bigraph-viz2 0.3.12

Lightweight read-only bigraph renderer with no graphviz dependency

bigraph-viz2

A lightweight, interactive, read-only renderer for process-bigraph composites. Drop-in replacement for bigraph-viz's static PNG output in HTML reports — no graphviz dependency, pan / zoom / click-to-inspect / double-click-to-collapse / Alt-drag-to-rearrange in the browser, and the entire renderer inlines into a self-contained ~40 KB snippet.

The example above shows a two-cell tissue with nested substores (membrane, cytoplasm, nucleus), processes living inside each, and wires reaching across container boundaries. Orange = input port, teal = output port.

Install

pip install bigraph-viz2

No graphviz. No node. No browser at install time. The JS bundle is vendored inside the Python package; consumers need only Python ≥ 3.10.

Use

The Python API has one main function and a Jupyter wrapper.

from bigraph_viz2 import emit_html

# one-shot: a self-contained HTML fragment you can paste anywhere
snippet = emit_html(composite_state, height="600px")
report_html = report_html.replace("{{BIGRAPH}}", snippet)

In a Jupyter notebook:

from bigraph_viz2 import BigraphViz
BigraphViz(composite_state)   # auto-displays via _repr_html_

Composite expansion + schema validation

A raw .pbg document references stores by wire path that may not exist until process_bigraph.Composite materializes them. To render the expanded structure (so all wire targets resolve and the spec is also type-checked), pass expand=True:

from bigraph_viz2 import emit_html
html = emit_html(spec, expand=True)

This mirrors what bigraph-viz did: it calls core.realize(schema, state) under the hood. Requires the expand extra:

pip install "bigraph-viz2[expand]"

For composites referencing custom process addresses (e.g. local:MyProcess), build a core with those registered and pass it:

from process_bigraph import allocate_core
import my_pkg                       # side-effect: registers process types
core = allocate_core()
html = emit_html(spec, expand=True, core=core)

There's also a stand-alone validator that returns a list of issues without rendering:

from bigraph_viz2 import validate_state
issues = validate_state(spec)       # [] if clean

Multi-instance pages

For pages with multiple viz instances, inline the bundle once and dedupe the rest:

snippets = [emit_html(specs[0], dedupe=False)]
for spec in specs[1:]:
    snippets.append(emit_html(spec, dedupe=True))

API

emit_html(state, *,
          height="500px",
          width="100%",
          inspector=True,         # show the right-side inspector panel
          theme="light",          # only "light" supported in v0.1
          dedupe=False,           # set True after the first call on a page
          id=None,                # explicit DOM id (auto-generated otherwise)
          max_row_width=480       # auto-wrap threshold inside each container
          ) -> str

Returns a self-contained HTML fragment.

Interactions

gesture	effect
drag (anywhere)	pan
wheel	zoom centered on cursor (0.25× – 4×)
hover a port	tooltip with port name
click a node	populate the inspector
double-click a node	collapse / expand subtree
Alt + drag a node	reorder siblings; drop into row / new row
Esc (while dragging)	cancel the drag

Collapse state persists in the URL hash and survives reload.

Concepts

bigraph-viz2 renders compositional bigraph schemas with three primitive shapes:

shape	meaning
circle	a variable — a leaf in the place graph
rounded rectangle	a store — a container nesting substores, processes, variables
sharp rectangle	a process — reads from / writes to its declared ports

A composite is a tree of stores; processes live anywhere inside that tree. Each process declares ports, which connect by wire to variables — possibly across multiple container boundaries. Ports render as small triangles on the edge of the process rectangle:

• orange ▶ — input port (variable feeds the process)
• teal ▶ — output port (process writes to the variable)
• gray · — undirected (direction not declared in the spec)

Port direction is read from the spec's inputs: / outputs: blocks (preferred), or from a single ports: block (treated as undirected for back-compat with existing bigraph-viz specs).

Example spec

spec = {
    "name": "cell",
    "stores": {
        "membrane": {
            "v":        {"_type": "variable", "value": -70},
            "channels": {"_type": "variable", "value": []},
        },
        "cytoplasm": {
            "M":   {"_type": "variable", "value": 1.0},
            "ATP": {"_type": "variable", "value": 2.0},
            "metabolism": {
                "_type": "process",
                "address": "fba.CobraStep",
                "config": {"model": "iJO1366"},
                "inputs":  {"substrate": ["M"]},
                "outputs": {"atp":       ["ATP"]},
            },
        },
        "diffusion": {
            "_type": "process",
            "address": "ode.IonFlux",
            "config": {},
            "inputs":  {"voltage":  ["membrane", "v"]},
            "outputs": {"channels": ["membrane", "channels"]},
        },
    },
}

from bigraph_viz2 import emit_html
html = emit_html(spec, height="500px")

Wire paths are relative to the process's enclosing store (["M"] = the sibling named M; ["..", "membrane", "v"] = up to the enclosing store, then into membrane.v).

Development

git clone https://github.com/vivarium-collective/bigraph-viz2
cd bigraph-viz2

# build the JS bundle and vendor it into py/
bash scripts/vendor.sh

# JS tests + typecheck
cd js && npm test && npm run typecheck

# JS end-to-end smoke (real browser)
cd js && npm run test:e2e

# Python tests (includes a Playwright round-trip)
cd py && pip install -e ".[test]" && pytest

Status

v0.1 — initial release.

License

Apache-2.0.