Merge pull request #32 from barahona-research-group/small_corrections

small corrections

examples/run_simple_example.sh

@@ -1,4 +1,3 @@
-<<<<<<< Updated upstream
 #!/bin/bash
 
 python create_graph.py
@@ -15,12 +14,6 @@ pygenstability run \
 #    sbm_graph.pkl
 
 pygenstability plot_scan --help
-=======
-#!/bin/zsh
-
-python create_graph.py
-pygenstability run --n-time 100 sbm_graph.pkl
->>>>>>> Stashed changes
 pygenstability plot_scan results.pkl
 
 pygenstability plot_communities --help

examples/simple_example.py

@@ -12,12 +12,13 @@ def simple_test():
 
     all_results = run(graph)
 
-    plotting.plot_scan(all_results, use_plotly=True)
+    plotting.plot_scan(all_results, use_plotly=False)
+    plotting.plot_scan(all_results, use_plotly=True, live=False)
 
     with open("sbm_graph.gpickle", "rb") as pickle_file:
         graph = pickle.load(pickle_file)
     plotting.plot_communities(graph, all_results)
-    plotting.plot_sankey(all_results)
+    plotting.plot_sankey(all_results, live=False)
 
 
 if __name__ == "__main__":

pygenstability/constructors.py

@@ -11,11 +11,13 @@
 DTYPE = "float128"
 
 
-def load_constructor(constructor):
+def load_constructor(constructor, graph, **kwargs):
     """Load a constructor from its name, or as a custom Constructor class."""
     if isinstance(constructor, str):
+        if graph is None:
+            raise Exception(f"No graph was provided with a generic constructor {constructor}")
         try:
-            return getattr(sys.modules[__name__], "constructor_%s" % constructor)
+            return getattr(sys.modules[__name__], "constructor_%s" % constructor)(graph, **kwargs)
         except AttributeError as exc:
             raise Exception("Could not load constructor %s" % constructor) from exc
     if not isinstance(constructor, Constructor):
@@ -53,10 +55,21 @@ def get_spectral_gap(laplacian):
 
 
 class Constructor:
-    """Parent constructor class."""
+    """Parent constructor class.
+
+    This class encodes method specific construction of quality matrix and null models.
+    Use the method prepare to load and compute time independent quantities, and the method get_data
+    to return quality matrix, null model, and possible global shift (for linearised stability).
+    """
 
     def __init__(self, graph, with_spectral_gap=False, **kwargs):
-        """Initialise constructor."""
+        """The constructor calls te prepare method upon initialisation.
+
+        Args:
+            graph (csgraph): graph for which to run clustering
+            with_spectral_gap (bool): set to True to use spectral gap time rescale if available
+            kwargs (dict): any other properties to pass to the constructor.
+        """
         self.graph = graph
         self.with_spectral_gap = with_spectral_gap
         self.spectral_gap = None