fix: updated Vagrantfile, fixed freesurfer test on osx, and fsl doctest with undefined environment variable

Author: satra

Vagrantfile

@@ -20,19 +20,20 @@ $script = <<SCRIPT
 # qconf -aattr queue slots "2, [neuro=3]" main.q
 
 # install anaconda
-wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
+wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
 chmod +x miniconda.sh
 ./miniconda.sh -b
-echo "export PATH=$HOME/miniconda/bin:\\$PATH" >> .bashrc
+echo "export PATH=$HOME/miniconda3/bin:\\$PATH" >> .bashrc
 
 # install nipype dependencies
-$HOME/miniconda/bin/conda update --yes conda
-$HOME/miniconda/bin/conda install --yes pip numpy scipy nose traits networkx
-$HOME/miniconda/bin/conda install --yes dateutil ipython-notebook matplotlib
-$HOME/miniconda/bin/pip install nibabel --use-mirrors
-$HOME/miniconda/bin/pip install https://github.com/RDFLib/rdflib/archive/master.zip
-$HOME/miniconda/bin/pip install https://github.com/trungdong/prov/archive/rdf.zip
-$HOME/miniconda/bin/pip install https://github.com/nipy/nipype/archive/master.zip
+$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 python-dateutil jupyter matplotlib
+$HOME/miniconda3/bin/pip install nibabel
+$HOME/miniconda3/bin/pip install prov
+$HOME/miniconda3/bin/pip install xvfbwrapper
+$HOME/miniconda3/bin/pip install traits
+$HOME/miniconda3/bin/pip install https://github.com/nipy/nipype/archive/master.zip
 SCRIPT
 
 Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|

nipype/interfaces/freesurfer/tests/test_model.py

@@ -14,7 +14,7 @@
 
 @skipif(no_freesurfer)
 def test_concatenate():
-    tmp_dir = tempfile.mkdtemp()
+    tmp_dir = os.path.realpath(tempfile.mkdtemp())
     cwd = os.getcwd()
     os.chdir(tmp_dir)
     in1 = os.path.join(tmp_dir, 'cont1.nii')

nipype/interfaces/fsl/utils.py

@@ -165,6 +165,7 @@ class Smooth(FSLCommand):
     Setting the kernel width using sigma:
 
     >>> sm = Smooth()
+    >>> sm.inputs.output_type = 'NIFTI_GZ'
     >>> sm.inputs.in_file = 'functional2.nii'
     >>> sm.inputs.sigma = 8.0
     >>> sm.cmdline #doctest: +ELLIPSIS
@@ -173,6 +174,7 @@ class Smooth(FSLCommand):
     Setting the kernel width using fwhm:
 
     >>> sm = Smooth()
+    >>> sm.inputs.output_type = 'NIFTI_GZ'
     >>> sm.inputs.in_file = 'functional2.nii'
     >>> sm.inputs.fwhm = 8.0
     >>> sm.cmdline #doctest: +ELLIPSIS
@@ -182,6 +184,7 @@ class Smooth(FSLCommand):
 
     >>> from nipype.interfaces.fsl import Smooth
     >>> sm = Smooth()
+    >>> sm.inputs.output_type = 'NIFTI_GZ'
     >>> sm.inputs.in_file = 'functional2.nii'
     >>> sm.cmdline #doctest: +ELLIPSIS
     Traceback (most recent call last):