At least some Nipype workflows fail with the dev version of networkx installed!

[dPys]

File "/usr/local/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py", line 586, in run
self._set_needed_outputs(flatgraph)
File "/usr/local/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py", line 679, in _set_needed_outputs
for edge in graph.out_edges_iter(node):
AttributeError: 'DiGraph' object has no attribute 'out_edges_iter'

[satra]

@dpisner453 - many thanks for reporting this. i'm assuming networkx had a proper deprecation cycle for this change.

@djarecka - could you please take a stab at this? it would be good to make sure that we are compatible with current and future versions. we don't have to support the future of every library, but to the extent we can it would be good.

[djarecka]

@satra - it looks like they removed all *_iter, http://networkx.readthedocs.io/en/latest/release/migration_guide_from_1.x_to_2.0.html.
And nodes() etc., is not a list anymore but dict-like object. Will have to change the way how we ask for nodes from a graph, not sure about ordering yet.

[djarecka]

@dpisner453 - i've updated nipype, and tests are passing. But if you have any specific example that didn't work for you, i can test it too. You can also try to run with my branch
https://github.com/djarecka/nipype/tree/graphx

[effigies]

@satra This is now affecting Travis builds.

[djarecka]

@effigies just rebased my PR, hopefully it works

[djarecka]

well, it doesn't... some tests are failing with py2.7, 3.5 and 3.6 (3.4 is perfectly fine), will try to fix it today

[oesteban]

For some reason 3.4 keeps networkx < 2. That's good news because it means that we are testing backwards compatibility on your PR :)

[djarecka]

we can just try to remember when we get errors only for python 3.4 ;-)

[caroleguedj]

I also have this error with my script...
File "/usr/local/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py", line 188, in connect
for edge in self._graph.in_edges_iter(destnode):
AttributeError: 'DiGraph' object has no attribute 'in_edges_iter'

Could anybody help me to fix it?