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bigraph-viz - npm Package Compare versions

Comparing version
0.1.10
 to
0.1.15
+217
-16
bigraph_viz.egg-info/PKG-INFO

@@ -1,26 +0,229 @@

Metadata-Version: 2.1
Metadata-Version: 2.4
Name: bigraph-viz
Version: 0.1.10
Summary: A graphviz-based plotting tool for compositional bigraph schema
Home-page: https://github.com/vivarium-collective/bigraph-viz
Author: Eran Agmon
Author-email: agmon.eran@gmail.com
License: UNKNOWN
Platform: UNKNOWN
Version: 0.1.15
Summary: A visualization method for displaying the structure of process bigraphs
Author-email: Eran Agmon <agmon.eran@gmail.com>
Maintainer-email: Eran Agmon <agmon.eran@gmail.com>
License: Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
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APPENDIX: How to apply the Apache License to your work.
To apply the Apache License to your work, attach the following
boilerplate notice, with the fields enclosed by brackets "[]"
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Copyright 2023 Ryan Spangler and Eran Agmon
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
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See the License for the specific language governing permissions and
limitations under the License.
Keywords: visualization,systems biology,bigraph,graphviz,vivarium
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Requires-Python: >=3.6
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Topic :: Software Development :: Libraries
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
License-File: AUTHORS.md
Requires-Dist: bigraph-schema
Requires-Dist: graphviz
Dynamic: license-file

@@ -94,3 +297,1 @@ # Bigraph-viz

Bigraph-viz is open-source software released under the [Apache 2 License](https://github.com/vivarium-collective/bigraph-viz/blob/main/LICENSE).
+1
-2
bigraph_viz.egg-info/requires.txt

@@ -0,3 +1,2 @@

bigraph-schema
graphviz
bigraph-schema>=0.0.51
numpy
+0
-1
bigraph_viz.egg-info/SOURCES.txt

@@ -5,3 +5,2 @@ AUTHORS.md

pyproject.toml
setup.py
bigraph_viz/__init__.py

@@ -8,0 +7,0 @@ bigraph_viz/convert.py

+487
-293
bigraph_viz/visualize_types.py

@@ -16,2 +16,3 @@ import os

# Utility: Label formatting

@@ -22,2 +23,3 @@ def make_label(label):

def get_graph_wires(ports_schema, wires, graph_dict, schema_key, edge_path, bridge_wires=None):

@@ -76,2 +78,3 @@ """

# Append a single port wire connection to graph_dict

@@ -108,2 +111,3 @@

# Plot a labeled edge from a port to a process

@@ -127,4 +131,14 @@ def plot_edges(graph, edge, port_labels, port_label_size, state_node_spec, constraint='false'):

# Add a node to the graph with optional value/type
def add_node_to_graph(graph, node, state_node_spec, show_values, show_types, significant_digits):
def add_node_to_graph(
graph,
node,
state_node_spec,
show_values,
show_types,
significant_digits,
value_char_limit,
type_char_limit,
):
"""

@@ -145,55 +159,88 @@ Add a state node to the Graphviz graph.

