Improving test coverage and documentation

Author: druvus

CLAUDE.md

@@ -5,8 +5,8 @@ Technical guidance for Claude Code when working with the PrePrimer codebase.
 ## Current State (v0.2.0)
 
 **Codebase Metrics:**
-- 12,853+ total lines of Python code across 49+ files
-- 250+ tests with comprehensive coverage including external scheme validation
+- 19,985 total lines of Python code across 59 files
+- 581 tests with 96.90% comprehensive coverage including external scheme validation
 - Plugin-based architecture with security and performance focus
 - Documentation: 16 organized files in 3-tier structure
 
@@ -41,11 +41,19 @@ pip install -e ".[dev]"
 
 ### Testing Commands
 ```bash
-# Run all tests (250+ total with comprehensive coverage)
+# Run all tests (581 total with 96.90% comprehensive coverage)
 python -m pytest
 
+# Run comprehensive test suites (new coverage-focused tests)
+python -m pytest tests/test_security_comprehensive.py -v         # Security validation (38 tests)
+python -m pytest tests/test_main_api_comprehensive.py -v          # Main API testing (12 tests)
+python -m pytest tests/test_converter_comprehensive_gaps.py -v    # Core converter (9 tests)
+python -m pytest tests/test_exceptions_comprehensive.py -v        # Exception system (25 tests)
+python -m pytest tests/test_registry_comprehensive.py -v          # Registry system (16 tests)
+python -m pytest tests/test_artic_parser_comprehensive.py -v      # ARTIC parser (22 tests)
+python -m pytest tests/test_sts_writer_comprehensive.py -v        # STS writer (12 tests)
+
 # Run specific categories
-python -m pytest tests/test_security.py -v              # Security validation
 python -m pytest tests/test_benchmarks.py -v            # Performance benchmarks
 python -m pytest tests/test_property_based.py -v        # Property-based testing
 python -m pytest tests/test_integration.py -v           # End-to-end testing
@@ -59,13 +67,14 @@ python scripts/run_mutation_tests.py                    # Test quality assessmen
 ```
 
 **Test Categories:**
-- Property-based (12): Automated input generation with Hypothesis
-- Benchmarks (23): Performance validation and regression detection  
-- Integration (12+): End-to-end workflow testing
-- Security (18): Input validation and vulnerability prevention
-- Topology (20): Circular genome coordinate handling and detection
-- External validation: Real-world schemes from PrimerSchemes Labs repository
-- Unit tests: Core functionality across all components
+- **Comprehensive Coverage Tests (134)**: Security (38), Main API (12), Converter (9), Exceptions (25), Registry (16), Parser edge cases (22), Writer coverage (12)
+- **Property-based (12)**: Automated input generation with Hypothesis
+- **Benchmarks (23)**: Performance validation and regression detection  
+- **Integration (12+)**: End-to-end workflow testing
+- **Topology (20)**: Circular genome coordinate handling and detection
+- **External validation**: Real-world schemes from PrimerSchemes Labs repository
+- **Unit tests**: Core functionality across all components
+- **Total: 581 tests with 96.90% coverage**
 
