Merge remote-tracking branch 'upstream/master' into fix/Py3UseBuiltinOpen

Author: oesteban

.travis.yml

@@ -8,6 +8,7 @@ python:
 env:
 - INSTALL_DEB_DEPENDECIES=true
 - INSTALL_DEB_DEPENDECIES=false
+- INSTALL_DEB_DEPENDECIES=true DUECREDIT_ENABLE=yes
 before_install:
 - wget http://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh
   -O /home/travis/.cache/miniconda.sh
@@ -32,6 +33,7 @@ install:
 #   conda install -y vtk mayavi; fi
 - conda install -y nipype
 - pip install python-coveralls coverage doctest-ignore-unicode
+- if [ ! -z "$DUECREDIT_ENABLE"]; then pip install duecredit; fi
 - rm -r /home/travis/miniconda/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype*
 - pip install -r requirements.txt
 - pip install -e .

nipype/__init__.py

@@ -13,6 +13,7 @@
 from .utils.config import NipypeConfig
 from .fixes.numpy.testing import nosetester
 from .utils.logger import Logging
+from .refs import due
 
 try:
     import faulthandler

nipype/external/due.py

@@ -0,0 +1,72 @@
+# emacs: at the end of the file
+# ex: set sts=4 ts=4 sw=4 et:
+# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### #
+"""
+
+Stub file for a guaranteed safe import of duecredit constructs:  if duecredit
+is not available.
+
+To use it, place it into your project codebase to be imported, e.g. copy as
+
+    cp stub.py /path/tomodule/module/due.py
+
+Note that it might be better to avoid naming it duecredit.py to avoid shadowing
+installed duecredit.
+
+Then use in your code as
+
+    from .due import due, Doi, BibTeX
+
+See  https://github.com/duecredit/duecredit/blob/master/README.md for examples.
+
+Origin:     Originally a part of the duecredit
+Copyright:  2015-2016  DueCredit developers
+License:    BSD-2
+"""
+
+__version__ = '0.0.5'
+
+
+class InactiveDueCreditCollector(object):
+    """Just a stub at the Collector which would not do anything"""
+    def _donothing(self, *args, **kwargs):
+        """Perform no good and no bad"""
+        pass
+
+    def dcite(self, *args, **kwargs):
+        """If I could cite I would"""
+        def nondecorating_decorator(func):
+            return func
+        return nondecorating_decorator
+
+    cite = load = add = _donothing
+
+    def __repr__(self):
+        return self.__class__.__name__ + '()'
+
+
+def _donothing_func(*args, **kwargs):
+    """Perform no good and no bad"""
+    pass
+
+try:
+    from duecredit import due, BibTeX, Doi, Url
+    if 'due' in locals() and not hasattr(due, 'cite'):
+        raise RuntimeError(
+            "Imported due lacks .cite. DueCredit is now disabled")
+except Exception as e:
+    if type(e).__name__ != 'ImportError':
+        import logging
+        logging.getLogger("duecredit").error(
+            "Failed to import duecredit due to %s" % str(e))
+    # Initiate due stub
+    due = InactiveDueCreditCollector()
+    BibTeX = Doi = Url = _donothing_func
+
+# Emacs mode definitions
+# Local Variables:
+# mode: python
+# py-indent-offset: 4
+# tab-width: 4
+# indent-tabs-mode: nil
+# End:

nipype/interfaces/base.py

@@ -41,6 +41,7 @@
 from .traits_extension import (
     traits, Undefined, TraitDictObject, TraitListObject, TraitError, isdefined, File,
     Directory, DictStrStr, has_metadata)
+from ..external.due import due
 
 runtime_profile = str2bool(config.get('execution', 'profile_runtime'))
 nipype_version = LooseVersion(__version__)
@@ -753,6 +754,7 @@ class BaseInterface(Interface):
     _version = None
     _additional_metadata = []
     _redirect_x = False
+    references_ = []
 
     def __init__(self, **inputs):
         if not self.input_spec:
@@ -775,12 +777,24 @@ 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
@@ -1005,6 +1019,13 @@ 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__
+            due.cite(**r)
+
     def run(self, **inputs):
         """Execute this interface.
 
@@ -1024,6 +1045,8 @@ 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(),

nipype/interfaces/spm/base.py

@@ -32,6 +32,8 @@
 from ..base import (BaseInterface, traits, isdefined, InputMultiPath,
                     BaseInterfaceInputSpec, Directory, Undefined)
 from ..matlab import MatlabCommand
+from ...external.due import due, Doi, BibTeX
+
 
 __docformat__ = 'restructuredtext'
 logger = logging.getLogger('interface')
@@ -234,6 +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/refs.py

@@ -0,0 +1,17 @@
+
+# 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 .external.due import due, Doi, BibTeX
+
+due.cite(Doi("10.3389/fninf.2011.00013"),
+         description="A flexible, lightweight and extensible neuroimaging data"
+                     " processing framework in Python",
+         path="nipype",
+         tags=["implementation"],)
+
+due.cite(Doi("10.5281/zenodo.50186"),
+         description="A flexible, lightweight and extensible neuroimaging data"
+                     " processing framework in Python",
+         path="nipype",
+         tags=["implementation"],)

setup.py

@@ -241,7 +241,7 @@ def _package_status(pkg_name, version, version_getter, checker):
 
 # Get version and release info, which is all stored in nipype/info.py
 ver_file = os.path.join('nipype', 'info.py')
-exec(open(ver_file).read())
+exec(open(ver_file).read(), locals())
 
 # Prepare setuptools args
 if 'setuptools' in sys.modules: