process-bigraph 1.8.3__tar.gz → 1.8.5__tar.gz

process_bigraph-1.8.5/PKG-INFO

@@ -0,0 +1,309 @@
+Metadata-Version: 2.4
+Name: process-bigraph
+Version: 1.8.5
+Summary: protocol and execution for compositional systems biology
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: AUTHORS.md
+Requires-Dist: bigraph-schema>=1.6.0
+Requires-Dist: requests>=2.31
+Requires-Dist: matplotlib
+Requires-Dist: pint>=0.24.4
+Requires-Dist: scipy>=1.8
+Requires-Dist: pandas
+Requires-Dist: sympy
+Provides-Extra: ray
+Requires-Dist: ray>=2.10; extra == "ray"
+Provides-Extra: server-rest
+Requires-Dist: fastapi>=0.116.1; extra == "server-rest"
+Requires-Dist: fastapi-utils>=0.8.0; extra == "server-rest"
+Requires-Dist: uvicorn>=0.35.0; extra == "server-rest"
+Requires-Dist: fire; extra == "server-rest"
+Requires-Dist: typing-inspect>=0.9.0; extra == "server-rest"
+Provides-Extra: ec2-ssm
+Requires-Dist: boto3>=1.28; extra == "ec2-ssm"
+Dynamic: license-file
+
+# Process-Bigraph
+
+[![PyPI](https://img.shields.io/pypi/v/process-bigraph.svg)](https://pypi.org/project/process-bigraph/)
+[![GitHub Pages](https://img.shields.io/badge/GitHub%20Pages-Tutorials-brightgreen)](https://vivarium-collective.github.io/process-bigraph/notebooks/index.html)
+
+**Process-Bigraph** is a compositional runtime and protocol for building and executing
+**multiscale biological models from interoperable processes**.
+
+It provides a shared architectural layer for:
+- declaring **process interfaces**
+- wiring processes through **typed shared state**
+- orchestrating execution across **heterogeneous timescales**
+- supporting **dynamic structure** (workflows, division, graph rewrites)
+
+Process-Bigraph is the execution core of **Vivarium 2.0**, designed to integrate models
+built with different formalisms—including ODEs, FBA, agent-based models, spatial solvers,
+and machine-learning components—into a single coherent simulation.
+
+<p align="center">
+  <img src="https://github.com/vivarium-collective/process-bigraph/blob/main/docs/_static/composition_framework.png?raw=true"
+       width="800"
+       alt="Process Bigraph composition framework">
+</p>
+
+---
+
+## 🧩 What is a Process Bigraph?
+
+A **process bigraph** combines:
+
+- **Typed stores** — hierarchical, schema-validated state defined with
+  [**bigraph-schema**](https://github.com/vivarium-collective/bigraph-schema)
+- **Processes** — executable components with explicit input/output ports
+- **Composites** — encapsulated sub-simulations with their own internal structure
+- **Orchestration patterns** — multi-timestepping, directed workflows, and event-driven rewrites
+
+Processes do **not** mutate state directly.
+Instead, they emit **typed deltas** that are merged by the runtime.
+
+This allows:
+- numerical updates
+- structural rewrites
+- scheduling and orchestration
+
+to coexist under a single execution semantics.
+
+In this sense, Process-Bigraph is a **composition protocol**, not a domain-specific simulator.
+
+---
+
+## 📄 Paper reference
+
+The conceptual framework and formal semantics of process bigraphs are introduced in:
+
+> **Agmon, E. & Spangler, R. K.**  
+> *Process Bigraphs and the Architecture of Compositional Systems Biology*  
+> https://arxiv.org/abs/2512.23754
+
+---
+
+## 🚀 Getting Started
+
+### Installation
+
+```console
+pip install process-bigraph
+```
+
+### Quickstart — composites, drafts & templates in code
+
+A runnable five-minute tour of the core concepts. Every block below runs as-is
+against `process-bigraph ≥ 1.8.3`. Concepts explained in
+[`docs/concepts/composites-and-templates.md`](docs/concepts/composites-and-templates.md).
+
+**1. A process wired into a composite over a shared store.** A composite is a `state`
+map of typed nodes; processes couple only by reading/writing shared stores.
+
+```python
+from process_bigraph import Composite, Process, allocate_core
+from process_bigraph.emitter import emitter_from_wires, gather_emitter_results
+
+class Grow(Process):                                  # a Process = ports + an update
+    config_schema = {'rate': 'float'}
+    def inputs(self):  return {'level': 'float'}
+    def outputs(self): return {'level': 'float'}
+    def update(self, state, interval):
+        return {'level': state['level'] * self.config['rate'] * interval}  # a delta
+
+core = allocate_core()
+core.register_link('Grow', Grow)                      # register it in the local registry
+
+composite = Composite({'state': {
+    'level': 1.0,                                     # a shared store
+    'grow': {'_type': 'process', 'address': 'local:Grow', 'config': {'rate': 0.5},
+             'interval': 1.0, 'inputs': {'level': ['level']}, 'outputs': {'level': ['level']}},
+    'emitter': emitter_from_wires({'level': ['level'], 'time': ['global_time']}),
+}}, core=core)
+composite.run(5.0)
+print(gather_emitter_results(composite))
+# {('emitter',): [{'level': 1.0, 'time': 0.0}, {'level': 1.5, ...}, ... {'level': 7.59, 'time': 5.0}]}
+```
+
+**2. A draft process — a present-but-inert placeholder node.** It declares a contract
+(ports + description) but has no `update`, so a composite containing it still runs; the
+draft just no-ops. Complementary to a *site* (step 3): a draft is a node that is *there
+but inert*, a site is an empty *hole*.
+
+```python
+from process_bigraph import DraftProcess, draft_process
+
+@draft_process(name="PTH secretion",
+    inputs={'ca_sense': 'float'}, outputs={'pth_out': 'float'},
+    contract={'summary': 'senses serum Ca, secretes PTH', 'senses': 'calcium', 'makes': 'PTH'})
+class PTHSecretion(DraftProcess):
+    pass
+
+core.register_link('PTHSecretion', PTHSecretion)
+print(PTHSecretion({}, core=core).describe())
+# DRAFT — senses serum Ca, secretes PTH  ·  makes: PTH  ·  senses: calcium  ·  status: draft - no update dynamics yet
+```
+
+A module-scope draft auto-registers, so it appears in the vivarium-workbench dashboard
+(Modules → Processes) marked **DRAFT** with its ports and contract — no code change
+needed. Replace it with a real `Process` once the mechanism is committed.
+
+**3. A template — a composite with an open site (hole).** A template is a document that
+isn't *ground*: it has open **sites** (`{"_type": "site"}`). `Composite` refuses to run
+one until every required site is filled.
+
+```python
+from process_bigraph import Step
+from process_bigraph.templates import open_sites, is_ground_document, template_document
+
+class ReportCard(Step):                               # a fixed downstream verdict
+    config_schema = {'threshold': 'float'}
+    def inputs(self):  return {'level': 'float'}
+    def outputs(self): return {'verdict': 'string'}
+    def update(self, state):
+        return {'verdict': 'pass' if state['level'] >= self.config['threshold'] else 'fail'}
+
+core.register_link('ReportCard', ReportCard)
+MODEL_FACE = {'_type': 'link', '_inputs': {'level': 'float'}, '_outputs': {'level': 'float'}}
+
+template = core.access({'study': {                     # analysis fixed, the model is a HOLE
+    'level': 1.0, 'verdict': 'string',
+    'model':  {'_type': 'site', '_sort': MODEL_FACE},
+    'report': {'_type': 'step', 'address': 'local:ReportCard', 'config': {'threshold': 2.0},
+               'inputs': {'level': ['level']}, 'outputs': {'verdict': ['verdict']}}}})
+
+print(open_sites(template), is_ground_document(template))   # [('study', 'model')] False
+
+def model(rate):                                      # any conforming composite fits the hole
+    return core.access({'_type': 'process', 'address': 'local:Grow', 'config': {'rate': rate},
+                        'interval': 1.0, 'inputs': {'level': ['level']}, 'outputs': {'level': ['level']}})
+
+sim = Composite({'state': template_document(core, template, {'study/model': model(0.5)})}, core=core)
+sim.run(4.0)
+print(sim.state['study']['verdict'])                  # pass  (a slower model → fail)
+# template_document(core, template, {}) → ValueError: not ground — required site 'study/model'
+```
+
+**4. An investigation — one site per member study; gating is *filling*.** Fill a
+member's site to admit it; leave it open and it is pruned from the built document, so a
+blocked prerequisite simply never runs.
