Merge pull request #934 from chrisfilo/fix/travis

WIP: fixing travis

Author: chrisgorgo

.travis.yml

@@ -4,19 +4,21 @@ language: python
 python:
   - 2.6
   - 2.7
+env:
+  - INSTALL_DEB_DEPENDECIES=true
+  - INSTALL_DEB_DEPENDECIES=false
 # Setup anaconda
 before_install:
   - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-3.6.0-Linux-x86_64.sh -O miniconda.sh; fi
   - chmod +x miniconda.sh
   - ./miniconda.sh -b
   - export PATH=/home/travis/miniconda/bin:$PATH
-  # The next couple lines fix a crash with multiprocessing on Travis
-  - sudo rm -rf /dev/shm
-  - sudo ln -s /run/shm /dev/shm
-  - bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
-  - travis_retry sudo apt-get install -qq --no-install-recommends fsl afni elastix
-  - travis_retry sudo apt-get install -qq fsl-atlases
-  - source /etc/fsl/fsl.sh
+  - if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi
+  - if $INSTALL_DEB_DEPENDECIES; then sudo ln -s /run/shm /dev/shm; fi
+  - if $INSTALL_DEB_DEPENDECIES; then bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh); fi
+  - if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -qq --no-install-recommends fsl afni elastix; fi
+  - if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -qq fsl-atlases; fi
+  - if $INSTALL_DEB_DEPENDECIES; then source /etc/fsl/fsl.sh; fi
 
 # Install packages
 install:

nipype/interfaces/fsl/epi.py

@@ -233,6 +233,7 @@ class TOPUP(FSLCommand):
     >>> topup = TOPUP()
     >>> topup.inputs.in_file = "b0_b0rev.nii"
     >>> topup.inputs.encoding_file = "topup_encoding.txt"
+    >>> topup.inputs.output_type = "NIFTI_GZ"
     >>> topup.cmdline #doctest: +ELLIPSIS
     'topup --config=b02b0.cnf --datain=topup_encoding.txt \
 --imain=b0_b0rev.nii --out=b0_b0rev_base --iout=b0_b0rev_corrected.nii.gz \
@@ -354,6 +355,7 @@ class ApplyTOPUP(FSLCommand):
     >>> applytopup.inputs.in_index = [1,2]
     >>> applytopup.inputs.in_topup_fieldcoef = "topup_fieldcoef.nii.gz"
     >>> applytopup.inputs.in_topup_movpar = "topup_movpar.txt"
+    >>> applytopup.inputs.output_type = "NIFTI_GZ"
     >>> applytopup.cmdline #doctest: +ELLIPSIS
     'applytopup --datain=topup_encoding.txt --imain=epi.nii,epi_rev.nii \
 --inindex=1,2 --topup=topup --out=epi_corrected.nii.gz'

nipype/interfaces/fsl/preprocess.py

@@ -532,10 +532,11 @@ class FLIRT(FSLCommand):
     >>> from nipype.interfaces import fsl
     >>> from nipype.testing import example_data
     >>> flt = fsl.FLIRT(bins=640, cost_func='mutualinfo')
-    >>> flt.inputs.in_file = example_data('structural.nii')
-    >>> flt.inputs.reference = example_data('mni.nii')
+    >>> flt.inputs.in_file = 'structural.nii'
+    >>> flt.inputs.reference = 'mni.nii'
+    >>> flt.inputs.output_type = "NIFTI_GZ"
     >>> flt.cmdline #doctest: +ELLIPSIS
-    'flirt -in .../structural.nii -ref .../mni.nii -out structural_flirt.nii.gz -omat structural_flirt.mat -bins 640 -searchcost mutualinfo'
+    'flirt -in structural.nii -ref mni.nii -out structural_flirt.nii.gz -omat structural_flirt.mat -bins 640 -searchcost mutualinfo'
     >>> res = flt.run() #doctest: +SKIP
 
