Conversation

effigies

Summary

Another attempt to fix Python 2.7 test failures. Numpy released 1.16.0 yesterday.

Acknowledgment

  • (Mandatory) I acknowledge that this contribution will be available under the Apache 2 license.

@effigieseffigies added this to the 1.1.8 milestone Jan 14, 2019
@effigies

Yup, this seems to be it. I thought our --pre checks should have caught this, but IDK what all has changed in numpy.

@codecov-io

Codecov Report

Merging #2855 into master will increase coverage by 0.53%.
The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #2855      +/-   ##
==========================================
+ Coverage    66.9%   67.44%   +0.53%     
==========================================
  Files         340      341       +1     
  Lines       43373    43392      +19     
  Branches     5380     5383       +3     
==========================================
+ Hits        29020    29267     +247     
+ Misses      13647    13427     -220     
+ Partials      706      698       -8
FlagCoverage Δ
#smoketests50.53% <100%> (ø)⬆️
#unittests64.85% <100%> (+0.81%)⬆️
Impacted FilesCoverage Δ
nipype/info.py94.2% <100%> (+0.08%)⬆️
nipype/testing/__init__.py88.88% <0%> (ø)
nipype/interfaces/spm/preprocess.py57.03% <0%> (+0.32%)⬆️
nipype/utils/filemanip.py79.65% <0%> (+0.43%)⬆️
nipype/interfaces/freesurfer/preprocess.py66.11% <0%> (+0.98%)⬆️
nipype/interfaces/freesurfer/model.py64.25% <0%> (+1.12%)⬆️
nipype/interfaces/io.py53.99% <0%> (+1.87%)⬆️
nipype/interfaces/spm/base.py87.12% <0%> (+1.98%)⬆️
nipype/interfaces/freesurfer/utils.py62.94% <0%> (+2.13%)⬆️
nipype/workflows/smri/freesurfer/autorecon1.py46.75% <0%> (+5.09%)⬆️
... and 8 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 041068b...f52df97. Read the comment docs.

@effigies

Looks like numpy/numpy#12157 is the culprit, which replaced checks that used isinstance(..., basestring) with something that doesn't accept unicode objects. I'm not sure if we can get them to re-allow unicode, so perhaps we'll just need to make sure that the test in question sends a str object.

@effigies

Upstreamed to numpy/numpy#12749, but we should probably go ahead and just fix up the test to not pass a unicode path in 2.7.

@effigieseffigies force-pushed the maint/numpy_version branch 2 times, most recently from 7871fb2 to dec30d5 Compare January 16, 2019 18:12
@effigieseffigies force-pushed the maint/numpy_version branch from dec30d5 to f52df97 Compare January 16, 2019 18:20
@effigieseffigies merged commit ede7020 into nipy:master Jan 16, 2019
@effigieseffigies deleted the maint/numpy_version branch January 16, 2019 19:39
yarikoptic added a commit to yarikoptic/nipype that referenced this pull request Feb 4, 2019
1.1.8 (January 28, 2019)

  * FIX: ANTS LaplacianThickness cmdline opts fixed up (nipy#2846)
  * FIX: Resolve LinAlgError during SVD (nipy#2838)
  * ENH: Add interfaces wrapping DIPY worflows (nipy#2830)
  * ENH: Update BIDSDataGrabber for pybids 0.7 (nipy#2737)
  * ENH: Add FSL `eddy_quad` interface (nipy#2825)
  * ENH: Support tckgen -select in MRtrix3 v3+ (nipy#2823)
  * ENH: Support for BIDS event files (nipy#2845)
  * ENH: CompositeTransformUtil, new ANTs interface (nipy#2785)
  * RF: Move pytest and pytest-xdist from general requirement into tests_required (nipy#2850)
  * DOC: Add S3DataGrabber example (nipy#2849)
  * DOC: Skip conftest module in API generation (nipy#2852)
  * DOC: Hyperlink DOIs to preferred resolver (nipy#2833)
  * MAINT: Install numpy!=1.16.0 from conda in Docker (nipy#2862)
  * MAINT: Drop pytest-xdist requirement, minimum pytest version  (nipy#2856)
  * MAINT: Disable numpy 1.16.0 for Py2.7 (nipy#2855)

* tag '1.1.8': (79 commits)
  MNT: Add @feilong to .zenodo, update ordering
  MNT: Update .mailmap
  MNT: Update .zenodo ordering
  Accept invitation as Zenodo release co-author (see nipy#2864)
  MAINT: Update .mailmap
  BF: allowing bids_event_file as alternate input
  MNT: Update .zenodo ordering
  MNT: Version 1.1.8
  DOC: 1.1.8 changelog
  Update nipype/interfaces/dipy/tracks.py
  Update nipype/interfaces/dipy/reconstruction.py
  MNT: Install numpy!=1.16.0 from conda in Docker
  Add FSL auto test
  remake specs
  Update nipype/interfaces/io.py
  Remove return type named tuple
  Update nipype/info.py
  STY: Whitespace, line length
  Remove out_ prefix from EddyQuad outputs
  Apply minor edits from code review
  ...
Sign up for free to join this conversation on . Already have an account? Sign in to comment
None yet
None yet

Successfully merging this pull request may close these issues.