Merge remote-tracking branch 'upstream/master' into oar_support

Conflicts:
	CHANGES

Author: demianw

.gitignore

@@ -5,6 +5,7 @@
 /nipype/build
 /nipype/nipype.egg-info
 /doc/_build
+/doc/preproc
 /doc/users/examples
 /doc/api/generated
 *.pyc
@@ -17,3 +18,6 @@
 .DS_Store
 nipype/testing/data/von-ray_errmap.nii.gz
 nipype/testing/data/von_errmap.nii.gz
+crash*.pklz
+.coverage
+htmlcov/

.travis.yml

@@ -3,16 +3,17 @@ cache:
 language: python
 python:
 - 2.7
+- 3.4
 env:
 - INSTALL_DEB_DEPENDECIES=true
 - INSTALL_DEB_DEPENDECIES=false
 before_install:
-- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
-  -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-3.6.0-Linux-x86_64.sh
+- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
+  -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
   -O miniconda.sh; fi
 - chmod +x miniconda.sh
 - "./miniconda.sh -b"
-- export PATH=/home/travis/miniconda/bin:$PATH
+- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then export PATH=/home/travis/miniconda2/bin:$PATH; else export PATH=/home/travis/miniconda3/bin:$PATH; fi
 - if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi
 - if $INSTALL_DEB_DEPENDECIES; then sudo ln -s /run/shm /dev/shm; fi
 - if $INSTALL_DEB_DEPENDECIES; then bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh);
@@ -27,15 +28,16 @@ install:
 - conda create -n testenv --yes pip python=$TRAVIS_PYTHON_VERSION
 - source activate testenv
 - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then pip install ordereddict; fi
-- conda install --yes numpy scipy nose traits networkx dateutil
-- pip install nibabel
+- conda install --yes numpy scipy nose networkx dateutil
+- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then conda install --yes traits; else pip install traits; fi
 - pip install python-coveralls
 - pip install nose-cov
+- pip install -r requirements.txt  # finish remaining requirements
 - pip install https://github.com/RDFLib/rdflib/archive/master.zip
 - pip install https://github.com/trungdong/prov/archive/rdf.zip
 - python setup.py install
 script:
-- nosetests --with-doctest --with-cov --cov nipype --cov-config .coveragerc --logging-level=INFO
+- python -W once:FSL:UserWarning:nipype `which nosetests` --with-doctest --with-cov --cover-package nipype --cov-config .coveragerc --logging-level=INFO
 after_success:
 - coveralls --config_file .coveragerc
 deploy:

CHANGES

@@ -2,6 +2,7 @@ Next Release
 ============
 
 * ENH: Added an OAR scheduler plugin (https://github.com/nipy/nipype/pull/1259)
+* ENH: New ANTs interface: antsBrainExtraction (https://github.com/nipy/nipype/pull/1231)
 * API: Default model level for the bedpostx workflow has been set to "2" following FSL 5.0.9 lead
 * ENH: New interfaces for interacting with AWS S3: S3DataSink and S3DataGrabber (https://github.com/nipy/nipype/pull/1201)
 

THANKS.rst

@@ -10,9 +10,11 @@ Contributors to Nipype include but are not limited to:
   * Aimi Watanabe
   * Alexander Schaefer
   * Alexandre Gramfort
+  * Alexandre Savio
   * Anisha Keshavan
   * Ariel Rokem
   * Ben Acland
+  * Ben Cipollini
   * Basile Pinsard
   * Brendan Moloney
   * Brian Cheung

build_docs.py

@@ -8,6 +8,8 @@
     python setup.py build_sphinx
 """
 
+from __future__ import print_function
+
 # Standard library imports
 import sys
 import os
@@ -27,23 +29,25 @@
 
 ################################################################################
 # Distutils Command class for installing nipype to a temporary location.
+
+
 class TempInstall(Command):
     temp_install_dir = os.path.join('build', 'install')
 
     def run(self):
         """ build and install nipype in a temporary location. """
         install = self.distribution.get_command_obj('install')
         install.install_scripts = self.temp_install_dir
-        install.install_base    = self.temp_install_dir
+        install.install_base = self.temp_install_dir
         install.install_platlib = self.temp_install_dir
         install.install_purelib = self.temp_install_dir
-        install.install_data    = self.temp_install_dir
-        install.install_lib     = self.temp_install_dir
+        install.install_data = self.temp_install_dir
+        install.install_lib = self.temp_install_dir
         install.install_headers = self.temp_install_dir
         install.run()
 
         # Horrible trick to reload nipype with our temporary instal
-        for key in sys.modules.keys():
+        for key in list(sys.modules.keys()):
             if key.startswith('nipype'):
                 sys.modules.pop(key, None)
         sys.path.append(os.path.abspath(self.temp_install_dir))
@@ -62,13 +66,12 @@ def finalize_options(self):
 # Distutils Command class for API generation
 class APIDocs(TempInstall):
     description = \
-    """generate API docs """
+        """generate API docs """
 
     user_options = [
         ('None', None, 'this command has no options'),
         ]
 