label_info = ''
value_char_limit = value_char_limit or 20
type_char_limit = type_char_limit or 20
rows = [label] # the node's name, already plain text
# Value row
if show_values and (val := node.get('value')) is not None:
if isinstance(val, float):
val = int(val) if val.is_integer() else round(val, significant_digits)
label_info += f":{val}"
val_str = str(val)
if len(val_str) > value_char_limit:
val_str = val_str[:value_char_limit] + "…"
rows.append(f"<FONT POINT-SIZE='10' COLOR='gray30'>value: {val_str}</FONT>")
# Type row
if show_types and (typ := node.get('type')):
label_info += f"<br/>[{typ if len(typ) <= 20 else '...'}]"
typ_str = str(typ)
if len(typ_str) > type_char_limit:
typ_str = typ_str[:type_char_limit] + "…"
rows.append(f"<FONT POINT-SIZE='10' COLOR='gray40'>type: {typ_str}</FONT>")
full_label = make_label(label + label_info) if label_info else make_label(label)
html_label = "<<TABLE BORDER='0' CELLBORDER='0' CELLSPACING='0'>"
for r in rows:
html_label += f"<TR><TD>{r}</TD></TR>"
html_label += "</TABLE>>"
# full_label = make_label(label + label_info) if label_info else make_label(label)
graph.attr('node', **state_node_spec)
graph.node(node_name, label=full_label)
graph.node(node_name, label=html_label)
return node_name
# make the Graphviz figure
import os
from collections import defaultdict
import graphviz
def get_graphviz_fig(
graph_dict,
label_margin='0.05',
node_label_size='12pt',
process_label_size=None,
size='16,10',
rankdir='TB',
aspect_ratio='auto',
dpi='70',
significant_digits=2,
undirected_edges=False,
show_values=False,
show_types=False,
port_labels=True,
port_label_size='10pt',
invisible_edges=None,
remove_process_place_edges=False,
node_border_colors=None,
node_fill_colors=None,
node_groups=None,
collapse_redundant_processes=False,
graph_dict,
label_margin='0.05',
node_label_size='12pt',
process_label_size=None,
size='16,10',
rankdir='TB',
aspect_ratio='auto',
dpi='70',
significant_digits=2,
undirected_edges=False,
show_values=False,
show_types=False,
value_char_limit=20,
type_char_limit=50,
port_labels=True,
port_label_size='10pt',
invisible_edges=None,
remove_process_place_edges=False,
node_border_colors=None,
node_fill_colors=None,
node_groups=None,
collapse_redundant_processes=False,
):
"""
Generate a Graphviz Digraph from a graph_dict describing a simulation architecture.
Generate a Graphviz Digraph from a graph_dict describing a simulation bigraph.
Parameters:
graph_dict: dict
Dictionary describing nodes and edges of a simulation bigraph.
collapse_redundant_processes: bool
Collapse processes with identical port wiring into a single node.
All other parameters configure visual style.
Parameters
----------
graph_dict : dict
Dictionary describing nodes and edges of a simulation bigraph.
collapse_redundant_processes : bool | str | Iterable | dict
Controls collapsing of processes that share identical port wiring:
Returns:
graphviz.Digraph
Graphviz representation of the graph.
- False / None : collapse no processes
- True or "all" : collapse all redundant processes
- Iterable : collapse only processes matching the selectors
- {"exclude": it} : collapse all redundant processes except those
matching selectors in `it`
A selector can be:
* str : matches the leaf process name or str(path)
* tuple : matches the exact process path
Returns
-------
graphviz.Digraph
"""
import difflib
from collections import defaultdict

@@ -205,20 +252,35 @@ invisible_edges = invisible_edges or []

graph = graphviz.Digraph(name='bigraph', engine='dot')
graph.attr(size=size, overlap='false', rankdir=rankdir, dpi=dpi, ratio=aspect_ratio, splines='true')
graph.attr(size=size, overlap='false', rankdir=rankdir, dpi=dpi,
ratio=aspect_ratio, splines='true')
# Define node styles
# Use the same label_margin parameter, but circles get a smaller
# effective margin so they don't balloon visually.
state_margin = str(float(label_margin) * 0.1)
process_margin = label_margin
# Node styles
state_node_spec = {
'shape': 'circle', 'penwidth': '2', 'constraint': 'false',
'margin': label_margin, 'fontsize': node_label_size
'shape': 'circle',
'penwidth': '2',
'constraint': 'false',
'margin': state_margin,
'fontsize': node_label_size,
}
process_node_spec = {
'shape': 'box', 'penwidth': '2', 'constraint': 'false',
'margin': label_margin, 'fontsize': process_label_size
'shape': 'box',
'penwidth': '2',
'constraint': 'false',
'margin': process_margin,
'fontsize': process_label_size,
}
# Define edge styles
# Edge styles
edge_styles = {
'input': {'style': 'dashed', 'penwidth': '1', 'arrowhead': 'normal', 'arrowsize': '1.0', 'dir': 'forward'},
'output': {'style': 'dashed', 'penwidth': '1', 'arrowhead': 'normal', 'arrowsize': '1.0', 'dir': 'back'},
'bidirectional': {'style': 'dashed', 'penwidth': '1', 'arrowhead': 'normal', 'arrowsize': '1.0', 'dir': 'both'},
'place': {'arrowhead': 'none', 'penwidth': '2'}
'input': {'style': 'dashed', 'penwidth': '1', 'arrowhead': 'normal',
'arrowsize': '1.0', 'dir': 'forward'},
'output': {'style': 'dashed', 'penwidth': '1', 'arrowhead': 'normal',
'arrowsize': '1.0', 'dir': 'back'},
'bidirectional': {'style': 'dashed', 'penwidth': '1', 'arrowhead': 'normal',
'arrowsize': '1.0', 'dir': 'both'},
'place': {'arrowhead': 'none', 'penwidth': '2'},
}

