Merge pull request #891 from fabratu/20220222_plotlybridge

Add new module vizbridges: Create visualization widgets in 2D and 3D with Cytoscape and Plotly.

.github/workflows/ci.yml

@@ -387,6 +387,7 @@ jobs:
           python -c 'import networkit'
           pip install -r requirements.txt
           python -m unittest discover -v networkit/test/
+          pip install ipycytoscape plotly seaborn
           python notebooks/test_notebooks.py "notebooks"
         env:
           NATIVE: ${{ matrix.os == 'full (native)' }}

.github/workflows/scripts/documentation.sh

@@ -12,6 +12,7 @@ pip3 install cython
 pip3 install 'sphinx<4.1' sphinx_bootstrap_theme numpydoc exhale nbsphinx breathe
 pip3 install sphinx_copybutton sphinxcontrib.bibtex sphinx_gallery sphinx_last_updated_by_git 
 pip3 install ipykernel ipython matplotlib nbconvert jupyter-client networkx tabulate
+pip3 install ipycytoscape plotly seaborn
 
 # Build the C++ core library (no need for optimizations).
 mkdir core_build && cd "$_"

.github/workflows/scripts/full.sh

@@ -40,4 +40,6 @@ pip3 install -r requirements.txt
 
 python3 -m unittest discover -v networkit/test/
 
+pip3 install ipycytoscape plotly seaborn
+
 python3 notebooks/test_notebooks.py 'notebooks/'

docs/python_api/modules.rst

@@ -54,5 +54,6 @@ Modules
    structures
    traversal
    viz
+   vizbridges
    viztasks
    workflows

networkit/csbridge.py

@@ -1,6 +1,7 @@
 # local imports
 from .support import MissingDependencyError
 from .structures import Partition
+from .vizbridges import widgetFromGraph
 
 # external imports
 try:
@@ -21,11 +22,15 @@ def widget_from_graph(G, node_scores = None, node_partition = None, node_palette
 	""" 
 	widget_from_graph(G, node_scores = None, node_partition = None, node_palette = None, show_ids = True)
 
+	Note
+	----
+	DEPRECATED. Use networkit.vizbridges.widgetFromGraph() instead.
+
 	Creates a ipycytoscape-widget from a given graph. The returned widget already contains
 	all nodes and edges from the graph. The graph is colored using an array of norm. rgb-values
 	based on seaborn perceptually uniform color map (rocket) or a user given custom color array. 
 	See matplotlib color maps for the correct formatting: 
-	https://matplotlib.org/api/_as_gen/matplotlib.colors.Colormap.html#matplotlib.colors.Colormap 
+	https://matplotlib.org/api/_as_gen/matplotlib.colors.Colormap.html#matplotlib.colors.Colormap
 
