bigraph-viz - npm Package Compare versions

Comparing version 0.1.3 to 0.1.5

bigraph_viz.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: bigraph-viz
-Version: 0.1.3
+Version: 0.1.5
 Summary: A graphviz-based plotting tool for compositional bigraph schema
@@ -8,4 +8,2 @@ Home-page: https://github.com/vivarium-collective/bigraph-viz
 Author-email: [e-mail]
-License: UNKNOWN
-Platform: UNKNOWN
 Classifier: Development Status :: 3 - Alpha
@@ -95,3 +93,1 @@ Classifier: Intended Audience :: Developers
 Bigraph-viz is open-source software released under the [Apache 2 License](https://github.com/vivarium-collective/bigraph-viz/blob/main/LICENSE).
-
-

bigraph_viz/visualize_types.py

 import os
 import inspect
 import graphviz
+import numpy as np
 
-from bigraph_schema import TypeSystem, is_schema_key
+from bigraph_schema import TypeSystem, is_schema_key, hierarchy_depth
 from bigraph_viz.dict_utils import absolute_path
@@ -40,2 +41,3 @@
     wires = wires or {}
+    ports_schema = ports_schema or {}
     inferred_ports = set(list(ports_schema.keys()) + list(wires.keys()))
@@ -61,17 +63,9 @@
         elif isinstance(wire, (list, tuple, str)):
-            # the wire is defined, add it to edges
-            if isinstance(wire, str):
-                wire = [wire]
-            target_path = absolute_path(edge_path[:-1], tuple(wire))  # TODO -- make sure this resolves ".."
-            if schema_key == 'inputs':
-                edge_key = 'input_edges'
-            elif schema_key == 'outputs':
-                edge_key = 'output_edges'
-            else:
-                raise Exception(f'invalid schema key {schema_key}')
-            graph_dict[edge_key].append({
-                'edge_path': edge_path,
-                'target_path': target_path,
-                'port': port,
-                'type': schema_key})
+            graph_dict = get_single_wire(edge_path, graph_dict, port, schema_key, wire)
+        elif isinstance(wire, dict):
+            flat_wires = hierarchy_depth(wires)
+            for subpath, subwire in flat_wires.items():
+                subport = '/'.join(subpath)
+                graph_dict = get_single_wire(edge_path, graph_dict, subport, schema_key, subwire)
+
         else:
@@ -98,2 +92,26 @@ raise ValueError(f"Unexpected wire type: {wires}")
 
+def get_single_wire(edge_path, graph_dict, port, schema_key, wire):
+    # the wire is defined, add it to edges
+    if isinstance(wire, str):
+        wire = [wire]
+    elif isinstance(wire, (list, tuple)):
+        # only use strings in the wire
+        # TODO -- make this more general so it only skips integers if they go into an array
+        wire = [item for item in wire if isinstance(item, str)]
+
+    target_path = absolute_path(edge_path[:-1], tuple(wire))  # TODO -- make sure this resolves ".."
+    if schema_key == 'inputs':
+        edge_key = 'input_edges'
+    elif schema_key == 'outputs':
+        edge_key = 'output_edges'
+    else:
+        raise Exception(f'invalid schema key {schema_key}')
+    graph_dict[edge_key].append({
+        'edge_path': edge_path,
+        'target_path': target_path,
+        'port': port,
+        'type': schema_key})
+    return graph_dict
+
+
 def plot_edges(
@@ -168,6 +186,9 @@ graph,
         node_label_size='12pt',
+        process_label_size=None,
         size='16,10',
         rankdir='TB',
+        aspect_ratio='auto', # 'compress', 'expand', 'auto', 'fill'
         dpi='70',
         significant_digits=2,
+        undirected_edges=False,
         show_values=False,
@@ -187,8 +208,9 @@ show_types=False,
     invisible_edges = invisible_edges or []
+    process_label_size = process_label_size or node_label_size
 
     # node specs
     state_node_spec = {
-        'shape': 'circle', 'penwidth': '2', 'margin': label_margin, 'fontsize': node_label_size}
+        'shape': 'circle', 'penwidth': '2', 'constraint': 'false', 'margin': label_margin, 'fontsize': node_label_size}
     process_node_spec = {
-        'shape': 'box', 'penwidth': '2', 'constraint': 'false', 'margin': label_margin, 'fontsize': node_label_size}
+        'shape': 'box', 'penwidth': '2', 'constraint': 'false', 'margin': label_margin, 'fontsize': process_label_size}
     input_edge_spec = {
@@ -198,6 +220,16 @@ 'style': 'dashed', 'penwidth': '1', 'arrowhead': 'normal', 'arrowsize': '1.0', 'dir': 'forward'}
         'style': 'dashed', 'penwidth': '1', 'arrowhead': 'normal', 'arrowsize': '1.0', 'dir': 'back'}
+    bidirectional_edge_spec = {
+        'style': 'dashed', 'penwidth': '1', 'arrowhead': 'normal', 'arrowsize': '1.0', 'dir': 'both'}
 