@@ -231,11 +293,75 @@ if undirected_edges:

# -------- collapse configuration ----------------------------------------
def normalize_collapse_arg(arg):
"""
Return (mode, selectors) where mode is:
'none' : collapse nothing
'all' : collapse all redundant processes
'subset' : collapse only selected processes
'all_except' : collapse all except selected processes
"""
if arg is False or arg is None:
return 'none', set()
if arg is True or arg == 'all':
return 'all', set()
if isinstance(arg, dict) and 'exclude' in arg:
try:
selectors = set(arg['exclude'])
except TypeError:
selectors = {arg['exclude']}
return 'all_except', selectors
# Iterable or single selector ⇒ subset
try:
selectors = set(arg)
except TypeError:
selectors = {arg}
return 'subset', selectors
collapse_mode, collapse_selectors = normalize_collapse_arg(
collapse_redundant_processes
)
def process_matches_selector(entry, selector):
"""Check if a process entry matches a single selector."""
path, path_str, name = entry
if isinstance(selector, (tuple, list)):
return tuple(selector) == tuple(path)
return selector == name or selector == path_str
def process_is_selected(entry):
"""Return True if this process is eligible to be collapsed."""
if collapse_mode == 'all':
return True
if collapse_mode == 'none':
return False
if not collapse_selectors:
return collapse_mode == 'all'
matches = any(
process_matches_selector(entry, sel)
for sel in collapse_selectors
)
if collapse_mode == 'subset':
return matches
if collapse_mode == 'all_except':
return not matches
return False
# -------- core helpers --------------------------------------------------
def get_name_template(names):
"""Create a generalized name with wildcards for collapsed process names."""
"""Create a generalized label for collapsed process names."""
if len(names) == 1:
return names[0]
import re
prefix = os.path.commonprefix(names)
suffix = os.path.commonprefix([n[::-1] for n in names])[::-1]
wildcard_middle = '*' if prefix != names[0] or suffix != names[0] else ''
return f"{prefix}{wildcard_middle}{suffix}"
middle = '*' if prefix != names[0] or suffix != names[0] else ''
return f"{prefix}{middle}{suffix}"

@@ -245,11 +371,18 @@ def add_state_nodes():

for node in graph_dict['state_nodes']:
name = add_node_to_graph(graph, node, state_node_spec, show_values, show_types, significant_digits)
name = add_node_to_graph(
graph, node, state_node_spec,
show_values, show_types, significant_digits,
value_char_limit, type_char_limit,
)
node_names.append(name)
def add_process_nodes():
"""Add process nodes to the graph, with optional collapse of redundant processes."""
"""
Add process nodes, with optional collapse of redundant ones
according to collapse_mode and collapse_selectors.
"""
graph.attr('node', **process_node_spec)
process_fingerprints = defaultdict(list)
# Build fingerprints for each process based on edge connectivity
# Group processes by connectivity "fingerprint"
for node in graph_dict['process_nodes']:

@@ -260,8 +393,12 @@ node_path = node['path']

fingerprint = []
for group, tag in [('input_edges', 'in'), ('output_edges', 'out'), ('bidirectional_edges', 'both')]:
fp = []
for group, tag in [
('input_edges', 'in'),
('output_edges', 'out'),
('bidirectional_edges', 'both'),
]:
for edge in graph_dict.get(group, []):
if edge['edge_path'] == node_path:
fingerprint.append((tag, edge['port'], str(edge.get('target_path'))))
fingerprint = tuple(sorted(fingerprint))
fp.append((tag, edge['port'], str(edge.get('target_path'))))
fingerprint = tuple(sorted(fp))
process_fingerprints[fingerprint].append((node_path, path_str, node_name))

