WIP

Author: sim51

.gitignore

@@ -1 +1,4 @@
-dist
+dist
+__pycache__
+.pytest_cache
+gephi-toolkit-all.jar

README.md

@@ -1 +1,112 @@
- # Gephipy
+ # Gephipy
+
+This project is Python wrapper of [Gephi toolkit](https://gephi.org/toolkit/), thanks to [Jpype](https://www.jpype.org) which does the bindings between Java and Python.
+
+It provides helpers to easy the use of Gephy toolkit for Pythonist, even if you still ned to know the Java API.
+
+## How to use 
+
+* Install the lib `pip install gephipy`
+
+* Initialize the GephiPy context
+
+```python
+from gephipy import gephipy
+
+gephipy.initialize()
+```
+
+Then you can use the Gephi toolkit or the GephiPy features.
+
+## Example 
+
+```python
+from gephipy import gephipy
+from org.gephi.statistics.plugin import Modularity, GraphDistance
+
+#
+# Init context
+#
+gephipy.initialize()
+
+#
+# Create a workspace
+#
+workspace = gephipy.create_workspace()
+
+#
+# Import a GEXF file
+#
+gephipy.import_gexf(workspace, "./graph.gexf")
+graphModel = gephipy.get_graph_model(workspace)
+
+#
+# Compute some metrics
+#
+
+# Louvain
+modularity = Modularity()
+modularity.execute(graphModel)
+
+# Betweeness centrality
+centrality = GraphDistance()
+centrality.setDirected(True)
+centrality.execute(graphModel)
+
+#
+# Apply appearance
+# Here it is really looks like java code
+#
+
+appearanceController = Lookup.getDefault().lookup(AppearanceController)
+appearanceModel = appearanceController.getModel()
+
+# Size Make node size based on centrality
+centralityColumn = graphModel.getNodeTable().getColumn(GraphDistance.BETWEENNESS)
+centralityRanking = appearanceModel.getNodeFunction(centralityColumn, RankingNodeSizeTransformer)
+centralityTransformer = centralityRanking.getTransformer()
+centralityTransformer.setMinSize(10)
+centralityTransformer.setMaxSize(100)
+appearanceController.transform(centralityRanking)
+
+
+# Color by community
+communityColumn = graphModel.getNodeTable().getColumn(Modularity.MODULARITY_CLASS)
+colorPartition = appearanceModel.getNodeFunction(communityColumn, PartitionElementColorTransformer)
+partition = colorPartition.getPartition()
+palette = PaletteManager.getInstance().generatePalette(partition.size(graphModel.getGraph()))
+partition.setColors(graphModel.getGraph(), palette.getColors())
+appearanceController.transform(colorPartition)
+
+
+#
+# Run Layouts
+#
+
+# Random layout
+random = Random().buildLayout()
+random.setGraphModel(gephipy.get_graph_model(workspace))
+random.initAlgo();
+random.goAlgo()
+random.endAlgo();
+
+# FA2 layout
+fa2 = ForceAtlas2Builder().buildLayout()
+fa2.setGraphModel(gephipy.get_graph_model(workspace))
+fa2.resetPropertiesValues();
+fa2.initAlgo();
+for x in range(1000):
+  fa2.goAlgo()
+
+# Noverlap layout
+noverlap = NoverlapLayoutBuilder().buildLayout()
+noverlap.setGraphModel(gephipy.get_graph_model(workspace))
+noverlap.initAlgo()
+noverlap.endAlgo()
+
+#
+# Export your graph
+#
+
+gephipy.export_gexf(workspace, "my-gephi-graph.gexf")
+```

dist/gephipy-0.0.1-py3-none-any.whl

@@ -1,11 +1,16 @@
 import jpype
+
 from pathlib import Path
 import urllib.request
 import networkx as nx
 
+from java.io import File
 from org.openide.util import Lookup
 from org.gephi.graph.api import GraphController
 from org.gephi.project.api import ProjectController
+from org.gephi.io.processor.plugin import DefaultProcessor
+from org.gephi.io.exporter.api import ExportController
+from org.gephi.io.importer.api import ImportController, EdgeDirectionDefault
 
 GTK_URL="https://repo1.maven.org/maven2/org/gephi/gephi-toolkit/0.10.1/gephi-toolkit-0.10.1-all.jar"
 
@@ -24,23 +29,27 @@ def initialize(gephi_jar_path="./gephi-toolkit-all.jar"):
       print(f"Warning: {e}")
 
 #
-# Create a new Gephi project in a fresh workspace and returns it associated graph model instance
+# Create a new Gephi workspace
 #
-def gephi_create_graph(): 
+def create_workspace(): 
   # Create a Gephi workspace
   pc = Lookup.getDefault().lookup(ProjectController)
   pc.newProject()
-  workspace = pc.getCurrentWorkspace()
-  # returns the graph model
+  return pc.getCurrentWorkspace()
+
+#
+# Get the graph model of
+#
+def get_graph_model(workspace): 
   return Lookup.getDefault().lookup(GraphController).getGraphModel(workspace)
 
