bigraph-viz - pypi Package Compare versions

Comparing version 0.1.5 to 0.1.6

bigraph_viz/convert.py

+import os
+from pdf2image import convert_from_path
+from PIL import Image
+
+# Print current working directory
+cwd = os.getcwd()
+print("Current working directory:", cwd)
+
+# Go up one level in the directory
+cwd = os.path.dirname(cwd)
+
+# Input PDF file (single page)
+pdf_path = os.path.join(cwd, "notebooks/out/ecoli.pdf")
+
+# Output directory and files
+output_dir = os.path.join(cwd, "notebooks/out/")
+output_full_res = os.path.join(output_dir, "ecoli_full_res.png")
+output_scaled = os.path.join(output_dir, "ecoli_google_slides.png")
+
+# Ensure the output directory exists
+os.makedirs(output_dir, exist_ok=True)
+
+# Convert PDF to an image at high DPI
+images = convert_from_path(pdf_path, dpi=1200)  # Use high DPI for sharpness
+
+if images:
+    # Save the **full resolution** image first
+    images[0].save(output_full_res, "PNG")
+    print(f"Full resolution image saved at: {output_full_res}")
+
+    # Resize image to match Google Slides width (3000 px)
+    target_width = 3000
+    aspect_ratio = images[0].width / images[0].height
+    target_height = int(target_width / aspect_ratio)
+
+    resized_image = images[0].resize((target_width, target_height), Image.LANCZOS)
+    resized_image.save(output_scaled, "PNG")
+
+    print(f"Resized Google Slides image saved at: {output_scaled}")
+else:
+    print("Error: No images found in PDF!")

pyproject.toml

+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "bigraph-viz"
+version = "0.1.6"
+description = "A visualization method for displaying the structure of process bigraphs"
+readme = "README.md"
+requires-python = "==3.12.9"
+license = { file = "LICENSE" }
+
+authors = [
+    { name = "Eran Agmon", email = "[e-mail]" }
+]
+maintainers = [
+    { name = "Eran Agmon", email = "[e-mail]" }
+]
+
+keywords = ["visualization", "systems biology", "bigraph", "graphviz", "vivarium"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Visualization",
+    "Topic :: Software Development :: Libraries"
+]
+
+dependencies = [
+    "bigraph-schema",
+    "graphviz"
+]
+
+[tool.setuptools]
+packages = ["bigraph_viz"]
+
+[tool.uv.sources]
+bigraph-schema = { path = "../bigraph-schema", editable = true }

bigraph_viz.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: bigraph-viz
-Version: 0.1.5
+Version: 0.1.6
 Summary: A graphviz-based plotting tool for compositional bigraph schema
@@ -8,2 +8,4 @@ Home-page: https://github.com/vivarium-collective/bigraph-viz
 Author-email: [e-mail]
+License: UNKNOWN
+Platform: UNKNOWN
 Classifier: Development Status :: 3 - Alpha
@@ -93,1 +95,3 @@ 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.egg-info/SOURCES.txt

 AUTHORS.md
 LICENSE
 README.md
+pyproject.toml
 setup.py
 bigraph_viz/__init__.py
+bigraph_viz/convert.py
 bigraph_viz/convert_vivarium_v1.py
@@ -7,0 +9,0 @@ bigraph_viz/dict_utils.py

bigraph_viz/visualize_types.py

 import os
 import inspect
 import graphviz
+from itertools import islice
 import numpy as np
@@ -9,3 +10,2 @@
 
