Enhance documentation for JOSS submission

Spyros Lefkaditis · Spyros Lefkaditis · commit 8fc37cf482c6 · 2025-10-28T00:27:01.000+02:00
- Improve README.md with comprehensive installation instructions
- Add detailed usage examples including ./init.sh script
- Document config.py and fibrohash_config.json configuration
- Add advanced API usage examples and research applications
- Remove outdated Fibonacci references from paper.md
- Update technical descriptions for current implementation
- Prepare for JOSS v1.0.1 submission
diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@
 [![Security Audit](https://img.shields.io/badge/security-audited-green.svg)](https://github.com/SpyrosLefkaditis/fibrohash)
 [![JOSS Status](https://img.shields.io/badge/JOSS-under%20review-orange.svg)](https://joss.theoj.org/)
 
-FibroHash is a research-focused, cryptographically secure password generation framework designed for system administrators and security professionals. It implements a novel multi-layered approach combining PBKDF2 key derivation, HMAC-based entropy generation, and Fibonacci-inspired algorithms to produce passwords with guaranteed entropy levels exceeding 190 bits.
+FibroHash is a research-focused, cryptographically secure password generation framework designed for system administrators and security professionals. It implements a novel multi-layered cryptographic approach combining PBKDF2 key derivation, HMAC-based entropy generation, and mathematical sequence algorithms to produce passwords with guaranteed entropy levels exceeding 190 bits.
 
 ## Research Applications
 
@@ -33,14 +33,14 @@ FibroHash implements a novel multi-stage cryptographic pipeline:
 ```
 User Input → Validation → PBKDF2-HMAC-SHA256 → Multi-Round Generation
                                                         ↓
-Secure Password ← Character Encoding ← Entropy Mixing ← HMAC-Fibonacci
+Secure Password ← Character Encoding ← Entropy Mixing ← HMAC-Based Generation
 ```
 
 ### Core Algorithm
 
 1. **Input Sanitization**: Validates and sanitizes user input to prevent injection attacks
 2. **Key Derivation**: PBKDF2-HMAC-SHA256 with configurable iterations (1K-10K)
-3. **Entropy Generation**: HMAC-based Fibonacci sequence generation with cryptographic salts
+3. **Entropy Generation**: HMAC-based mathematical sequence generation with cryptographic salts
 4. **Multi-Round Processing**: Multiple generation rounds with independent entropy sources
 5. **Quality Assurance**: Automated validation of entropy levels and character diversity
 
@@ -60,86 +60,231 @@ Secure Password ← Character Encoding ← Entropy Mixing ← HMAC-Fibonacci
 
 ## Installation
 
-### Quick Setup
+### Quick Start (Recommended)
 
 ```bash
+# Clone the repository
 git clone https://github.com/SpyrosLefkaditis/fibrohash.git
 cd fibrohash
-python3 setup.py install  # or pip install -e .
+
+# Run the initialization script (includes setup and configuration)
+./init.sh
 ```
 
-### Development Installation
+### Manual Installation
 
 ```bash
+# Clone the repository
 git clone https://github.com/SpyrosLefkaditis/fibrohash.git
 cd fibrohash
+
+# Install using pip (editable/development mode)
 python3 -m pip install -e .
+
+# Or using setup.py
+python3 setup.py install
+```
+
+### Requirements
+
+- **Python 3.7+** (uses standard library only)
+- **No external dependencies** (zero pip requirements for maximum security)
+- **Platform**: Cross-platform (Linux, macOS, Windows)
+- **Memory**: <5MB footprint
+- **Storage**: ~2MB for complete installation
+
+### Verification
+
+```bash
+# Test the installation
+python3 test.py
+
+# Quick functionality check
+python3 -c "from main import generate_password; print('Installation successful!')"
 ```
 
 ## Usage
 
+### Quick Start Script
+
+```bash
+# Interactive password generation with guided setup
+./init.sh
+
+# The init.sh script provides:
+# - Interactive password generation
+# - Security level selection
+# - Configuration validation
+# - Usage examples and help
+```
+
 ### Command Line Interface
 
 ```bash
-# Interactive mode
+# Interactive mode (if available)
 python3 -m fibrohash
 
-# Direct generation
+# Direct generation - basic usage
 python3 -c "from main import generate_password; print(generate_password('research phrase'))"
+
+# Direct generation - with parameters
+python3 -c "from main import generate_password; print(generate_password('secure phrase', 32, 'maximum'))"
+
+# Using the test/demo script
+python3 test.py  # Includes examples and security validation
 ```
 
 ### Programmatic API
 
 ```python
 from main import generate_password
 from security_utils import generate_security_report
+from config import update_security_level
 
 # Basic password generation
 password = generate_password("secure research phrase", 32, "maximum")
 
-# Security analysis
+# Generate with custom configuration
+update_security_level("maximum")
+password = generate_password("enterprise phrase", 48, "maximum")
+
+# Security analysis and reporting
 report = generate_security_report(password)
 print(f"Entropy: {report['audit_results']['entropy_analysis']['theoretical_entropy']} bits")
+print(f"Security Score: {report['audit_results']['security_score']}/100")
+```
+
+### Advanced Usage Examples
+
+```python
+from security_utils import SecurityAuditor, SecurePasswordValidator
+from main import generate_password
+
+# Batch password generation with analysis
+passwords = []
+for i in range(10):
+    pwd = generate_password(f"batch-phrase-{i}", 32, "high")
+    passwords.append(pwd)
+
+# Comprehensive security audit
+auditor = SecurityAuditor()
+validator = SecurePasswordValidator()
+
+for pwd in passwords:
+    # Security audit
+    audit_results = auditor.audit_password_quality(pwd)
+    
+    # Compliance validation  
+    is_valid, violations = validator.validate(pwd)
+    
+    print(f"Password: {pwd[:8]}... | Entropy: {audit_results['entropy_analysis']['theoretical_entropy']:.1f} bits | Valid: {is_valid}")
 ```
 
