Merge remote-tracking branch 'upstream/master' into rel/1.1.1

Author: effigies

.travis.yml

@@ -53,6 +53,7 @@ before_install:
     export FSLOUTPUTTYPE=NIFTI_GZ;
   fi;
 
+- travis_retry pip install --upgrade pytest>=3.4  # Work around pip failure
 - travis_retry pip install -r requirements.txt
 - travis_retry pip install grabbit==0.1.2
 - travis_retry git clone https://github.com/INCF/pybids.git ${HOME}/pybids &&

Makefile

@@ -3,7 +3,6 @@
 # rsync -e ssh nipype-0.1-py2.5.egg cburns,[email protected]:/home/frs/project/n/ni/nipy/nipype/nipype-0.1/
 
 PYTHON ?= python
-NOSETESTS=`which nosetests`
 
 .PHONY: zipdoc sdist egg upload_to_pypi trailing-spaces clean-pyc clean-so clean-build clean-ctags clean in inplace test-code test-coverage test html specs check-before-commit check gen-base-dockerfile gen-main-dockerfile gen-dockerfiles
 

Vagrantfile

@@ -27,7 +27,7 @@ echo "export PATH=$HOME/miniconda3/bin:\\$PATH" >> .bashrc
 
 # install nipype dependencies
 $HOME/miniconda3/bin/conda update --yes conda
-$HOME/miniconda3/bin/conda install --yes pip scipy nose networkx lxml future simplejson
+$HOME/miniconda3/bin/conda install --yes pip scipy networkx lxml future simplejson
 $HOME/miniconda3/bin/conda install --yes python-dateutil jupyter matplotlib
 $HOME/miniconda3/bin/pip install nibabel
 $HOME/miniconda3/bin/pip install prov

doc/links_names.txt

@@ -56,7 +56,6 @@
 .. _doctest-mode: http://www.cis.upenn.edu/~edloper/projects/doctestmode/
 .. _bazaar: http://bazaar-vcs.org/
 .. _subversion: http://subversion.tigris.org/
-.. _nose: http://nose.readthedocs.io/en/latest/
 .. _`python coverage tester`: http://nedbatchelder.com/code/modules/coverage.html
 
 .. Other python projects

nipype/interfaces/fsl/epi.py

@@ -199,16 +199,12 @@ class TOPUPInputSpec(FSLCommandInputSpec):
     # TODO: the following traits admit values separated by commas, one value
     # per registration level inside topup.
     warp_res = traits.Float(
-        10.0, usedefault=True,
         argstr='--warpres=%f',
         desc=('(approximate) resolution (in mm) of warp '
-              'basis for the different sub-sampling levels'
-              '.'))
-    subsamp = traits.Int(1, usedefault=True,
-                         argstr='--subsamp=%d', desc='sub-sampling scheme')
+              'basis for the different sub-sampling levels'))
+    subsamp = traits.Int(argstr='--subsamp=%d',
+                         desc='sub-sampling scheme')
     fwhm = traits.Float(
-        8.0,
-        usedefault=True,
         argstr='--fwhm=%f',
         desc='FWHM (in mm) of gaussian smoothing kernel')
     config = traits.String(
@@ -218,13 +214,12 @@ class TOPUPInputSpec(FSLCommandInputSpec):
         desc=('Name of config file specifying command line '
               'arguments'))
     max_iter = traits.Int(
-        5, usedefault=True,
-        argstr='--miter=%d', desc='max # of non-linear iterations')
+        argstr='--miter=%d',
+        desc='max # of non-linear iterations')
     reg_lambda = traits.Float(
-        1.0, usedefault=True,
-        argstr='--miter=%0.f',
-        desc=('lambda weighting value of the '
-              'regularisation term'))
+        argstr='--lambda=%0.f',
+        desc=('Weight of regularisation, default '
+              'depending on --ssqlambda and --regmod switches.'))
     ssqlambda = traits.Enum(
         1,
         0,
@@ -259,7 +254,6 @@ class TOPUPInputSpec(FSLCommandInputSpec):
         desc=('Minimisation method 0=Levenberg-Marquardt, '
               '1=Scaled Conjugate Gradient'))
     splineorder = traits.Int(
-        3, usedefault=True,
         argstr='--splineorder=%d',
         desc=('order of spline, 2->Qadratic spline, '
               '3->Cubic spline'))
@@ -321,11 +315,9 @@ class TOPUP(FSLCommand):
     >>> topup.inputs.output_type = "NIFTI_GZ"
     >>> topup.cmdline # doctest: +ELLIPSIS
     'topup --config=b02b0.cnf --datain=topup_encoding.txt \
---fwhm=8.000000 --imain=b0_b0rev.nii --miter=5 \
---out=b0_b0rev_base --iout=b0_b0rev_corrected.nii.gz \
+--imain=b0_b0rev.nii --out=b0_b0rev_base --iout=b0_b0rev_corrected.nii.gz \
 --fout=b0_b0rev_field.nii.gz --jacout=jac --logout=b0_b0rev_topup.log \
---rbmout=xfm --dfout=warpfield --miter=1 --splineorder=3 --subsamp=1 \
---warpres=10.000000'
+--rbmout=xfm --dfout=warpfield'
     >>> res = topup.run() # doctest: +SKIP
 
