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Make Unit, CompositeUnit, and Substrate stateless: state is now passed explicitly to compute_tpm(), network(), and subsystem() rather than stored as mutable instance attributes. This eliminates side effects from TPM computation and makes the API safer for concurrent use. - Replace BaseUnit/Unit/TPMDict with stateless Unit, CompositeUnit, and TPMCache - Update unit function signatures to accept (unit, state, input_state) explicitly instead of reading state from the unit - Remove System class and visualization methods from Substrate - Remove state/input_state properties and setters Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Add type annotations to mechanism_combinations functions and registry - Fix utils.py to use relative import instead of top-level pyphi import - Add public API exports to __init__.py Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Test Unit construction, equality, hashing, state-independent and state-dependent mechanisms, TPM caching, CompositeUnit, Substrate construction, TPM computation, connectivity matrix, network/subsystem creation, serialization, and an end-to-end integration test. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Adds substrate modeler capability into pyphi with several major changes: