Metadata-Version: 2.4
Name: bioshield
Version: 1.0.0
Summary: BioShield: Intelligent Soil Monitoring & Auto-Adjustment System
Home-page: https://github.com/emerladcompass/BioShield
Author: Samir Baladi
Author-email: emerladcompass@gmail.com
Keywords: agriculture,soil-monitoring,ai,machine-learning,environmental-science
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy>=1.21.0
Requires-Dist: pandas>=1.3.0
Requires-Dist: scikit-learn>=1.0.0
Requires-Dist: matplotlib>=3.4.0
Requires-Dist: requests>=2.26.0
Dynamic: author
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
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Dynamic: keywords
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# BioShield-B – Agro-Systemic Immunity & Genetic Integrity  
## A Network-Based Intelligence Framework (2026–2046)  

**Author:** Samir Baladi  
**Organization:** Emerlad Compass Research  

![BioShield-B](https://img.shields.io/badge/BioShield-B-Agro_Systemic_Immunity-4CAF50?style=for-the-badge&logo=github)
![BioShield](https://img.shields.io/badge/BioShield-Genetic_Integrity-4CAF50?style=for-the-badge&logo=dna)
![Version](https://img.shields.io/badge/version-3.3.5-blue?style=flat-square)
![PyPI Version](https://img.shields.io/pypi/v/bioshield?style=flat-square&color=blue)
![PyPI Downloads](https://img.shields.io/pypi/dm/bioshield?style=flat-square&color=green)
![Python](https://img.shields.io/badge/python-3.8+-blue?style=flat-square&logo=python&logoColor=white)
![License](https://img.shields.io/badge/license-MIT-green?style=flat-square)
![Status](https://img.shields.io/badge/status-research_beta-orange?style=flat-square)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18224754.svg)](https://doi.org/10.5281/zenodo.18224754)
[![GitHub](https://img.shields.io/badge/GitHub-Repository-black?style=flat-square&logo=github)](https://github.com/emerladcompass/BioShield)
[![Documentation](https://img.shields.io/badge/docs-online-success?style=flat-square&logo=readthedocs)](https://emerladcompass.github.io/bioshield/)
[![Live Dashboard](https://img.shields.io/badge/Live_Dashboard-bioshield--b1.netlify.app-blue?style=flat-square&logo=netlify)](https://bioshield-b1.netlify.app)

### 🔗 Contact & Profiles

📧 **Email:** [emerladcompass@gmail.com](mailto:emerladcompass@gmail.com)  
🔬 **ORCID:** [0009-0003-8903-0029](https://orcid.org/0009-0003-8903-0029)  
🌐 **Website:** [emerladcompass.github.io/bioshield](https://emerladcompass.github.io/bioshield)  
💼 **GitHub:** [@emerladcompass](https://github.com/emerladcompass)  
🏢 **GitLab:** [@emerladcompass1](https://gitlab.com/emerladcompass1/BioShield)  
🧭 **Affiliation:** Interdisciplinary AI Researcher  

**📂 Repositories:**  
• **GitHub:** [github.com/emerladcompass/BioShield](https://github.com/emerladcompass/BioShield)  
• **GitLab:** [gitlab.com/emerladcompass1/BioShield](https://gitlab.com/emerladcompass1/BioShield)  

**🔗 Live Dashboard:** [bioshield-b1.netlify.app](https://bioshield-b1.netlify.app)

---

## 🌱 Overview

**BioShield-B** represents a paradigm shift in agricultural systems intelligence—moving beyond traditional monitoring toward **network-based systemic immunity** and **genetic integrity preservation**. This framework integrates **AI-driven analytics, quantum-inspired algorithms, and ecological network theory** to create resilient agricultural ecosystems capable of self-regulation, adaptation, and long-term sustainability.

### 🎯 Framework Timeline & Evolution

| Phase | Period | Focus | Key Innovations |
|-------|--------|-------|-----------------|
| **Phase 1** | 2023–2025 | Soil Monitoring & Basic Analytics | Traditional sensors, basic AI models |
| **Phase 2** | 2026–2030 | Agro-Systemic Intelligence | Network immunity, predictive adaptation |
| **Phase 3** | 2031–2035 | Genetic Integrity Systems | DNA-based monitoring, epigenetic tracking |
| **Phase 4** | 2036–2040 | Quantum-Agriculture Integration | Quantum sensors, entanglement-based networks |
| **Phase 5** | 2041–2046 | Planetary-Scale Agricultural Immunity | Global network, autonomous ecosystem regulation |

---

## 📦 PyPI Package

**BioShield is now available on PyPI!** 🎉

### Installation via PyPI (Recommended)

```bash
# Install latest version
pip install bioshield

# Install specific version
pip install bioshield==3.3.5

# Upgrade to latest
pip install --upgrade bioshield
```

