fix for networkx and afni #2196

satra · 2017-09-23T18:53:10Z

this is a replacement for #2171 to get merged so that master is back on track.

(Fix/close lines edited by @effigies)

…(*) in a few places (nodes_iter, in_edges_iter, etc., dont exist in ver 2, but nodes, in_edges, etc., are iterators); had to add .copy to .subgraph for ver 2 (otherwise its a view), but had to keep original code for ver 1

…more (so changed to **dict); some updates related to changes in .nodes method (its not a list anymore)

…ve no tests, so no idea if changes work

…they have no tests, so no idea if changes work

codecov-io · 2017-09-23T21:38:04Z

Codecov Report

Merging #2196 into master will decrease coverage by 0.06%.
The diff coverage is 43.87%.

@@            Coverage Diff             @@
##           master    #2196      +/-   ##
==========================================
- Coverage   72.28%   72.22%   -0.07%     
==========================================
  Files        1171     1171              
  Lines       58622    58620       -2     
  Branches     8433     8434       +1     
==========================================
- Hits        42377    42339      -38     
- Misses      14887    14921      +34     
- Partials     1358     1360       +2

Flag	Coverage Δ
#smoketests	`72.22% <43.87%> (-0.07%)`	⬇️
#unittests	`69.89% <42.85%> (-0.07%)`	⬇️

Impacted Files	Coverage Δ
nipype/utils/misc.py	`78.19% <ø> (-5.27%)`	⬇️
nipype/interfaces/cmtk/cmtk.py	`18.77% <0%> (ø)`	⬆️
nipype/interfaces/afni/preprocess.py	`81.27% <0%> (+0.25%)`	⬆️
nipype/interfaces/cmtk/nx.py	`19.39% <0%> (ø)`	⬆️
nipype/pipeline/plugins/tests/test_somaflow.py	`50% <0%> (ø)`	⬆️
nipype/pipeline/plugins/tests/test_pbs.py	`71.79% <0%> (ø)`	⬆️
nipype/interfaces/cmtk/parcellation.py	`14.46% <0%> (ø)`	⬆️
nipype/interfaces/cmtk/nbs.py	`36.55% <0%> (ø)`	⬆️
nipype/pipeline/plugins/tests/test_oar.py	`71.05% <0%> (ø)`	⬆️
nipype/pipeline/plugins/tests/test_linear.py	`100% <100%> (ø)`	⬆️
... and 10 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 4a0bd3d...9ced114. Read the comment docs.

codecov-io · 2017-09-23T21:38:13Z

Codecov Report

Merging #2196 into master will decrease coverage by 0.06%.
The diff coverage is 43.87%.

@@            Coverage Diff             @@
##           master    #2196      +/-   ##
==========================================
- Coverage   72.28%   72.22%   -0.07%     
==========================================
  Files        1171     1171              
  Lines       58622    58620       -2     
  Branches     8433     8434       +1     
==========================================
- Hits        42377    42339      -38     
- Misses      14887    14921      +34     
- Partials     1358     1360       +2

Flag	Coverage Δ
#smoketests	`72.22% <43.87%> (-0.07%)`	⬇️
#unittests	`69.89% <42.85%> (-0.07%)`	⬇️

Impacted Files	Coverage Δ
nipype/utils/misc.py	`78.19% <ø> (-5.27%)`	⬇️
nipype/interfaces/cmtk/parcellation.py	`14.46% <0%> (ø)`	⬆️
nipype/pipeline/plugins/tests/test_somaflow.py	`50% <0%> (ø)`	⬆️
nipype/interfaces/cmtk/nx.py	`19.39% <0%> (ø)`	⬆️
nipype/pipeline/plugins/tests/test_oar.py	`71.05% <0%> (ø)`	⬆️
nipype/interfaces/cmtk/nbs.py	`36.55% <0%> (ø)`	⬆️
nipype/interfaces/cmtk/cmtk.py	`18.77% <0%> (ø)`	⬆️
nipype/interfaces/afni/preprocess.py	`81.27% <0%> (+0.25%)`	⬆️
nipype/pipeline/plugins/tests/test_pbs.py	`71.79% <0%> (ø)`	⬆️
nipype/pipeline/engine/tests/test_engine.py	`93.43% <100%> (ø)`	⬆️
... and 10 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 4a0bd3d...9ced114. Read the comment docs.

codecov-io · 2017-09-23T21:38:43Z

Codecov Report

Merging #2196 into master will decrease coverage by 0.06%.
The diff coverage is 43.87%.

