Merge branch 'master' into bug/fixEddyWrapper

Conflicts:
	nipype/interfaces/fsl/epi.py

Author: oesteban

.travis.yml

@@ -12,7 +12,7 @@ before_install:
   - sudo rm -rf /dev/shm
   - sudo ln -s /run/shm /dev/shm
   - bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
-  - travis_retry sudo apt-get install -qq --no-install-recommends fsl afni
+  - travis_retry sudo apt-get install -qq --no-install-recommends fsl afni elastix
   - travis_retry sudo apt-get install -qq fsl-atlases
   - source /etc/fsl/fsl.sh
 

CHANGES

@@ -1,11 +1,34 @@
 Next Release
 ============
 
-* API: Interfaces to external packages are no longer available in the top-level ``nipype`` namespace, and must be imported directly (e.g. ``from nipype.interfaces import fsl``).
+* ENH: New FSL interfaces: WarpPoints, WarpPointsToStd.
+* ENH: New Freesurfer interface: MRIPretess
+* ENH: New miscelaneous interface: AddCSVRow
+* ENH: FUGUE interface has been refactored to use the name_template system, 3 examples 
+       added to doctests, some bugs solved.
+* ENH: Added new interfaces (fsl.utils.WarpUtils, ConvertWarp) to fnirtfileutils and convertwarp
+* API: Interfaces to external packages are no longer available in the top-level
+       ``nipype`` namespace, and must be imported directly (e.g.
+       ``from nipype.interfaces import fsl``).
+* ENH: New FSL interface: ProbTrackX2
+* ENH: New misc algorithm: NormalizeProbabilityMapSet
+* ENH: Support for elastix via a set of new interfaces: Registration, ApplyWarp, 
+       AnalyzeWarp, PointsWarp, and EditTransform
 * ENH: New ANTs interface: ApplyTransformsToPoints
+* ENH: New metrics group in algorithms. Now Distance, Overlap, and FuzzyOverlap
+       are found in nipype.algorithms.metrics instead of misc
+* ENH: New interface in algorithms.metrics: ErrorMap (a voxel-wise diff map).
 * ENH: New FreeSurfer workflow: create_skullstripped_recon_flow()
 * ENH: New data grabbing interface that works over SSH connections, SSHDataGrabber
+* ENH: New color mode for write_graph
+* ENH: You can now force MapNodes to be run serially
+* ENH: New ANTs interface: LaplacianThickness
 * FIX: MRTrix tracking algorithms were ignoring mask parameters.
+* FIX: FNIRT registration pathway and associated OpenFMRI example script
+* FIX: spm12b compatibility for Model estimate
+* FIX: Batch scheduler controls the number of maximum jobs properly
+* FIX: Update for FSL 5.0.7 which deprecated Contrast Manager
+* ENH: Added ANTS based openfmri workflow
 
 Release 0.9.2 (January 31, 2014)
 ============
@@ -26,7 +49,8 @@ Release 0.9.0 (December 20, 2013)
 * ENH: new tools for defining workflows: JoinNode, synchronize and itersource
 * ENH: W3C PROV support with optional RDF export built into Nipype
 * ENH: Added support for Simple Linux Utility Resource Management (SLURM)
-* ENH: AFNI interfaces refactor, prefix, suffix are replaced by "flexible_%s_templates"
+* ENH: AFNI interfaces refactor, prefix, suffix are replaced by
+       "flexible_%s_templates"
 * ENH: New SPM interfaces:
 		- spm.ResliceToReference,
 		- spm.DicomImport

README.rst

@@ -8,6 +8,25 @@ NIPYPE: Neuroimaging in Python: Pipelines and Interfaces
 .. image:: https://coveralls.io/repos/nipy/nipype/badge.png
   :target: https://coveralls.io/r/nipy/nipype
 
+.. image:: https://pypip.in/version/nipype/badge.png
+    :target: https://pypi.python.org/pypi/nipype/
+    :alt: Latest Version
+
+.. image:: https://pypip.in/download/nipype/badge.png
+    :target: https://pypi.python.org/pypi/nipype/
+    :alt: Downloads
+
+.. image:: https://pypip.in/py_versions/nipype/badge.png
+    :target: https://pypi.python.org/pypi/nipype/
+    :alt: Supported Python versions
+
+.. image:: https://pypip.in/status/nipype/badge.png
+    :target: https://pypi.python.org/pypi/nipype/
+    :alt: Development Status
+
+.. image:: https://pypip.in/license/nipype/badge.png
+    :target: https://pypi.python.org/pypi/nipype/
+    :alt: License
 
 Current neuroimaging software offer users an incredible opportunity to
 analyze data using a variety of different algorithms. However, this has

doc/_templates/indexsidebar.html

@@ -5,8 +5,9 @@ <h3>{{ _('Links') }}</h3>
     <li>Docs: <a href="http://nipy.org/nipype">Stable</a> · <a href="http://www.mit.edu/~satra/nipype-nightly/">Nightly</a></li>
     <li>Code: <a href="http://github.com/nipy/nipype">Github</a> · <a href="http://github.com/nipy/nipype/issues">Bugs-Requests</a></li>
     <li>Forum: <a href="http://groups.google.com/group/nipy-user">User</a> · <a href="http://projects.scipy.org/mailman/listinfo/nipy-devel">Developer</a></li>
-    <li>Info: <a href="http://nipy.org/software/license/index.html">License</a> · <a href="http://nipy.org/about/funding.html">Funding</a></li>
+    <li><a href="http://nipy.org/software/license/index.html"><img src="https://pypip.in/license/nipype/badge.png" alt="License"></a> · <a href="http://nipy.org/about/funding.html">Funding</a></li>
     <li><a href="https://travis-ci.org/nipy/nipype"><img src="https://travis-ci.org/nipy/nipype.png?branch=master" alt="travis"></a> · <a href='https://coveralls.io/r/nipy/nipype'><img src='https://coveralls.io/repos/nipy/nipype/badge.png' alt='Coverage Status' /></a></li>
+    <li><a href="https://pypi.python.org/pypi/nipype/"><img src="https://pypip.in/download/nipype/badge.png" alt="Downloads"></a> · <a href='https://pypi.python.org/pypi/nipype/'><img src='https://pypip.in/py_versions/nipype/badge.png' alt='Python Versions' /></a></li>
 </ul>
 
 {% endblock %}

doc/conf.py

@@ -38,7 +38,9 @@
               'sphinx.ext.autosummary',
               'numpy_ext.numpydoc',
               'matplotlib.sphinxext.plot_directive',
-              'matplotlib.sphinxext.only_directives'
+              'matplotlib.sphinxext.only_directives',
+              'matplotlib.sphinxext.ipython_directive',
+              'ipython_console_highlighting'
               ]
 
 # Add any paths that contain templates here, relative to this directory.

doc/users/install.rst

@@ -10,7 +10,7 @@ Download
 --------
 
 Release 0.9.2: [`zip <https://github.com/nipy/nipype/archive/0.9.2.zip>`__ `tar.gz
-<https://github.com/nipy/nipype/archive/0.9.1.tar.gz>`__]
+<https://github.com/nipy/nipype/archive/0.9.2.tar.gz>`__]
 
 Development: [`zip <http://github.com/nipy/nipype/zipball/master>`__ `tar.gz
 <http://github.com/nipy/nipype/tarball/master>`__]