+
+```python
+from process_bigraph.templates import investigation_document
+
+study = lambda: {'level': 1.0, 'verdict': 'string',
+    'model':  {'_type': 'site', '_sort': MODEL_FACE},
+    'report': {'_type': 'step', 'address': 'local:ReportCard', 'config': {'threshold': 2.0},
+               'inputs': {'level': ['level']}, 'outputs': {'verdict': ['verdict']}}}
+
+inv = core.access({'investigation': {'study_A': study(), 'study_B': study()}})
+document, blocked = investigation_document(
+    core, inv, {'investigation/study_A/model': model(0.5)}, member_depth=2)  # fill A only
+print(blocked, sorted(document['investigation']))     # ['investigation/study_B'] ['study_A']
+```
+
+> This same template/site machinery is what viva-superpowers uses to compile a whole
+> **investigation into a composite** (one `StudyStep` per member). The study/investigation
+> layer is documented in viva-superpowers
+> `docs/concepts/composites-templates-and-the-study-investigation-stack.md`.
+
+## 📘 Tutorials
+
+The Process-Bigraph tutorials are executable Jupyter notebooks,
+rendered to HTML and published automatically on GitHub Pages.
+
+- 📚 **Tutorial Index (all tutorials)**  
+  https://vivarium-collective.github.io/process-bigraph/notebooks/index.html
+
+### Learning Path (Featured Tutorials)
+
+- **Tutorial 0 — A Process in 12 Lines (quickstart)**  
+  *The new front door: define a process with the `@process` decorator, wire and
+  run it end-to-end on one screen, and watch a `_units`-bearing port auto-convert*  
+  https://vivarium-collective.github.io/process-bigraph/notebooks/tutorial_0_quickstart.html
+
+- **Tutorial 1 — Process-Bigraph Basics**  
+  *Processes, Steps, ports, Composites, workflows, and emitters*  
+  https://vivarium-collective.github.io/process-bigraph/notebooks/tutorial_1.html
+
+- **Tutorial 2 — Wrapping an ODE Solver (`odeint`)**  
+  *How to expose an existing scientific API as a Process*  
+  https://vivarium-collective.github.io/process-bigraph/notebooks/tutorial_2.html
+
+- **Tutorial 3 — Declarative Math**  
+  *Defining mathematical relationships, signal pipelines, and events using `MathExpressionStep`*  
+  https://vivarium-collective.github.io/process-bigraph/notebooks/tutorial_3.html
+
+- **Tutorial 4 — Composing a Biological Model**  
+  *The central dogma from four small processes: composition over shared molecular state, biological units in the port types, and adding regulation by adding a wire*  
+  https://vivarium-collective.github.io/process-bigraph/notebooks/tutorial_4.html
+
+More tutorials are added continuously and appear automatically in the index.
+
+### Architecture
+
+- **The framework, end to end** — *start here to understand the whole system:
+  what the objects are (documents, sites, handles), how they compose, the
+  higher-order DAG, templates and gating, content-addressed artifacts, the
+  `git:` protocol, and the laws everything else follows from.*
+  [docs/architecture.md](docs/architecture.md)
+
+### Topic Guides
+
+- **Emitters — Recording Simulation Results**
+  *Built-in emitters (RAM, console, JSON, SQLite), how to wire them, retrieve results, store runs long-term, and write your own.*
+  [docs/emitters.md](docs/emitters.md)
+
+- **Tick lifecycle** — *how a step network is ordered and advanced, and how a
+  protocol runtime batches remote dispatch.*
+  [docs/tick_lifecycle.md](docs/tick_lifecycle.md)
+
+- **Distributed lifecycles** — *running parts of a composite off-process.*
+  [docs/distributed_lifecycles.md](docs/distributed_lifecycles.md)
+
+- **Deploying a Step network to Nextflow** — *opt-in: compile a composite's
+  Step network into a Nextflow DSL2 workflow and run it on a batch backend
+  (local / SLURM). Nothing changes about `Composite.run()`.*
+  [docs/nextflow.md](docs/nextflow.md)
+
+---
+
+## 🧪 Reference Implementation: spatio-flux
+
+Process-Bigraph is exercised end-to-end in **spatio-flux**, a multiscale reference
+model built entirely using the process-bigraph protocol.