@@            Coverage Diff             @@
##           master    #2196      +/-   ##
==========================================
- Coverage   72.28%   72.22%   -0.07%     
==========================================
  Files        1171     1171              
  Lines       58622    58620       -2     
  Branches     8433     8434       +1     
==========================================
- Hits        42377    42339      -38     
- Misses      14887    14921      +34     
- Partials     1358     1360       +2

Flag	Coverage Δ
#smoketests	`72.22% <43.87%> (-0.07%)`	⬇️
#unittests	`69.89% <42.85%> (-0.07%)`	⬇️

Impacted Files	Coverage Δ
nipype/utils/misc.py	`78.19% <ø> (-5.27%)`	⬇️
nipype/interfaces/cmtk/cmtk.py	`18.77% <0%> (ø)`	⬆️
nipype/interfaces/cmtk/nx.py	`19.39% <0%> (ø)`	⬆️
nipype/interfaces/afni/preprocess.py	`81.27% <0%> (+0.25%)`	⬆️
nipype/pipeline/plugins/tests/test_somaflow.py	`50% <0%> (ø)`	⬆️
nipype/interfaces/cmtk/parcellation.py	`14.46% <0%> (ø)`	⬆️
nipype/interfaces/cmtk/nbs.py	`36.55% <0%> (ø)`	⬆️
nipype/pipeline/plugins/tests/test_pbs.py	`71.79% <0%> (ø)`	⬆️
nipype/pipeline/plugins/tests/test_oar.py	`71.05% <0%> (ø)`	⬆️
nipype/info.py	`84.61% <100%> (+0.24%)`	⬆️
... and 10 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 4a0bd3d...9ced114. Read the comment docs.

Includes nipy/nipype#2196

djarecka and others added 9 commits September 22, 2017 10:03

updating to networkx ver.2 (dev): add_edge doesnt have attr_dict any…

1c16fca

…more (so changed to **dict); some updates related to changes in .nodes method (its not a list anymore)

updating to networkx ver.2 (dev): updating interfaces/cmtk - they ha…

bff81b2

…ve no tests, so no idea if changes work

updating to networkx ver.2 (dev): more updates to interfaces/cmtk - …

f799adf

…they have no tests, so no idea if changes work

changing pydotplus to pydot in the requirements

c052581

restoring pydotplus, adding min version to pydot

9fa38d1

small changes in networkx min versions to be consistent

33758eb

removing package_check('networkx'

6876a38

fix: afni version check

9ced114

effigies approved these changes Sep 23, 2017

View reviewed changes

This was referenced Sep 23, 2017

FIX: Set networkx max version until 2.0 fixes are finalized #2195

Closed

Remove afni_vcheck from container? nipreps/fmriprep#724

Closed

[RTM] PIN: Upgrade niworkflows.nipype to include networkx fix nipreps/fmriprep#723

Merged

satra merged commit 6a8318f into nipy:master Sep 23, 2017

effigies added a commit to effigies/fmriprep that referenced this pull request Sep 23, 2017

PIN: poldracklab/niworkflows master

e83d89d

Includes nipy/nipype#2196

effigies mentioned this pull request Oct 10, 2017

ENH: Remove AFNI version check monkey patch nipreps/fmriprep#750

Closed

satra added this to the 0.14.0 milestone Oct 20, 2017

satra deleted the fix/timeout branch October 30, 2017 15:16

oesteban mentioned this pull request Nov 1, 2017

Nipype fails with new networkx (>=2.0) because of API changes #2270

Closed

effigies mentioned this pull request Mar 19, 2018

may be pydotplus would be sufficient? #2494

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

fix for networkx and afni #2196

fix for networkx and afni #2196

Uh oh!

satra commented Sep 23, 2017 •

edited by effigies

Loading

Uh oh!

codecov-io commented Sep 23, 2017

Uh oh!

codecov-io commented Sep 23, 2017

Uh oh!

codecov-io commented Sep 23, 2017

Uh oh!

Uh oh!

fix for networkx and afni #2196

fix for networkx and afni #2196

Uh oh!

Conversation

satra commented Sep 23, 2017 • edited by effigies Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

codecov-io commented Sep 23, 2017

Codecov Report

Uh oh!

codecov-io commented Sep 23, 2017

Codecov Report

Uh oh!

codecov-io commented Sep 23, 2017

Codecov Report

Uh oh!

Uh oh!

satra commented Sep 23, 2017 •

edited by effigies

Loading