Merge pull request nipy#224 from satra/killspaces

sty: removed trailing spaces (thanks alex)
mattfeld · Sep 9, 2011 · c146692 · c146692
2 parents 7df211b + 1c11e63
commit c146692
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Showing 109 changed files with 1,252 additions and 1,254 deletions.
diff --git a/Makefile b/Makefile
@@ -53,7 +53,8 @@ inplace:
 	$(PYTHON) setup.py build_ext -i
 
 test-code: in
-	$(NOSETESTS) -s nipype
+	$(NOSETESTS) -s nipype --with-doctest
+
 test-doc:
 	$(NOSETESTS) -s --with-doctest --doctest-tests --doctest-extension=rst \
 	--doctest-fixtures=_fixture doc/
@@ -62,5 +63,5 @@ test-coverage:
 	$(NOSETESTS) -s --with-coverage --cover-html --cover-html-dir=coverage \
 	--cover-package=nipype nipype
 
-test: test-code test-doc
+test: test-code
 
diff --git a/build_docs.py b/build_docs.py
@@ -25,7 +25,7 @@
 DOC_DOCTREES_DIR = os.path.join('doc', '_build', 'doctrees')
 
 ################################################################################
-# Distutils Command class for installing nipype to a temporary location. 
+# Distutils Command class for installing nipype to a temporary location.
 class TempInstall(Command):
     temp_install_dir = os.path.join('build', 'install')
 
@@ -34,11 +34,11 @@ def run(self):
         install = self.distribution.get_command_obj('install')
         install.install_scripts = 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_headers = 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_headers = self.temp_install_dir
         install.run()
 
         # Horrible trick to reload nipype with our temporary instal
@@ -52,13 +52,13 @@ def run(self):
 
     def initialize_options(self):
         pass
-    
+
     def finalize_options(self):
         pass
 
 
 ################################################################################
-# Distutils Command class for API generation 
+# Distutils Command class for API generation
 class APIDocs(TempInstall):
     description = \
     """generate API docs """
@@ -99,7 +99,7 @@ def relative_path(filename):
 
 
 ################################################################################
-# Distutils Command class build the docs 
+# Distutils Command class build the docs
 class MyBuildDoc(BuildDoc):
     """ Sub-class the standard sphinx documentation building system, to
         add logics for API generation and matplotlib's plot directive.
@@ -121,7 +121,7 @@ def run(self):
         # in case I'm missing something?
         BuildDoc.run(self)
         self.zip_docs()
-    
+
     def zip_docs(self):
         if not os.path.exists(DOC_BUILD_DIR):
             raise OSError, 'Doc directory does not exist.'
@@ -131,19 +131,19 @@ def zip_docs(self):
         # for it. ZIP_STORED produces an uncompressed zip, but does not
         # require zlib.
         try:
-            zf = zipfile.ZipFile(target_file, 'w', 
+            zf = zipfile.ZipFile(target_file, 'w',
                                         compression=zipfile.ZIP_DEFLATED)
         except RuntimeError:
             warnings.warn('zlib not installed, storing the docs '
                             'without compression')
-            zf = zipfile.ZipFile(target_file, 'w', 
-                                        compression=zipfile.ZIP_STORED)    
+            zf = zipfile.ZipFile(target_file, 'w',
+                                        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), 
+                    zf.write(os.path.join(root, f),
                             os.path.join(relative, 'html_docs', f))
         zf.close()
 
@@ -171,7 +171,7 @@ def run(self):
             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

diff --git a/doc/sphinxext/docscrape.py b/doc/sphinxext/docscrape.py
@@ -185,7 +185,7 @@ def _parse_param_list(self,content):
 
         return params
 
-    
+
     _name_rgx = re.compile(r"^\s*(:(?P<role>\w+):`(?P<name>[a-zA-Z0-9_.-]+)`|"
                            r" (?P<name2>[a-zA-Z0-9_.-]+))\s*", re.X)
     def _parse_see_also(self, content):
@@ -218,7 +218,7 @@ def push_item(name, rest):
 
         current_func = None
         rest = []
-        
+
         for line in content:
             if not line.strip(): continue
 
@@ -260,7 +260,7 @@ def strip_each_in(lst):
             if len(line) > 2:
                 out[line[1]] = strip_each_in(line[2].split(','))
         return out
-    
+
     def _parse_summary(self):
         """Grab signature (if given) and summary"""
         if self._is_at_section():
@@ -277,7 +277,7 @@ def _parse_summary(self):
 
         if not self._is_at_section():
             self['Extended Summary'] = self._read_to_next_section()
-    
+
     def _parse(self):
         self._doc.reset()
         self._parse_summary()
@@ -442,7 +442,7 @@ def get_func(self):
         else:
             func = self._f
         return func, func_name
-            
+
     def __str__(self):
         out = ''
 

diff --git a/doc/sphinxext/ipython_console_highlighting.py b/doc/sphinxext/ipython_console_highlighting.py
@@ -43,7 +43,7 @@ class IPythonConsoleLexer(Lexer):
 
