Merge pull request #5 from nipy/master

Update nipype fork.

Author: sgiavasis

.travis.yml

@@ -4,7 +4,7 @@ python:
   - 2.7
 # Setup anaconda
 before_install:
-  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-2.0.3-Linux-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-2.0.3-Linux-x86_64.sh -O miniconda.sh; fi
+  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-2.2.2-Linux-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-2.2.2-Linux-x86_64.sh -O miniconda.sh; fi
   - chmod +x miniconda.sh
   - ./miniconda.sh -b
   - export PATH=/home/travis/anaconda/bin:$PATH
@@ -40,4 +40,4 @@ script:
 
 # Calculate coverage
 after_success:
-  - coveralls --config_file .coveragerc
+  - coveralls --config_file .coveragerc

doc/_templates/indexsidebar.html

@@ -6,7 +6,7 @@ <h3>{{ _('Links') }}</h3>
     <li>Code: <a href="http://github.com/nipy/nipype">Github</a> · <a href="http://github.com/nipy/nipype/issues">Bugs-Requests</a></li>
     <li>Forum: <a href="http://groups.google.com/group/nipy-user">User</a> · <a href="http://projects.scipy.org/mailman/listinfo/nipy-devel">Developer</a></li>
     <li>Info: <a href="http://nipy.org/software/license/index.html">License</a> · <a href="http://nipy.org/about/funding.html">Funding</a></li>
-    <li><a href="https://travis-ci.org/nipy/nipy"><img src="https://travis-ci.org/nipy/nipype.png?branch=master" alt="travis"></a> · <a href='https://coveralls.io/r/nipy/nipype'><img src='https://coveralls.io/repos/nipy/nipype/badge.png' alt='Coverage Status' /></a></li>
+    <li><a href="https://travis-ci.org/nipy/nipype"><img src="https://travis-ci.org/nipy/nipype.png?branch=master" alt="travis"></a> · <a href='https://coveralls.io/r/nipy/nipype'><img src='https://coveralls.io/repos/nipy/nipype/badge.png' alt='Coverage Status' /></a></li>
 </ul>
 
-{% endblock %}
+{% endblock %}

doc/index.rst

@@ -34,7 +34,7 @@
 
    Gorgolewski K, Burns CD, Madison C, Clark D, Halchenko YO, Waskom ML, Ghosh SS.
    (2011). Nipype: a flexible, lightweight and extensible neuroimaging data
-   processing framework in Python. Front. Neuroimform. 5:13. `Download`__
+   processing framework in Python. Front. Neuroinform. 5:13. `Download`__
 
    __ paper_
 

examples/fmri_openfmri.py

@@ -388,12 +388,16 @@ def get_subs(subject_id, conds, model_id, task_id):
 
 if __name__ == '__main__':
     import argparse
+    defstr = ' (default %(default)s)'
     parser = argparse.ArgumentParser(prog='fmri_openfmri.py',
                                      description=__doc__)
     parser.add_argument('-d', '--datasetdir', required=True)
-    parser.add_argument('-s', '--subject', default=None)
-    parser.add_argument('-m', '--model', default=1)
-    parser.add_argument('-t', '--task', default=1)
+    parser.add_argument('-s', '--subject', default=None,
+                        help="Subject name (e.g. 'sub001')")
+    parser.add_argument('-m', '--model', default=1,
+                        help="Model index" + defstr)
+    parser.add_argument('-t', '--task', default=1,
+                        help="Task index" + defstr)
     parser.add_argument("-o", "--output_dir", dest="outdir",
                         help="Output directory base")
     parser.add_argument("-w", "--work_dir", dest="work_dir",

examples/fmri_spm.py

@@ -15,6 +15,9 @@
 
 Import necessary modules from nipype."""
 
+from nipype import config
+config.enable_provenance()
+
 from nipype import spm, fsl
 
 # In order to use this example with SPM's matlab common runtime
@@ -389,6 +392,4 @@ def getstripdir(subject_id):
 
 if __name__ == '__main__':
     l1pipeline.run('MultiProc')
-#    l2pipeline.run()
-#    l1pipeline.write_graph()
-
+    l2pipeline.run('MultiProc')

nipype/external/provcopy.py

@@ -14,6 +14,7 @@
 import datetime
 import json
 import re
+import dateutil.parser
 import collections
 from collections import defaultdict
 
