API reference

The modules a user of PyPhi works with, grouped by what they do. Each entry opens the module’s page: its functions, classes, and submodules. Modules that only serve the package’s internals (import deferral, registries, protocols, type aliases, utilities) are not listed.

The top-level namespace

import pyphi gives the everyday API in one place: Substrate, System, analyze, sweep, examples, and config.

The example networks page shows every registered example rendered from the objects themselves.

pyphi

PyPhi

Substrates and systems

pyphi.substrate	Represents the substrate of interest.
pyphi.system	System value type — (Substrate, state, node_subset, partition).
pyphi.substrate_generator	High-level interface for creating systems by specifying architecture.
pyphi.examples	Example substrates and systems to go along with the documentation.
pyphi.estimate	Estimate substrates from observed transitions, with epistemic uncertainty.
pyphi.labels	Helper class representing labels of substrate nodes.
pyphi.connectivity	Functions for determining substrate connectivity properties.
pyphi.convert	Conversion functions.
pyphi.validate	Methods for validating user input.

Analysis

pyphi.analyze(substrate, state, *[, subset, ...])	Analyze one candidate system over substrate in state, or run a grain search over the whole substrate.
pyphi.sweep(substrates, *, states[, ...])	Run a computation across the cartesian product of axes into a tidy table.
pyphi.cost	Analytic workload counting for single-system analyses.
pyphi.conf	Layered configuration system for PyPhi.
pyphi.formalism	Phi formalisms — strategies for computing integrated information.
pyphi.partition	Utilities for generating partitions.
pyphi.direction	Causal directions.
pyphi.relations	Implements the formalism for computing relations.
pyphi.resolve_ties	Resolve ties between IIT objects.
pyphi.condensation	Condensation of candidate systems into complexes.
pyphi.compositional_state
pyphi.macro	Intrinsic-units macro framework (Marshall et al. 2026).
pyphi.actual	Methods for computing actual causation of systems and mechanisms.
pyphi.matching	The matching formalism: perception and matching.
pyphi.landscape	Continuous-parameter analysis of IIT quantities over substrate space.
pyphi.optimize(builder, state, bounds, *, seed)	Search a substrate's weights for a maximizer of an IIT quantity.
pyphi.dynamics	Functions for simulating system state trajectories.

Results

pyphi.models	See pyphi.models.sia, pyphi.models.mice, and pyphi.models.partitions for documentation.
pyphi.display	Unified object display: declarative descriptions rendered by pluggable backends.
pyphi.numerics	Tolerant scalar comparison of φ, Φ, and α values.
pyphi.measures	Distance functions.
pyphi.serialize	Typed, compact (de)serialization of PyPhi results via msgspec.
pyphi.provenance	Provenance record attached to top-level result objects.
pyphi.graph	Bridge between PyPhi value types and graph representations.
pyphi.visualize	Provides visualization capabilities for PyPhi objects.
pyphi.exceptions	PyPhi exceptions.

Infrastructure

pyphi.parallel	Provides an interface for parallel computation.
pyphi.cache	Memoization and caching utilities.
pyphi.campaign	Distribute PyPhi computations across an HTCondor pool as batch campaigns.
pyphi.mcp	Model Context Protocol server exposing PyPhi to AI agents.
pyphi.log	Utilities for logging and progress bars.

Lower-level building blocks

pyphi.core	Lower-level value types and primitives shared across PyPhi.
pyphi.distribution	Functions for manipulating probability distributions.
pyphi.timescale	Functions for manipulating the timescale of TPMs.
pyphi.automorphism	Behavior-aware substrate canonicalization.