@@ -271,18 +408,27 @@

# Only collapse if flag is enabled
if collapse_redundant_processes:
for fingerprint, entries in process_fingerprints.items():
names = [entry[2] for entry in entries]
template = get_name_template(names)
count = len(entries)
label = template if count == 1 else f"{template} (x{count})"
representative = str(entries[0][0])
graph.node(representative, label=label)
node_names.append(representative)
for path, path_str, _ in entries:
if str(path) != representative:
collapse_map[str(path)] = representative
else:
# Add all process nodes without collapsing
for entries in process_fingerprints.values():
# For each fingerprint group, possibly collapse some or all
for fingerprint, entries in process_fingerprints.items():
selected = [e for e in entries if process_is_selected(e)]
if len(selected) > 1:
# Create collapsed representative
names = [e[2] for e in selected]
label = f"{get_name_template(names)} (x{len(selected)})"
rep_path = selected[0][0]
rep_str = str(rep_path)
graph.node(rep_str, label=label)
node_names.append(rep_str)
# Map collapsed entries (except representative)
for path, path_str, _ in selected[1:]:
collapse_map[str(path)] = rep_str
# Draw remaining (unselected) entries individually
remaining = [e for e in entries if e not in selected]
for path, path_str, name in remaining:
graph.node(path_str, label=name)
node_names.append(path_str)
else:
# No effective collapse here: draw all individually
for path, path_str, name in entries:

@@ -292,11 +438,24 @@ graph.node(path_str, label=name)

return [entry[0] for entries in process_fingerprints.values() for entry in entries], collapse_map
# Return original process paths and collapse map
return [
entry[0]
for entries in process_fingerprints.values()
for entry in entries
], collapse_map
def rewrite_collapsed_edges(collapse_map):
"""Update edge endpoints to point to collapsed representatives."""
removed_keys = set(collapse_map.keys())
for group in ['input_edges', 'output_edges', 'bidirectional_edges', 'disconnected_input_edges',
'disconnected_output_edges']:
if not removed_keys:
return
for group in [
'input_edges',
'output_edges',
'bidirectional_edges',
'disconnected_input_edges',
'disconnected_output_edges',
]:
edges = graph_dict.get(group, [])
new_edges = []
seen = set()
new_edges, seen = [], set()
for edge in edges:

@@ -307,3 +466,2 @@ key = str(edge['edge_path'])

if key not in removed_keys:
# Build a tuple that uniquely identifies this edge after collapse
edge_key = (

@@ -313,3 +471,3 @@ group,

edge.get('port'),
str(edge.get('target_path'))
str(edge.get('target_path')),
)

@@ -321,3 +479,3 @@ if edge_key not in seen:

# Remove any place_edges associated with collapsed processes
# Remove place edges involving removed processes
new_place_edges = []

@@ -342,13 +500,27 @@ for edge in graph_dict.get('place_edges', []):

graph.attr('edge', **edge_styles[style])
plot_edges(graph, edge, port_labels, port_label_size, state_node_spec, constraint=constraint)
plot_edges(
graph, edge, port_labels, port_label_size,
state_node_spec, constraint=constraint,
)
def add_place_edges(process_paths):
for edge in graph_dict['place_edges']:
visible = not ((remove_process_place_edges and edge['child'] in process_paths) or (edge in invisible_edges))
for edge in graph_dict.get('place_edges', []):
visible = not (
(remove_process_place_edges and edge['child'] in process_paths)
or (edge in invisible_edges)
)
graph.attr('edge', style='filled' if visible else 'invis')
graph.edge(str(edge['parent']), str(edge['child']), **edge_styles['place'], constraint='true')
graph.edge(
str(edge['parent']),
str(edge['child']),
**edge_styles['place'],
constraint='true',
)
def add_disconnected_edges():
for direction, style_key in [('disconnected_input_edges', 'input'), ('disconnected_output_edges', 'output')]:
for edge in graph_dict[direction]:
for direction, style_key in [
('disconnected_input_edges', 'input'),
('disconnected_output_edges', 'output'),
]:
for edge in graph_dict.get(direction, []):
path = edge['edge_path']

@@ -361,3 +533,6 @@ port = edge['port']

graph.attr('edge', **edge_styles[style_key])
plot_edges(graph, edge, port_labels, port_label_size, state_node_spec, constraint='true')
plot_edges(
graph, edge, port_labels, port_label_size,
state_node_spec, constraint='true',
)