+
+spatio-flux composes spatial fields, particle dynamics, and metabolic processes
+using typed shared state and declarative orchestration.
+
+GitHub: https://github.com/vivarium-collective/spatio-flux  
+Live test report: https://vivarium-collective.github.io/spatio-flux/report/index.html
+
+---
+
+## 🔗 Related Resources
+
+- **Bigraph Schema Basics**  
+  https://vivarium-collective.github.io/bigraph-viz/notebooks/basics.html  
+  *Introduction to the schema language underlying Process-Bigraph*
+
+- **Visualization of Bigraph Document** — diagramming and rendering with
+  [**bigraph-viz**](https://github.com/vivarium-collective/bigraph-viz)  
+  https://vivarium-collective.github.io/bigraph-viz/notebooks/format.html
+
+- **E. coli Whole-Cell Wiring Diagram**  
+  https://raw.githubusercontent.com/vivarium-collective/bigraph-viz/main/doc/_static/ecoli.png
+
+- **Claude Code skills** — wrap simulators, compose `pbg-*` packages, and
+  scaffold process-bigraph research workspaces with the
+  [**pbg-superpowers**](https://github.com/vivarium-collective/pbg-superpowers)
+  Claude Code plugin (install with `/plugin install pbg-superpowers`).
+
+---
+
+## 📜 License
+
+Process-Bigraph is open-source software released under the  
+[Apache 2 License](https://github.com/vivarium-collective/process-bigraph/blob/main/LICENSE).

process_bigraph-1.8.5/README.md

@@ -0,0 +1,282 @@
+# Process-Bigraph
+
+[![PyPI](https://img.shields.io/pypi/v/process-bigraph.svg)](https://pypi.org/project/process-bigraph/)
+[![GitHub Pages](https://img.shields.io/badge/GitHub%20Pages-Tutorials-brightgreen)](https://vivarium-collective.github.io/process-bigraph/notebooks/index.html)
+
+**Process-Bigraph** is a compositional runtime and protocol for building and executing
+**multiscale biological models from interoperable processes**.
+
+It provides a shared architectural layer for:
+- declaring **process interfaces**
+- wiring processes through **typed shared state**
+- orchestrating execution across **heterogeneous timescales**
+- supporting **dynamic structure** (workflows, division, graph rewrites)
+
+Process-Bigraph is the execution core of **Vivarium 2.0**, designed to integrate models
+built with different formalisms—including ODEs, FBA, agent-based models, spatial solvers,
+and machine-learning components—into a single coherent simulation.
+
+<p align="center">
+  <img src="https://github.com/vivarium-collective/process-bigraph/blob/main/docs/_static/composition_framework.png?raw=true"
+       width="800"
+       alt="Process Bigraph composition framework">
+</p>
+
+---
+
+## 🧩 What is a Process Bigraph?
+
+A **process bigraph** combines:
+
+- **Typed stores** — hierarchical, schema-validated state defined with
+  [**bigraph-schema**](https://github.com/vivarium-collective/bigraph-schema)
+- **Processes** — executable components with explicit input/output ports
+- **Composites** — encapsulated sub-simulations with their own internal structure
+- **Orchestration patterns** — multi-timestepping, directed workflows, and event-driven rewrites
+
+Processes do **not** mutate state directly.
+Instead, they emit **typed deltas** that are merged by the runtime.
+
+This allows:
+- numerical updates
+- structural rewrites
+- scheduling and orchestration
+
+to coexist under a single execution semantics.
+
+In this sense, Process-Bigraph is a **composition protocol**, not a domain-specific simulator.
