Merge branch 'master' into enh/GraftWorkflow

Conflicts:
	CHANGES

Author: oesteban

CHANGES

@@ -2,6 +2,18 @@ Next release
 ============
 
 * ENH: [Interfaced|Graft]Workflows (https://github.com/nipy/nipype/pull/882)
+* FIX: Enable absolute path definitions in DCMStack (https://github.com/nipy/nipype/pull/1089,
+       replaced by https://github.com/nipy/nipype/pull/1093)
+* ENH: New algorithm: mesh.WarpPoints applies displacements fields to point sets.
+* ENH: New mesh.MeshWarpMaths to operate on surface-defined warpings
+       (https://github.com/nipy/nipype/pull/1016)
+* FIX: Refactor P2PDistance, change name to ComputeMeshWarp, add regression tests,
+       fix bug in area weighted distance, and added optimizations
+       (https://github.com/nipy/nipype/pull/1016)
+* ENH: Add an option not to resubmit Nodes that finished running when using SGEGraph (https://github.com/nipy/nipype/pull/1002)
+* FIX: FUGUE is now properly listing outputs. (https://github.com/nipy/nipype/pull/978)
+* ENH: Improved FieldMap-Based (FMB) workflow for correction of susceptibility distortions in EPI seqs.
+       (https://github.com/nipy/nipype/pull/1019)
 * ENH: Dropped support for now 7 years old Python 2.6 (https://github.com/nipy/nipype/pull/1069)
 * FIX: terminal_output is not mandatory anymore (https://github.com/nipy/nipype/pull/1070)
 * ENH: Added "nipype_cmd" tool for running interfaces from the command line (https://github.com/nipy/nipype/pull/795)
@@ -41,6 +53,8 @@ Next release
 * ENH: Usability improvements in cluster environments (https://github.com/nipy/nipype/pull/1025)
 * ENH: ANTs JointFusion() (https://github.com/nipy/nipype/pull/1042)
 * ENH: Added csvReader() utility (https://github.com/nipy/nipype/pull/1044)
+* FIX: typo in nipype.interfaces.freesurfer.utils.py Tkregister2 (https://github.com/nipy/nipype/pull/1083)
+* FIX: SSHDataGrabber outputs now return full path to the grabbed/downloaded files. (https://github.com/nipy/nipype/pull/1086)
 
 Release 0.10.0 (October 10, 2014)
 ============

doc/quickstart.rst

@@ -16,7 +16,7 @@ Downloading and installing
 Beginner's guide
 ================
 
-Beginner's tutorials (IPython Notebooks). `Availible here`__
+Beginner's tutorials (IPython Notebooks). `Available here`__
 
 Michael Notter's Nipype guide. `Available here`__
 

doc/users/plugins.rst

@@ -136,13 +136,28 @@ particular node might use more resources than other nodes in a workflow.
   this local configuration::
 
      node.plugin_args = {'qsub_args': '-l nodes=1:ppn=3', 'overwrite': True}
+	 
+SGEGraph
+~~~~~~~~
+SGEGraph_ is a exuction plugin working with Sun Grid Engine that allows for
+submitting entire graph of dependent jobs at once. This way Nipype does not 
+need to run a monitoring process - SGE takes care of this.
+
+.. note::
+
+  When rerunning unfinished workflows using SGEGraph you may decide not to 
+  submit jobs for Nodes that previously finished running. This can speed up
+  execution, but new or modified inputs that would previously trigger a Node
+  to rerun will be ignored. The following option turns on this functionality::
+
+     workflow.run(plugin='SGEGraph', plugin_args = {'dont_resubmit_completed_jobs': True})
 
 LSF
 ---
 
-Submitting via LSF is almost identical to SGE above above except for the optional arguments field:
+Submitting via LSF is almost identical to SGE above above except for the optional arguments field::
 
-       workflow.run(plugin='LSF')
+    workflow.run(plugin='LSF')
 
 Optional arguments::
 
@@ -168,7 +183,7 @@ DAGMan
 ~~~~~~
 
 With its DAGMan_ component HTCondor_ (previously Condor) allows for submitting
-entire graphs of dependent jobs at once. With the ``CondorDAGMan`` plug-in
+entire graphs of dependent jobs at once (similar to SGEGraph_). With the ``CondorDAGMan`` plug-in
 Nipype can utilize this functionality to submit complete workflows directly and
 in a single step.  Consequently, and in contrast to other plug-ins, workflow
 execution returns almost instantaneously -- Nipype is only used to generate the