renamed conversors corneto<->networkx

saezlab · Jul 3, 2024 · 9b31209 · 9b31209
1 parent cdfce23
commit 9b31209
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diff --git a/docs/src/vignettes/1_simple_example.ipynb b/docs/src/vignettes/1_simple_example.ipynb
diff --git a/networkcommons/methods/_causal.py b/networkcommons/methods/_causal.py
@@ -20,7 +20,8 @@
 from __future__ import annotations
 
 __all__ = [
-    'convert_cornetograph',
+    'to_cornetograph',
+    'to_networkx',
     'run_corneto_carnival',
 ]
 
@@ -30,7 +31,7 @@
 cn_nx = lazy_import.lazy_module('corneto.contrib.networkx')
 
 
-def convert_cornetograph(graph):
+def to_cornetograph(graph):
     """
     Convert a networkx graph to a corneto graph, if needed.
 
@@ -43,11 +44,38 @@ def convert_cornetograph(graph):
     if isinstance(graph, cn._graph.Graph):
         corneto_graph = graph
     elif isinstance(graph, (nx.Graph, nx.DiGraph)):
-        corneto_graph = cn_nx.networkx_to_corneto_graph(graph)
+        # substitute 'sign' for 'interaction' in the graph
+        for u, v, data in graph.edges(data=True):
+            data['interaction'] = data.pop('sign')
+
+        corneto_graph = networkx_to_corneto_graph(graph)
 
     return corneto_graph
 
 
+def to_networkx(graph, skip_unsupported_edges=True):
+    """
+    Convert a corneto graph to a networkx graph, if needed.
+
+    Args:
+        graph (cn.Graph): The corneto graph.
+
+    Returns:
+        nx.Graph: The networkx graph.
+    """
+    if isinstance(graph, nx.Graph) or isinstance(graph, nx.DiGraph):
+        networkx_graph = graph
+    elif isinstance(graph, cn._graph.Graph):
+        networkx_graph = corneto_graph_to_networkx(
+            graph,
+            skip_unsupported_edges=skip_unsupported_edges)
+        # rename interaction for sign
+        for u, v, data in networkx_graph.edges(data=True):
+            data['sign'] = data.pop('interaction')
+
+    return networkx_graph
+
+
 def run_corneto_carnival(network,
                          source_dict,
                          target_dict,
@@ -68,7 +96,7 @@ def run_corneto_carnival(network,
         nx.Graph: The subnetwork containing the paths found by CARNIVAL.
         list: A list containing the paths found by CARNIVAL.
     """
-    corneto_net = convert_cornetograph(network)
+    corneto_net = to_cornetograph(network)
 
     problem, graph = cn.methods.runVanillaCarnival(
         perturbations=source_dict,
@@ -83,10 +111,7 @@ def run_corneto_carnival(network,
         cn.methods.carnival.get_selected_edges(problem, graph),
     )
 
-    network_nx = cn_nx.corneto_graph_to_networkx(
-        network_sol,
-        skip_unsupported_edges=True,
-    )
+    network_nx = to_networkx(network_sol, skip_unsupported_edges=True)
 
     network_nx.remove_nodes_from(['_s', '_pert_c0', '_meas_c0'])