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

* upstream/master: (153 commits)
  DOC: fix path to links_names.txt
  FIX: remove improper space from import in freesurfer/io.py
  BLD: add doctest to Travis matrix
  DOC: fix ImportErrors in apigen.py for Python 3
  DOC: remove another nipy.github.io link
  DOC: remove last vestiges of nipy-devel list
  DOC: fix mailing list and website link in README
  ENH: ls test -- take Matthew's snippet with better msg
  DOC: add additional sorting details to the parrec API docs
  BF: allow for int type string in ls on BE begin with <i
  DOC: add info on sorting to API docs for PAR/REC
  STY: PEP8 in doc/tools
  DOC: python 3 compatibility fixes in doc/tools
  RF: update code to remove deprecated imp module
  BF: make MPL viewer tests require MPL 1.3
  NF: add min version argumemt to optpkg and test
  ENH: limit number of unique counts to be processed by 1000 and add --all-counts to override
  RF(no functional changes): flake8 nib-ls
  ENH: drop use of Counter in favor of MB's shared snippet using recipe from scipy
  DOC: mention that -c reports 0s if -z
  ...

Author: satra

.gitmodules

@@ -10,3 +10,6 @@
 [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

.travis.yml

@@ -3,6 +3,7 @@
 # munges each line before executing it to print out the exit status.  It's okay
 # for it to be on multiple physical lines, so long as you remember: - There
 # can't be any leading "-"s - All newlines will be removed, so use ";"s
+
 language: python
 
 # Run jobs on container-based infrastructure, can be overridden per job
@@ -11,15 +12,15 @@ sudo: false
 cache:
   directories:
     - $HOME/.cache/pip
-
 addons:
   apt:
     packages:
       - libhdf5-serial-dev
-
+      # For numpy --pre wheels
+      - libatlas-base-dev
 env:
     global:
-        - DEPENDS="numpy scipy matplotlib h5py"
+        - DEPENDS="numpy scipy matplotlib h5py pillow"
         - PYDICOM=1
         - INSTALL_TYPE="setup"
 python:
@@ -36,14 +37,26 @@ matrix:
     - python: 2.7
       env:
         - DEPENDS=numpy==1.5.1 PYDICOM=0
+    # Absolute minimum dependencies plus oldest MPL
+    - python: 2.7
+      env:
+        - DEPENDS="numpy==1.5.1 matplotlib==1.3.1" PYDICOM=0
     # Minimum pydicom dependency
     - python: 2.7
       env:
-        - DEPENDS="numpy==1.5.1 pydicom==0.9.7"
+        - DEPENDS="numpy==1.5.1 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 against pre-release builds
+    - python: 2.7
+      env:
+        - EXTRA_PIP_FLAGS="--pre"
     # Documentation doctests
     - python: 2.7
       env:
@@ -63,14 +76,17 @@ matrix:
     - python: 3.5
       env:
         - STYLE=1
+    - python: 3.5
+      env:
+        - DOC_DOC_TEST=1
 before_install:
     - source tools/travis_tools.sh
     - 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
+    - wheelhouse_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 [ "$PYDICOM" == "1" ]; then
@@ -82,6 +98,7 @@ before_install:
     - if [ "${COVERAGE}" == "1" ]; then
       pip install coverage;
       pip install coveralls;
+      pip install codecov;
       fi
 # command to install dependencies
 install:
@@ -91,13 +108,13 @@ 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
+          wheelhouse_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
+          wheelhouse_pip_install $EXTRA_PIP_FLAGS dist/*.whl
       elif [ "$INSTALL_TYPE" == "requirements" ]; then
-          wheelhouse_pip_install -r requirements.txt
+          wheelhouse_pip_install $EXTRA_PIP_FLAGS -r requirements.txt
           python setup.py install
       fi
     # Point to nibabel data directory
@@ -117,16 +134,16 @@ script:
               COVER_ARGS="--with-coverage --cover-package nibabel";
           fi
           if [ "$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

Changelog

@@ -26,6 +26,8 @@ References like "pr/298" refer to github pull request numbers.
 
 * Upcoming
 
+  * Read and write support for DICOM tags in NIfTI Extended Header using
+    pydicom (pr/296);
   * Trackvis reader will now allow final streamline to have fewer points that
     tne numbe declared in the header, with ``strict=False`` argument to
     ``read`` function;

Makefile

@@ -221,8 +221,8 @@ deb-src: check-debian distclean
 bdist_rpm:
 	$(PYTHON) setup.py bdist_rpm \
 	  --doc-files "doc" \
-	  --packager "nibabel authors <http://mail.scipy.org/mailman/listinfo/nipy-devel>"
-	  --vendor "nibabel authors <http://mail.scipy.org/mailman/listinfo/nipy-devel>"
+	  --packager "nibabel authors <http://mail.python.org/mailman/listinfo/neuroimaging>"
+	  --vendor "nibabel authors <http://mail.python.org/mailman/listinfo/neuroimaging>"
 
 
 # build MacOS installer -- depends on patched bdist_mpkg for Leopard

README.rst

@@ -41,14 +41,13 @@ Website
 =======
 
 Current documentation on nibabel can always be found at the `NIPY nibabel
-website <https://nipy.github.io/nibabel>`_.
+website <http://nipy.org/nibabel>`_.
 
 Mailing Lists
 =============
 
-Please see the `nipy devel list
-<http://mail.scipy.org/mailman/listinfo/nipy-devel>`_. The nipy devel list is
-fine for user and developer questions about nibabel.
+Please send any questions or suggestions to the `neuroimaging mailing list
+<https://mail.python.org/mailman/listinfo/neuroimaging>`_.
 
 Code
 ====
@@ -62,7 +61,7 @@ You can find our sources and single-click downloads:
 * Downloads of all `available releases`_.
 
 .. _main repository: https://github.com/nipy/nibabel
-.. _Documentation: https://nipy.github.io/nibabel
+.. _Documentation: http://nipy.org/nibabel
 .. _current release: https://pypi.python.org/pypi/nibabel
 .. _current development version: https://github.com/nipy/nibabel/archive/master.zip
 .. _available releases: https://github.com/nipy/nibabel/releases

bin/nib-dicomfs

@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!python
 # emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##