Core Framework Modules

```python
# Import BioShield-B Framework Modules
from bioshield import (
    SoilMonitor,           # Advanced soil analysis
    SoilAutoAdjuster,      # Auto-correction system
    AIPredictor,          # Predictive analytics
    ReportGenerator,      # Automated reporting
    LiveDashboard,        # Real-time visualization
    AlertManager,         # Notification system
    DirectoryManager      # System organization
)

# Initialize complete system
from bioshield.core.engine import BioShieldEngine

engine = BioShieldEngine()
engine.initialize_system()
results = engine.run_full_analysis()
```

---

🏗️ Project Structure

```
BioShield/
├── src/
│   ├── main.py                 # CLI entry point - Complete system interface
│   ├── final_system.py         # Integrated system - Production deployment
│   ├── core/                   # Core engine - Framework foundation
│   │   ├── __init__.py
│   │   └── engine.py          # Main orchestration engine
│   └── modules/                # Functional modules - Specialized components
│       ├── __init__.py
│       ├── soil_monitor.py     # Soil parameter monitoring & analysis
│       ├── auto_adjuster.py    # Automatic correction algorithms
│       ├── ai_predictor.py     # Predictive analytics & forecasting
│       ├── report_generator.py # Automated report generation
│       ├── live_dashboard.py   # Real-time visualization interface
│       ├── alert_manager.py    # Notification & alert system
│       ├── banner.py           # System branding & display
│       └── directory_manager.py# File system organization
├── config/
│   └── config.json            # System configuration & parameters
├── data/                      # Data storage - Input/output datasets
├── logs/                      # System logs - Activity & error tracking
├── reports/                   # Generated reports - Analysis outputs
├── tests/                     # Test suite - Quality assurance
├── vault/                     # Secure storage - Sensitive data
├── docs/                      # Documentation - User & developer guides
├── README.md                  # Project overview - This file
├── LICENSE                    # Licensing terms - MIT License
└── requirements.txt           # Dependencies - Python package requirements
```

Module Descriptions

Core Engine (core/engine.py)

```python
class BioShieldEngine:
    """
    Main orchestration engine coordinating all system modules
    - System initialization and configuration
    - Module coordination and data flow
    - Error handling and recovery
    - Performance optimization
    """
```

Soil Monitor (modules/soil_monitor.py)

```python
class SoilMonitor:
    """
    Advanced soil parameter monitoring system
    - pH level detection and analysis
    - Moisture content measurement
    - Temperature monitoring
    - Nutrient level assessment
    - Sensor data simulation (for testing)
    """
```

Auto Adjuster (modules/auto_adjuster.py)

```python
class SoilAutoAdjuster:
    """
    Intelligent correction system
    - Automatic pH balancing
    - Irrigation control algorithms
    - Nutrient supplementation
    - Environmental adaptation
    - Feedback loop optimization
    """
```

AI Predictor (modules/ai_predictor.py)

```python
class AIPredictor:
    """
    Predictive analytics framework
    - Soil health forecasting
    - Crop yield prediction
    - Disease risk assessment
    - Climate impact analysis
    - Trend identification
    """
```

Live Dashboard (modules/live_dashboard.py)

```python
class LiveDashboard:
    """
    Real-time visualization interface
    - Sensor data visualization
    - System status monitoring
    - Performance metrics display
    - Interactive controls
    - Alert notifications
    """
```

---

🚀 Quick Start

Prerequisites

```bash
# System Requirements
- Python 3.8+ (recommended 3.10+)
- 4GB+ RAM (for data processing)
- 500MB+ disk space
- Network connectivity (for updates)
```

Installation & Setup

```bash
# 1. Clone the repository
git clone https://github.com/emerladcompass/BioShield.git
cd BioShield

# 2. Install dependencies
pip install -r requirements.txt

# 3. Run system tests
python -m pytest tests/

# 4. Initialize configuration
python src/main.py --init
```

Running the System

```bash
# Full system mode (all modules)
python src/main.py --mode all

# Demo mode (simulated data)
python src/main.py --mode demo

# Auto-adjustment only
python src/main.py --mode auto

# Custom configuration
python src/main.py --config custom_config.json --log-level debug
```

PyPI Installation & Usage

```bash
# Install from PyPI
pip install bioshield

# Import and use
python
>>> from bioshield import SoilMonitor
>>> monitor = SoilMonitor()
>>> data = monitor.simulate_sensor_reading()
>>> print(f"pH: {data['ph']:.2f}, Moisture: {data['moisture']}%")
```

---

📊 Research & Applications

Academic Research Applications

· Soil science and agronomy studies
· Environmental monitoring research
· AI/ML algorithm development
· Predictive analytics validation
· Climate change impact studies

Agricultural Implementation

· Precision farming systems
· Smart irrigation management
· Soil health optimization
· Crop yield improvement
· Sustainable agriculture practices

Environmental Conservation

· Ecosystem health monitoring
· Biodiversity assessment
· Pollution detection
· Habitat restoration
· Conservation planning

Educational Use

· STEM education programs
· Agricultural training
· Data science projects
· Environmental awareness
· Research methodology

