Casper/factored processes

[casperlchristensen]

Note

Introduce a unified FactoredGenerativeProcess with pluggable conditional structures and builders, plus utilities and extensive tests/configs.

• Generative Processes:
  • Add FactoredGenerativeProcess supporting composite vocabularies and per-factor state transitions.
  • Implement observation/log-probability, emission, and transition updates via encoder-based factorization.
• Conditional Structures (simplexity/generative_processes/structures):
  • New protocols and implementations: IndependentStructure, SequentialConditional, FullyConditional, ConditionalTransitions.
  • Provide variant selection and joint distribution computation for each structure.
• Builder Enhancements (builder.py):
  • Add build_factored_process and build_factored_process_from_spec factories.
  • Add helpers: build_matrices_from_spec, build_chain_from_spec, build_symmetric_from_spec, build_transition_coupled_from_spec.
  • Minor: return HiddenMarkovModel without device arg in nonergodic builder.
• Utilities (utils/factoring_utils.py):
  • Add compute_obs_dist_for_variant, transition_with_obs, and TokenEncoder for factor encoding/updates.
• GHMM:
  • Strengthen validate_transition_matrices with eigenvalue check and normalization warning.
• Tests & Examples:
  • Add comprehensive unit/integration tests for builders, structures, factored process, and utils.
  • Add end-to-end YAML configs demonstrating independent, chain, symmetric, and transition_coupled structures.
  • Update analysis and structured-config tests to use jax.Array types.

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