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fix: updated Vagrantfile, fixed freesurfer test on osx, and fsl doctest #1421

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Merged
merged 1 commit into from
Apr 7, 2016
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fix: updated Vagrantfile, fixed freesurfer test on osx, and fsl doctest #1421

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19 changes: 10 additions & 9 deletions Vagrantfile
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Original file line number Diff line number Diff line change
Expand Up @@ -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|
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2 changes: 1 addition & 1 deletion nipype/interfaces/freesurfer/tests/test_model.py
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Expand Up @@ -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')
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3 changes: 3 additions & 0 deletions nipype/interfaces/fsl/utils.py
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Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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):
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