@@ -379,15 +554,25 @@ def rank_node_groups():

def apply_custom_colors():
state_paths = [entry['path'] for entry in graph_dict['state_nodes']]
process_paths = [entry['path'] for entry in graph_dict['process_nodes']]
if node_border_colors:
for name, color in node_border_colors.items():
graph.node(str(name), color=color)
if name in state_paths or name in process_paths:
graph.node(str(name), color=color)
if node_fill_colors:
for name, color in node_fill_colors.items():
graph.node(str(name), color=color, style='filled')
if name in state_paths or name in process_paths:
graph.node(str(name), color=color, style='filled')
# -------- build graph ---------------------------------------------------
add_state_nodes()
process_paths, collapse_map = add_process_nodes()
if collapse_redundant_processes:
rewrite_collapsed_edges(collapse_map)
rewrite_collapsed_edges(collapse_map)
add_place_edges(process_paths)
add_edges([('input_edges', 'input'), ('output_edges', 'output'), ('bidirectional_edges', 'bidirectional')])
add_edges([
('input_edges', 'input'),
('output_edges', 'output'),
('bidirectional_edges', 'bidirectional'),
])
add_state_nodes()

@@ -402,9 +587,9 @@ add_disconnected_edges()

def plot_bigraph(
state,
schema=None,
core=None,
out_dir=None,
filename=None,
file_format='png',
**kwargs
state,
schema=None,
core=None,
out_dir=None,
filename=None,
file_format='png',
**kwargs
):

@@ -477,4 +662,6 @@ """

def graphviz_edge(core, schema, state, path, options, graph):
"""Visualize a process node with input/output/bridge wiring."""
schema = schema or {}
node_spec = {

@@ -494,7 +681,11 @@ 'name': path[-1],

# Wiring
graph = get_graph_wires(schema.get('_inputs', {}), state.get('inputs', {}), graph, 'inputs', path, state.get('bridge', {}).get('inputs', {}))
graph = get_graph_wires(schema.get('_outputs', {}), state.get('outputs', {}), graph, 'outputs', path, state.get('bridge', {}).get('outputs', {}))
graph = get_graph_wires(schema.get('_inputs', {}), state.get('inputs', {}), graph, 'inputs', path,
state.get('bridge', {}).get('inputs', {}))
graph = get_graph_wires(schema.get('_outputs', {}), state.get('outputs', {}), graph, 'outputs', path,
state.get('bridge', {}).get('outputs', {}))
# Merge bidirectional edges
def key(edge): return (tuple(edge['edge_path']), tuple(edge['target_path']), edge['port'])
def key(edge):
return (tuple(edge['edge_path']), tuple(edge['target_path']), edge['port'])
input_set = {key(e): e for e in graph['input_edges']}

@@ -589,3 +780,3 @@ output_set = {key(e): e for e in graph['output_edges']}

},
'map':{
'map': {
'_graphviz': graphviz_map,

@@ -605,2 +796,3 @@ },

# TODO: we want to visualize things that are not yet complete

@@ -1097,2 +1289,3 @@

def generate_spec_and_schema(n_rows, n_cols):

@@ -1145,2 +1338,3 @@ spec = {'cells': {}}

def test_array_paths():

@@ -1163,3 +1357,3 @@ core = VisualizeTypes()

n_rows, n_cols = 6, 6 # or any desired shape
n_rows, n_cols = 6, 6 # or any desired shape
spec, schema = generate_spec_and_schema(n_rows, n_cols)