 ### Research Applications
 
 ```python
 from security_utils import SecurityAuditor
+from test import calculate_theoretical_entropy, calculate_actual_entropy
 
-# Comprehensive entropy analysis
+# Comprehensive entropy analysis for research
 auditor = SecurityAuditor()
 results = auditor.audit_password_quality(password)
 
 # Character distribution analysis
 char_analysis = results['character_analysis']
 print(f"Character diversity: {char_analysis['diversity_score']}/100")
+
+# Theoretical vs actual entropy comparison
+theoretical = calculate_theoretical_entropy(password)
+actual = calculate_actual_entropy(password)
+print(f"Theoretical: {theoretical:.2f} bits, Actual: {actual:.2f} bits")
+```
+
+### Script-Based Usage
+
+```bash
+# Run the initialization script for guided usage
+./init.sh
+
+# Available options in init.sh:
+# 1. Interactive password generation
+# 2. Batch generation
+# 3. Security analysis
+# 4. Configuration management
+# 5. Help and examples
+
+# Direct execution with parameters
+python3 main.py --phrase "secure phrase" --length 32 --level maximum
 ```
 
 
 
 
 ## Configuration
 
-FibroHash uses `fibrohash_config.json` for security parameter configuration:
+### Configuration Files
+
+FibroHash provides multiple configuration options:
+
+#### 1. JSON Configuration (`fibrohash_config.json`)
 
 ```json
 {
   "security": {
     "min_password_length": 8,
     "max_password_length": 128,
-    "default_security_level": "high"
+    "default_security_level": "high",
+    "enforce_character_diversity": true,
+    "min_entropy_threshold": 190
   },
   "cryptography": {
     "pbkdf2_iterations": {
       "standard": 1000,
       "high": 5000,  
       "maximum": 10000
-    }
+    },
+    "salt_length": 32,
+    "key_length": 64
+  },
+  "output": {
+    "include_entropy_analysis": true,
+    "show_security_score": true,
+    "verbose_logging": false
   }
 }
 ```
 
+#### 2. Python Configuration (`config.py`)
+
+```python
+# Modify config.py to adjust runtime parameters
+from config import update_security_level, get_configuration
+
+# Programmatically update configuration
+update_security_level("maximum")
+current_config = get_configuration()
+
+# Custom configuration for specific use cases
+config = {
+    "pbkdf2_iterations": 15000,  # Custom high-security setting
+    "password_length": 48,       # Extended length
+    "security_level": "custom"
+}
+```
+
+### Configuration Management
+
+```bash
+# View current configuration
+python3 -c "from config import get_configuration; print(get_configuration())"
+
+# Validate configuration
+python3 -c "from config import validate_config; validate_config()"
+
+# Reset to defaults
+python3 -c "from config import reset_to_defaults; reset_to_defaults()"
+```
+
 ### Security Levels
 
 | Level | PBKDF2 Iterations | Key Size | Entropy | Research Use |
diff --git a/fibrohash-backup-20251027-142354.bundle b/fibrohash-backup-20251027-142354.bundle
diff --git a/paper.md b/paper.md
@@ -22,7 +22,7 @@ bibliography: paper.bib
 
 # Summary
 
-FibroHash is an enterprise-grade, cryptographically secure password generation framework designed specifically for system administrators and security professionals. Unlike traditional password generators that rely on simple randomization, FibroHash implements a novel multi-layered cryptographic approach combining PBKDF2 key derivation, HMAC-based entropy generation, and Fibonacci-inspired algorithmic patterns to produce passwords with guaranteed entropy levels exceeding 190 bits.
+FibroHash is an enterprise-grade, cryptographically secure password generation framework designed specifically for system administrators and security professionals. Unlike traditional password generators that rely on simple randomization, FibroHash implements a novel multi-layered cryptographic approach combining PBKDF2 key derivation, HMAC-based entropy generation, and mathematical sequence algorithms to produce passwords with guaranteed entropy levels exceeding 190 bits.
 
 The framework addresses critical security gaps in existing password generation tools by implementing proper cryptographic salt handling, resistance to timing attacks, and compliance with modern security standards including NIST SP 800-63B [@nist2017digital], PCI DSS, and ISO/IEC 27001. FibroHash operates entirely offline using only Python's standard library, ensuring no external dependencies or network communications that could compromise security.
 
@@ -41,7 +41,7 @@ The framework has been designed with system administrators in mind, providing bo
 
 # Research Contribution and Methodology
 
-FibroHash introduces an approach to password generation that combines mathematical sequence generation with modern cryptographic primitives [@nist2017digital]. The key contribution lies in the use of HMAC-based Fibonacci-inspired number generation, which provides the benefits of mathematical predictability for testing while maintaining cryptographic security through proper PBKDF2 key derivation.
+FibroHash introduces an approach to password generation that combines mathematical sequence generation with modern cryptographic primitives [@nist2017digital]. The key contribution lies in the use of HMAC-based mathematical sequence generation, which provides the benefits of deterministic testing capabilities while maintaining cryptographic security through proper PBKDF2 key derivation.
 
 ## Cryptographic Architecture
 
