Merge remote-tracking branch 'upstream/master' into enh/cifti2

* upstream/master:
  BF: adapt sphinx doctests to numpy 1.12
  MAINT: update numpy dependency; add Python 3.6
  Addressed @matthew-brett's comments
  DOC: better warning when nibabel not on path
  RF: add bottom left 1 to affine for tests
  PEP8
  TST: add test for fix in PR 500
  Supports extending empty tractograms
  PEP8
  RF: Add function to easily make fake streamline for testing purposes.
  Addressed @matthew-brett's comments
  Support __add__. Remove unnecessary syntatic sugar.
  Add docstrings
  Add Tractogram concatenation
  PEP8
  BF: boolean indexing now requires matching dimension

Author: satra

.travis.yml

@@ -23,10 +23,12 @@ env:
         - DEPENDS="numpy scipy matplotlib h5py pillow"
         - PYDICOM=1
         - INSTALL_TYPE="setup"
+        - EXTRA_WHEELS="https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
+        - EXTRA_PIP_FLAGS="--find-links=$EXTRA_WHEELS"
 python:
-    - 3.3
     - 3.4
     - 3.5
+    - 3.6
 matrix:
   include:
     - python: 2.7
@@ -35,19 +37,19 @@ matrix:
     # Absolute minimum dependencies
     - python: 2.7
       env:
-        - DEPENDS=numpy==1.5.1 PYDICOM=0
+        - DEPENDS=numpy==1.6.0 PYDICOM=0
     # Absolute minimum dependencies plus oldest MPL
     # Check these against:
+    # nibabel/info.py
     # doc/source/installation.rst
     # requirements.txt
-    # .travis.yml
     - python: 2.7
       env:
-        - DEPENDS="numpy==1.5.1 matplotlib==1.3.1" PYDICOM=0
+        - DEPENDS="numpy==1.6.0 matplotlib==1.3.1" PYDICOM=0
     # Minimum pydicom dependency
     - python: 2.7
       env:
-        - DEPENDS="numpy==1.5.1 pydicom==0.9.7 pillow==2.6"
+        - DEPENDS="numpy==1.6.0 pydicom==0.9.7 pillow==2.6"
     # test against numpy 1.7
     - python: 2.7
       env:
@@ -59,7 +61,7 @@ matrix:
     # test against pre-release builds
     - python: 2.7
       env:
-        - EXTRA_PIP_FLAGS="--pre"
+        - EXTRA_PIP_FLAGS="--pre --find-links=$EXTRA_WHEELS"
     # Documentation doctests
     - python: 2.7
       env:
@@ -84,12 +86,14 @@ matrix:
         - DOC_DOC_TEST=1
 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
+    - pip install -U pip wheel  # needed at one point
     - retry pip install nose flake8 mock  # always
-    - wheelhouse_pip_install $EXTRA_PIP_FLAGS $DEPENDS
+    - pip install $EXTRA_PIP_FLAGS $DEPENDS
     # pydicom <= 0.9.8 doesn't install on python 3
     - if [ "${TRAVIS_PYTHON_VERSION:0:1}" == "2" ]; then
         if [ "$PYDICOM" == "1" ]; then
@@ -111,13 +115,13 @@ install:
       elif [ "$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 $EXTRA_PIP_FLAGS 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 $EXTRA_PIP_FLAGS dist/*.whl
+          pip install $EXTRA_PIP_FLAGS dist/*.whl
       elif [ "$INSTALL_TYPE" == "requirements" ]; then
-          wheelhouse_pip_install $EXTRA_PIP_FLAGS -r requirements.txt
+          pip install $EXTRA_PIP_FLAGS -r requirements.txt
           python setup.py install
       fi
     # Point to nibabel data directory

doc/source/conf.py

@@ -22,8 +22,6 @@
 import sys
 import os
 
-import nibabel
-
 # Check for external Sphinx extensions we depend on
 try:
     import numpydoc
@@ -34,6 +32,13 @@
 except ImportError:
     raise RuntimeError('Need to install "texext" package for doc build')
 
+# Need nibabel installed as well
+try:
+    import nibabel
+except ImportError:
+    raise RuntimeError('Need nibabel on Python PATH; consider "make htmldoc" '
+                       'from nibabel root directory')
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
@@ -82,7 +87,7 @@
 
