Merge branch 'master' of https://github.com/nipy/nipype into nipy-master

Conflicts:
	nipype/interfaces/fsl/preprocess.py

Author: sgiavasis

.travis.yml

@@ -20,5 +20,12 @@ before_install:
     - source /etc/fsl/fsl.sh
     - virtualenv --system-site-packages ~/virtualenv/this
     - source ~/virtualenv/this/bin/activate
-install: python setup.py build_ext --inplace
-script: make test
+    - pip install https://github.com/RDFLib/rdflib/archive/master.zip
+    - pip install https://github.com/satra/prov/archive/enh/rdf.zip
+install:
+    - source ~/virtualenv/this/bin/activate
+    - python setup.py build_ext --inplace
+script:
+    - source ~/virtualenv/this/bin/activate
+    - make test
+

CHANGES

@@ -1,7 +1,9 @@
 Next release
 ============
 
-* ENH: New interfaces: spm.ResliceToReference
+* ENH: SelectFiles: a streamlined version of DataGrabber
+* ENH: New interfaces: spm.ResliceToReference, FuzzyOverlap, afni.AFNItoNIFTI
+* ENH: W3C PROV support with optional RDF export built into Nipype
 
 * FIX: Deals properly with 3d files in SPM Realign
 

doc/devel/index.rst

@@ -17,6 +17,7 @@ conventions documented in the `NIPY Developers Guide
    writing_custom_interfaces
    gitwash/index   
    architecture
+   provenance
 
 
 .. include:: ../links_names.txt

doc/devel/provenance.rst

@@ -0,0 +1,21 @@
+================
+W3C PROV support
+================
+
+Overview
+--------
+
+We're using the the `W3C PROV data model <http://www.w3.org/TR/prov-dm/`_ to
+capture and represent provenance in Nipype.
+
+For an overview see:
+
+`PROV-DM overview <http://slideviewer.herokuapp.com/url/raw.github.com/ni-/notebooks/master/NIDMIntro.ipynb>`_
+
+Each interface writes out a provenance.json (currently prov-json) or
+provenance.rdf (if rdflib is available) file. The workflow engine can also
+write out a provenance of the workflow if instructed.
+
+This is very much an experimental feature as we continue to refine how exactly
+the provenance should be stored and how such information can be used for
+reporting or reconstituting workflows.

doc/sphinxext/README.txt

@@ -5,13 +5,10 @@
 We've copied these sphinx extensions over from nipy-core.  Any edits
 should be done upstream in nipy-core, not here in nipype!
 
-Thesea are a few sphinx extensions we are using to build the nipy
+These a are a few sphinx extensions we are using to build the nipy
 documentation.  In this file we list where they each come from, since we intend
 to always push back upstream any modifications or improvements we make to them.
 
-* From matploltlib:
-  * inheritance_diagram.py
-
 * From numpy:
   * numpy_ext
 

doc/sphinxext/autosummary_generate.py

@@ -54,7 +54,7 @@ def main():
     for name, path in sorted(names.items()):
         if options.output_dir is not None:
             path = options.output_dir
-        
+
         if not os.path.isdir(path):
             os.makedirs(path)
 
@@ -121,7 +121,7 @@ def get_documented_in_docstring(name, module=None, filename=None):
     """
     Find out what items are documented in the given object's docstring.
     See `get_documented_in_lines`.
-    
+
     """
     try:
         obj, real_name = import_by_name(name)
@@ -136,7 +136,7 @@ def get_documented_in_docstring(name, module=None, filename=None):
 def get_documented_in_lines(lines, module=None, filename=None):
     """
     Find out what items are documented in the given lines
-    
+
     Returns
     -------
     documented : dict of list of (filename, title, keyword, toctree)
@@ -153,15 +153,15 @@ def get_documented_in_lines(lines, module=None, filename=None):
     module_re = re.compile(r'^\.\.\s+(current)?module::\s*([a-zA-Z0-9_.]+)\s*$')
     autosummary_item_re = re.compile(r'^\s+([_a-zA-Z][a-zA-Z0-9_.]*)\s*.*?')
     toctree_arg_re = re.compile(r'^\s+:toctree:\s*(.*?)\s*$')
-    
+
     documented = {}
-   
+
     current_title = []
     last_line = None
     toctree = None
     current_module = module
     in_autosummary = False
-    
+
     for line in lines:
         try:
             if in_autosummary: