Merge branch 'master' into fsl_model

* master: (209 commits)
  fix: label2vol test
  fix: randomise - removed os.getcwd
  fix: label2vol mistake
  fix: randomise outputs
  sty: white space
  BUG: Process Directories as data sinks
  fixed matlab example
  DOC: fix link to caching example
  fix: afni tests
  fix: use correct outfile name generation routine
  fix: first filename bug
  fix: absolute path on outputs from fslmaths
  fix: changed sge to use subprocess directly
  fix: check for pbs
  fix: example fixed to import TraitedSpec
  fix: removed extra parenthesis
  fix: refined pbs to directly use subprocess instead of CommandLine
  Fixed mapnode isdefined bug
  Added hash_files description.
  Fixed output files hashing and returned paths.
  ...

Author: bpinsard

CHANGES

@@ -1,3 +1,26 @@
+Release 0.6.0 (Jun 30, 2012)
+============================
+
+* API: display variable no longer encoded as inputs in commandline interfaces
+
+* 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, 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)
 ============================
 

build_docs.py

@@ -21,7 +21,7 @@
 # Sphinx import.
 from sphinx.setup_command import BuildDoc
 
-_info_fname = pjoin('nipype', 'info.py')
+_info_fname = pjoin(os.path.dirname(__file__), 'nipype', 'info.py')
 INFO_VARS = {}
 exec(open(_info_fname, 'rt').read(), {}, INFO_VARS)
 

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/matlab_interface_devel.rst

@@ -90,13 +90,10 @@ By subclassing **MatlabCommand** for your main class, and **MatlabInputSpec** fo
 	    Examples
 	    --------
 
-            >>> hello = HelloWorld(matlab_cmd = 'mymatlab')
-            >>> hello.inputs.name = 'Monty'
-            >>> hello.inputs.mfile = True #creates mfile
-            >>> hello.inputs.paths = '/path/to/matlab/toolbox'
-            >>> hello.inputs.script_file = 'helloworld_pyscript.m'
+            >>> hello = HelloWorld()
+            >>> hello.inputs.name = 'hello_world'
             >>> out = hello.run()
-            >>> out.outputs['matlab_output'] 
+            >>> print out.outputs.matlab_output 
             """
             input_spec = HelloWorldInputSpec
             output_spec = HelloWorldOutputSpec

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/index.rst

@@ -1,3 +1,10 @@
+.. admonition:: Announcement
+
+   Nipype Connectivity Workshop 2012 in Magdeburg, Germany: Sep 8-9, 2012: 
+   `Information and Registration`__
+
+   __ http://nipype.blogspot.com
+
 .. list-table::
 
  * -  .. image:: images/nipype_architecture_overview2.png
@@ -14,11 +21,11 @@
       to existing neuroimaging software and facilitates interaction between
       these packages within a single workflow. Nipype provides an environment
       that encourages interactive exploration of algorithms from different
-      packages (e.g., SPM_, FSL_, FreeSurfer_, Camino_, MRtrix_, AFNI_, Slicer_),
-      eases the design of workflows within and between packages, and reduces the
-      learning curve necessary to use different packages. Nipype is creating a
-      collaborative platform for neuroimaging software development in a
-      high-level language and addressing limitations of existing pipeline
+      packages (e.g., SPM_, FSL_, FreeSurfer_, Camino_, MRtrix_, MNE_, AFNI_, 
+      Slicer_), eases the design of workflows within and between packages, and
+      reduces the learning curve necessary to use different packages. Nipype is
+      creating a collaborative platform for neuroimaging software development 
+      in a high-level language and addressing limitations of existing pipeline
       systems.
 
       *Nipype* allows you to:

doc/links_names.txt

@@ -91,6 +91,7 @@
 .. _Camino: http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php
 .. _Camino2Trackvis: http://camino-trackvis.sourceforge.net/
 .. _MRtrix: http://www.brain.org.au/software/mrtrix/index.html
+.. _MNE: https://martinos.org/mne/index.html
 
 .. General software
 .. _gcc: http://gcc.gnu.org

doc/quickstart.rst

@@ -15,8 +15,11 @@ Downloading and installing
 Beginner's guide
 ================
 
-By Michael Notter. `Available here`__
+Introductory slides. `Available here`__
 
+Michael Notter's guide. `Available here`__
+
+__ http://satra.github.com/intro2nipype
 __ http://miykael.github.com/nipype-beginner-s-guide/index.html
 
 User guides