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fix: Code quality improvements, comprehensive tests, and documentation fixes#9

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coredipper merged 19 commits intomainfrom
fix/code-quality-and-testing
Dec 26, 2025
Merged

fix: Code quality improvements, comprehensive tests, and documentation fixes#9
coredipper merged 19 commits intomainfrom
fix/code-quality-and-testing

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@coredipper coredipper commented Dec 26, 2025 •
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Summary

Comprehensive code quality overhaul addressing critical issues, testing gaps, and documentation problems.

Critical Fixes

  • Thread safety: Added threading.Lock() to Membrane rate limiting
  • DoS protection: Added expression length limit (10KB) to Mitochondria
  • Error handling: Fixed silent exception handling in Lysosome with proper logging
  • Error context: Enhanced Mitochondria exceptions with pathway information

Testing (~200 new tests)

  • Ribosome: 42 tests (templates, filters, conditionals, loops)
  • Lysosome: 30 tests (waste processing, autophagy, recycling)
  • Nucleus: 25 tests (transcription, tools, statistics)
  • WAgent: 33 tests (wiring diagrams, connections, capabilities)
  • Oscillator: 52 tests (phases, waveforms, states)
  • Integration: 26 tests (multi-organelle workflows)

Code Consistency

  • Standardized type hints to Python 3.10+ syntax (T | None)
  • Added docstrings to Ribosome private methods
  • Fixed silent flag behavior in Lysosome

Documentation Fixes

  • Oscillator example: Added missing function definitions
  • Chaperone example: Added FoldingStrategy usage
  • Membrane example: Defined other_membrane variable
  • Ribosome example: Added mRNA usage

Test Plan

  • All 645 tests pass
  • No regressions to existing functionality
  • README examples are now copy-paste runnable

coredipper and others added 19 commits December 26, 2025 01:45
@coredipper @claude
fix: add thread safety to Membrane rate limiting
cd6a4b6 
Added thread-safe rate limiting to prevent race conditions in concurrent
requests. The rate limiting counter now uses a threading.Lock to ensure
atomic check-then-act operations.

Changes:
- Added threading.Lock (_rate_lock) to Membrane.__init__
- Extracted rate limiting logic to _check_rate_limit() method
- Protected _request_times access with lock to prevent race conditions
- Added comprehensive thread safety tests

Tests verify:
- Concurrent requests maintain exact rate limit boundary
- No race conditions when multiple threads make simultaneous requests
- Rate limiting triggers at precisely the configured threshold

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@coredipper @claude
fix: add expression length limit to Mitochondria (DoS protection)
b5d941d 
🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@coredipper @claude
fix: add proper error logging to Lysosome (no silent failures)
aae8d3c 
🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@coredipper @claude
fix: add error context to Mitochondria exceptions
42178eb 
- Added pathway field to MetabolicResult dataclass
- Enhanced error messages to include pathway information and error type
- Error messages now show: "Metabolic failure in {pathway}: {ErrorType}: {message}"
- All MetabolicResult returns now include pathway information
- Created error_context dict for potential future use (expression, error_type, error_message)
- Tests verify errors contain both expression context and pathway info

Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@coredipper @claude
test: add comprehensive Ribosome tests (42 test cases)
c90e86a 
Add comprehensive test coverage for the Ribosome prompt template engine:

- TestRibosomeBasics (8 tests): Template creation, translation, required/optional variables
- TestRibosomeFilters (7 tests): upper, lower, trim, title filters, custom filters
- TestRibosomeConditionals (6 tests): if/else blocks, truthy/falsy values
- TestRibosomeLoops (6 tests): iteration, index access, dict items, first/last markers
- TestRibosomeIncludes (3 tests): template inclusion, nested includes
- TestRibosomeEdgeCases (12 tests): error handling, dataclass structure, statistics

All 42 tests pass, providing complete coverage of the Ribosome API.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@coredipper @claude
test: add comprehensive Lysosome tests (30 test cases)
9d7df4a 
Add comprehensive test coverage for Lysosome organelle including:
- Basic functionality (ingest, digest, waste count)
- All waste types (FAILED_OPERATION, EXPIRED_CACHE, TOXIC, ORPHANED, MISFOLDED)
- Autophagy and self-cleaning mechanisms
- Recycling and insight extraction
- Sensitive data handling and secure disposal
- Statistics and monitoring
- Emergency digest behavior
- Custom digesters

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@coredipper @claude
test: expand Nucleus tests (25 test cases)
fe3dda4 
Add comprehensive test coverage for the Nucleus organelle including:

1. TestNucleusBasics (6 tests):
   - Creating with explicit MockProvider
   - Custom mock responses
   - Auto-detect provider fallback with warning
   - Basic transcribe functionality
   - History logging
   - Metadata capture

2. TestNucleusConfiguration (4 tests):
   - Custom base energy cost
   - Per-transcription energy cost override
   - Custom ProviderConfig
   - Custom max_retries

