pyphi_config.yml

# PyPhi configuration
# ~~~~~~~~~~~~~~~~~~~
# See the documentation for ``pyphi.config`` for more info.
---

# Approximations and theoretical options
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# In certain cases, making a cut can actually cause a previously reducible
# concept to become a proper, irreducible concept. Assuming this can never
# happen can increase performance significantly, however the obtained results
# are not strictly accurate.
ASSUME_CUTS_CANNOT_CREATE_NEW_CONCEPTS: false
# When determining the MIP for Φ, this restricts the set of system cuts that
# are considered to only those that cut the inputs or outputs of a single node.
# This restricted set of cuts scales linearly with the size of the system; the
# full set of all possible bipartitions scales exponentially. This
# approximation is more likely to give theoretically accurate results with
# modular, sparsely-connected, or homogeneous networks.
CUT_ONE_APPROXIMATION: false
# The measure to use when computing phi ("EMD", "KLD", "L1", ...)
MEASURE: "EMD"
# Controls the number of parts in a partition.
PARTITION_TYPE: "BI"
# Controls how to resolve phi-ties when computing MICE.
PICK_SMALLEST_PURVIEW: false
# Use the difference in sum of small phi for the cause-effect structure
# distance
USE_SMALL_PHI_DIFFERENCE_FOR_CES_DISTANCE: false
# The type of system cuts to use
SYSTEM_CUTS: "3.0_STYLE"
# In some applications of this library, you may want to allow single
# micro-nodes with a self-loop to have nonzero Phi. See ``pyphi.config`` for
# details.
SINGLE_MICRO_NODES_WITH_SELFLOOPS_HAVE_PHI: false
# Controls whether a subsystem's state is validated when the subsystem is
# created.
VALIDATE_SUBSYSTEM_STATES: true
# Controls whether a system is validated for conditional independence.
VALIDATE_CONDITIONAL_INDEPENDENCE: true

# Parallelization and system resources
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Controls whether concepts are evaluated in parallel.
PARALLEL_CONCEPT_EVALUATION: false
# Controls whether cuts are evaluated in parallel, which requires more memory.
# If cuts are evaluated sequentially, only two SIAs need to be in memory at a
# time.
PARALLEL_CUT_EVALUATION: true
# Controls whether complexes are evaluated in parallel.
PARALLEL_COMPLEX_EVALUATION: false
# The number of CPU cores to use in parallel cut evaluation. -1 means all
# available cores, -2 means all but one available cores, etc.
NUMBER_OF_CORES: -1
# Some functions are memoized using an in-memory cache. This is the maximum
# percentage of memory that these caches can collectively use.
MAXIMUM_CACHE_MEMORY_PERCENTAGE: 100

# Memoization and caching
# ~~~~~~~~~~~~~~~~~~~~~~~
# Controls whether SIAs are cached.
CACHE_SIAS: false
# Controls whether cause and effect repertoires are cached.
CACHE_REPERTOIRES: true
# Controls whether the potential purviews of the mechanisms of a network are
# cached. Speeds up calculations when the same network is used repeatedly, but
# takes up additional memory, and makes network initialization slow.
CACHE_POTENTIAL_PURVIEWS: true
# Controls whether subsystem caches are automatically cleared after computing
# the SIA for the subsystem.
CLEAR_SUBSYSTEM_CACHES_AFTER_COMPUTING_SIA: false
# The caching system to use. "fs" means cache the results on the local
# filesystem, in a subdirectory of the current directory; "db" means connect to
# a database and store the results there.
CACHING_BACKEND: "fs"
# The verbosity of filesystem caching (integer from 0 to 11).
FS_CACHE_VERBOSITY: 0
# The directory to use for local persistent caching on the filesystem. This
# only has an effect if the caching backend is the filesystem and not a
# database.
FS_CACHE_DIRECTORY: "__pyphi_cache__"
# These are the settings for the MongoDB database used in the 'db' caching
# backend.
MONGODB_CONFIG:
    host: "localhost"
    port: 27017
    database_name: "pyphi"
    collection_name: "test"
# Use a Redis server as a MICE cache
REDIS_CACHE: false
# Redis connection configuration
REDIS_CONFIG:
    host: "localhost"
    port: 6379
    db: 0
    test_db: 1

# Logging
# ~~~~~~~
# The log level to write to stdout.
LOG_STDOUT_LEVEL: "WARNING"
# The log level to write to `LOG_FILE`.
LOG_FILE_LEVEL: "INFO"
# The file to log to.
LOG_FILE: "pyphi.log"
# Enable/disable progress bars
PROGRESS_BARS: true
# Use pretty __str__-like formatting in repr calls.
REPR_VERBOSITY: 2
# Print numbers as fractions if the denominator isn't too big.
PRINT_FRACTIONS: true

# Numerical precision
# ~~~~~~~~~~~~~~~~~~~
# The number of decimal places to which Phi values are considered accurate.
PRECISION: 6