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?

[djarecka]

@carolege : are you using the current master?

[caroleguedj]

I don't really know... I upgrade nipype using pip install...

[djarecka]

@carolege , so you're probably using 0.13, you can always the version with this command: python -c "import nipype;print(nipype.__version__)"

So this problem is related to the new version of networkx (you're probably using 2.0) and we updated the code some weeks ago. You can either wait for a new release (should be this week) or try to install our master.

[mgxd]

@carolege you can install our current master through pip with the following command

pip install -U https://github.com/nipy/nipype/archive/master.zip

[SebastianSpeer]

Hi, I am experiencing the same problem and installing the master did not help. Are there other suggestions?
I have upgraded nipype to 0.13.1 through conda install instead of pip install. Is that an issue?

[mgxd]

@SebastianSpeer yes, the fixed version is not yet available on conda - we will hopefully be releasing a new version this coming week

[djarecka]

@SebastianSpeer just to add to @mgxd answer, you will have the same problem when you install the last released version with pip. You can either wait for new version or install master as @mgxd
suggested in an earlier answer

[caroleguedj]

Thank you, it seems to fix this problem but I have now and other error message:

_Traceback (most recent call last):
File "/usr/local/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 51, in run_node
result['result'] = node.run(updatehash=updatehash)
File "/usr/local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 407, in run
self._run_interface()
File "/usr/local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 517, in _run_interface
self._result = self._run_command(execute)
File "/usr/local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 650, in _run_command
result = self.interface.run()
File "/usr/local/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1101, in run
runtime.traceback_args = ('\n'.join(['%s' % arg for arg in exc_args]),)
UnicodeDecodeError: 'ascii' codec can't decode byte 0xff in position 35: ordinal not in range(128)

Do you know from where it could come from?

[caroleguedj]

Finally, I successfully fix it. Thanks again!!