@@ -179,31 +180,10 @@
 
 
 #  Datatypes
-_r_xsd_dateTime = re.compile(""" ^
-    (?P<year>-?[0-9]{4}) - (?P<month>[0-9]{2}) - (?P<day>[0-9]{2})
-    T (?P<hour>[0-9]{2}) : (?P<minute>[0-9]{2}) : (?P<second>[0-9]{2})
-    (?P<microsecond>\.[0-9]{1,6})?
-    (?P<tz>
-      Z | (?P<tz_hr>[-+][0-9]{2}) : (?P<tz_min>[0-9]{2})
-    )?
-    $ """, re.X)
-
 attr2rdf = lambda attr: PROV[PROV_ID_ATTRIBUTES_MAP[attr].split('prov:')[1]].rdf_representation()
 
 def _parse_xsd_dateTime(s):
-    """Returns datetime or None."""
-    m = _r_xsd_dateTime.match(s)
-    if m is not None:
-        values = m.groupdict()
-        if values["microsecond"] is None:
-            values["microsecond"] = 0
-        else:
-            values["microsecond"] = values["microsecond"][1:]
-            values["microsecond"] += "0" * (6 - len(values["microsecond"]))
-        values = dict((k, int(v)) for k, v in values.iteritems() if not k.startswith("tz"))
-        return datetime.datetime(**values)
-    else:
-        return None
+    return dateutil.parser.parse(s)
 
 
 def _ensure_datetime(time):
@@ -359,7 +339,7 @@ def provn_representation(self):
 
     def json_representation(self):
         return {'$': self._uri, 'type': u'xsd:anyURI'}
-
+    
     def rdf_representation(self):
         return URIRef(self.get_uri())
 
@@ -773,7 +753,7 @@ def rdf(self, graph=None, subj=None):
                     obj = RDFLiteral(value)
                 graph.add((subj, pred, obj))
         return graph
-
+        
     def is_asserted(self):
         return self._asserted
 
@@ -788,7 +768,7 @@ def is_relation(self):
 class ProvElement(ProvRecord):
     def is_element(self):
         return True
-
+    
     def rdf(self, graph=None):
         if graph is None:
             graph = Graph()
@@ -1666,15 +1646,15 @@ def rdf(self, graph=None):
             # graph should not None here
             uri = self.get_identifier().rdf_representation()
             graph = Graph(graph.store, uri)
-
+        
         for prefix, namespace in self._namespaces.items():
             graph.bind(prefix, namespace.get_uri())
-
+        
         for record in self._records:
             if record.is_asserted():
                 record.rdf(graph)
         return graph
-
+    
     def get_provjson(self, **kw):
         """Return the `PROV-JSON <http://www.w3.org/Submission/prov-json/>`_ representation for the bundle/document.
 

nipype/interfaces/afni/tests/test_auto_Volreg.py

@@ -20,24 +20,27 @@ def test_Volreg_inputs():
     args=dict(argstr='%s',
     ),
     outputtype=dict(),
-    md1dfile=dict(position=-4,
-    argstr='-maxdisp1D %s',
-    ),
     zpad=dict(position=-5,
     argstr='-zpad %d',
     ),
     terminal_output=dict(mandatory=True,
     nohash=True,
     ),
-    environ=dict(nohash=True,
-    usedefault=True,
+    md1d_file=dict(name_source='in_file',
+    keep_extension=True,
+    position=-4,
+    name_template='%s_md.1D',
+    argstr='-maxdisp1D %s',
     ),
     in_file=dict(position=-1,
     mandatory=True,
     argstr='%s',
     ),
     copyorigin=dict(argstr='-twodup',
     ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
     out_file=dict(name_source='in_file',
     name_template='%s_volreg',
     argstr='-prefix %s',

nipype/interfaces/base.py

@@ -1116,6 +1116,8 @@ def run_command(runtime, output=None, timeout=0.01):
                              cwd=runtime.cwd,
                              env=runtime.environ)
     result = {}
+    errfile = os.path.join(runtime.cwd, 'stderr.nipype')
+    outfile = os.path.join(runtime.cwd, 'stdout.nipype')
     if output == 'stream':
         streams = [Stream('stdout', proc.stdout), Stream('stderr', proc.stderr)]
 
@@ -1152,8 +1154,6 @@ def _process(drain=0):
         result['stderr'] = stderr.split('\n')
         result['merged'] = ''
     if output == 'file':
-        errfile = os.path.join(runtime.cwd, 'stderr.nipype')
-        outfile = os.path.join(runtime.cwd, 'stdout.nipype')
         stderr = open(errfile, 'wt')
         stdout = open(outfile, 'wt')
         proc = subprocess.Popen(runtime.cmdline,

nipype/interfaces/cmtk/convert.py

@@ -23,7 +23,6 @@
     package_check('cfflib')
 except Exception, e:
     have_cfflib = False
-    warnings.warn('cfflib not installed')
 else:
     import cfflib as cf
 

nipype/interfaces/cmtk/nbs.py

@@ -17,7 +17,6 @@
     package_check('cviewer')
 except Exception, e:
     have_cv = False
-    warnings.warn('ConnectomeViewer not installed')
 else:
     import cviewer.libs.pyconto.groupstatistics.nbs as nbs