 #
 # Function to load a NetworkX instance in Gephi
 # This function takes a networkX instance and returns a Gephi graphModel
 #
-def networkx_to_gephi(graphX):
+def networkx_to_gephi(workspace, graphX):
   # Get the Graph
-  graphModel = gephi_create_graph()
+  graphModel = Lookup.getDefault().lookup(GraphController).getGraphModel(workspace)
   directedGraph = graphModel.getDirectedGraph()
 
   # Cast NetworkX graph to Gephi
@@ -61,12 +70,12 @@ def networkx_to_gephi(graphX):
     # TODO: add edge attributes
     directedGraph.addEdge(edge)
 
-  return graphModel
 
 #
 # Gephi to NetworkX
 #
-def gephi_to_networkx(graphModel):
+def gephi_to_networkx(workspace):
+  graphModel = Lookup.getDefault().lookup(GraphController).getGraphModel(workspace)
   directedGraph = graphModel.getDirectedGraph()
   graphX = nx.Graph()
 
@@ -83,33 +92,47 @@ def gephi_to_networkx(graphModel):
   return graphX
 
 #
+# Import a GEXF
+#
+def import_gexf(workspace, file_path=""):
+  importController = Lookup.getDefault().lookup(ImportController)
+  file = File(file_path)
+  container = importController.importFile(file)
+  container.getLoader().setEdgeDefault(EdgeDirectionDefault.DIRECTED)
+  importController.process(container, DefaultProcessor(), workspace);
+#
 # Export the current Gephi graph to an GEXF file
 #
-def export_gexf(file_path="./graph.gexf"):
+def export_gexf(workspace, file_path="./graph.gexf"):
   export = Lookup.getDefault().lookup(ExportController)
+  gexf = export.getExporter("gexf")
+  gexf.setWorkspace(workspace)
   export.exportFile(File(file_path))
 
 
 #
 # Export the current Gephi graph to an PDF file
 #
-def export_pdf(file_path="./graph.pdf"):
+def export_pdf(workspace, file_path="./graph.pdf"):
   export = Lookup.getDefault().lookup(ExportController)
   pdf = export.getExporter("pdf")
+  pdf.setWorkspace(workspace)
   export.exportFile(File(file_path),pdf)
 
 #
 # Export the current Gephi graph to an SVG file
 #
-def export_svg(file_path="./graph.svg"):
+def export_svg(workspace, file_path="./graph.svg"):
   export = Lookup.getDefault().lookup(ExportController)
   svg = export.getExporter("svg")
+  svg.setWorkspace(workspace)
   export.exportFile(File(file_path), svg)
 
 #
 # Export the current Gephi graph to an PNG file
 #
-def export_png(file_path="./graph.png"):
+def export_png(workspace, file_path="./graph.png"):
   export = Lookup.getDefault().lookup(ExportController)
   png = export.getExporter("png")
+  png.setWorkspace(workspace)
   export.exportFile(File(file_path), png)

dist/gephipy-0.0.1.tar.gz

@@ -0,0 +1,26 @@
+from IPython.display import HTML
+
+#
+# Display a SVG in Jupyter notebook with pan & zoom  
+#
+def display_svg(file_path, width="100%", height="500px"):
+  with open(file_path, 'r') as file_svg:
+    svg = file_svg.read()
+
+  html_code = f"""
+    <script src="//bumbu.me/svg-pan-zoom/dist/svg-pan-zoom.js"></script>
+    <div id="svg-container">
+    {svg}
+    </div>
+    <script>
+    var svgElement = document.getElementById("svg-container").children[0];
+    svgElement.style.width = "{width}";
+    svgElement.style.height = "{height}";
+    svgPanZoom(svgElement, {{
+        zoomEnabled: true,
+        controlIconsEnabled: true
+    }});
+    </script>
+  """
+
+  HTML(html_code)

gephipy/gephipy.py

@@ -0,0 +1,20 @@
+import jpype
+
+from pathlib import Path
+import urllib.request
+
+GTK_URL="https://repo1.maven.org/maven2/org/gephi/gephi-toolkit/0.10.1/gephi-toolkit-0.10.1-all.jar"
+
+#
+# Initialize the context
+#
+def initialize(gephi_jar_path="./gephi-toolkit-all.jar"):
+    gtk_jar = Path(gephi_jar_path)
+    if not gtk_jar.is_file():
+      print("Download the Gephi toolkit jar")
+      urllib.request.urlretrieve(GTK_URL, gephi_jar_path)
+    # Starts the JVM with the GTK in the classpath
+    try:
+      jpype.startJVM(classpath=[gephi_jar_path])
+    except OSError as e: 
+      print(f"Warning: {e}")

gephipy/jupyter.py

@@ -2,7 +2,7 @@
 name = "Gephipy"
 version = "0.0.1"
 description = "A wrapper of Gephi toolkit for Python"
-authors = ["OuestWare <contact@ouestware.com>"]
+authors = ["Gephi <contact@gephi.org>"]
 readme = "README.md"
 license="MIT"
 
@@ -11,6 +11,9 @@ python = "^3.11"
 JPype1 = "^1.6.0"
 networkx = "^3.5"
 
+[tool.poetry.group.test.dependencies]  
+pytest = "^8.2.0"  
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"