Merge pull request #3 from bcipolli/satra/enh/cifti2

Base CiftiImage on the xml.expat framework

Author: bcipolli

.mailmap

@@ -29,3 +29,5 @@ Basile Pinsard <[email protected]> bpinsard <[email protected]>
 Nguyen, Ly <[email protected]> lxn2 <[email protected]>
 Ben Cipollini <[email protected]> Ben Cipollini <[email protected]>
 Chris Markiewicz <[email protected]> Christopher J. Markiewicz <[email protected]>
+Chris Markiewicz <[email protected]> Christopher J. Markiewicz <[email protected]>
+Chris Markiewicz <[email protected]> Chris Johnson <[email protected]>

.travis.yml

@@ -24,7 +24,6 @@ env:
         - INSTALL_TYPE="setup"
 python:
     - 2.6
-    - 3.2
     - 3.3
     - 3.4
     - 3.5
@@ -58,13 +57,19 @@ matrix:
     - python: 2.7
       env:
         - INSTALL_TYPE=requirements
+    - python: 2.7
+      env:
+        - STYLE=1
+    - python: 3.5
+      env:
+        - STYLE=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  # upgrade to latest pip to find 3.5 wheels
-    - retry pip install nose # always
+    - 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 $DEPENDS
     # pydicom <= 0.9.8 doesn't install on python 3
     - if [ "${TRAVIS_PYTHON_VERSION:0:1}" == "2" ]; then
@@ -99,20 +104,29 @@ install:
     - export NIBABEL_DATA_DIR="$PWD/nibabel-data"
 # command to run tests, e.g. python setup.py test
 script:
-    # Change into an innocuous directory and find tests from installation
-    - mkdir for_testing
-    - cd for_testing
-    - if [ "${COVERAGE}" == "1" ]; then
-      cp ../.coveragerc .;
-      COVER_ARGS="--with-coverage --cover-package nibabel";
-      fi
-    - if [ "$DOC_DOC_TEST" == "1" ]; then
-      pip install sphinx;
-      cd ../doc;
-      make html;
-      make doctest;
+    - |
+      if [ "${STYLE}" == "1" ]; then
+          # Run styles only on core nibabel code.
+          flake8 nibabel
       else
-      nosetests --with-doctest $COVER_ARGS nibabel;
+          # Change into an innocuous directory and find tests from installation
+          mkdir for_testing
+          cd for_testing
+          if [ "${COVERAGE}" == "1" ]; then
+              cp ../.coveragerc .;
+              COVER_ARGS="--with-coverage --cover-package nibabel";
+          fi
+          if [ "$DOC_DOC_TEST" == "1" ]; then
+              pip install sphinx numpydoc texext;
+              cd ../doc;
+              make html;
+              make doctest;
+          else
+              nosetests --with-doctest $COVER_ARGS nibabel;
+          fi
       fi
 after_success:
     - if [ "${COVERAGE}" == "1" ]; then coveralls; fi
+
+notifications:
+    webhooks: http://nipy.bic.berkeley.edu:54856/travis

Changelog

@@ -34,6 +34,19 @@ References like "pr/298" refer to github pull request numbers.
     are raising a DataError if the track is truncated when ``strict=True``
     (the default), rather than a TypeError when trying to create the points
     array.
+
+* 2.0.2 (Monday 23 November 2015)
+
+  * Fix for integer overflow on large images (pr/325) (MB);
+  * Fix for Freesurfer nifti files with unusual dimensions (pr/332) (Chris
+    Markiewicz);
+  * Fix typos on benchmarks and tests (pr/336, pr/340, pr/347) (Chris
+    Markiewicz);
+  * Fix Windows install script (pr/339) (MB);
+  * Support for Python 3.5 (pr/363) (MB) and numpy 1.10 (pr/358) (Chris
+    Markiewicz);
+  * Update pydicom imports to permit version 1.0 (pr/379) (Chris Markiewicz);
+  * Workaround for Python 3.5.0 gzip regression (pr/383) (Ben Cipollini).
   * tripwire.TripWire object now raises subclass of AttributeError when trying
     to get an attribute, rather than a direct subclass of Exception.  This
     prevents Python 3.5 triggering the tripwire when doing inspection prior to

doc/source/conf.py

@@ -11,45 +11,55 @@
 # nipype documentation build configuration file, created by
 # sphinx-quickstart on Mon Jul 20 12:30:18 2009.
 #
-# This file is execfile()d with the current directory set to its containing dir.
+# This file is exec()d with the current directory set to its containing dir.
 #
 # Note that not all possible configuration values are present in this
 # autogenerated file.
 #
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys, os
+import sys
+import os
 
 import nibabel
 
+# Check for external Sphinx extensions we depend on
+try:
+    import numpydoc
+except ImportError:
+    raise RuntimeError('Need to install "numpydoc" package for doc build')
+try:
+    import texext
+except ImportError:
+    raise RuntimeError('Need to install "texext" package for doc build')
+
 # 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.
 sys.path.append(os.path.abspath('../sphinxext'))
 