+
+---
+
+## 📄 Paper reference
+
+The conceptual framework and formal semantics of process bigraphs are introduced in:
+
+> **Agmon, E. & Spangler, R. K.**  
+> *Process Bigraphs and the Architecture of Compositional Systems Biology*  
+> https://arxiv.org/abs/2512.23754
+
+---
+
+## 🚀 Getting Started
+
+### Installation
+
+```console
+pip install process-bigraph
+```
+
+### Quickstart — composites, drafts & templates in code
+
+A runnable five-minute tour of the core concepts. Every block below runs as-is
+against `process-bigraph ≥ 1.8.3`. Concepts explained in
+[`docs/concepts/composites-and-templates.md`](docs/concepts/composites-and-templates.md).
+
+**1. A process wired into a composite over a shared store.** A composite is a `state`
+map of typed nodes; processes couple only by reading/writing shared stores.
+
+```python
+from process_bigraph import Composite, Process, allocate_core
+from process_bigraph.emitter import emitter_from_wires, gather_emitter_results
+
+class Grow(Process):                                  # a Process = ports + an update
+    config_schema = {'rate': 'float'}
+    def inputs(self):  return {'level': 'float'}
+    def outputs(self): return {'level': 'float'}
+    def update(self, state, interval):
+        return {'level': state['level'] * self.config['rate'] * interval}  # a delta
+
+core = allocate_core()
+core.register_link('Grow', Grow)                      # register it in the local registry
+
+composite = Composite({'state': {
+    'level': 1.0,                                     # a shared store
+    'grow': {'_type': 'process', 'address': 'local:Grow', 'config': {'rate': 0.5},
+             'interval': 1.0, 'inputs': {'level': ['level']}, 'outputs': {'level': ['level']}},
+    'emitter': emitter_from_wires({'level': ['level'], 'time': ['global_time']}),
+}}, core=core)
+composite.run(5.0)
+print(gather_emitter_results(composite))
+# {('emitter',): [{'level': 1.0, 'time': 0.0}, {'level': 1.5, ...}, ... {'level': 7.59, 'time': 5.0}]}
+```
+
+**2. A draft process — a present-but-inert placeholder node.** It declares a contract
+(ports + description) but has no `update`, so a composite containing it still runs; the
+draft just no-ops. Complementary to a *site* (step 3): a draft is a node that is *there
+but inert*, a site is an empty *hole*.
+
+```python
+from process_bigraph import DraftProcess, draft_process
+
+@draft_process(name="PTH secretion",
+    inputs={'ca_sense': 'float'}, outputs={'pth_out': 'float'},
+    contract={'summary': 'senses serum Ca, secretes PTH', 'senses': 'calcium', 'makes': 'PTH'})
+class PTHSecretion(DraftProcess):
+    pass
+
+core.register_link('PTHSecretion', PTHSecretion)
+print(PTHSecretion({}, core=core).describe())
+# DRAFT — senses serum Ca, secretes PTH  ·  makes: PTH  ·  senses: calcium  ·  status: draft - no update dynamics yet
+```
+
+A module-scope draft auto-registers, so it appears in the vivarium-workbench dashboard
+(Modules → Processes) marked **DRAFT** with its ports and contract — no code change
+needed. Replace it with a real `Process` once the mechanism is committed.
+
+**3. A template — a composite with an open site (hole).** A template is a document that
+isn't *ground*: it has open **sites** (`{"_type": "site"}`). `Composite` refuses to run
+one until every required site is filled.