@@ -1181,194 +1375,194 @@

state = {
"particles": {
"rddyhz3IRHaZIKnpyROvGw": {
"id": "rddyhz3IRHaZIKnpyROvGw",
"position": ["1.6170202476993778", "2.6965198046441277"],
"size": "0.0",
"mass": "0.7708618958003092",
"local": {
"glucose": "2.1129479416859507", "acetate": "0.0"},
"exchange": {
"glucose": "0.0", "acetate": "0.0"},
"dFBA": {
"inputs": {
"substrates": ["local"],
"biomass": ["mass"]},
"outputs": {
"substrates": ["exchange"],
"biomass": ["mass"]},
"interval": 1.0,
"address": "local:DynamicFBA",
"config": {
"model_file": "textbook",
"kinetic_params": {
"glucose": ["0.5", "1.0"],
"acetate": ["0.5", "2.0"]},
"substrate_update_reactions": {
"glucose": "EX_glc__D_e",
"acetate": "EX_ac_e"},
"bounds": {
"EX_o2_e": {
"lower": "-2.0",
"upper": "!nil"},
"ATPM": {
"lower": "1.0",
"upper": "1.0"}}},
"shared": {}
}
},
state = {
"particles": {
"rddyhz3IRHaZIKnpyROvGw": {
"id": "rddyhz3IRHaZIKnpyROvGw",
"position": ["1.6170202476993778", "2.6965198046441277"],
"size": "0.0",
"mass": "0.7708618958003092",
"local": {
"glucose": "2.1129479416859507", "acetate": "0.0"},
"exchange": {
"glucose": "0.0", "acetate": "0.0"},
"dFBA": {
"inputs": {
"substrates": ["local"],
"biomass": ["mass"]},
"outputs": {
"substrates": ["exchange"],
"biomass": ["mass"]},
"interval": 1.0,
"address": "local:DynamicFBA",
"config": {
"model_file": "textbook",
"kinetic_params": {
"glucose": ["0.5", "1.0"],
"acetate": ["0.5", "2.0"]},
"substrate_update_reactions": {
"glucose": "EX_glc__D_e",
"acetate": "EX_ac_e"},
"bounds": {
"EX_o2_e": {
"lower": "-2.0",
"upper": "!nil"},
"ATPM": {
"lower": "1.0",
"upper": "1.0"}}},
"shared": {}
}
},
"global_time": "0.0",
"particle_movement": {
'_type': 'process',
"inputs": {
"particles": ["particles"],
"fields": ["fields"]},
"outputs": {
"particles": ["particles"],
"fields": ["fields"]},
"interval": 1.0,
"address": "local:Particles",
"config": {},
},
"fields": {
"glucose": {
"list": [
[
6.682473038698228,
6.138508047074471,
5.932822055376635,
1.2275655546440918,
7.184289576021444,
5.802540321285436,
3.158370346023715,
6.191878825605585,
7.417057892118427,
9.619194357104389
],
[
7.384059587748178,
8.640811575012702,
2.1129479416859507,
3.1057148920618385,
8.05289155553335,
4.399086558257299,
7.193948745260049,
5.035688862165517,
5.219923411699781,
4.539653707209219
],
[
1.9082739815105203,
8.99864529956811,
6.5195511089756675,
1.957101992521509,
3.1907575508941806,
4.5623876367245195,
9.68212403622312,
4.419905700021853,
8.71921956750521,
8.163620432115913
],
[
9.478709499822921,
8.675323729741326,
4.226239950967384,
1.6634413475982608,
4.2399161776694365,
1.8032704088212483,
8.029077191030485,
3.5987760418726706,
1.0827071604629657,
4.939077862941639
],
[
2.2055610319311745,
8.052040372657313,
5.325939740703682,
5.915877670139153,
9.335157497844655,
5.8973761480277584,
7.503363745465629,
1.2530328598811558,
7.58703729093062,
2.4382507126877866
]
},
"global_time": "0.0",
"particle_movement": {
'_type': 'process',
"inputs": {
"particles": ["particles"],
"fields": ["fields"]},
"outputs": {
"particles": ["particles"],
"fields": ["fields"]},
"interval": 1.0,
"address": "local:Particles",
"config": {},
},
"fields": {
"glucose": {
"list": [
[
6.682473038698228,
6.138508047074471,
5.932822055376635,
1.2275655546440918,
7.184289576021444,
5.802540321285436,
3.158370346023715,
6.191878825605585,
7.417057892118427,
9.619194357104389
],
"data": "float",
"shape": [
5,
10
[
7.384059587748178,
8.640811575012702,
2.1129479416859507,
3.1057148920618385,
8.05289155553335,
4.399086558257299,
7.193948745260049,
5.035688862165517,
5.219923411699781,
4.539653707209219
],
[
1.9082739815105203,
8.99864529956811,
6.5195511089756675,
1.957101992521509,
3.1907575508941806,
4.5623876367245195,
9.68212403622312,
4.419905700021853,
8.71921956750521,
8.163620432115913
],
[
9.478709499822921,
8.675323729741326,
4.226239950967384,
1.6634413475982608,
4.2399161776694365,
1.8032704088212483,
8.029077191030485,
3.5987760418726706,
1.0827071604629657,
4.939077862941639
],
[
2.2055610319311745,
8.052040372657313,
5.325939740703682,
5.915877670139153,
9.335157497844655,
5.8973761480277584,
7.503363745465629,
1.2530328598811558,
7.58703729093062,
2.4382507126877866
]
},
"acetate": {
"list": [
[
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0
],
[
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0
],
[
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0
],
[
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0
],
[
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0
]
],
"data": "float",
"shape": [
5,
10
]
},
"acetate": {
"list": [
[
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0
],
"data": "float",
"shape": [
5,
10
[
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0
],
[
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0
],
[
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0
],
[
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0
]
}
],
"data": "float",
"shape": [
5,
10
]
}
}
}

