[ENH] update for networkx dev version (should fix #2159)

[djarecka]

The new code should work with both versions -- ver 1.x and 2.x (dev).

summary of changes:

• *_iter has been removed, changing nodes_iter to nodes, etc. nodes gives dict-like NodeView (iterate or change to list first to access a specific element)

• .node has been removed, changing to nodes[node]

• add_node and add_edge don't have attr_dict anymore, have to change **dict

• subgraph gives a view and .copy() has different depth, created two versions of this part . Suggestions how to simplify are welcome, don't understand all details of those various copies.

Note, I changed also interfaces.cmtk, but don't have any tests, so don't know if it works.

Edit (by @effigies):

Closes #2159
Closes #2194

[codecov-io]

Codecov Report

Merging #2171 into master will decrease coverage by 0.04%.
The diff coverage is 42.68%.

@@            Coverage Diff             @@
##           master    #2171      +/-   ##
==========================================
- Coverage   72.28%   72.24%   -0.05%     
==========================================
  Files        1171     1171              
  Lines       58622    58626       +4     
  Branches     8433     8434       +1     
==========================================
- Hits        42377    42352      -25     
- Misses      14887    14918      +31     
+ Partials     1358     1356       -2

Flag	Coverage Δ
#smoketests	72.24% <42.68%> (-0.05%)	⬇️
#unittests	69.9% <41.46%> (-0.05%)	⬇️

Impacted Files	Coverage Δ
nipype/pipeline/plugins/tests/test_somaflow.py	50% <0%> (ø)	⬆️
nipype/interfaces/cmtk/nx.py	19.39% <0%> (ø)	⬆️
nipype/interfaces/cmtk/cmtk.py	18.77% <0%> (ø)	⬆️
nipype/interfaces/cmtk/nbs.py	36.55% <0%> (ø)	⬆️
nipype/pipeline/plugins/tests/test_oar.py	71.05% <0%> (ø)	⬆️
nipype/interfaces/cmtk/parcellation.py	14.46% <0%> (ø)	⬆️
nipype/pipeline/plugins/tests/test_pbs.py	71.79% <0%> (ø)	⬆️
nipype/info.py	84.61% <100%> (+0.24%)	⬆️
nipype/pipeline/engine/tests/test_engine.py	93.43% <100%> (ø)	⬆️
...pipeline/plugins/tests/test_multiproc_nondaemon.py	53.52% <100%> (ø)	⬆️
... and 7 more

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[effigies]

At a glance, this looks reasonable to me, but I'm not as conversant with networkx as I'd like to be to sign off on this. We're starting to run up against this issue in our tests, so hopefully this can go in soon.

[effigies]

@djarecka could you merge master? I can set fmriprep to running with this branch, which should at least smoke test most of these changes (and get our tests working agaiin).

[djarecka]

@effigies - i'm trying quickly to check the error. It works fine on a few environments on my OSX and i noticed that python complains about ModuleNotFoundError: No module named 'pydot'. It doesn't complain for py3.4. Any thoughts?

[effigies]

Need to switch pydotplus in requirements and nipype/info.py to pydot.

networkx/networkx@481f3e8

Edit: Actually, here are all the instances of pydotplus: https://github.com/nipy/nipype/search?utf8=%E2%9C%93&q=pydotplus&type=

[djarecka]

@effigies thanks, i indeed installed pydot but completely forgot that it's not already in nipype... Still not sure, why it works for 3.4, but will update.

[effigies]

Realizing that switching from pydotplus to pydot is going to break compatibility with networkx < 2. @satra is this okay (in which case we should update the minimum networkx), or should we have both pydot>=1.2.3 and pydotplus in the extras?

Also, we should set the minimum version on pydot to match networkx's.

[djarecka]

@effigies : I tried to write my PR in a way that it works with networkx < 2 and networkx > 2. What about I will keep both pydotplus and pydot?

[effigies]

That's reasonable. It just assumes that we care enough about supporting multiple versions of networkx.

[effigies]

Can you sync the networkx min versions, while you're at it? (rtd_)requirements says 1.7, info says 1.9. I'm assuming info is correct.

[djarecka]

changed it.

regarding multiple versions support, the 2.0 is brand new (I was using dev version for my PR), so @satra wanted to support them both. Not sure for how long we want to do it, but my point was that in this PR I did try to check my changes with both versions, so we can just keep pydotplus for some time.

[effigies]

Sounds good. If this passes (and nipreps/niworkflows#196, nipreps/fmriprep#723), I'm 👍 for merging as is.

[effigies]

Downstream tests are passing.

[oesteban]

I have tested this with both networkx 1.x and 2.x and worked. Great job @djarecka !

[oesteban]

On your branch:

$ git grep "package_check('networkx"
examples/dmri_dtk_dti.py:package_check('networkx', '1.0', 'tutorial1')
examples/dmri_dtk_odf.py:package_check('networkx', '1.0', 'tutorial1')
examples/dmri_fsl_dti.py:package_check('networkx', '1.0', 'tutorial1')
examples/fmri_slicer_coregistration.py:package_check('networkx', '1.0', 'tutorial1')
nipype/pipeline/engine/utils.py:package_check('networkx', '1.3')
nipype/pipeline/engine/workflows.py:package_check('networkx', '1.3')
nipype/utils/misc.py:    package_check('networkx', '1.0', 'tutorial1')

We probably don't need any of those.

[effigies]

I don't understand what's changed to cause afni.preprocess.Hist to repeatedly stall.

[satra]

@effigies - i have restarted the build several times yesterday with the same result, and it's only happening on 3.6.

i'll build a neurodocker environment locally to test.