-
     def run(self):
         # First build the project and install it to a temporary location.
         TempInstall.run(self)
@@ -131,30 +134,29 @@ def run(self):
 
         def zip_docs(self):
             if not os.path.exists(DOC_BUILD_DIR):
-                raise OSError, 'Doc directory does not exist.'
+                raise OSError('Doc directory does not exist.')
             target_file = os.path.join('doc', 'documentation.zip')
             # ZIP_DEFLATED actually compresses the archive. However, there
             # will be a RuntimeError if zlib is not installed, so we check
             # for it. ZIP_STORED produces an uncompressed zip, but does not
             # require zlib.
             try:
                 zf = zipfile.ZipFile(target_file, 'w',
-                                            compression=zipfile.ZIP_DEFLATED)
+                                     compression=zipfile.ZIP_DEFLATED)
             except RuntimeError:
                 warnings.warn('zlib not installed, storing the docs '
-                                'without compression')
+                              'without compression')
                 zf = zipfile.ZipFile(target_file, 'w',
-                                            compression=zipfile.ZIP_STORED)
+                                     compression=zipfile.ZIP_STORED)
 
             for root, dirs, files in os.walk(DOC_BUILD_DIR):
                 relative = relative_path(root)
                 if not relative.startswith('.doctrees'):
                     for f in files:
                         zf.write(os.path.join(root, f),
-                                os.path.join(relative, 'html_docs', f))
+                                 os.path.join(relative, 'html_docs', f))
             zf.close()
 
-
         def finalize_options(self):
             """ Override the default for the documentation build
                 directory.
@@ -164,23 +166,25 @@ def finalize_options(self):
 
 ################################################################################
 # Distutils Command class to clean
+
+
 class Clean(clean):
 
     def run(self):
         clean.run(self)
         api_path = os.path.join('doc', 'api', 'generated')
         if os.path.exists(api_path):
-            print "Removing %s" % api_path
+            print("Removing %s" % api_path)
             shutil.rmtree(api_path)
         interface_path = os.path.join('doc', 'interfaces', 'generated')
         if os.path.exists(interface_path):
-            print "Removing %s" % interface_path
+            print("Removing %s" % interface_path)
             shutil.rmtree(interface_path)
         if os.path.exists(DOC_BUILD_DIR):
-            print "Removing %s" % DOC_BUILD_DIR
+            print("Removing %s" % DOC_BUILD_DIR)
             shutil.rmtree(DOC_BUILD_DIR)
         if os.path.exists(DOC_DOCTREES_DIR):
-            print "Removing %s" % DOC_DOCTREES_DIR
+            print("Removing %s" % DOC_DOCTREES_DIR)
             shutil.rmtree(DOC_DOCTREES_DIR)
 
 

circle.yml

@@ -15,7 +15,7 @@ dependencies:
     - if [[ ! -d ~/fsl ]]; then wget "http://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.9-centos6_64.tar.gz"; tar zxvf fsl-5.0.9-centos6_64.tar.gz; mv fsl ~/fsl; fi
     - if [[ ! -d ~/examples/data ]]; then wget "http://tcpdiag.dl.sourceforge.net/project/nipy/nipype/nipype-0.2/nipype-tutorial.tar.bz2"; tar jxvf nipype-tutorial.tar.bz2; mkdir ~/examples; mv nipype-tutorial/* ~/examples/; fi
     # we download this manually because CircleCI does not cache apt
-    - if [[ ! -d ~/examples/feeds ]]; then wget "http://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.8-feeds.tar.gz"; tar zxvf fsl-5.0.8-feeds.tar.gz; mv feeds ~/examples/; fi
+    - if [[ ! -d ~/examples/feeds ]]; then wget "http://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.9-feeds.tar.gz"; tar zxvf fsl-5.0.8-feeds.tar.gz; mv feeds ~/examples/; fi
     - if [[ ! -d ~/examples/fsl_course_data ]]; then wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt1.tar.gz" ; wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt2.tar.gz"; wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/tbss.tar.gz"; mkdir ~/examples/fsl_course_data; tar zxvf fdt1.tar.gz -C ~/examples/fsl_course_data; tar zxvf fdt2.tar.gz -C ~/examples/fsl_course_data; tar zxvf tbss.tar.gz -C ~/examples/fsl_course_data; fi
     - bash ~/nipype/tools/install_spm_mcr.sh
     - mkdir -p ~/.nipype && echo "[logging]" > ~/.nipype/nipype.cfg && echo "workflow_level = DEBUG" >> ~/.nipype/nipype.cfg && echo "interface_level = DEBUG" >> ~/.nipype/nipype.cfg && echo "filemanip_level = DEBUG" >> ~/.nipype/nipype.cfg

doc/conf.py

@@ -15,7 +15,7 @@
 import sys, os
 
 nipypepath = os.path.abspath('..')
-sys.path.insert(1,nipypepath)
+sys.path.insert(1, nipypepath)
 
 import nipype
 
@@ -168,9 +168,9 @@
 #html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-html_sidebars = {'**': ['gse.html','localtoc.html', 'sidebar_versions.html', 'indexsidebar.html'],
-                 'searchresults' : ['sidebar_versions.html', 'indexsidebar.html'],
-                 'version' : []}
+html_sidebars = {'**': ['gse.html', 'localtoc.html', 'sidebar_versions.html', 'indexsidebar.html'],
+                 'searchresults': ['sidebar_versions.html', 'indexsidebar.html'],
+                 'version': []}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.