3. TestNucleusToolIntegration (4 tests):
   - Transcribe with tools (no tool calls)
   - Transcribe with tools (executes tool)
   - Max iterations respected
   - Auto-execute flag behavior

4. TestNucleusErrorHandling (3 tests):
   - Empty prompt handling
   - Provider error propagation
   - Invalid response handling

5. TestNucleusStatistics (5 tests):
   - Total energy consumed tracking
   - Total tokens used tracking
   - Transcription count
   - Clear log functionality
   - Timing information capture

6. TestNucleusAdvanced (3 tests):
   - Chronological order maintenance
   - Same prompt different responses
   - Provider name logging

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@coredipper @claude
test: expand WAgent tests (33 test cases)
c9d6894 
Add comprehensive test coverage for typed wiring diagrams:
- TestWiringDiagramBasics (5 tests): empty diagram, add modules, duplicate detection
- TestWiringConnections (9 tests): valid connections, type/integrity validation, error handling
- TestCapabilities (6 tests): capability tracking and aggregation
- TestIntegrityLabels (7 tests): integrity flow rules (UNTRUSTED/VALIDATED/TRUSTED)
- TestComplexDiagrams (6 tests): multi-module chains, fanout patterns, complex scenarios

All tests validate the type-safe composition with integrity labels and capability tracking.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@coredipper @claude
test: add Oscillator topology tests
72d8708 
🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@coredipper @claude
style: add missing return type hints to Ribosome
27a056d 
🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@coredipper @claude
style: standardize to Python 3.10+ union syntax in types.py
522ea42 
🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@coredipper @claude
docs: add docstrings to Ribosome private methods
8fe47f6 
Added comprehensive docstrings to all private methods in the Ribosome class:
- mRNA._detect_codons(): Documents variable detection logic
- Ribosome._process_variables(): Details variable substitution with filters
- Ribosome._process_conditionals(): Explains if/else block handling
- Ribosome._process_loops(): Documents loop iteration and context
- Ribosome._process_includes(): Describes template composition

All docstrings follow the standard format with descriptions, args, and
return values. Improves code maintainability and developer experience.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@coredipper @claude
fix: respect silent flag in Lysosome auto_digest
aa8e0bd 
Add silent flag check to _auto_digest method so it respects
the silent setting before printing auto-digest messages.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@coredipper @claude
test: add multi-organelle integration tests
d1d84ad 
Add comprehensive integration tests for multi-organelle workflows that verify
the "cell" functions as a cohesive system. Tests cover realistic scenarios
combining multiple organelles:

Test Coverage:
- TestMembraneToMitochondria: Filtering -> Execution workflows
  * Safe signals pass and execute correctly
  * Dangerous signals blocked by membrane
  * Suspicious signals with lenient thresholds

- TestChaperoneValidation: Output validation workflows
  * Valid JSON folding to Pydantic models
  * Invalid output routing to Lysosome
  * JSON extraction from markdown blocks

- TestRibosomeToNucleus: Template rendering -> LLM execution
  * Template variable substitution
  * Conditional sections (if/else)
  * Loop expansion for lists

- TestFullCellWorkflow: Complete signal processing pipelines
  * End-to-end workflow: Signal -> Filter -> Template -> Execute -> Validate
  * Membrane blocking with waste logging
  * Tool execution integration

- TestATPBudgetWorkflow: Energy budget tracking
  * ATP depletion across operations
  * ROS accumulation stopping work
  * Mitochondrial repair restoring function

- TestMultiOrganelleErrorHandling: Error handling across organelles
  * Membrane -> Lysosome threat pipeline
  * Chaperone -> Lysosome error pipeline
  * Autophagy cleaning old waste

- TestOrganelleStatistics: Monitoring and metrics
  * Statistics tracking for all organelles
  * Success/failure rates

- TestRealWorldScenarios: Realistic use cases
  * Safe math query through full pipeline
  * Injection attack blocking
  * Malformed output recovery
  * JSON repair (trailing commas)

Total: 26 integration test cases covering all major organelles and their
interactions in realistic workflows.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@coredipper @claude
docs: fix Oscillator example with undefined functions
0457631 
- Define health_check, do_work, do_rest functions
- Remove unnecessary lambda wrapper
- Add comment about stopping oscillators

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@coredipper @claude
docs: fix Chaperone example to use FoldingStrategy import
2c7dbca 
- Add example showing how to control folding strategies
- Replace coercions_applied with strategy_used (more useful)

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@coredipper @claude
docs: fix Membrane example with undefined other_membrane
2bb19b7 
🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@coredipper @claude
docs: fix Ribosome example to use mRNA import
c7dc190 
🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@coredipper @claude
docs: fix more README examples with undefined variables
e8e3877 
- Lysosome: Remove unused Waste import, use concrete example
- Metabolism: Define other_metabolism instead of other_agent
- Quorum: Define budget variable
- Cascade: Use concrete lambda functions and input
- Telomere: Replace undefined functions with concrete loop

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@coredipper coredipper merged commit 532d90f into main Dec 26, 2025
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