 # General information about the project.
 project = u'NiBabel'
-copyright = u'2006-2016, %(MAINTAINER)s <%(AUTHOR_EMAIL)s>' % rel
+copyright = u'2006-2017, %(MAINTAINER)s <%(AUTHOR_EMAIL)s>' % rel
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

doc/source/coordinate_systems.rst

@@ -97,11 +97,11 @@ middle voxel in the EPI data array like this:
     :nofigs:
 
     >>> n_i, n_j, n_k = epi_img_data.shape
-    >>> center_i = (n_i - 1) / 2.
-    >>> center_j = (n_j - 1) / 2.
-    >>> center_k = (n_k - 1) / 2.
+    >>> center_i = (n_i - 1) // 2  # // for integer division
+    >>> center_j = (n_j - 1) // 2
+    >>> center_k = (n_k - 1) // 2
     >>> center_i, center_j, center_k
-    (26.0, 30.0, 16.0)
+    (26, 30, 16)
     >>> center_vox_value = epi_img_data[center_i, center_j, center_k]
     >>> center_vox_value
     81.549287796020508

doc/source/installation.rst

@@ -86,8 +86,8 @@ Requirements
     requirements.txt
     .travis.yml
 
-*  Python_ 2.7 or greater
-*  NumPy_ 1.5 or greater
+*  Python_ 2.7, or >= 3.4
+*  NumPy_ 1.6 or greater
 *  SciPy_ (optional, for full SPM-ANALYZE support)
 *  PyDICOM_ 0.9.7 or greater (optional, for DICOM support)
 *  `Python Imaging Library`_ (optional, for PNG conversion in DICOMFS)

doc/source/nifti_images.rst

@@ -401,7 +401,7 @@ Now we save the image and load it again:
 The data array has the scaling applied:
 
 >>> scaled_img.get_data()
-memmap([[[ 10.,  12.,  14.,  16.],
+...([[[ 10.,  12.,  14.,  16.],
         [ 18.,  20.,  22.,  24.],
         [ 26.,  28.,  30.,  32.]],
 <BLANKLINE>

nibabel/benchmarks/bench_streamlines.py

@@ -91,5 +91,6 @@ def bench_load_trk():
         for s1, s2 in zip(scalars_new, scalars_old):
             assert_array_equal(s1, s2)
 
+
 if __name__ == '__main__':
     bench_load_trk()

nibabel/casting.py

@@ -165,6 +165,7 @@ def shared_range(flt_type, int_type):
     _SHARED_RANGES[key] = (mn, mx)
     return mn, mx
 
+
 # ----------------------------------------------------------------------------
 # Routines to work out the next lowest representable integer in floating point
 # types.

nibabel/imageclasses.py

@@ -42,6 +42,7 @@ class ClassMapDict(dict):
     def __getitem__(self, *args, **kwargs):
         return super(ClassMapDict, self).__getitem__(*args, **kwargs)
 
+
 class_map = ClassMapDict(
     analyze={'class': AnalyzeImage,  # Image class
              'ext': '.img',  # characteristic image extension
@@ -97,6 +98,7 @@ class ExtMapRecoder(Recoder):
     def __getitem__(self, *args, **kwargs):
         return super(ExtMapRecoder, self).__getitem__(*args, **kwargs)
 
+
 # mapping of extensions to default image class names
 ext_map = ExtMapRecoder((
     ('nifti_single', '.nii'),

nibabel/info.py

@@ -186,7 +186,7 @@ def cmp_pkg_version(version_str, pkg_version_str=__version__):
 # doc/source/installation.rst
 # requirements.txt
 # .travis.yml
-NUMPY_MIN_VERSION = '1.5.1'
+NUMPY_MIN_VERSION = '1.6.0'
 PYDICOM_MIN_VERSION = '0.9.7'
 
 # Main setup parameters

nibabel/orientations.py

@@ -63,7 +63,7 @@ def io_orientation(affine, tol=None):
     RS = RZS / zooms
     # Transform below is polar decomposition, returning the closest
     # shearless matrix R to RS
-    P, S, Qs = npl.svd(RS)
+    P, S, Qs = npl.svd(RS, full_matrices=False)
     # Threshold the singular values to determine the rank.
     if tol is None:
         tol = S.max() * max(RS.shape) * np.finfo(S.dtype).eps