-
 PROCESS_SCHEMA_KEYS = [
@@ -22,2 +22,8 @@ 'config',
 
+def chunked(iterable, size):
+    """Yield successive chunks from iterable."""
+    it = iter(iterable)
+    return iter(lambda: tuple(islice(it, size)), ())
+
+
 def make_label(label):
@@ -32,6 +38,6 @@ # Insert line breaks after every max_length characters
 def get_graph_wires(
-        ports_schema,     # the ports schema
-        wires,      # the wires, from port to path
-        graph_dict, # the current graph dict that is being built
-        schema_key, # inputs or outputs
+        ports_schema,  # the ports schema
+        wires,  # the wires, from port to path
+        graph_dict,  # the current graph dict that is being built
+        schema_key,  # inputs or outputs
         edge_path,  # the path up to this process
@@ -79,3 +85,3 @@ bridge_wires=None,
                 graph_dict['input_edges'].append({
-                    'edge_path': edge_path ,
+                    'edge_path': edge_path,
                     'target_path': target_path,
@@ -190,3 +196,3 @@ 'port': f'bridge_{port}',
         rankdir='TB',
-        aspect_ratio='auto', # 'compress', 'expand', 'auto', 'fill'
+        aspect_ratio='auto',  # 'compress', 'expand', 'auto', 'fill'
         dpi='70',
@@ -204,2 +210,3 @@ significant_digits=2,
         node_groups=False,
+        max_nodes_per_row=None,
 ):
@@ -233,3 +240,3 @@ """make a graphviz figure from a graph_dict"""
                ratio=aspect_ratio,  # "fill",
-               splines = 'true',
+               splines='true',
                )
@@ -239,18 +246,57 @@
     graph.attr('node', **state_node_spec)
-    for node in graph_dict['state_nodes']:
-        node_path = node['path']
-        node_name = add_node_to_graph(graph, node, state_node_spec, show_values, show_types, significant_digits)
-        node_names.append(node_name)
+    state_nodes = graph_dict['state_nodes']
+    if max_nodes_per_row:
+        previous_node = None
+        for i, chunk in enumerate(chunked(state_nodes, max_nodes_per_row)):
+            with graph.subgraph(name=f'state_row_{i}') as row:
+                row.attr(rank='same')
+                chunk_node_names = []
+                for node in chunk:
+                    node_name = add_node_to_graph(graph, node, state_node_spec, show_values, show_types,
+                                                  significant_digits)
+                    node_names.append(node_name)
+                    chunk_node_names.append(node_name)
 
+                # Add invisible edge to stack rows
+                if previous_node and chunk_node_names:
+                    graph.edge(previous_node, chunk_node_names[0], style='invis', weight='10')
+                if chunk_node_names:
+                    previous_node = chunk_node_names[-1]
+    else:
+        for node in state_nodes:
+            node_name = add_node_to_graph(graph, node, state_node_spec, show_values, show_types, significant_digits)
+            node_names.append(node_name)
+
     # process nodes
     process_paths = []
     graph.attr('node', **process_node_spec)
-    for node in graph_dict['process_nodes']:
-        node_path = node['path']
-        process_paths.append(node_path)
-        node_name = str(node_path)
-        node_names.append(node_name)
-        label = make_label(node_path[-1])
-        graph.node(node_name, label=label)
+    process_nodes = graph_dict['process_nodes']
+    if max_nodes_per_row:
+        previous_node = None
+        for i, chunk in enumerate(chunked(process_nodes, max_nodes_per_row)):
+            with graph.subgraph(name=f'process_row_{i}') as row:
+                row.attr(rank='same')
+                chunk_node_names = []
+                for node in chunk:
+                    node_path = node['path']
+                    process_paths.append(node_path)
+                    node_name = str(node_path)
+                    node_names.append(node_name)
+                    chunk_node_names.append(node_name)
+                    label = make_label(node_path[-1])
+                    row.node(node_name, label=label)
 
+                if previous_node and chunk_node_names:
+                    graph.edge(previous_node, chunk_node_names[0], style='invis', weight='10')
+                if chunk_node_names:
+                    previous_node = chunk_node_names[-1]
+    else:
+        for node in process_nodes:
+            node_path = node['path']
+            process_paths.append(node_path)
+            node_name = str(node_path)
+            node_names.append(node_name)
+            label = make_label(node_path[-1])
+            graph.node(node_name, label=label)
+
     # place edges
@@ -278,3 +324,3 @@ graph.attr('edge', arrowhead='none', penwidth='2')
         if edge['type'] == 'bridge_inputs':
-            graph.attr('edge', **output_edge_spec) # reverse arrow direction to go from composite to store
+            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')
@@ -287,3 +333,3 @@ else:
         if edge['type'] == 'bridge_outputs':
-            graph.attr('edge', **input_edge_spec) # reverse arrow direction to go from store to composite
+            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')
@@ -300,6 +346,6 @@ else:
             if 'bridge_outputs' in edge['type']:
-                graph.attr('edge', **input_edge_spec) # reverse arrow direction to go from store to composite
+                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
+                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')
@@ -396,3 +442,3 @@
         (),
-        options=viztype_kwargs   # TODO
+        options=viztype_kwargs  # TODO
     )
@@ -431,3 +477,3 @@
             if not is_schema_key(key):
-                subpath = path + (key,)                
+                subpath = path + (key,)
                 graph = core.get_graph_dict(
@@ -441,4 +487,4 @@ schema.get(key, {}),
     return graph
-        
 