---

🔬 Core Features

1. Comprehensive Soil Analysis

· Multi-parameter monitoring (pH, moisture, temperature, nutrients)
· Real-time data collection and processing
· Historical trend analysis
· Comparative assessment

2. Intelligent Auto-Correction

· Automated parameter adjustment
· Smart irrigation control
· Nutrient balance optimization
· Environmental adaptation

3. Advanced AI Analytics

· Predictive modeling and forecasting
· Pattern recognition and anomaly detection
· Risk assessment and mitigation
· Optimization algorithms

4. Automated Reporting

· Daily, weekly, and custom reports
· Data visualization and charts
· Export capabilities (PDF, CSV, JSON)
· Customizable templates

5. Real-Time Dashboard

· Live data visualization
· Interactive controls
· System status monitoring
· Alert notifications

6. Robust Alert System

· Custom threshold configuration
· Multi-channel notifications
· Escalation protocols
· Historical alert tracking

---

📚 How to Cite

Primary Citation

```bibtex
@software{baladi2026bioshieldb,
  author       = {Baladi, Samir},
  title        = {{BioShield-B: Agro-Systemic Immunity & Genetic Integrity Framework}},
  year         = {2026},
  publisher    = {Zenodo},
  version      = {3.3.5},
  doi          = {10.5281/zenodo.18224754},
  url          = {https://doi.org/10.5281/zenodo.18224754}
}
```

Related Publications

```bibtex
@article{baladi2026intelligentsoil,
  title={Intelligent Soil Monitoring Systems for Sustainable Agriculture},
  author={Baladi, Samir},
  journal={Journal of Agricultural Informatics},
  year={2026},
  volume={12},
  pages={45–78}
}
```

---

🤝 Contributing

We welcome contributions from researchers, developers, and agriculture professionals:

Development Areas

1. Algorithm Enhancement
   · Improved prediction models
   · Optimization algorithms
   · Data processing efficiency
2. New Features
   · Additional sensor integrations
   · Mobile application development
   · API expansion
3. Documentation
   · User guides and tutorials
   · API documentation
   · Research case studies

Contribution Process

```bash
# 1. Fork the repository
# 2. Create feature branch
git checkout -b feature/improvement-name

# 3. Make changes and test
python -m pytest tests/

# 4. Update documentation
# 5. Submit pull request
```

Testing Guidelines

```bash
# Run all tests
python -m pytest tests/

# Run specific test module
python -m pytest tests/test_soil_monitor.py

# Generate coverage report
python -m pytest --cov=src tests/
```

---

📄 License

MIT License

This project is licensed under the MIT License - see the LICENSE file for details.

Usage Terms

1. Academic Use: Free for research and education
2. Commercial Use: Contact for enterprise licensing
3. Modifications: Allowed with proper attribution
4. Distribution: Permitted with license inclusion

Attribution

```markdown
Based on "BioShield-B: Agro-Systemic Intelligence Framework"
by Samir Baladi, Emerlad Compass Research (2026)
DOI: 10.5281/zenodo.18224754
```

---

🔮 Future Development Roadmap

Short Term (2026)

· Mobile application development
· Additional sensor integrations
· Cloud deployment options
· Multi-language support

Medium Term (2027-2028)

· Satellite data integration
· Drone-based monitoring
· Blockchain for data integrity
· IoT device compatibility

Long Term (2029-2030)

· Quantum computing integration
· Global soil health network
· Autonomous farming systems
· Climate prediction models

---

🆘 Support & Resources

Documentation

· User Guide - Complete usage instructions
· API Reference - Developer documentation
· Tutorials - Step-by-step guides
· FAQ - Common questions and solutions

Community & Support

· GitHub Issues: Report bugs & request features
· Email Support: emerladcompass@gmail.com
· Discussion Forum: GitHub Discussions

Training & Workshops

· Online training sessions available
· Custom workshop arrangements
· Academic collaboration opportunities
· Industry partnership programs

---

## 🧭 Connect & Collaborate

**📧 Email:** [emerladcompass@gmail.com](mailto:emerladcompass@gmail.com)  
**🔗 Website:** [emerladcompass.github.io/bioshield](https://emerladcompass.github.io/bioshield)  
**💼 GitHub:** [github.com/emerladcompass](https://github.com/emerladcompass)  
**🔬 Research Portal:** [Emerlad Compass Research](https://emerladcompass.github.io)  

**🌱 Join our growing community of researchers and developers!**

---

**BioShield-B Framework** • **Version 3.3.5** • **© 2026 Emerlad Compass Research**  
*"Intelligent Soil Monitoring for Sustainable Agriculture"*

[![PyPI Version](https://img.shields.io/pypi/v/bioshield?style=for-the-badge)](https://pypi.org/project/bioshield/)
[![GitHub Stars](https://img.shields.io/github/stars/emerladcompass/BioShield?style=for-the-badge)](https://github.com/emerladcompass/BioShield/stargazers)
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