@@ -1375,0 +1569,0 @@ composition = {

+217
-16
PKG-INFO

@@ -1,26 +0,229 @@

Metadata-Version: 2.1
Metadata-Version: 2.4
Name: bigraph-viz
Version: 0.1.10
Summary: A graphviz-based plotting tool for compositional bigraph schema
Home-page: https://github.com/vivarium-collective/bigraph-viz
Author: Eran Agmon
Author-email: agmon.eran@gmail.com
License: UNKNOWN
Platform: UNKNOWN
Version: 0.1.15
Summary: A visualization method for displaying the structure of process bigraphs
Author-email: Eran Agmon <agmon.eran@gmail.com>
Maintainer-email: Eran Agmon <agmon.eran@gmail.com>
License: Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
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END OF TERMS AND CONDITIONS
APPENDIX: How to apply the Apache License to your work.
To apply the Apache License to your work, attach the following
boilerplate notice, with the fields enclosed by brackets "[]"
replaced with your own identifying information. (Don't include
the brackets!) The text should be enclosed in the appropriate
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identification within third-party archives.
Copyright 2023 Ryan Spangler and Eran Agmon
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
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Unless required by applicable law or agreed to in writing, software
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WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
Keywords: visualization,systems biology,bigraph,graphviz,vivarium
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Requires-Python: >=3.6
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Topic :: Software Development :: Libraries
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
License-File: AUTHORS.md
Requires-Dist: bigraph-schema
Requires-Dist: graphviz
Dynamic: license-file

@@ -94,3 +297,1 @@ # Bigraph-viz

Bigraph-viz is open-source software released under the [Apache 2 License](https://github.com/vivarium-collective/bigraph-viz/blob/main/LICENSE).
+6
-2
pyproject.toml

@@ -7,6 +7,6 @@ [build-system]

name = "bigraph-viz"
version = "0.1.10"
version = "0.1.15"
description = "A visualization method for displaying the structure of process bigraphs"
readme = "README.md"
requires-python = "==3.12.9"
requires-python = ">=3.9"
license = { file = "LICENSE" }

@@ -28,2 +28,6 @@

"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",

@@ -30,0 +34,0 @@ "Topic :: Scientific/Engineering :: Visualization",

-51
setup.py
import re
from setuptools import setup, find_packages
VERSION = '0.1.10'
with open("README.md", "r") as readme:
description = readme.read()
# Patch the relative links to absolute URLs that will work on PyPI.
description2 = re.sub(
r']\(([\w/.-]+\.png)\)',
r'](https://github.com/vivarium-collective/bigraph-viz/raw/main/\1)',
description)
long_description = re.sub(
r']\(([\w/.-]+)\)',
r'](https://github.com/vivarium-collective/bigraph-viz/blob /main/\1)',
description2)
setup(
name="bigraph-viz",
version=VERSION,
author="Eran Agmon",
author_email="agmon.eran@gmail.com",
description="A graphviz-based plotting tool for compositional bigraph schema",
long_description=long_description,
long_description_content_type="text/markdown",
url="https://github.com/vivarium-collective/bigraph-viz",
packages=find_packages(),
classifiers=[
"Development Status :: 3 - Alpha",
"Intended Audience :: Developers",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.6",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
],
python_requires=">=3.6",
install_requires=[
# List your package dependencies here
"graphviz",
"bigraph-schema>=0.0.51",
"numpy"
],
)