+
+```python
+from process_bigraph import Step
+from process_bigraph.templates import open_sites, is_ground_document, template_document
+
+class ReportCard(Step):                               # a fixed downstream verdict
+    config_schema = {'threshold': 'float'}
+    def inputs(self):  return {'level': 'float'}
+    def outputs(self): return {'verdict': 'string'}
+    def update(self, state):
+        return {'verdict': 'pass' if state['level'] >= self.config['threshold'] else 'fail'}
+
+core.register_link('ReportCard', ReportCard)
+MODEL_FACE = {'_type': 'link', '_inputs': {'level': 'float'}, '_outputs': {'level': 'float'}}
+
+template = core.access({'study': {                     # analysis fixed, the model is a HOLE
+    'level': 1.0, 'verdict': 'string',
+    'model':  {'_type': 'site', '_sort': MODEL_FACE},
+    'report': {'_type': 'step', 'address': 'local:ReportCard', 'config': {'threshold': 2.0},
+               'inputs': {'level': ['level']}, 'outputs': {'verdict': ['verdict']}}}})
+
+print(open_sites(template), is_ground_document(template))   # [('study', 'model')] False
+
+def model(rate):                                      # any conforming composite fits the hole
+    return core.access({'_type': 'process', 'address': 'local:Grow', 'config': {'rate': rate},
+                        'interval': 1.0, 'inputs': {'level': ['level']}, 'outputs': {'level': ['level']}})
+
+sim = Composite({'state': template_document(core, template, {'study/model': model(0.5)})}, core=core)
+sim.run(4.0)
+print(sim.state['study']['verdict'])                  # pass  (a slower model → fail)
+# template_document(core, template, {}) → ValueError: not ground — required site 'study/model'
+```
+
+**4. An investigation — one site per member study; gating is *filling*.** Fill a
+member's site to admit it; leave it open and it is pruned from the built document, so a
+blocked prerequisite simply never runs.
+
+```python
+from process_bigraph.templates import investigation_document
+
+study = lambda: {'level': 1.0, 'verdict': 'string',
+    'model':  {'_type': 'site', '_sort': MODEL_FACE},
+    'report': {'_type': 'step', 'address': 'local:ReportCard', 'config': {'threshold': 2.0},
+               'inputs': {'level': ['level']}, 'outputs': {'verdict': ['verdict']}}}
+
+inv = core.access({'investigation': {'study_A': study(), 'study_B': study()}})
+document, blocked = investigation_document(
+    core, inv, {'investigation/study_A/model': model(0.5)}, member_depth=2)  # fill A only
+print(blocked, sorted(document['investigation']))     # ['investigation/study_B'] ['study_A']
+```
+
+> This same template/site machinery is what viva-superpowers uses to compile a whole
+> **investigation into a composite** (one `StudyStep` per member). The study/investigation
+> layer is documented in viva-superpowers
+> `docs/concepts/composites-templates-and-the-study-investigation-stack.md`.
+
+## 📘 Tutorials
+
+The Process-Bigraph tutorials are executable Jupyter notebooks,
+rendered to HTML and published automatically on GitHub Pages.
+
+- 📚 **Tutorial Index (all tutorials)**  
+  https://vivarium-collective.github.io/process-bigraph/notebooks/index.html
+
+### Learning Path (Featured Tutorials)
+
+- **Tutorial 0 — A Process in 12 Lines (quickstart)**  
+  *The new front door: define a process with the `@process` decorator, wire and
+  run it end-to-end on one screen, and watch a `_units`-bearing port auto-convert*  
+  https://vivarium-collective.github.io/process-bigraph/notebooks/tutorial_0_quickstart.html
+
+- **Tutorial 1 — Process-Bigraph Basics**  
+  *Processes, Steps, ports, Composites, workflows, and emitters*  
+  https://vivarium-collective.github.io/process-bigraph/notebooks/tutorial_1.html
+
+- **Tutorial 2 — Wrapping an ODE Solver (`odeint`)**  
+  *How to expose an existing scientific API as a Process*  
+  https://vivarium-collective.github.io/process-bigraph/notebooks/tutorial_2.html
+
+- **Tutorial 3 — Declarative Math**  
+  *Defining mathematical relationships, signal pipelines, and events using `MathExpressionStep`*  
+  https://vivarium-collective.github.io/process-bigraph/notebooks/tutorial_3.html
+
+- **Tutorial 4 — Composing a Biological Model**  
+  *The central dogma from four small processes: composition over shared molecular state, biological units in the port types, and adding regulation by adding a wire*  
+  https://vivarium-collective.github.io/process-bigraph/notebooks/tutorial_4.html
+
+More tutorials are added continuously and appear automatically in the index.