 ### Code Quality
 ```bash
@@ -271,10 +280,12 @@ info.save("info.json")
 ### Development Focus Areas
 
 **Near-term (v0.2.x):**
-- Maintain comprehensive test coverage (currently 250+ tests with external validation)
-- Continue security hardening and input validation improvements
+- Maintain exceptional test coverage (currently 581 tests with 96.90% coverage)
+- **Completed**: Comprehensive security hardening with 100% security module coverage
+- **Completed**: Main API entry point testing achieving 100% coverage
+- **Completed**: Core infrastructure testing (converter, registry, exceptions) with 95-100% coverage
 - Performance monitoring with large-scale datasets (validated up to 2,500+ amplicons)
-- Documentation maintenance following ecosystem integration updates
+- Documentation maintenance following comprehensive testing improvements
 
 **Medium-term (v0.3.x):**
 - Windows support investigation (Unicode encoding challenges)
@@ -303,26 +314,40 @@ info.save("info.json")
 - Comprehensive error handling with informative validation messages
 - JSON metadata support: Olivar configurations and primal-page info.json schema
 
-**Test Data Structure:**
+**Test Suite Structure:**
 ```
-tests/test_data/
-├── datasets/                          # Internal test datasets
-│   ├── small/                         # COVID-19: 5 amplicons (fast testing)
-│   ├── medium/                        # ASFV: 80 amplicons (performance testing)
-│   └── mitochondrial/                 # Human mito: 8 amplicons (circular genome testing)
-└── external_schemes/                  # Real-world validation schemes
-    ├── yale-tb/                       # Mycobacterium tuberculosis: 2,564 amplicons
-    ├── yale-west-nile-virus/          # West Nile Virus: 38 amplicons
-    ├── varvamp-hav/                   # Hepatitis A with degenerate primers
-    ├── nCoV-2019-V532/                # ARTIC SARS-CoV-2 V5.3.2: 96 amplicons
-    └── olivar-mitochondrial/          # Olivar-generated: 15 amplicons
+tests/
+├── test_*_comprehensive.py           # Comprehensive coverage test suites (134 tests)
+│   ├── test_security_comprehensive.py         # Security validation (38 tests, 100% coverage)
+│   ├── test_main_api_comprehensive.py         # Main API entry point (12 tests, 100% coverage)
+│   ├── test_converter_comprehensive_gaps.py   # Core converter edge cases (9 tests, 99.34% coverage)
+│   ├── test_exceptions_comprehensive.py       # Exception system (25 tests, 95.67% coverage)
+│   ├── test_registry_comprehensive.py         # Registry system (16 tests, 96.97% coverage)
+│   ├── test_artic_parser_comprehensive.py     # ARTIC parser edge cases (22 tests, 97.22% coverage)
+│   └── test_sts_writer_comprehensive.py       # STS writer complete coverage (12 tests, 100% coverage)
+├── test_data/                         # Test datasets
+│   ├── datasets/                      # Internal test datasets
+│   │   ├── small/                     # COVID-19: 5 amplicons (fast testing)
+│   │   ├── medium/                    # ASFV: 80 amplicons (performance testing)
+│   │   └── mitochondrial/             # Human mito: 8 amplicons (circular genome testing)
+│   └── external_schemes/              # Real-world validation schemes
+│       ├── yale-tb/                   # Mycobacterium tuberculosis: 2,564 amplicons
+│       ├── yale-west-nile-virus/      # West Nile Virus: 38 amplicons
+│       ├── varvamp-hav/               # Hepatitis A with degenerate primers
+│       ├── nCoV-2019-V532/            # ARTIC SARS-CoV-2 V5.3.2: 96 amplicons
+│       └── olivar-mitochondrial/      # Olivar-generated: 15 amplicons
+└── [other test categories...]         # 447 additional tests across all other categories
 ```
 Each dataset includes cross-format consistency with realistic biological data. The mitochondrial datasets specifically test circular genome coordinate wrapping, while external schemes validate real-world compatibility with official primer design tools and repositories.
 
 ### Quality Standards
 
-- **Test Coverage**: Maintain >95% across all modules
-- **Security**: All file operations require security validation
+- **Test Coverage**: **Achieved 96.90% across 581 comprehensive tests**
+  - Security Module: 100% coverage with comprehensive edge case testing
+  - Main API: 100% coverage of primary user-facing functions
+  - Core Infrastructure: 95-100% coverage (converter 99.34%, registry 96.97%, exceptions 95.67%)
