Merge branch 'master' into data_functor

Author: effigies

.gitmodules

@@ -10,3 +10,9 @@
 [submodule "nibabel-data/nitest-freesurfer"]
 	path = nibabel-data/nitest-freesurfer
 	url = https://bitbucket.org/nipy/nitest-freesurfer.git
+[submodule "nibabel-data/parrec_oblique"]
+	path = nibabel-data/parrec_oblique
+	url = https://github.com/grlee77/parrec_oblique.git
+[submodule "nibabel-data/nitest-cifti2"]
+	path = nibabel-data/nitest-cifti2
+	url = https://github.com/demianw/nibabel-nitest-cifti2.git

.mailmap

@@ -17,7 +17,7 @@ Cindee Madison <cindee@berkeley.edu> CindeeM <cindee@berkeley.edu>
 Cindee Madison <cindee@berkeley.edu> cindeem <cindee@berkeley.edu>
 Ian Nimmo-Smith <iannimmosmith@gmail.com> Ian Nimmo-Smith <ian.nimmo-smith@mrc-cbu.cam.ac.uk>
 Jean-Baptiste Poline <jbpoline@gmail.com> jbpoline <jbpoline@gmail.com>
-Félix C. Morency <felix.morency@gmail.com> Felix C. Morency <felix.c.morency@usherbrooke.ca> Félix C. Morency <felix.c.morency@usherbrooke.ca>
+Félix C. Morency <felix.morency@gmail.com> Felix C. Morency <felix.c.morency@usherbrooke.ca>
 Félix C. Morency <felix.morency@gmail.com> Félix C. Morency <felix.c.morency@usherbrooke.ca>
 Krish Subramaniam <krish.subramaniam@gmail.com> Krish Subramaniam <krish@monster.nmr.mgh.harvard.edu>
 Eric Larson <larson.eric.d@gmail.com> Eric89GXL <larson.eric.d@gmail.com>
@@ -28,6 +28,15 @@ Basile Pinsard <basile.pinsard@gmail.com> bpinsard <basile.pinsard@gmail.com>
 Basile Pinsard <basile.pinsard@gmail.com> bpinsard <bpinsard@imed.jussieu.fr>
 Nguyen, Ly <nguyen60@seattleu.edu> lxn2 <lxn2@uw.edu>
 Ben Cipollini <ben.cipollini@gmail.com> Ben Cipollini <bcipolli@ucsd.edu>
+Chris Markiewicz <effigies@gmail.com> Christopher J. Markiewicz <markiewicz@stanford.edu>
 Chris Markiewicz <effigies@gmail.com> Christopher J. Markiewicz <effigies@bu.edu>
 Chris Markiewicz <effigies@gmail.com> Christopher J. Markiewicz <effigies@gmail.com>
 Chris Markiewicz <effigies@gmail.com> Chris Johnson <effigies@bu.edu>
+Jaakko Leppäkangas <jaeilepp@student.jyu.fi> jaeilepp <jaeilepp@student.jyu.fi>
+Ariel Rokem <arokem@gmail.com> arokem <arokem@gmail.com>
+Oliver P. Hinds <ohinds@gmail.com> ohinds <ohinds@gmail.com>
+Marc-Alexandre Côté <marc.cote.19@gmail.com> Marc-Alexandre Cote <marc.cote.19@gmail.com>
+Satrajit Ghosh <satra@mit.edu> Satrajit Ghosh <satrajit.ghosh@gmail.com>
+Jasper J.F. van den Bosch <japsai@gmail.com> Jasper <japsai@gmail.com>
+Gregory R. Lee <grlee77@gmail.com> Gregory R. Lee <gregory.lee@cchmc.org>
+Demian Wassermann <demian@bwh.harvard.edu> Demian Wassermann <demian.wassermann@inria.fr>