+
 def graphviz_edge(core, schema, state, path, options, graph):
@@ -490,3 +536,2 @@ # add process node to graph
                     (input_edge['edge_path'] == output_edge['edge_path']):
-
                 graph['bidirectional_edges'].append({
@@ -523,5 +568,7 @@ 'edge_path': input_edge['edge_path'],
 
+
 def graphviz_none(core, schema, state, path, options, graph):
     return graph
 
+
 def graphviz_composite(core, schema, state, path, options, graph):
@@ -591,3 +638,2 @@ # add the composite edge
 
-
     def get_graph_dict(self, schema, state, path, options, graph=None):
@@ -621,3 +667,2 @@ path = path or ()
 
-
     def generate_graph_dict(self, schema, state, path, options):
@@ -627,3 +672,2 @@ full_schema, full_state = self.generate(schema, state)
 
-
     def plot_graph(self,
@@ -657,3 +701,2 @@ graph_dict,
 
-
 # Begin Tests
@@ -667,2 +710,3 @@ ###############
 
+
 def test_simple_store():
@@ -677,2 +721,3 @@ simple_store_state = {
 
+
 def test_forest():
@@ -692,2 +737,3 @@ forest = {
 
+
 def test_nested_composite():
@@ -708,27 +754,27 @@ state = {
                     'config': {'_type': 'quote',
-                              'state': {'grow': {'_type': 'process',
-                                                 'address': 'local:grow',
-                                                 'config': {'rate': 0.03},
-                                                 'inputs': {'mass': ['mass']},
-                                                 'outputs': {'mass': ['mass']}},
-                                        'divide': {'_type': 'process',
-                                                   'address': 'local:divide',
-                                                   'config': {'agent_id': '0',
-                                                              'agent_schema': {'mass': 'float'},
-                                                              'threshold': 2.0,
-                                                              'divisions': 2},
-                                                   'inputs': {'trigger': ['mass']},
-                                                   'outputs': {'environment': ['environment']}},
-                                        'global_time': 0.0},
-                              'bridge': {'inputs': {'mass': ['mass']},
-                                         'outputs': {'mass': ['mass'],
-                                                     'environment': ['environment']}},
-                              'composition': {'global_time': 'float'},
-                              'interface': {'inputs': {}, 'outputs': {}},
-                              'emitter': {'path': ['emitter'],
-                                          'address': 'local:ram-emitter',
-                                          'config': {},
-                                          'mode': 'none',
-                                          'emit': {}},
-                              'global_time_precision': None}
+                               'state': {'grow': {'_type': 'process',
+                                                  'address': 'local:grow',
+                                                  'config': {'rate': 0.03},
+                                                  'inputs': {'mass': ['mass']},
+                                                  'outputs': {'mass': ['mass']}},
+                                         'divide': {'_type': 'process',
+                                                    'address': 'local:divide',
+                                                    'config': {'agent_id': '0',
+                                                               'agent_schema': {'mass': 'float'},
+                                                               'threshold': 2.0,
+                                                               'divisions': 2},
+                                                    'inputs': {'trigger': ['mass']},
+                                                    'outputs': {'environment': ['environment']}},
+                                         'global_time': 0.0},
+                               'bridge': {'inputs': {'mass': ['mass']},
+                                          'outputs': {'mass': ['mass'],
+                                                      'environment': ['environment']}},
+                               'composition': {'global_time': 'float'},
+                               'interface': {'inputs': {}, 'outputs': {}},
+                               'emitter': {'path': ['emitter'],
+                                           'address': 'local:ram-emitter',
+                                           'config': {},
+                                           'mode': 'none',
+                                           'emit': {}},
+                               'global_time_precision': None}
                 }}}}
@@ -739,2 +785,3 @@ plot_bigraph(state,
 
