Add Py_AASequence wrapper for amino acid sequence operations

[Copilot]

Add Py_AASequence class to wrap pyOpenMS AASequence with common operations

Plan

• Create py_aasequence.py module with Py_AASequence class
  • Wrap pyOpenMS AASequence with pythonic properties
  • Add reverse() and reverse_with_enzyme() methods using DecoyGenerator
  • Add shuffle() and shuffle_with_enzyme() methods using DecoyGenerator
  • Add from_string() class method for easy creation
  • Support iteration and string representation
  • Add Pythonic properties (sequence, mono_weight, average_weight, formula, etc.)
• Create comprehensive tests in test_py_aasequence.py
  • Test basic wrapper functionality
  • Test reverse operations (with and without enzyme)
  • Test shuffle operations (with and without enzyme)
  • Test properties and string operations
• Export Py_AASequence in __init__.py
• Run tests to validate implementation (all 140 tests pass)
• Run code formatting (Black) and linting (flake8)
• Run security check with codeql_checker (0 alerts)
• Add documentation to README.md
  • Added "Working with Amino Acid Sequences" section with examples
  • Added Py_AASequence to API Reference section
  • Added AASequence examples to comparison table

Original prompt

add a Py_AASequence class

• that supports common operations used in other parts of this library (DRY principle)
• for example reversing or shuffle a sequence, optionally by specifying an enzyme.
  It should use existing pyopenms functionality for that so minimal reimplementation is done

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[timosachsenberg]

@copilot whats wrong with you? Always add to the readme so new stuff is documented

[timosachsenberg]

@copilot add to the readme.md!!!

[Copilot]

@copilot add to the readme.md!!!

Added comprehensive documentation for Py_AASequence to README.md in commit ff18081. The documentation includes:

• A new "Working with Amino Acid Sequences" section with usage examples
• Full API reference in the "API Reference" section
• Comparison examples in the pyOpenMS vs openms-python table

The documentation covers all key features: sequence creation, properties, reverse/shuffle operations, m/z calculations, and sequence queries.