       - It assumes the default IPython prompts, not customized ones.
     """
-    
+
     name = 'IPython console session'
     aliases = ['ipython']
     mimetypes = ['text/x-ipython-console']

diff --git a/doc/sphinxext/numpydoc.py b/doc/sphinxext/numpydoc.py
@@ -90,7 +90,7 @@ def initialize(app):
 def setup(app, get_doc_object_=get_doc_object):
     global get_doc_object
     get_doc_object = get_doc_object_
-    
+
     app.connect('autodoc-process-docstring', mangle_docstrings)
     app.connect('builder-inited', initialize)
     app.add_config_value('numpydoc_edit_link', None, True)

diff --git a/examples/camino_dti_tutorial.py b/examples/camino_dti_tutorial.py
@@ -136,7 +136,7 @@ def get_affine(volume):
 
 """
 In this tutorial we implement probabilistic tractography using the PICo algorithm.
-PICo tractography requires an estimate of the fibre direction and a model of its 
+PICo tractography requires an estimate of the fibre direction and a model of its
 uncertainty in each voxel; this is produced using the following node.
 """
 

diff --git a/examples/connectivity_tutorial.py b/examples/connectivity_tutorial.py
@@ -29,7 +29,7 @@
 These are written by Stephan Gerhard and can be obtained from:
 
     http://www.cmtk.org/
-    
+
 Or on github at:
 
     CFFlib: https://github.com/LTS5/cfflib

diff --git a/examples/dartmouth_workshop_2010.py b/examples/dartmouth_workshop_2010.py
@@ -1,32 +1,32 @@
 """
 =================================
- Dartmouth College Workshop 2010 
+ Dartmouth College Workshop 2010
 =================================
 
-First lets go to the directory with the data we'll be working on and start the interactive python interpreter 
-(with some nipype specific configuration). Note that nipype does not need to be run through ipython - it is 
+First lets go to the directory with the data we'll be working on and start the interactive python interpreter
+(with some nipype specific configuration). Note that nipype does not need to be run through ipython - it is
 just much nicer to do interactive work in it.
 
 .. sourcecode:: bash
-    
+
     cd $TDPATH
     ipython -p nipype
-    
-For every neuroimaging procedure supported by nipype there exists a wrapper - a small piece of code managing 
+
+For every neuroimaging procedure supported by nipype there exists a wrapper - a small piece of code managing
 the underlying software (FSL, SPM, AFNI etc.). We call those interfaces. They are standarised so we can hook them up
 together. Lets have a look at some of them.
-    
+
 .. sourcecode:: ipython
 
     In [1]: import nipype.interfaces.fsl as fsl
-    
+
     In [2]: fsl.BET.help()
     Inputs
     ------
-    
+
     Mandatory:
      in_file: input file to skull strip
-    
+
     Optional:
      args: Additional parameters to the command
      center: center of gravity in voxels
@@ -46,7 +46,7 @@
      skull: create skull image
      threshold: apply thresholding to segmented brain image and mask
      vertical_gradient: vertical gradient in fractional intensity threshold (-1, 1)
-    
+
     Outputs
     -------
     mask_file: path/name of binary brain mask (if generated)
@@ -59,16 +59,16 @@
     In [4]: fs.Smooth.help()
     Inputs
     ------
-    
+
     Mandatory:
      in_file: source volume
      num_iters: number of iterations instead of fwhm
       mutually exclusive: surface_fwhm
-     reg_file: registers volume to surface anatomical 
+     reg_file: registers volume to surface anatomical
      surface_fwhm: surface FWHM in mm
       mutually exclusive: num_iters
       requires: reg_file
-    
+
     Optional:
      args: Additional parameters to the command
      environ: Environment variables (default={})
@@ -79,15 +79,15 @@
      smoothed_file: output volume
      subjects_dir: subjects directory
      vol_fwhm: volumesmoothing outside of surface
-    
+
     Outputs
     -------
     args: Additional parameters to the command
     environ: Environment variables
     smoothed_file: smoothed input volume
     subjects_dir: subjects directory
-    
-You can read about all of the interfaces implemented in nipype at our online documentation at http://nipy.sourceforge.net/nipype/documentation.html#documentation . 
+
+You can read about all of the interfaces implemented in nipype at our online documentation at http://nipy.sourceforge.net/nipype/documentation.html#documentation .
 Check it out now.
 
