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

Merged

coredipper merged 19 commits intomainfrom

fix/code-quality-and-testing

Dec 26, 2025

Commits on Dec 26, 2025

fix: add thread safety to Membrane rate limiting

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claude
committed
fix: add expression length limit to Mitochondria (DoS protection)

coredipper
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claude
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fix: add proper error logging to Lysosome (no silent failures)

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fix: add error context to Mitochondria exceptions

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test: add comprehensive Ribosome tests (42 test cases)

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test: add comprehensive Lysosome tests (30 test cases)

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test: expand Nucleus tests (25 test cases)

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test: expand WAgent tests (33 test cases)

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test: add Oscillator topology tests

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style: add missing return type hints to Ribosome

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style: standardize to Python 3.10+ union syntax in types.py

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docs: add docstrings to Ribosome private methods

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fix: respect silent flag in Lysosome auto_digest

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test: add multi-organelle integration tests

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docs: fix Oscillator example with undefined functions

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docs: fix Chaperone example to use FoldingStrategy import

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docs: fix Membrane example with undefined other_membrane

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docs: fix Ribosome example to use mRNA import

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docs: fix more README examples with undefined variables

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

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

Commits on Dec 26, 2025

fix: add thread safety to Membrane rate limiting

fix: add expression length limit to Mitochondria (DoS protection)

fix: add proper error logging to Lysosome (no silent failures)

fix: add error context to Mitochondria exceptions

test: add comprehensive Ribosome tests (42 test cases)

test: add comprehensive Lysosome tests (30 test cases)

test: expand Nucleus tests (25 test cases)

test: expand WAgent tests (33 test cases)

test: add Oscillator topology tests

style: add missing return type hints to Ribosome

style: standardize to Python 3.10+ union syntax in types.py

docs: add docstrings to Ribosome private methods

fix: respect silent flag in Lysosome auto_digest

test: add multi-organelle integration tests

docs: fix Oscillator example with undefined functions

docs: fix Chaperone example to use FoldingStrategy import

docs: fix Membrane example with undefined other_membrane

docs: fix Ribosome example to use mRNA import

docs: fix more README examples with undefined variables