Merge branch 'master' into spm/gzip

* master: (76 commits)
  fixed paths
  Back to dev
  0.7 release
  Code cleanup.
  doc: updated inputs help to indicate FSL and AFNI inaccuracy when using bounds_by_brainmask
  Fix nipy#493
  Fixes nipy#459
  fixed doctests
  changelog
  fix: ants workflows setup
  BF: Fixed several issues with GroupAndStack interface
  DOC: Various clean up an improvements to docstrings.
  DOC: Added example to LookupMeta docstring
  ENH: Allow meta_keys input to LookupMeta be a mapping.
  minor fixes
  deprecated version should be a string, added AFNITraitedSpec for backward compatibility
  docs
  PEP8
  name_source can be a list, make "infolder" a deprecated name
  Removed unnecessary outputsspecs
  ...

Author: bpinsard

CHANGES

@@ -1,12 +1,18 @@
 Next release
 ============
 
+
+Release 0.7.0 (Dec 18, 2012)
+============================
+
 * ENH: Add basic support for LSF plugin.
-* ENH: New interfaces: ICC, Meshfix, ants.Register, C3dAffineTool, ants.JacobianDeterminant
+* ENH: New interfaces: ICC, Meshfix, ants.Register, C3dAffineTool, ants.JacobianDeterminant,
+       afni.AutoTcorrelate, DcmStack
 * ENH: New workflows: ants template building (both using 'ANTS' and the new 'antsRegistration')
 * ENH: New examples: how to use ANTS template building workflows (smri_ants_build_tmeplate), 
 	  how to set SGE specific options (smri_ants_build_template_new)
 * ENH: added no_flatten option to Merge
+* ENH: added versioning option and checking to traits
 * ENH: added deprecation metadata to traits
 * ENH: Slicer interfaces were updated to version 4.1
 

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">0.6.0</td><td align="right">pre-0.7</td>
+                <td align="left">0.7.0</td><td align="right">pre-0.8</td>
             </tr>
             <tr>
                 <td align="left"><a href="{{pathto('users/install')}}">Download</a></td>

doc/devel/interface_specs.rst

@@ -263,7 +263,15 @@ Common
 	should be symlinked, while `True` indicates that the contents should be 
 	copied over.
 
-``deprecated``
+``min_ver`` and ``max_ver``
+    These metadata determine if a particular trait will be available when a
+    given version of the underlying interface runs. Note that this check is
+    performed at runtime.::
+
+	    class RealignInputSpec(BaseInterfaceInputSpec):
+	        jobtype = traits.Enum('estwrite', 'estimate', 'write', min_ver='5',
+	                              usedefault=True)
+``deprecated`` and ``new_name``
     This is metadata for removing or renaming an input field from a spec.::
 
         class RealignInputSpec(BaseInterfaceInputSpec):
@@ -277,8 +285,8 @@ Common
     from current release. Raises `TraitError` after package version crosses the
     deprecation version.
 
-``new_name``
-    For inputs that are being renamed, one can specify the new name of the field.::
+    For inputs that are being renamed, one can specify the new name of the
+    field.::
 
         class RealignInputSpec(BaseInterfaceInputSpec):
             jobtype = traits.Enum('estwrite', 'estimate', 'write',
@@ -293,6 +301,11 @@ Common
     When `new_name` is provided it must exist as a trait, otherwise an exception
     will be raised.
 
+.. note::
+
+   The version information for `min_ver`, `max_ver` and `deprecated` has to be
+   provided as a string. For example, `min_ver='0.1'`.
+
 CommandLine
 ^^^^^^^^^^^
 

doc/documentation.rst

@@ -9,7 +9,7 @@ Documentation
    :Release: |version|
    :Date: |today|
 
-Previous versions: `0.5.3 <http://nipy.org/nipype/0.5.3>`_ `0.4.1 <http://nipy.org/nipype/0.4.1>`_
+Previous versions: `0.6 <http://nipy.org/nipype/0.6>`_ `0.5.3 <http://nipy.org/nipype/0.5.3>`_ 
 
 .. container:: doc2
 

doc/users/config_file.rst

@@ -109,6 +109,11 @@ Execution
 	data through (without copying) (possible values: ``true`` and
 	``false``; default value: ``false``)
 
+*stop_on_unknown_version*
+    If this is set to True, an underlying interface will raise an error, when no
+    version information is available. Please notify developers or submit a
+    patch.
+
 Example
 ~~~~~~~
 

doc/users/install.rst

@@ -9,8 +9,8 @@ This page covers the necessary steps to install Nipype.
 Download
 --------
 
-Release 0.6.0: [`zip <http://github.com/nipy/nipype/zipball/0.6.0>`_ `tar
-<http://github.com/nipy/nipype/tarball/0.6.0>`_]
+Release 0.7.0: [`zip <https://github.com/nipy/nipype/archive/0.7.zip>`_ `tar.gz
+<https://github.com/nipy/nipype/archive/0.7.tar.gz>`_]
 
 Development: [`zip <http://github.com/nipy/nipype/zipball/master>`_ `tar
 <http://github.com/nipy/nipype/tarball/master>`_]