pyphi: 0.5.0

Optimizations

• Concepts are only recomputed if they could have been changed by a cut.
• Cuts are evaluated individually, rather than in bidirectional pairs, which allows for better parallel performance.

• Removed the unused validate.nodelist function.

• The new configuration option ASSUME_CUTS_CANNOT_CREATE_NEW_CONCEPTS gives an approximation of Φ by only recomputing concepts that exist in the unpartitioned constellation. This is much faster in certain cases.
• The methods used in determining whether a cut could effect a concept are exposed via the utils module as:
  • utils.cut_mechanism_indices
  • utils.cut_concepts
  • utils.uncut_concepts
• Added the pyphi.Subsystem.connections_relevant_for_concept method.
• Added the pyphi.Subsystem.cut_matrix property.

• pyphi.compute.main_complex now returns an empty BigMip if there are no proper complexes.
• No longer using LRU-caches implemented as a circular, doubly-linked list; this was causing a huge number of recursive calls when pickling a Subsystem object (since caches are stored on subsystems since v0.3.6) as pickle traversed the (potentially very large) cache.
• pyphi.json.make_encodable now properly handles NumPy numeric types.