Merge branch 'sgiavasis-master' into new_interfaces

Author: pintohutch

.travis.yml

@@ -16,24 +16,43 @@ before_install:
 - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then export PATH=/home/travis/miniconda2/bin:$PATH; else export PATH=/home/travis/miniconda3/bin:$PATH; fi
 - 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
+- bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
+- sudo apt-get update
+- sudo apt-get install xvfb
 - 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
 - if $INSTALL_DEB_DEPENDECIES; then source /etc/afni/afni.sh; fi
 - export FSLOUTPUTTYPE=NIFTI_GZ
+# Install vtk and fix numpy installation problem
+# Fix numpy problem: https://github.com/enthought/enable/issues/34#issuecomment-2029381
+- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then travis_retry sudo apt-get install -qq libx11-dev swig;
+  echo '[x11]' >> $HOME/.numpy-site.cfg; 
+  echo 'library_dirs = /usr/lib64:/usr/lib:/usr/lib/x86_64-linux-gnu' >> $HOME/.numpy-site.cfg;
+  echo 'include_dirs = /usr/include:/usr/include/X11' >> $HOME/.numpy-site.cfg;
+  fi
 install:
 - conda update --yes conda
 - conda create -n testenv --yes pip python=$TRAVIS_PYTHON_VERSION
 - source activate testenv
 - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then pip install ordereddict; fi
 - conda install --yes numpy scipy nose networkx dateutil
 - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then conda install --yes traits; else pip install traits; fi
+- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then conda install --yes vtk; fi
 - pip install python-coveralls
 - pip install nose-cov
+# Add tvtk (PIL is required by blockcanvas)
+# Install mayavi (see https://github.com/enthought/mayavi/issues/271)
+- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then
+  pip install http://effbot.org/downloads/Imaging-1.1.7.tar.gz;
+  pip install -e git+https://github.com/enthought/etsdevtools.git#egg=etsdevtools;
+  pip install -e git+https://github.com/enthought/blockcanvas.git#egg=blockcanvas;
+  pip install -e git+https://github.com/enthought/etsproxy.git#egg=etsproxy;
+  pip install https://github.com/dmsurti/mayavi/archive/4d4aaf315a29d6a86707dd95149e27d9ed2225bf.zip;
+  pip install -e git+https://github.com/enthought/ets.git#egg=ets;
+  fi
 - pip install -r requirements.txt  # finish remaining requirements
 - python setup.py install
 script:

CHANGES

@@ -1,6 +1,12 @@
 Next release
 ============
 
+* FIX: Prevent crash when tvtk is loaded - ETS_TOOLKIT=null (https://github.com/nipy/nipype/pull/973)
+* ENH: New interfaces in dipy: RESTORE, EstimateResponseSH, CSD and StreamlineTractography
+       (https://github.com/nipy/nipype/pull/1090)
+* ENH: Added interfaces of AFNI (https://github.com/nipy/nipype/pull/1360,
+       https://github.com/nipy/nipype/pull/1361)
+* ENH: Provides a Nipype wrapper for antsJointFusion (https://github.com/nipy/nipype/pull/1351)
 * ENH: Added support for PETPVC (https://github.com/nipy/nipype/pull/1335)
 * ENH: Merge S3DataSink into DataSink, added AWS documentation (https://github.com/nipy/nipype/pull/1316)
 * TST: Cache APT in CircleCI (https://github.com/nipy/nipype/pull/1333)

circle.yml

@@ -9,19 +9,25 @@ dependencies:
   pre:
     # Let CircleCI cache the apt archive
     - sudo rm -rf /var/cache/apt/archives && sudo ln -s ~/.apt-cache /var/cache/apt/archives && mkdir -p ~/.apt-cache/partial
-    - wget -O- http://neuro.debian.net/lists/precise.us-ca.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
-    - sudo apt-key adv --recv-keys --keyserver hkp://pgp.mit.edu:80 0xA5D32F012649A5A9
-    - sudo apt-get update
+    - bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
   override:
     # Install apt packages
-    - sudo apt-get install -y fsl-core fsl-atlases fsl-mni152-templates fsl-feeds afni
-    - echo "source /etc/fsl/fsl.sh" >> $HOME/.profile
-    - echo "source /etc/afni/afni.sh" >> $HOME/.profile
+    - sudo apt-get install -y fsl-core fsl-atlases fsl-mni152-templates fsl-feeds afni swig python-vtk xvfb
+    - echo 'source /etc/fsl/fsl.sh' >> $HOME/.profile
+    - echo 'source /etc/afni/afni.sh' >> $HOME/.profile
     - mkdir -p ~/examples/ && ln -sf /usr/share/fsl-feeds/ ~/examples/feeds
+    # Enable system-wide vtk
+    - ln -sf /usr/lib/pymodules/python2.7/vtk ~/virtualenvs/venv-system/lib/python2.7/site-packages/
     # Set up python environment
     - pip install --upgrade pip
     - pip install -e .
-    - pip install matplotlib sphinx ipython boto coverage
+    - pip install matplotlib sphinx ipython boto coverage dipy
+    # Add tvtk
+    - pip install http://effbot.org/downloads/Imaging-1.1.7.tar.gz
+    - pip install -e git+https://github.com/enthought/etsdevtools.git#egg=etsdevtools
+    - pip install -e git+https://github.com/enthought/blockcanvas.git#egg=blockcanvas
+    - pip install -e git+https://github.com/enthought/etsproxy.git#egg=etsproxy
+    - pip install -e git+https://github.com/enthought/ets.git#egg=ets
     - gem install fakes3
     - if [[ ! -d ~/examples/data ]]; then wget "http://tcpdiag.dl.sourceforge.net/project/nipy/nipype/nipype-0.2/nipype-tutorial.tar.bz2" && tar jxvf nipype-tutorial.tar.bz2 && mv nipype-tutorial/* ~/examples/; fi
     - if [[ ! -d ~/examples/fsl_course_data ]]; then wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt1.tar.gz" && wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt2.tar.gz" && wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/tbss.tar.gz" && mkdir ~/examples/fsl_course_data && tar zxvf fdt1.tar.gz -C ~/examples/fsl_course_data && tar zxvf fdt2.tar.gz -C ~/examples/fsl_course_data && tar zxvf tbss.tar.gz -C ~/examples/fsl_course_data; fi