+
+### Architecture
+
+- **The framework, end to end** — *start here to understand the whole system:
+  what the objects are (documents, sites, handles), how they compose, the
+  higher-order DAG, templates and gating, content-addressed artifacts, the
+  `git:` protocol, and the laws everything else follows from.*
+  [docs/architecture.md](docs/architecture.md)
+
+### Topic Guides
+
+- **Emitters — Recording Simulation Results**
+  *Built-in emitters (RAM, console, JSON, SQLite), how to wire them, retrieve results, store runs long-term, and write your own.*
+  [docs/emitters.md](docs/emitters.md)
+
+- **Tick lifecycle** — *how a step network is ordered and advanced, and how a
+  protocol runtime batches remote dispatch.*
+  [docs/tick_lifecycle.md](docs/tick_lifecycle.md)
+
+- **Distributed lifecycles** — *running parts of a composite off-process.*
+  [docs/distributed_lifecycles.md](docs/distributed_lifecycles.md)
+
+- **Deploying a Step network to Nextflow** — *opt-in: compile a composite's
+  Step network into a Nextflow DSL2 workflow and run it on a batch backend
+  (local / SLURM). Nothing changes about `Composite.run()`.*
+  [docs/nextflow.md](docs/nextflow.md)
+
+---
+
+## 🧪 Reference Implementation: spatio-flux
+
+Process-Bigraph is exercised end-to-end in **spatio-flux**, a multiscale reference
+model built entirely using the process-bigraph protocol.
+
+spatio-flux composes spatial fields, particle dynamics, and metabolic processes
+using typed shared state and declarative orchestration.
+
+GitHub: https://github.com/vivarium-collective/spatio-flux  
+Live test report: https://vivarium-collective.github.io/spatio-flux/report/index.html
+
+---
+
+## 🔗 Related Resources
+
+- **Bigraph Schema Basics**  
+  https://vivarium-collective.github.io/bigraph-viz/notebooks/basics.html  
+  *Introduction to the schema language underlying Process-Bigraph*
+
+- **Visualization of Bigraph Document** — diagramming and rendering with
+  [**bigraph-viz**](https://github.com/vivarium-collective/bigraph-viz)  
+  https://vivarium-collective.github.io/bigraph-viz/notebooks/format.html
+
+- **E. coli Whole-Cell Wiring Diagram**  
+  https://raw.githubusercontent.com/vivarium-collective/bigraph-viz/main/doc/_static/ecoli.png
+
+- **Claude Code skills** — wrap simulators, compose `pbg-*` packages, and
+  scaffold process-bigraph research workspaces with the
+  [**pbg-superpowers**](https://github.com/vivarium-collective/pbg-superpowers)
+  Claude Code plugin (install with `/plugin install pbg-superpowers`).
+
+---
+
+## 📜 License
+
+Process-Bigraph is open-source software released under the  
+[Apache 2 License](https://github.com/vivarium-collective/process-bigraph/blob/main/LICENSE).

{process_bigraph-1.8.3 → process_bigraph-1.8.5}/process_bigraph/__init__.py

@@ -18,9 +18,10 @@ except ImportError:                   # pragma: no cover — py<3.8
 
 from process_bigraph.composite import (  # noqa: F401
     Process, Step, Composite, TimingSummary, interval_time_precision, wire_step_layers,
+    process, step, as_process, as_step,
 )
 from process_bigraph.composite_spec import (  # noqa: F401
-    CompositeSpec, discover_specs, regenerate_default_state,
+    CompositeSpec, discover_specs, register_spec_generator, regenerate_default_state,
     normalize_type, CANONICAL_TYPES,
 )
 from process_bigraph.bundle import load_bundle  # noqa: F401
@@ -39,6 +40,7 @@ from process_bigraph.composite_generator import (  # noqa: F401
 from process_bigraph.composite_discovery import discover_all  # noqa: F401
 from process_bigraph.config_helpers import normalize_config_list  # noqa: F401
 from process_bigraph.visualization import Visualization, as_visualization, render_results  # noqa: F401
+from process_bigraph.workflow import run_workflow  # noqa: F401
 
 
 import pprint

{process_bigraph-1.8.3 → process_bigraph-1.8.5}/process_bigraph/artifacts.py

@@ -22,7 +22,7 @@ import hashlib
 import json
 import os
 from dataclasses import dataclass, field
-from typing import Any, Callable
+from typing import Callable
 
 # ── content address ─────────────────────────────────────────────────
 #