     """

nipype/interfaces/fsl/tests/test_auto_TOPUP.py

@@ -26,19 +26,13 @@ def test_TOPUP_inputs():
             usedefault=True,
         ),
         estmov=dict(argstr='--estmov=%d', ),
-        fwhm=dict(
-            argstr='--fwhm=%f',
-            usedefault=True,
-        ),
+        fwhm=dict(argstr='--fwhm=%f', ),
         in_file=dict(
             argstr='--imain=%s',
             mandatory=True,
         ),
         interp=dict(argstr='--interp=%s', ),
-        max_iter=dict(
-            argstr='--miter=%d',
-            usedefault=True,
-        ),
+        max_iter=dict(argstr='--miter=%d', ),
         minmet=dict(argstr='--minmet=%d', ),
         numprec=dict(argstr='--numprec=%s', ),
         out_base=dict(
@@ -87,26 +81,14 @@ def test_TOPUP_inputs():
             requires=['encoding_direction'],
             xor=['encoding_file'],
         ),
-        reg_lambda=dict(
-            argstr='--miter=%0.f',
-            usedefault=True,
-        ),
+        reg_lambda=dict(argstr='--lambda=%0.f', ),
         regmod=dict(argstr='--regmod=%s', ),
         regrid=dict(argstr='--regrid=%d', ),
         scale=dict(argstr='--scale=%d', ),
-        splineorder=dict(
-            argstr='--splineorder=%d',
-            usedefault=True,
-        ),
+        splineorder=dict(argstr='--splineorder=%d', ),
         ssqlambda=dict(argstr='--ssqlambda=%d', ),
-        subsamp=dict(
-            argstr='--subsamp=%d',
-            usedefault=True,
-        ),
-        warp_res=dict(
-            argstr='--warpres=%f',
-            usedefault=True,
-        ),
+        subsamp=dict(argstr='--subsamp=%d', ),
+        warp_res=dict(argstr='--warpres=%f', ),
     )
     inputs = TOPUP.input_spec()
 

nipype/pipeline/plugins/tests/test_base.py

@@ -16,7 +16,7 @@ def test_scipy_sparse():
 
 '''
 Can use the following code to test that a mapnode crash continues successfully
-Need to put this into a nose-test with a timeout
+Need to put this into a unit-test with a timeout
 
 import nipype.interfaces.utility as niu
 import nipype.pipeline.engine as pe

nipype/pipeline/plugins/tests/test_tools.py

@@ -38,7 +38,7 @@ def test_report_crash():
 
 '''
 Can use the following code to test that a mapnode crash continues successfully
-Need to put this into a nose-test with a timeout
+Need to put this into a unit-test with a timeout
 
 import nipype.interfaces.utility as niu
 import nipype.pipeline.engine as pe