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Tentative =>networkx-3.0 support #3535

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TheChymera
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@TheChymera TheChymera commented Jan 26, 2023 •
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Closes: #3530

Well, except it doesn't really fix the issue.

Without the patch: https://ppb.chymera.eu/b4e05b.log
With the patch: https://ppb.chymera.eu/9e1476.log

Basically instead of AttributeError: module 'networkx' has no attribute 'to_scipy_sparse_matrix' we now get IndexError: tuple index out of range... which, dunno, I guess solves the issue in the most narrow and unhelpful sense.

It seems our parameter usage is still correct, at least per the documentation of the new function... Any ideas?

@TheChymera TheChymera mentioned this pull request Jan 26, 2023
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codecov bot commented Jan 26, 2023 •
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Codecov Report

Base: 63.63% // Head: 48.26% // Decreases project coverage by -15.38% ⚠️

Coverage data is based on head (8c0fe16) compared to base (7382b3d).
Patch coverage: 4.00% of modified lines in pull request are covered.

Additional details and impacted files 
@@             Coverage Diff             @@
##           master    #3535       +/-   ##
===========================================
- Coverage   63.63%   48.26%   -15.38%     
===========================================
  Files         309      309               
  Lines       40873    40884       +11     
  Branches     5381     5381               
===========================================
- Hits        26011    19734     -6277     
- Misses      13838    21020     +7182     
+ Partials     1024      130      -894
Impacted Files Coverage Δ
nipype/interfaces/cmtk/cmtk.py 15.97% <0.00%> (-1.92%) ⬇️
nipype/interfaces/cmtk/nx.py 17.61% <0.00%> (-0.19%) ⬇️
nipype/pipeline/plugins/base.py 12.93% <0.00%> (-45.29%) ⬇️
nipype/interfaces/cmtk/nbs.py 31.91% <14.28%> (-1.06%) ⬇️
nipype/utils/imagemanip.py 16.66% <0.00%> (-83.34%) ⬇️
nipype/interfaces/dipy/stats.py 0.00% <0.00%> (-83.34%) ⬇️
nipype/interfaces/dipy/registration.py 0.00% <0.00%> (-83.34%) ⬇️
nipype/utils/functions.py 22.72% <0.00%> (-77.28%) ⬇️
nipype/utils/subprocess.py 14.07% <0.00%> (-72.60%) ⬇️
nipype/pipeline/plugins/linear.py 12.50% <0.00%> (-70.84%) ⬇️
... and 114 more

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@TheChymera
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Caught a few more live ones, but there are still 20 test failures, at least they appear to be nipype-internal now:

https://ppb.chymera.eu/fdae94.log

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The errors seem likely to stem from previously having 2D matrices with a single row (so you index by [0, idx]) and now having 1D vectors. We'll need to thoroughly purge matrices and switch to ndarrays.

@TheChymera TheChymera changed the title Tentative =>networkx-3.0 support Tentative =>networkx-3.0 support Jan 26, 2023
@TheChymera TheChymera mentioned this pull request Jan 27, 2023
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@effigies effigies mentioned this pull request Jan 28, 2023
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@TheChymera TheChymera mentioned this pull request Jan 29, 2023
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TheChymera commented Jan 29, 2023 •
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Superseded by #3538

@TheChymera TheChymera closed this Jan 29, 2023
@TheChymera TheChymera deleted the networkx branch January 29, 2023 13:27
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networkx >= 3.0 unsupported
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@TheChymera @effigies