+    if undirected_edges:
+        input_edge_spec['dir'] = 'none'
+        output_edge_spec['dir'] = 'none'
+        bidirectional_edge_spec['dir'] = 'none'
+
     # initialize graph
     graph = graphviz.Digraph(name='bigraph', engine='dot')
-    graph.attr(size=size, overlap='false', rankdir=rankdir, dpi=dpi)
+    graph.attr(size=size, overlap='false', rankdir=rankdir, dpi=dpi,
+               ratio=aspect_ratio,  # "fill",
+               splines = 'true',
+               )
 
@@ -257,2 +289,14 @@ # state nodes
             plot_edges(graph, edge, port_labels, port_label_size, state_node_spec, constraint='true')
+    # bidirectional edges
+    for edge in graph_dict['bidirectional_edges']:
+        if 'bridge_outputs' not in edge['type'] and 'bridge_inputs' not in edge['type']:
+            graph.attr('edge', **bidirectional_edge_spec)
+            plot_edges(graph, edge, port_labels, port_label_size, state_node_spec, constraint='true')
+        else:
+            if 'bridge_outputs' in edge['type']:
+                graph.attr('edge', **input_edge_spec) # reverse arrow direction to go from store to composite
+                plot_edges(graph, edge, port_labels, port_label_size, state_node_spec, constraint='false')
+            if 'bridge_inputs' in edge['type']:
+                graph.attr('edge', **output_edge_spec) # reverse arrow direction to go from composite to store
+                plot_edges(graph, edge, port_labels, port_label_size, state_node_spec, constraint='false')
 
@@ -290,2 +334,5 @@ # state nodes again
     for group in node_groups:
+        # convert lists to tuples
+        group = [tuple(item) for item in group]
+
         group_name = str(group)
@@ -321,2 +368,3 @@ with graph.subgraph(name=group_name) as c:
         filename=None,
+        file_format='png',
         **kwargs
@@ -353,2 +401,3 @@ ):
         out_dir=out_dir,
+        file_format=file_format,
         options=get_graphviz_kwargs)
@@ -429,2 +478,29 @@
 
