Merge remote-tracking branch 'upstream/master' into label2vol

Author: akeshavan

CHANGES

@@ -1,12 +1,24 @@
-Since last release
-==================
+Release 0.6.0 (Jun 30, 2012)
+============================
 
 * API: display variable no longer encoded as inputs in commandline interfaces
 
-* ENH: New interfaces: MySQLSink, nipy.Similarity, WatershedBEM,
+* ENH: input hash not modified when environment DISPLAY is changed
+* ENH: support for 3d files for TSNR calculation
+* ENH: Preliminary support for graph submission with SGE, PBS and Soma Workflow
+* ENH: New interfaces: MySQLSink, nipy.Similarity, WatershedBEM, MRIsSmooth,
        NetworkBasedStatistic, Atropos, N4BiasFieldCorrection, ApplyTransforms,
-       fs.MakeAverageSubject
-
+       fs.MakeAverageSubject, epidewarp.fsl, WarpTimeSeriesImageMultiTransform,
+       AVScale, mri_ms_LDA
+* ENH: simple interfaces for spm
+
+* FIX: CompCor component calculation was erroneous
+* FIX: filename generation for AFNI and PRELUDE
+* FIX: improved slicer module autogeneration
+* FIX: added missing options for BBRegsiter
+* FIX: functionality of remove_unnecessary_ouputs cleaned up
+* FIX: local hash check works with appropriate inputs
+* FIX: Captures all stdout from commandline programs
 * FIX: Afni outputs should inherit from TraitedSpec
 
 Release 0.5.3 (Mar 23, 2012)

doc/_templates/sidebar_versions.html

@@ -17,7 +17,7 @@ <h3>{{ _('Versions') }}</h3>
                 <td align="left">Release</td><td align="right">Devel</td>
             </tr>
             <tr>
-                <td align="left">0.5.3</td><td align="right">pre-0.6</td>
+                <td align="left">0.6.0</td><td align="right">pre-0.7</td>
             </tr>
             <tr>
                 <td align="left"><a href="{{pathto('users/install')}}">Download</a></td>

doc/devel/interface_specs.rst

@@ -194,6 +194,9 @@ Common
 	    TraitError: The 'infile' trait of a BetInputSpec instance must be a file 
 	    name, but a value of 'does_not_exist.nii' <type 'str'> was specified.
 	    
+``hash_files``
+	To be used with inputs that are defining output filenames. When this flag is set to false any Nipype will not try to hash any files described by this input. This is useful to avoid rerunning when the specified output file already exists and has changed.
+	    
 ``desc``
 	All trait objects have a set of default metadata attributes.  ``desc``
 	is one of those and is used as a simple, one-line docstring.  The

doc/devel/python_interface_devel.rst

@@ -10,7 +10,7 @@ do is to define inputs, outputs, _run_interface() (not run()), and _list_outputs
 .. testcode::
 
     from nipype.interfaces.base import BaseInterface, \
-        BaseInterfaceInputSpec, traits, File
+        BaseInterfaceInputSpec, traits, File, TraitedSpec
     from nipype.utils.filemanip import split_filename
 
     import nibabel as nb

doc/documentation.rst

@@ -9,7 +9,7 @@ Documentation
    :Release: |version|
    :Date: |today|
 
-Previous version: `0.4.1 <http://nipy.org/nipype/0.4.1>`_
+Previous versions: `0.5.3 <http://nipy.org/nipype/0.5.3>`_ `0.4.1 <http://nipy.org/nipype/0.4.1>`_
 
 .. container:: doc2
 

doc/quickstart.rst

@@ -16,6 +16,7 @@ Beginner's guide
 ================
 
 Introductory slides. `Available here`__
+
 Michael Notter's guide. `Available here`__
 
 __ http://satra.github.com/intro2nipype

doc/users/install.rst

@@ -9,8 +9,8 @@ This page covers the necessary steps to install Nipype.
 Download
 --------
 
-Release 0.5.3: [`zip <http://github.com/nipy/nipype/zipball/0.5.3>`_ `tar
-<http://github.com/nipy/nipype/tarball/0.5.3>`_]
+Release 0.6.0: [`zip <http://github.com/nipy/nipype/zipball/0.6.0>`_ `tar
+<http://github.com/nipy/nipype/tarball/0.6.0>`_]
 
 Development: [`zip <http://github.com/nipy/nipype/zipball/master>`_ `tar
 <http://github.com/nipy/nipype/tarball/master>`_]
@@ -114,7 +114,7 @@ Must Have
 
 Python_ 2.6 -2.7
 
-Nibabel_ 1.0
+Nibabel_ 1.0 - 1.2
   Neuroimaging file i/o library
 
 NetworkX_ 1.0 - 1.4
@@ -135,7 +135,7 @@ Enthought_ Traits_ 4.0.0
 Strong Recommendations
 ~~~~~~~~~~~~~~~~~~~~~~
 
-IPython_ 0.10.2 - 0.12
+IPython_ 0.10.2 - 0.13
   Interactive python environment. This is necessary for some parallel
   components of the pipeline engine.
 

nipype/info.py

@@ -8,7 +8,7 @@
 # full release.  '.dev' as a _version_extra string means this is a development
 # version
 _version_major = 0
-_version_minor = 6
+_version_minor = 7
 _version_micro = 0
 _version_extra = '.dev'
 

nipype/interfaces/afni/base.py

@@ -21,9 +21,9 @@
 class Info(object):
     """Handle afni output type and version information.
     """
-    __outputtype = 'NIFTI_GZ'
+    __outputtype = 'AFNI'
     ftypes = {'NIFTI': '.nii',
-              'AFNI': '.BRIK',
+              'AFNI': '+orig.BRIK',
               'NIFTI_GZ': '.nii.gz'}
 
     @staticmethod
@@ -69,7 +69,7 @@ def outputtype_to_ext(cls, outputtype):
     def outputtype(cls):
         """AFNI has no environment variables,
         Output filetypes get set in command line calls
-        Nipype uses NIFTI_GZ as default
+        Nipype uses AFNI as default
 
 
         Returns
@@ -78,7 +78,7 @@ def outputtype(cls):
         """
         #warn(('AFNI has no environment variable that sets filetype '
         #      'Nipype uses NIFTI_GZ as default'))
-        return 'NIFTI_GZ'
+        return 'AFNI'
 
 
     @staticmethod
@@ -96,7 +96,7 @@ def standard_image(img_name):
 
 
 class AFNITraitedSpec(CommandLineInputSpec):
-    outputtype =  traits.Enum('NIFTI_GZ', Info.ftypes.keys(),
+    outputtype =  traits.Enum('AFNI', Info.ftypes.keys(),
                               desc = 'AFNI output filetype')