-# -- General configuration -----------------------------------------------------
+# -- General configuration ----------------------------------------------------
 
 # We load the nibabel release info into a dict by explicit execution
 rel = {}
-execfile('../../nibabel/info.py', rel)
+with open(os.path.join('..', '..', 'nibabel', 'info.py'), 'r') as fobj:
+    exec(fobj.read(), rel)
 
 # Write long description from info
 with open('_long_description.inc', 'wt') as fobj:
     fobj.write(rel['LONG_DESCRIPTION'])
 
-# Add any Sphinx extension module names here, as strings. They can be extensions
-# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = ['sphinx.ext.autodoc',
               'sphinx.ext.doctest',
               #'sphinx.ext.intersphinx',
               'sphinx.ext.todo',
               'sphinx.ext.mathjax',
               'sphinx.ext.inheritance_diagram',
               'sphinx.ext.autosummary',
-              'math_dollar', # has to go before numpydoc
-              # we have a local copy of the extension, imported from NumPy 1.3
-              # this also includes the docscrape* extensions
+              'texext.math_dollar',  # has to go before numpydoc
               'numpydoc',
               'only_directives',
               'plot_directive',
@@ -104,7 +114,7 @@
 # for source files.
 exclude_trees = ['_build']
 
-# The reST default role (used for this markup: `text`) to use for all documents.
+# The reST default role (used for this markup: `text`) to use for all documents
 #default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
@@ -124,7 +134,7 @@
 # A list of ignored prefixes for module index sorting.
 #modindex_common_prefix = []
 
-# -- Sphinxext configuration ---------------------------------------------------
+# -- Sphinxext configuration --------------------------------------------------
 
 # Set attributes for layout of inheritance diagrams
 inheritance_graph_attrs = dict(rankdir="LR", size='"6.0, 8.0"', fontsize=14,
@@ -135,7 +145,7 @@
 # Flag to show todo items in rendered output
 todo_include_todos = True
 
-# -- Options for HTML output ---------------------------------------------------
+# -- Options for HTML output --------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  Major themes that come with
 # Sphinx are currently 'default' and 'sphinxdoc'.
@@ -218,7 +228,7 @@
 
 mathjax_path = 'https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
 
-# -- Options for LaTeX output --------------------------------------------------
+# -- Options for LaTeX output -------------------------------------------------
 
 # The paper size ('letter' or 'a4').
 #latex_paper_size = 'letter'
@@ -227,11 +237,11 @@
 #latex_font_size = '10pt'
 
 # Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title, author, documentclass [howto/manual]).
+# (source start file, target name, title, author,
+#  documentclass [howto/manual]).
 latex_documents = [
-  ('index', 'nibabel.tex', u'NiBabel Documentation',
-   u'NiBabel Authors', 'manual'),
-]
+    ('index', 'nibabel.tex', u'NiBabel Documentation', u'NiBabel Authors',
+     'manual')]
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.

doc/source/devel/advanced_testing.rst

@@ -0,0 +1,32 @@
+.. -*- mode: rst -*-
+.. ex: set sts=4 ts=4 sw=4 et tw=79:
+  ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
+  #
+  #   See COPYING file distributed along with the NiBabel package for the
+  #   copyright and license terms.
+  #
+  ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
+
+.. _advanced_testing:
+
+************
+Advanced Testing
+************
+
+Setup
+-----
+
+Before running advanced tests, please update all submodules of nibabel, by running ``git submodule update --init``
+
+
+Long-running tests
+------------------
+
+Long-running tests are not enabled by default, and can be resource-intensive. To run these tests:
+
+* Set environment variable ``NIPY_EXTRA_TESTS=slow``
+* Run ``nosetests``.
+
+Note that some tests may require a machine with >4GB of RAM.
+
+.. include:: ../links_names.txt

doc/source/devel/index.rst

@@ -14,3 +14,4 @@ Developer documentation page
     add_image_format
     devdiscuss
     make_release
+    advanced_testing