+
 def test_graphviz():
@@ -744,3 +791,3 @@ cell = {
             '_type': 'map[float]',
-            'a': 11.0,  #{'_type': 'float', '_value': 11.0},
+            'a': 11.0,  # {'_type': 'float', '_value': 11.0},
             'b': 3333.33},
@@ -782,2 +829,3 @@ 'cell': {
 
+
 def test_bigraph_cell():
@@ -787,3 +835,3 @@ cell = {
             '_type': 'map[float]',
-            'a': 11.0,  #{'_type': 'float', '_value': 11.0},
+            'a': 11.0,  # {'_type': 'float', '_value': 11.0},
             'b': 3333.33},
@@ -793,3 +841,3 @@ 'cell': {
             'config': {},
-            'address': 'local:cell',   # TODO -- this is where the ports/inputs/outputs come from
+            'address': 'local:cell',  # TODO -- this is where the ports/inputs/outputs come from
             'internal': 1.0,
@@ -820,2 +868,3 @@ '_inputs': {
 
+
 def test_bio_schema():
@@ -852,3 +901,3 @@ core = VisualizeTypes()
                 'inputs': {
-                    'fields': ['fields',]
+                    'fields': ['fields', ]
                 },
@@ -864,2 +913,3 @@ 'outputs': {
 
+
 def test_flat_composite():
@@ -893,2 +943,3 @@ flat_composite_spec = {
 
+
 def test_multi_processes():
@@ -915,2 +966,3 @@ process_schema = {
 
+
 def test_nested_processes():
@@ -947,2 +999,3 @@ nested_process_spec = {
 
+
 def test_cell_hierarchy():
@@ -983,5 +1036,5 @@ core = VisualizeTypes()
     core.register('cell', {
-            'membrane': 'membrane',
-            'cytoplasm': 'cytoplasm',
-            'nucleoid': 'nucleoid'})
+        'membrane': 'membrane',
+        'cytoplasm': 'cytoplasm',
+        'nucleoid': 'nucleoid'})
 
@@ -1009,2 +1062,3 @@ # state
 
+
 def test_multiple_disconnected_ports():
@@ -1034,2 +1088,3 @@ core = VisualizeTypes()
 
+
 def test_composite_process():
@@ -1052,3 +1107,3 @@ core = VisualizeTypes()
                 '_inputs': {'port3': 'any'},
-                '_outputs': {'port4': 'any',},
+                '_outputs': {'port4': 'any', },
                 'inputs': {'port3': ['store1']},
@@ -1063,2 +1118,3 @@ 'outputs': {'port4': ['store2']}}}}
 
+
 def test_bidirectional_edges():
@@ -1089,2 +1145,3 @@ core = VisualizeTypes()
 
+
 def test_array_paths():
@@ -1150,4 +1207,4 @@ core = VisualizeTypes()
             'acetate': np.array([[1.0], [2.0]]),
-            'biomass': np.array([[3.0],[4.0]]),
-            'glucose': np.array([[5.0],[6.0]])
+            'biomass': np.array([[3.0], [4.0]]),
+            'glucose': np.array([[5.0], [6.0]])
         }
@@ -1154,0 +1211,0 @@ }

PKG-INFO

 Metadata-Version: 2.1
 Name: bigraph-viz
-Version: 0.1.5
+Version: 0.1.6
 Summary: A graphviz-based plotting tool for compositional bigraph schema
@@ -8,2 +8,4 @@ Home-page: https://github.com/vivarium-collective/bigraph-viz
 Author-email: [e-mail]
+License: UNKNOWN
+Platform: UNKNOWN
 Classifier: Development Status :: 3 - Alpha
@@ -93,1 +95,3 @@ 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 = '0.1.5'
+VERSION = '0.1.6'
 
@@ -8,0 +8,0 @@

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Improved metrics

Total package byte prevSize

82820

5.96%

Number of package files

18

12.5%

Lines of code

1522

5.11%