doc/devel/matlab_interface_devel.rst

@@ -93,7 +93,7 @@ By subclassing **MatlabCommand** for your main class, and **MatlabInputSpec** fo
             >>> hello = HelloWorld()
             >>> hello.inputs.name = 'hello_world'
             >>> out = hello.run()
-            >>> print out.outputs.matlab_output
+            >>> print(out.outputs.matlab_output)
             """
             input_spec = HelloWorldInputSpec
             output_spec = HelloWorldOutputSpec

doc/sphinxext/autosummary_generate.py

@@ -16,6 +16,8 @@
             ./ext/autosummary_generate.py -o source/generated source/*.rst
 
 """
+
+from __future__ import print_function
 import glob, re, inspect, os, optparse, pydoc
 from autosummary import import_by_name
 
@@ -24,6 +26,7 @@
 except ImportError:
     import_phantom_module = lambda x: x
 
+
 def main():
     p = optparse.OptionParser(__doc__.strip())
     p.add_option("-p", "--phantom", action="store", type="string",
@@ -44,7 +47,7 @@ def main():
 
     # read
     names = {}
-    for name, loc in get_documented(args).items():
+    for name, loc in list(get_documented(args).items()):
         for (filename, sec_title, keyword, toctree) in loc:
             if toctree is not None:
                 path = os.path.join(os.path.dirname(filename), toctree)
@@ -60,8 +63,8 @@ def main():
 
         try:
             obj, name = import_by_name(name)
-        except ImportError, e:
-            print "Failed to import '%s': %s" % (name, e)
+        except ImportError as e:
+            print("Failed to import '%s': %s" % (name, e))
             continue
 
         fn = os.path.join(path, '%s.rst' % name)
@@ -93,16 +96,19 @@ def main():
         finally:
             f.close()
 
+
 def format_modulemember(name, directive):
     parts = name.split('.')
     mod, name = '.'.join(parts[:-1]), parts[-1]
     return ".. currentmodule:: %s\n\n.. %s:: %s\n" % (mod, directive, name)
 
+
 def format_classmember(name, directive):
     parts = name.split('.')
     mod, name = '.'.join(parts[:-2]), '.'.join(parts[-2:])
     return ".. currentmodule:: %s\n\n.. %s:: %s\n" % (mod, directive, name)
 
+
 def get_documented(filenames):
     """
     Find out what items are documented in source/*.rst
@@ -117,6 +123,7 @@ def get_documented(filenames):
         f.close()
     return documented
 
+
 def get_documented_in_docstring(name, module=None, filename=None):
     """
     Find out what items are documented in the given object's docstring.
@@ -129,10 +136,11 @@ def get_documented_in_docstring(name, module=None, filename=None):
         return get_documented_in_lines(lines, module=name, filename=filename)
     except AttributeError:
         pass
-    except ImportError, e:
-        print "Failed to import '%s': %s" % (name, e)
+    except ImportError as e:
+        print("Failed to import '%s': %s" % (name, e))
     return {}
 
+
 def get_documented_in_lines(lines, module=None, filename=None):
     """
     Find out what items are documented in the given lines
@@ -171,7 +179,7 @@ def get_documented_in_lines(lines, module=None, filename=None):
                     continue
 
                 if line.strip().startswith(':'):
-                    continue # skip options
+                    continue  # skip options
 
                 m = autosummary_item_re.match(line)
                 if m:

doc/sphinxext/ipython_console_highlighting.py

@@ -3,7 +3,7 @@
 """reST directive for syntax-highlighting ipython interactive sessions.
 """
 
-#-----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
 # Needed modules
 
 # Standard library
@@ -18,13 +18,14 @@
 from sphinx import highlighting
 
 
-#-----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
 # Global constants
 line_re = re.compile('.*?\n')
 
-#-----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
 # Code begins - classes and functions
 
+
 class IPythonConsoleLexer(Lexer):
     """
     For IPython console output or doctests, such as:
@@ -95,6 +96,6 @@ def get_tokens_unprocessed(self, text):
                                       pylexer.get_tokens_unprocessed(curcode)):
                 yield item
 
-#-----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
 # Register the extension as a valid pygments lexer
 highlighting.lexers['ipython'] = IPythonConsoleLexer()