     """
@@ -1262,6 +1263,7 @@ class FUGUE(FSLCommand):
     >>> fugue.inputs.mask_file = 'epi_mask.nii'
     >>> fugue.inputs.shift_in_file = 'vsm.nii'  # Previously computed with fugue as well
     >>> fugue.inputs.unwarp_direction = 'y'
+    >>> fugue.inputs.output_type = "NIFTI_GZ"
     >>> fugue.cmdline #doctest: +ELLIPSIS
     'fugue --in=epi.nii --mask=epi_mask.nii --loadshift=vsm.nii --unwarpdir=y --unwarp=epi_unwarped.nii.gz'
     >>> fugue.run() #doctest: +SKIP
@@ -1276,6 +1278,7 @@ class FUGUE(FSLCommand):
     >>> fugue.inputs.mask_file = 'epi_mask.nii'
     >>> fugue.inputs.shift_in_file = 'vsm.nii'  # Previously computed with fugue as well
     >>> fugue.inputs.unwarp_direction = 'y'
+    >>> fugue.inputs.output_type = "NIFTI_GZ"
     >>> fugue.cmdline #doctest: +ELLIPSIS
     'fugue --in=epi.nii --mask=epi_mask.nii --loadshift=vsm.nii --unwarpdir=y --warp=epi_warped.nii.gz'
     >>> fugue.run() #doctest: +SKIP
@@ -1290,6 +1293,7 @@ class FUGUE(FSLCommand):
     >>> fugue.inputs.dwell_to_asym_ratio = (0.77e-3 * 3) / 2.46e-3
     >>> fugue.inputs.unwarp_direction = 'y'
     >>> fugue.inputs.save_shift = True
+    >>> fugue.inputs.output_type = "NIFTI_GZ"
     >>> fugue.cmdline #doctest: +ELLIPSIS
     'fugue --dwelltoasym=0.9390243902 --mask=epi_mask.nii --phasemap=epi_phasediff.nii --saveshift=epi_phasediff_vsm.nii.gz --unwarpdir=y'
     >>> fugue.run() #doctest: +SKIP

nipype/interfaces/fsl/utils.py

@@ -1359,6 +1359,7 @@ class InvWarp(FSLCommand):
     >>> invwarp = InvWarp()
     >>> invwarp.inputs.warp = "struct2mni.nii"
     >>> invwarp.inputs.reference = "anatomical.nii"
+    >>> invwarp.inputs.output_type = "NIFTI_GZ"
     >>> invwarp.cmdline
     'invwarp --out=struct2mni_inverse.nii.gz --ref=anatomical.nii --warp=struct2mni.nii'
     >>> res = invwarp.run() # doctest: +SKIP
@@ -1576,6 +1577,7 @@ class WarpUtils(FSLCommand):
     >>> warputils.inputs.reference = "T1.nii"
     >>> warputils.inputs.out_format = 'spline'
     >>> warputils.inputs.warp_resolution = (10,10,10)
+    >>> warputils.inputs.output_type = "NIFTI_GZ"
     >>> warputils.cmdline # doctest: +ELLIPSIS
     'fnirtfileutils --in=warpfield.nii --outformat=spline --ref=T1.nii --warpres=10.0000,10.0000,10.0000 --out=warpfield_coeffs.nii.gz'
     >>> res = invwarp.run() # doctest: +SKIP
@@ -1706,6 +1708,7 @@ class ConvertWarp(FSLCommand):
     >>> warputils.inputs.warp1 = "warpfield.nii"
     >>> warputils.inputs.reference = "T1.nii"
     >>> warputils.inputs.relwarp = True
+    >>> warputils.inputs.output_type = "NIFTI_GZ"
     >>> warputils.cmdline # doctest: +ELLIPSIS
     'convertwarp --ref=T1.nii --rel --warp1=warpfield.nii --out=T1_concatwarp.nii.gz'
     >>> res = invwarp.run() # doctest: +SKIP