,0 @@
-# Changelog
-
---8<-- "CHANGELOG.md"

docs/citation.md

@@ -12,22 +12,22 @@ How to cite Semantica in academic papers and research.
   author = {Hawksight AI},
   year = {2026},
   url = {https://github.com/Hawksight-AI/semantica},
-  version = {0.2.1},
+  version = {0.2.7},
   doi = {10.5281/zenodo.XXXXXXX}
 }
 ```
 
 ### APA
-Hawksight AI. (2026). *Semantica: An Open Source Framework for Semantic Layers and Knowledge Engineering* (Version 0.2.1) [Computer software]. https://github.com/Hawksight-AI/semantica
+Hawksight AI. (2026). *Semantica: An Open Source Framework for Semantic Layers and Knowledge Engineering* (Version 0.2.7) [Computer software]. https://github.com/Hawksight-AI/semantica
 
 ### MLA
-Hawksight AI. *Semantica: An Open Source Framework for Semantic Layers and Knowledge Engineering*. Version 0.2.1, GitHub, 2026, https://github.com/Hawksight-AI/semantica.
+Hawksight AI. *Semantica: An Open Source Framework for Semantic Layers and Knowledge Engineering*. Version 0.2.7, GitHub, 2026, https://github.com/Hawksight-AI/semantica.
 
 ### Chicago
-Hawksight AI. *Semantica: An Open Source Framework for Semantic Layers and Knowledge Engineering*. Version 0.2.1. GitHub, 2026. https://github.com/Hawksight-AI/semantica.
+Hawksight AI. *Semantica: An Open Source Framework for Semantic Layers and Knowledge Engineering*. Version 0.2.7. GitHub, 2026. https://github.com/Hawksight-AI/semantica.
 
 ### IEEE
-Hawksight AI, "Semantica: An Open Source Framework for Semantic Layers and Knowledge Engineering," Version 0.2.1, GitHub, 2026. [Online]. Available: https://github.com/Hawksight-AI/semantica
+Hawksight AI, "Semantica: An Open Source Framework for Semantic Layers and Knowledge Engineering," Version 0.2.7, GitHub, 2026. [Online]. Available: https://github.com/Hawksight-AI/semantica
 
 ---