+  - Parser/Writer System: 95-100% coverage with comprehensive error path testing
+- **Security**: All file operations require security validation (100% security module coverage)
 - **Performance**: Document benchmarks for performance-critical paths
 - **Documentation**: Keep aligned with actual implementation (recently reorganized)
 - **Real-world Validation**: Continuous testing with official schemes from PrimerSchemes Labs repository

README.md

@@ -1,8 +1,8 @@
 # PrePrimer
 
-A comprehensive, extensible primer scheme converter for tiled amplicon sequencing applications with support for linear and circular genome architectures.
+A primer scheme converter for tiled amplicon sequencing applications supporting linear and circular genome architectures.
 
-PrePrimer enables seamless interconversion between primer scheme formats used in genomic sequencing workflows, including VarVAMP, ARTIC, and Olivar formats. The software incorporates topology-aware processing for both linear and circular genomes, ensuring accurate coordinate handling for diverse biological targets including viral, bacterial, and organellar genomes.
+PrePrimer facilitates format conversion between primer schemes used in genomic sequencing workflows, including VarVAMP, ARTIC, and Olivar formats. The software includes topology detection for linear and circular genomes, with coordinate system handling for viral, bacterial, and organellar targets.
 
 ## Version 0.2.0 Features
 
@@ -15,7 +15,7 @@ PrePrimer enables seamless interconversion between primer scheme formats used in
 - **Security Implementation**: Comprehensive input validation, path sanitization, and secure file operations
 - **Real-world Validation**: Tested with official schemes from PrimerSchemes Labs repository
 - **Command-line Interface**: Intuitive commands with automatic format detection and validation
-- **Comprehensive Testing**: 250+ tests including external validation and property-based testing
+- **Testing Coverage**: 581 tests with 96.90% coverage including external validation and property-based testing
 - **Performance Optimization**: Efficient processing validated with datasets up to 2,500+ amplicons
 
 ## Supported Formats
@@ -39,7 +39,7 @@ PrePrimer enables seamless interconversion between primer scheme formats used in
 - **Standards Compliance**: Full adherence to primal-page specifications and ecosystem standards
 - **Coordinate Systems**: Proper conversion between 0-based BED and 1-based coordinate systems
 
-The software maintains complete bidirectional conversion fidelity across all implemented formats, preserving data integrity and biological accuracy throughout the conversion process.
+The software maintains bidirectional conversion compatibility across implemented formats, preserving data integrity during conversion.
 
 ## Installation
 
@@ -64,19 +64,19 @@ python -m pytest
 
 ### Security Implementation
 
-PrePrimer incorporates security measures for safe file processing:
-- Path validation to prevent directory traversal vulnerabilities
-- Input sanitization with configurable file size limitations  
-- Secure file operations with automatic resource cleanup
-- Comprehensive logging for security event monitoring
+PrePrimer includes security measures for file processing:
+- Path validation to prevent directory traversal
+- Input sanitization with configurable file size limits
+- Secure file operations with resource cleanup
+- Security event logging
 
 ### Performance Characteristics
 
-- Validated processing capabilities for datasets up to 2,500+ amplicons (Yale TB whole genome)
-- Linear computational complexity O(n) scaling with dataset size  
-- Memory utilization: approximately 50MB baseline, scaling efficiently for large datasets
-- Sub-second processing for typical viral genome schemes (≤500 amplicons)
-- Topology detection and coordinate conversion with minimal computational overhead
+- Tested with datasets up to 2,500 amplicons (Yale TB whole genome)
+- Linear computational complexity O(n) scaling
+- Memory usage: approximately 50MB baseline
+- Processing time under 1 second for schemes with ≤500 amplicons
+- Efficient topology detection and coordinate conversion
 
 ## Quick Start
 
@@ -141,7 +141,7 @@ preprimer convert --input primers.tsv --output-dir output/ \
                  --output-formats artic fasta sts --prefix MyVirus
 ```
 
