fix due approach: use references_ member

Author: alexsavio

nipype/__init__.py

@@ -18,10 +18,6 @@
 from .fixes.numpy.testing import nosetester
 from .refs import due
 
-<<<<<<< 5129557c96d5481bb93d64e157a0faf4caa729eb
-
-=======
->>>>>>> fix merge
 try:
     import faulthandler
     faulthandler.enable()

nipype/due.py

@@ -748,6 +748,7 @@ class BaseInterface(Interface):
     _version = None
     _additional_metadata = []
     _redirect_x = False
+    references_ = []
 
     def __init__(self, **inputs):
         if not self.input_spec:
@@ -770,12 +771,24 @@ def help(cls, returnhelp=False):
             docstring = ['']
 
         allhelp = '\n'.join(docstring + cls._inputs_help() + [''] +
-                            cls._outputs_help() + [''])
+                            cls._outputs_help() + [''] +
+                            cls._refs_help() + [''])
         if returnhelp:
             return allhelp
         else:
             print(allhelp)
 
+    @classmethod
+    def _refs_help(cls):
+        """ Prints interface references.
+        """
+        helpstr = ['References::']
+
+        for r in cls.references_:
+            helpstr += [repr(r['entry'])]
+
+        return helpstr
+
     @classmethod
     def _get_trait_desc(self, inputs, name, spec):
         desc = spec.desc
@@ -1000,6 +1013,13 @@ def _run_interface(self, runtime):
         """
         raise NotImplementedError
 
+    def _duecredit_cite(self):
+        """ Add the interface references to the duecredit citations
+        """
+        for r in self._references:
+            r['path'] = self.__module__ # TODO: check if this is correct
+            due.cite(**r, path=self.__module__)
+
     def run(self, **inputs):
         """Execute this interface.
 
@@ -1019,6 +1039,8 @@ def run(self, **inputs):
         self._check_mandatory_inputs()
         self._check_version_requirements(self.inputs)
         interface = self.__class__
+        self._duecredit_cite()
+
         # initialize provenance tracking
         env = deepcopy(dict(os.environ))
         runtime = Bunch(cwd=os.getcwd(),
@@ -1197,7 +1219,7 @@ def _read(self, drain):
 # Get number of threads for process
 def _get_num_threads(proc):
     """Function to get the number of threads a process is using
-    NOTE: If 
+    NOTE: If
 
     Parameters
     ----------

nipype/interfaces/base.py

@@ -12,5 +12,3 @@
                     PairedTTestDesign, MultipleRegressionDesign)
 from .utils import (Analyze2nii, CalcCoregAffine, ApplyTransform, Reslice,
                     ApplyInverseDeformation, ResliceToReference, DicomImport)
-
-from .refs import due

nipype/interfaces/spm/__init__.py

@@ -35,6 +35,7 @@
 from ..matlab import MatlabCommand
 from ...utils import spm_docs as sd
 from ...external.six import string_types
+from ...external.due import due, Doi, BibTeX
 from ... import logging
 logger = logging.getLogger('interface')
 
@@ -235,6 +236,17 @@ class SPMCommand(BaseInterface):
     _paths = None
     _use_mcr = None
 
+    references_ = [{'entry': BibTeX("@book{FrackowiakFristonFrithDolanMazziotta1997,"
+                                    "author={R.S.J. Frackowiak, K.J. Friston, C.D. Frith, R.J. Dolan, and J.C. Mazziotta},"
+                                    "title={Human Brain Function},"
+                                    "publisher={Academic Press USA},"
+                                    "year={1997},"
+                                    "}"),
+                    'description': 'The fundamental text on Statistical Parametric Mapping (SPM)',
+                    # 'path': "nipype.interfaces.spm",
+                    'tags': ['implementation'],
+                    }]
+
     def __init__(self, **inputs):
         super(SPMCommand, self).__init__(**inputs)
         self.inputs.on_trait_change(self._matlab_cmd_update, ['matlab_cmd',

nipype/interfaces/spm/base.py

@@ -2,7 +2,7 @@
 # Use duecredit (duecredit.org) to provide a citation to relevant work to
 # be cited. This does nothing, unless the user has duecredit installed,
 # And calls this with duecredit (as in `python -m duecredit script.py`):
-from .due import due, Doi, BibTeX
+from .external.due import due, Doi, BibTeX
 
 due.cite(Doi("10.3389/fninf.2011.00013"),
          description="A flexible, lightweight and extensible neuroimaging data"