updating to networkx ver.2 (dev): add_edge doesnt have attr_dict anymore (so changed to **dict); some updates related to changes in .nodes method (its not a list anymore)

Author: djarecka

nipype/pipeline/engine/utils.py

@@ -847,7 +847,7 @@ def make_field_func(*pair):
                             logger.debug("Qualified the %s -> %s join field"
                                          " %s as %s." %
                                          (in_node, jnode, dest_field, slot_field))
-                    graph_in.add_edge(in_node, jnode, newdata)
+                    graph_in.add_edge(in_node, jnode, **newdata)
                     logger.debug("Connected the join node %s subgraph to the"
                                  " expanded join point %s" % (jnode, in_node))
 
@@ -1289,8 +1289,8 @@ def write_workflow_prov(graph, filename=None, format='all'):
     # add dependencies (edges)
     # Process->Process
     for idx, edgeinfo in enumerate(graph.in_edges()):
-        ps.g.wasStartedBy(processes[nodes.index(edgeinfo[1])],
-                          starter=processes[nodes.index(edgeinfo[0])])
+        ps.g.wasStartedBy(processes[list(nodes).index(edgeinfo[1])],
+                          starter=processes[list(nodes).index(edgeinfo[0])])
 
     # write provenance
     ps.write_provenance(filename, format=format)

nipype/pipeline/plugins/tests/test_linear.py

@@ -41,6 +41,6 @@ def test_run_in_series(tmpdir):
     mod1.inputs.input1 = 1
     execgraph = pipe.run(plugin="Linear")
     names = ['.'.join((node._hierarchy, node.name)) for node in execgraph.nodes()]
-    node = execgraph.nodes()[names.index('pipe.mod1')]
+    node = list(execgraph.nodes())[names.index('pipe.mod1')]
     result = node.get_output('output1')
     assert result == [1, 1]

nipype/pipeline/plugins/tests/test_multiproc.py

@@ -46,7 +46,7 @@ def test_run_multiproc(tmpdir):
     pipe.config['execution']['poll_sleep_duration'] = 2
     execgraph = pipe.run(plugin="MultiProc")
     names = ['.'.join((node._hierarchy, node.name)) for node in execgraph.nodes()]
-    node = execgraph.nodes()[names.index('pipe.mod1')]
+    node = list(execgraph.nodes())[names.index('pipe.mod1')]
     result = node.get_output('output1')
     assert result == [1, 1]
 

nipype/pipeline/plugins/tests/test_multiproc_nondaemon.py

@@ -123,7 +123,7 @@ def run_multiproc_nondaemon_with_flag(nondaemon_flag):
                                       'non_daemon': nondaemon_flag})
 
     names = ['.'.join((node._hierarchy, node.name)) for node in execgraph.nodes()]
-    node = execgraph.nodes()[names.index('pipe.f2')]
+    node = list(execgraph.nodes())[names.index('pipe.f2')]
     result = node.get_output('sum_out')
     os.chdir(cur_dir)
     rmtree(temp_dir)

nipype/pipeline/plugins/tests/test_oar.py

@@ -50,7 +50,7 @@ def test_run_oar():
         '.'.join((node._hierarchy, node.name))
         for node in execgraph.nodes()
     ]
-    node = execgraph.nodes()[names.index('pipe.mod1')]
+    node = list(execgraph.nodes())[names.index('pipe.mod1')]
     result = node.get_output('output1')
     assert result == [1, 1]
     os.chdir(cur_dir)

nipype/pipeline/plugins/tests/test_pbs.py

@@ -48,7 +48,7 @@ def test_run_pbsgraph():
     mod1.inputs.input1 = 1
     execgraph = pipe.run(plugin="PBSGraph")
     names = ['.'.join((node._hierarchy, node.name)) for node in execgraph.nodes()]
-    node = execgraph.nodes()[names.index('pipe.mod1')]
+    node = list(execgraph.nodes())[names.index('pipe.mod1')]
     result = node.get_output('output1')
     assert result == [1, 1]
     os.chdir(cur_dir)

nipype/pipeline/plugins/tests/test_somaflow.py

@@ -46,6 +46,6 @@ def test_run_somaflow(tmpdir):
     mod1.inputs.input1 = 1
     execgraph = pipe.run(plugin="SomaFlow")
     names = ['.'.join((node._hierarchy, node.name)) for node in execgraph.nodes()]
-    node = execgraph.nodes()[names.index('pipe.mod1')]
+    node = list(execgraph.nodes())[names.index('pipe.mod1')]
     result = node.get_output('output1')
     assert result == [1, 1]