+    # get bidirectional wires
+    input_edges_to_remove = []
+    output_edges_to_remove = []
+    for input_edge in graph['input_edges']:
+        for output_edge in graph['output_edges']:
+            if (input_edge['target_path'] == output_edge['target_path']) and \
+                    (input_edge['port'] == output_edge['port']) and \
+                    (input_edge['edge_path'] == output_edge['edge_path']):
+
+                graph['bidirectional_edges'].append({
+                    'edge_path': input_edge['edge_path'],
+                    'target_path': input_edge['target_path'],
+                    'port': input_edge['port'],
+                    'type': (input_edge['type'], output_edge['type']),
+                    # 'type': 'bidirectional'
+                })
+                input_edges_to_remove.append(input_edge)
+                output_edges_to_remove.append(output_edge)
+                break  # prevent matching the same input_edge with multiple output_edges
+
+    # Remove matched edges after iteration
+    for edge in input_edges_to_remove:
+        graph['input_edges'].remove(edge)
+
+    for edge in output_edges_to_remove:
+        graph['output_edges'].remove(edge)
+
     # get the input and output bridge wires
@@ -474,2 +550,3 @@ if bridge_wires:
                 graph)
+
     return graph
@@ -519,2 +596,3 @@
             'output_edges': [],
+            'bidirectional_edges': [],
             'disconnected_input_edges': [],
@@ -938,43 +1016,138 @@ 'disconnected_output_edges': []}
             '_type': 'composite',
-            '_inputs': {
-                'port1': 'any',
-            },
-            '_outputs': {
-                'port2': 'any',
-            },
-            'inputs': {
-                'port1': ['external store'],
-            },
+            '_inputs': {'port1': 'any'},
+            '_outputs': {'port2': 'any'},
+            'inputs': {'port1': ['external store']},
             'store1': 'any',
             'store2': 'any',
             'bridge': {
-                'inputs': {
-                    'port1': ['store1'],
-                },
-                'outputs': {
-                    'port2': ['store2'],
-                }
-            },
+                'inputs': {'port1': ['store1']},
+                'outputs': {'port2': ['store2']}},
             'process1': {
                 '_type': 'process',
-                '_inputs': {
-                    'port3': 'any',
-                },
-                '_outputs': {
-                    'port4': 'any',
-                },
-                'inputs': {
-                    'port3': ['store1'],
-                },
-                'outputs': {
-                    'port4': ['store2'],
-                }
-            },
+                '_inputs': {'port3': 'any'},
+                '_outputs': {'port4': 'any',},
+                'inputs': {'port3': ['store1']},
+                'outputs': {'port4': ['store2']}}}}
+
+    plot_bigraph(
+        spec,
+        core=core,
+        filename='composite_process',
+        **plot_settings)
+
+def test_bidirectional_edges():
+    core = VisualizeTypes()
+
+    spec = {
+        'process1': {
+            '_type': 'process',
+            '_inputs': {'port1': 'any'},
+            '_outputs': {'port1': 'any'},
+            'inputs': {'port1': ['external store']},
+            'outputs': {'port1': ['external store']}},
+        'process2': {
+            '_type': 'process',
+            '_inputs': {'port3': 'any'},
+            '_outputs': {'port4': 'any'},
+            'inputs': {'port3': ['external store']},
+            'outputs': {'port4': ['external store']}
+        }
+    }
+
+    plot_bigraph(
+        spec,
+        core=core,
+        filename='bidirectional_edges',
+        **plot_settings)
+
+def test_array_paths():
+    core = VisualizeTypes()
+
+    spec = {
+        'dFBA[0,0]': {
+            '_type': 'process',
+            'address': 'local:DynamicFBA',
+            # 'config': {},
+            'inputs': {
+                'substrates': {
+                    'acetate': ['fields', 'acetate',
+                                0, 0
+                                ],
+                    'biomass': ['fields', 'biomass',
+                                0, 0
+                                ],
+                    'glucose': ['fields', 'glucose',
+                                0, 0
+                                ]}},
+            'outputs': {
+                'substrates': {
+                    'acetate': ['fields', 'acetate',
+                                0, 0
+                                ],
+                    'biomass': ['fields', 'biomass',
+                                0, 0
+                                ],
+                    'glucose': ['fields', 'glucose',
+                                0, 0
+                                ]}},
         },
+        'dFBA[1,0]': {
+            '_type': 'process',
+            'address': 'local:DynamicFBA',
+            # 'config': {},
+            'inputs': {
+                'substrates': {
+                    'acetate': ['fields', 'acetate',
+                                1, 0
+                                ],
+                    'biomass': ['fields', 'biomass',
+                                1, 0
+                                ],
+                    'glucose': ['fields', 'glucose',
+                                1, 0
+                                ]}},
+            'outputs': {
+                'substrates': {
+                    'acetate': ['fields', 'acetate',
+                                1, 0
+                                ],
+                    'biomass': ['fields', 'biomass',
+                                1, 0
+                                ],
+                    'glucose': ['fields', 'glucose',
+                                1, 0
+                                ]}},
+        },
+        'fields': {
+            'acetate': np.array([[1.0], [2.0]]),
+            'biomass': np.array([[3.0],[4.0]]),
+            'glucose': np.array([[5.0],[6.0]])
+        }
     }
 
+    schema = {
+        'fields': {
+            'acetate': {
+                '_type': 'array',
+                '_shape': (2, 1),
+                '_data': 'float'
+            },
+            'biomass': {
+                '_type': 'array',
+                '_shape': (2, 1),
+                '_data': 'float',
+            },
+            'glucose': {
+                '_type': 'array',
+                '_shape': (2, 1),
+                '_data': 'float',
+            }
+        }
+    }
+
     plot_bigraph(
         spec,
+        schema=schema,
         core=core,
-        filename='composite_process',
+        filename='array_paths',
         **plot_settings)
@@ -996,1 +1169,3 @@
     test_composite_process()
+    test_bidirectional_edges()
+    test_array_paths()

PKG-INFO

 Metadata-Version: 2.1
 Name: bigraph-viz
-Version: 0.1.3
+Version: 0.1.5
 Summary: A graphviz-based plotting tool for compositional bigraph schema
@@ -8,4 +8,2 @@ Home-page: https://github.com/vivarium-collective/bigraph-viz
 Author-email: [e-mail]
-License: UNKNOWN
-Platform: UNKNOWN
 Classifier: Development Status :: 3 - Alpha
@@ -95,3 +93,1 @@ Classifier: Intended Audience :: Developers
 Bigraph-viz is open-source software released under the [Apache 2 License](https://github.com/vivarium-collective/bigraph-viz/blob/main/LICENSE).
-
-

setup.py

@@ -5,3 +5,3 @@ import re
 
-VERSION = '0.1.3'
+VERSION = '0.1.5'
 
@@ -18,3 +18,3 @@
         r']\(([\w/.-]+)\)',
-        r'](https://github.com/vivarium-collective/bigraph-viz/blob/main/\1)',
+        r'](https://github.com/vivarium-collective/bigraph-viz/blob /main/\1)',
         description2)
@@ -21,0 +21,0 @@

Alert delta unavailable

Currently unable to show alert delta for PyPI packages.

Improved metrics

Total package byte prevSize

78161

9.34%

Lines of code

1448

12.16%