 	Parameters
 	----------
@@ -34,119 +39,14 @@ def widget_from_graph(G, node_scores = None, node_partition = None, node_palette
 	node_scores : list of numbers, optional
 		List of scores for each nodes, for example scores from a centrality measure. This is 
 		used for color-calculation of the nodes (continuous distribution). Provide either 
-		node_scores or node_partition - not both.
+		node_scores or node_partition - not both. Default: None
 	node_partition : networkit.structures.Partition, optional
 		Partition object. This is used for color-calculation of the nodes (discrete distribution). 
-		Provide either node_scores or node_partition - not both. 	
+		Provide either node_scores or node_partition - not both. Default: None 	
 	node_palette : list of tuples, optional
-		Array consisting of normalized rgb-values. If none is given, seaborn.color_palette.colors is used
+		Array consisting of normalized rgb-values. If none is given, seaborn.color_palette.colors is used.  Default: None
 	show_ids : 	boolean, optional
-		Set whether node ids should be visible in plot-widget. Is set to True by default. 
+		Set whether node ids should be visible in plot-widget. Is set to True by default. Default: None
 	"""
-	# Sanity checks
-	if not have_cyto:
-		raise MissingDependencyError("ipycytoscape")
-
-	if node_scores is not None:
-		if node_partition is not None:
-			raise Exception("Provide either node_scores or node_partition - not both.")
-		if len(node_scores) != G.upperNodeIdBound():
-			raise Exception("node_scores should include scores for every node.")
-
-	# Set color palettes (maybe overwritten below)
-	if node_palette is not None:
-		palette = node_palette
-	else:
-		if not have_seaborn:
-			raise MissingDependencyError("seaborn")
-		palette = seaborn.color_palette("rocket_r", as_cmap=True).colors
-
-	# Color calculation: score = continuous distribution, partition = discrete distribution
-	hc_colors = []
-
-	# Partition
-	if node_partition is not None:
-		if node_palette is None:
-			palette = seaborn.color_palette("hls", node_partition.numberOfSubsets())
-		else:
-			if len(node_palette) < node_partition.numberOfSubsets():
-				raise Exception("Number of partitions higher than number of colors in provided palette. Provide node_palette with enough colors.")
-
-		partitions = node_partition.getVector()
-
-		if len(palette) < node_partition.numberOfSubsets():
-			raise Exception("Number of partitions to high for default coloring. Provide node_palette with enough colors.")
-
-		for i in G.iterNodes():
-			hc_colors.append((palette[partitions[i]][0] * 255, palette[partitions[i]][1] * 255, palette[partitions[i]][2] * 255))
-
-	# Score
-	elif node_scores is not None:
-
-		minhc = min(node_scores)
-		maxhc = max(node_scores)
-
-		# calculate coloring of nodes
-		def get_rgb(minimum, maximum, value):
-			minimum, maximum, value = float(minimum), float(maximum), float(value)
-			ratio = int((len(palette) - 1) * (value-minimum) / (maximum - minimum) * (value-minimum) / (maximum - minimum))
-			r = int(palette[ratio][0] * 255)
-			g = int(palette[ratio][1] * 255)
-			b = int(palette[ratio][2] * 255)
-			return r, g, b
-
-		if abs(maxhc - minhc) > 0:
-			for score in node_scores:
-				hc_colors.append(get_rgb(minhc, maxhc, score))
-		else:
-			color = palette[int((len(palette) -1) / 2)];
-			for i in G.iterNodes():
-				hc_colors.append((color[0] * 255, color[1] * 255, color[2] * 255))
-
-	# No node values
-	else:
-		color = palette[0];
-		for i in G.iterNodes():
-			hc_colors.append((color[0] * 255, color[1] * 255, color[2] * 255))
-
-	# Set styling
-	if show_ids:
-		s = [{
-			'selector': 'node',
-				'css': {
-					'background-color': 'data(color)',
-					'content': 'data(id)'
-				}}]
-	else:
-		s = [{
-			'selector': 'node',
-				'css': {
-					'background-color': 'data(color)'
-				}}]
-
-	# Create widget
-	cytoWidget = ipycytoscape.CytoscapeWidget()
-
-	nodes = []
-	edges = []
-
-	if G.isDirected():
-		edge_class = "directed "
-	else:
-		edge_class = "undirected "
-
-	for i in G.iterNodes():
-		n = ipycytoscape.Node(data={"id": i, "color": hc_colors[i] })
-		nodes.append(n)
-
-	for u,v in G.iterEdges():
-		e = ipycytoscape.Edge(data={"source": u, "target": v, "classes": edge_class })
-		edges.append(e)
-
-	# It is much faster to add edges and nodes in bulk.
-	cytoWidget.graph.add_nodes(nodes)
-	cytoWidget.graph.add_edges(edges, G.isDirected())
-
-	cytoWidget.set_style(s)
-	cytoWidget.set_layout(name='cose')
-	return cytoWidget
+	print("WARNING: Module csbridge is deprecated and will be removed in future updates. Use networkit.vizbridges.widgetFromGraph() instead.")
+	return widgetFromGraph(G, nodeScores = node_scores, nodePartition = node_partition, nodePalette = node_palette, showIds = show_ids)

networkit/test/test_graphtools.py

@@ -521,7 +521,7 @@ def generateGraph(directed):
 				self.assertLess(indexNode0, indexNode2)
 				self.assertLess(indexNode4, indexNode2)
 				self.assertLess(indexNode2, indexNode1)
-				self.assertLess(indexNode1, indexNode3)		
+				self.assertLess(indexNode1, indexNode3)
 
 if __name__ == "__main__":
 	unittest.main()