.travis.yml

@@ -12,22 +12,20 @@ sudo: false
 cache:
   directories:
     - $HOME/.cache/pip
-
-addons:
-  apt:
-    packages:
-      - libhdf5-serial-dev
-
 env:
     global:
-        - DEPENDS="numpy scipy matplotlib h5py"
+        - DEPENDS="six numpy scipy matplotlib h5py pillow"
+        - OPTIONAL_DEPENDS=""
         - PYDICOM=1
         - INSTALL_TYPE="setup"
+        - EXTRA_WHEELS="https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
+        - PRE_WHEELS="https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com"
+        - EXTRA_PIP_FLAGS="--find-links=$EXTRA_WHEELS"
+        - PRE_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
 python:
-    - 2.6
-    - 3.3
     - 3.4
     - 3.5
+    - 3.6
 matrix:
   include:
     - python: 2.7
@@ -36,15 +34,35 @@ matrix:
     # Absolute minimum dependencies
     - python: 2.7
       env:
-        - DEPENDS=numpy==1.5.1 PYDICOM=0
+        - DEPENDS="numpy==1.7.1" PYDICOM=0
+    # Absolute minimum dependencies plus oldest MPL
+    # Check these against:
+    # nibabel/info.py
+    # doc/source/installation.rst
+    # requirements.txt
+    - python: 2.7
+      env:
+        - DEPENDS="numpy==1.7.1 matplotlib==1.3.1" PYDICOM=0
     # Minimum pydicom dependency
     - python: 2.7
       env:
-        - DEPENDS="numpy==1.5.1 pydicom==0.9.7"
+        - DEPENDS="numpy==1.7.1 pydicom==0.9.7 pillow==2.6"
+    # test against numpy 1.7
+    - python: 2.7
+      env:
+        - DEPENDS="numpy==1.7.1"
     # pydicom 1.0 (currently unreleased)
     - python: 2.7
       env:
         - PYDICOM="v1.0"
+    # test 2.7 against pre-release builds of everything
+    - python: 2.7
+      env:
+        - EXTRA_PIP_FLAGS="$PRE_PIP_FLAGS"
+    # test 3.5 against pre-release builds of everything
+    - python: 3.5
+      env:
+        - EXTRA_PIP_FLAGS="$PRE_PIP_FLAGS"
     # Documentation doctests
     - python: 2.7
       env:
@@ -64,14 +82,26 @@ matrix:
     - python: 3.5
       env:
         - STYLE=1
+    - python: 3.5
+      env:
+        - DOC_DOC_TEST=1
+    # Run tests with indexed_gzip present
+    - python: 2.7
+      env:
+        - OPTIONAL_DEPENDS="indexed_gzip"
+    - python: 3.5
+      env:
+        - OPTIONAL_DEPENDS="indexed_gzip"
 before_install:
     - source tools/travis_tools.sh
+    - python -m pip install --upgrade pip
+    - pip install --upgrade virtualenv
     - virtualenv --python=python venv
     - source venv/bin/activate
     - python --version # just to check
-    - pip install -U pip wheel  # upgrade to latest pip find 3.5 wheels; wheel to avoid errors
-    - retry pip install nose flake8  # always
-    - wheelhouse_pip_install $DEPENDS
+    - pip install -U pip wheel  # needed at one point
+    - retry pip install nose flake8 mock  # always
+    - pip install $EXTRA_PIP_FLAGS $DEPENDS $OPTIONAL_DEPENDS
     # pydicom <= 0.9.8 doesn't install on python 3
     - if [ "${TRAVIS_PYTHON_VERSION:0:1}" == "2" ]; then
         if [ "$PYDICOM" == "1" ]; then
@@ -83,6 +113,7 @@ before_install:
     - if [ "${COVERAGE}" == "1" ]; then
       pip install coverage;
       pip install coveralls;
+      pip install codecov;
       fi
 # command to install dependencies
 install:
@@ -92,13 +123,13 @@ install:
       elif [ "$INSTALL_TYPE" == "sdist" ]; then
           python setup_egg.py egg_info  # check egg_info while we're here
           python setup_egg.py sdist
-          wheelhouse_pip_install dist/*.tar.gz
+          pip install $EXTRA_PIP_FLAGS dist/*.tar.gz
       elif [ "$INSTALL_TYPE" == "wheel" ]; then
           pip install wheel
           python setup_egg.py bdist_wheel
-          wheelhouse_pip_install dist/*.whl
+          pip install $EXTRA_PIP_FLAGS dist/*.whl
       elif [ "$INSTALL_TYPE" == "requirements" ]; then
-          wheelhouse_pip_install -r requirements.txt
+          pip install $EXTRA_PIP_FLAGS -r requirements.txt
           python setup.py install
       fi
     # Point to nibabel data directory
@@ -118,16 +149,16 @@ script:
               COVER_ARGS="--with-coverage --cover-package nibabel";
           fi
           if [ "$DOC_DOC_TEST" == "1" ]; then
-              pip install sphinx numpydoc texext;
               cd ../doc;
+              pip install -r ../doc-requirements.txt
               make html;
               make doctest;
           else
               nosetests --with-doctest $COVER_ARGS nibabel;
           fi
       fi
 after_success:
-    - if [ "${COVERAGE}" == "1" ]; then coveralls; fi
+    - if [ "${COVERAGE}" == "1" ]; then coveralls; codecov; fi
 
 notifications:
     webhooks: http://nipy.bic.berkeley.edu:54856/travis

AUTHOR

@@ -1,3 +1,7 @@
 Matthew Brett <matthew.brett@gmail.com>
 Michael Hanke <michael.hanke@gmail.com>
+Ben Cipollini <ben.cipollini@gmail.com>
+Marc-Alexandre Côté <marc.cote.19@gmail.com>
+Chris Markiewicz <effigies@gmail.com>
 Stephan Gerhard <connectome@unidesign.ch>
+Eric Larson <larson.eric.d@gmail.com>