pbg-basic-processes 0.1.0

Reusable, composite-agnostic process-bigraph processes — Clock, Intervention, MathExpression, and beyond

pbg-basic-processes

Reusable, composite-agnostic process-bigraph processes — the small, generic building blocks that show up in almost every workspace.

Process	What it does
Clock	Emits an integer tick step counter each step — the one temporal quantity the engine does not expose as a store. (Absolute simulation time, global_time, is already maintained by the engine in every composite; wire any input to ['global_time'] to read it.)
Intervention	Applies a specific perturbation to one target store — set / knockout / scale / add / decouple / invert, optionally within a time window. The building block for negative controls and counterfactuals.
MathExpressionStep	Evaluates a list of named symbolic (SymPy) expressions as one Step, inferring input ports from free symbols and resolving inter-expression dependencies in topological order.

Auto-registration

Like pbg-emitters, these processes auto-register into any workspace core. allocate_core() walks every installed distribution that depends on bigraph-schema and registers its Process/Step subclasses — no entry points, no register_* boilerplate:

from bigraph_schema import allocate_core

core = allocate_core()
assert 'Clock' in core.link_registry          # just by being installed
assert 'Intervention' in core.link_registry
assert 'MathExpressionStep' in core.link_registry

Add pbg-basic-processes as a dependency of your workspace (it is a base dependency of pbg-superpowers, so every pbg workspace gets it) and reference the processes by local:Clock, local:Intervention, local:MathExpressionStep.

Install

pip install pbg-basic-processes            # from PyPI (when published)
pip install -e .                           # from a checkout

Usage

Node-builder helpers make wiring into a composite easy:

from pbg_basic_processes import clock_node, intervention_node

state = {
    'tick': 0,
    'nutrient': 5.0,
    'clock': clock_node(interval=1.0),          # writes a step counter to ['tick']
    # hold nutrient at 0 only between t=10 and t=20 of absolute sim time.
    # use_global_time wires the window to the engine's reserved global_time store.
    'starve': intervention_node(['nutrient'], mode='set', value=0.0,
                                window=[10, 20], use_global_time=True),
}

Develop

pip install -e '.[dev]'
pytest -q

MIT-licensed. Part of the vivarium-collective process-bigraph ecosystem.