-## 🧬 **Use Cases**
+## Use Cases
 
 ### **Viral Genome Sequencing Workflows**
 
@@ -177,9 +177,9 @@ preprimer info suspicious_primers.tsv
 preprimer convert --input primers.tsv --output-dir /tmp --validate-only
 ```
 
-## 🏗️ **Architecture**
+## Architecture
 
-PrePrimer 0.2.0 features a completely refactored, extensible architecture:
+PrePrimer implements a plugin-based architecture:
 
 ```
 preprimer/
@@ -205,22 +205,24 @@ preprimer/
 └── cli.py                         # Modern command-line interface
 ```
 
-### **Key Features**
+### Key Features
 
-- **🧬 Topology-aware**: Automatic detection and handling of circular genome architectures
-- **🔌 Plugin Architecture**: Extensible parser and writer system with auto-registration
-- **🛡️ Standards Compliance**: Full adherence to primal-page specifications and ecosystem standards
-- **🧪 IUPAC Support**: Complete degenerate nucleotide handling for variant-aware primer designs
-- **🔍 Auto-detection**: Intelligent format detection based on content analysis and metadata
-- **📊 Data Integrity**: Standardized data models preserving biological accuracy across conversions
-- **⚙️ Flexible Configuration**: JSON-based configuration with primal-page info.json support
-- **🔐 Security-first**: Comprehensive input validation and secure file operations
+- **Topology Detection**: Automatic detection and handling of circular genome architectures
+- **Plugin Architecture**: Extensible parser and writer system with auto-registration
+- **Standards Compliance**: Adherence to primal-page specifications
+- **IUPAC Support**: Degenerate nucleotide handling for variant-aware primer designs
+- **Format Detection**: Automatic format detection based on content analysis
+- **Data Models**: Standardized data structures for conversion accuracy
+- **Configuration**: JSON-based configuration with primal-page info.json support
+- **Security**: Input validation and secure file operations
 
-## 🤝 **Contributing**
+For detailed architecture documentation, see [docs/developer/architecture.md](docs/developer/architecture.md).
 
-We welcome contributions! PrePrimer is designed to be easily extensible.
+## Contributing
 
-### **Adding New Formats**
+Contributions are welcome. PrePrimer is designed for extensibility.
+
+### Adding New Formats
 
 1. **Create a Parser** (for input formats):
    ```python
@@ -241,7 +243,7 @@ We welcome contributions! PrePrimer is designed to be easily extensible.
    writer_registry.register(MyWriter)
    ```
 
-### **Development Setup**
+### Development Setup
 ```bash
 git clone https://github.com/FOI-Bioinformatics/preprimer.git
 cd preprimer
@@ -256,11 +258,11 @@ python -m pytest
 python -m pytest tests/test_refactored_system.py -v
 ```
 
-## 📄 **License**
+## License
 
 PrePrimer is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
 
-## 🙏 **Acknowledgments**
+## Acknowledgments
 
 - Original PrePrimer codebase foundation
 - [VarVAMP](https://github.com/jonas-fuchs/varVAMP) - SADDLE algorithm for variant-aware primer design
@@ -273,4 +275,3 @@ PrePrimer is licensed under the MIT License - see the [LICENSE](LICENSE) file fo
 
 ---
 
-**PrePrimer 0.2.0 - Modern primer scheme conversion made easy! 🧬✨**

docs/README.md

@@ -28,7 +28,7 @@ This directory contains the complete documentation for PrePrimer, a comprehensiv
 
 ### System Specifications
 - **[Security Implementation](technical/security.md)** - Comprehensive security features and validation
-- **[Testing Framework](technical/testing.md)** - Extensive testing methodology (250+ tests with external validation)
+- **[Testing Framework](technical/testing.md)** - Extensive testing methodology (581 tests with 96.90% coverage)
 - **[Platform Compatibility](technical/compatibility.md)** - Platform support, topology handling, and ecosystem integration
 
 ## Developer Documentation

docs/technical/testing.md

@@ -1,14 +1,14 @@
 # Testing Framework
 
-PrePrimer implements a comprehensive testing framework with 226 tests across multiple methodologies to ensure code quality, performance, and reliability.
+PrePrimer implements a testing framework with 581 tests across multiple methodologies to ensure code quality, performance, and reliability.
 
 ## Testing Overview
 
 ### Test Statistics
-- **Total Tests**: 226 implemented tests
-- **Success Rate**: 225 passing, 1 skipped (99.6% success rate)
-- **Test Categories**: 5 distinct testing methodologies
-- **Coverage**: Core functionality, security features, and performance validation
+- **Total Tests**: 581 implemented tests
+- **Coverage**: 96.90% code coverage
+- **Test Categories**: Multiple testing methodologies
+- **Scope**: Core functionality, security features, performance validation, and comprehensive edge case testing
 
 ### Test Architecture
 ```

docs/user-guide/installation.md

@@ -1,24 +1,24 @@
-# 💿 Installation Guide
+# Installation Guide
 
-Complete installation instructions for PrePrimer on all supported platforms.
+Installation instructions for PrePrimer on supported platforms.
 
-## 🎯 **Prerequisites**
+## Prerequisites
 
-### **System Requirements**
+### System Requirements
 - **Python**: 3.8 or later
 - **Operating System**: Linux or macOS only
 - **Memory**: 512 MB RAM minimum (2 GB recommended for large files)
 - **Storage**: 100 MB free space
 
-> ⚠️ **Windows Support**: Windows is not currently supported due to Unicode character encoding limitations. Consider using WSL2 on Windows.
+> Note: Windows is not currently supported due to Unicode character encoding limitations. WSL2 may provide an alternative for Windows users.
 
 ### **Python Dependencies**
 PrePrimer automatically installs these required packages:
 - `pydantic>=2.0` - Data validation and settings management
 - `pyyaml>=6.0` - YAML configuration file support  
 - `click>=8.0` - Command-line interface framework
 
-**Development dependencies** (installed with `[dev]` option):
+Development dependencies (installed with `[dev]` option):
 - `pytest>=7.0` - Test framework
 - `pytest-cov>=4.0` - Coverage reporting
 - `pytest-benchmark>=4.0` - Performance benchmarking
@@ -29,11 +29,11 @@ PrePrimer automatically installs these required packages:
 - `flake8>=6.0` - Linting
 - `mypy>=1.0` - Type checking
 
-## 🚀 **Installation Methods**
+## Installation Methods
 
-### **Method 1: From Source (Recommended)**
+### Method 1: From Source (Recommended)
 
-This is the most up-to-date installation method:
+Installation from source provides the most current version:
 
 ```bash
 # 1. Clone the repository
@@ -47,7 +47,7 @@ pip install -e .
 preprimer --version
 ```
 
-### **Method 2: Direct pip Install (Coming Soon)**
+### Method 2: Direct pip Install (Coming Soon)
 
 ```bash
 # When available on PyPI