 Using interfaces
@@ -101,7 +101,7 @@
 print result
 
 """
-Running a single program is not much of a breakthrough. Lets run motion correction followed by smoothing 
+Running a single program is not much of a breakthrough. Lets run motion correction followed by smoothing
 (isotropic - in other words not using SUSAN). Notice that in the first line we are setting the output data type
 for all FSL interfaces.
 """
@@ -132,15 +132,15 @@
 motion_correct_and_smooth.base_dir = os.path.abspath('.') # define where will be the root folder for the workflow
 motion_correct_and_smooth.connect([
                                    (motion_correct, smooth, [('out_file', 'in_file')])
-                                   ]) 
+                                   ])
 # we are connecting 'out_file' output of motion_correct to 'in_file' input of smooth
 motion_correct_and_smooth.run()
 
 """
 Another workflow
 ----------------
 
-Another example of a simple workflow (calculate the mean of fMRI signal and subtract it). 
+Another example of a simple workflow (calculate the mean of fMRI signal and subtract it).
 This time we'll be assigning inputs after defining the workflow.
 """
 
@@ -205,7 +205,7 @@
 
 Datasink is a special interface for copying and arranging results.
 """
- 
+
 import nipype.interfaces.io as nio
 
 preproc.inputs.inputspec.func = os.path.abspath('data/s1/f3.nii')
@@ -218,15 +218,15 @@
                                          ('maskfunc3.out_file', 'funcruns')])
                     ])
 preprocess.run()
-    
+
 """
 Datagrabber
 -----------
 
 Datagrabber is (surprise, surprise) an interface for collecting files from hard drive. It is very flexible and
-supports almost any file organisation of your data you can imagine. 
+supports almost any file organisation of your data you can imagine.
 """
-    
+
 datasource1 = nio.DataGrabber()
 datasource1.inputs.template = 'data/s1/f3.nii'
 results = datasource1.run()
@@ -248,13 +248,13 @@
 datasource4.inputs.run = [3, 7]
 datasource4.inputs.subject_id = ['s1', 's3']
 results = datasource4.run()
-print results.outputs    
+print results.outputs
 
 """
 Iterables
 ---------
 
-Iterables is a special field of the Node class that enables to iterate all workfloes/nodes connected to it over 
+Iterables is a special field of the Node class that enables to iterate all workfloes/nodes connected to it over
 some parameters. Here we'll use it to iterate over two subjects.
 """
 

diff --git a/examples/dtk_dti_tutorial.py b/examples/dtk_dti_tutorial.py
@@ -22,7 +22,7 @@
 import nipype.interfaces.io as nio           # Data i/o
 import nipype.interfaces.fsl as fsl          # fsl
 import nipype.workflows.fsl as fsl_wf          # fsl
-import nipype.interfaces.diffusion_toolkit as dtk 
+import nipype.interfaces.diffusion_toolkit as dtk
 import nipype.interfaces.utility as util     # utility
 import nipype.pipeline.engine as pe          # pypeline engine
 import os                                    # system functions
@@ -102,7 +102,7 @@
 
 datasource.inputs.template = "%s/%s"
 
-# This needs to point to the fdt folder you can find after extracting 
+# This needs to point to the fdt folder you can find after extracting
 # http://www.fmrib.ox.ac.uk/fslcourse/fsl_course_data2.tar.gz
 datasource.inputs.base_directory = os.path.abspath('fsl_course_data/fdt/')
 

diff --git a/examples/dtk_odf_tutorial.py b/examples/dtk_odf_tutorial.py
@@ -22,7 +22,7 @@
 import nipype.interfaces.io as nio           # Data i/o
 import nipype.interfaces.fsl as fsl          # fsl
 import nipype.workflows.fsl as fsl_wf          # fsl
-import nipype.interfaces.diffusion_toolkit as dtk 
+import nipype.interfaces.diffusion_toolkit as dtk
 import nipype.interfaces.utility as util     # utility
 import nipype.pipeline.engine as pe          # pypeline engine
 import os                                    # system functions
@@ -102,7 +102,7 @@
 
 datasource.inputs.template = "%s/%s"
 
-# This needs to point to the fdt folder you can find after extracting 
+# This needs to point to the fdt folder you can find after extracting
 # http://www.fmrib.ox.ac.uk/fslcourse/fsl_course_data2.tar.gz
 datasource.inputs.base_directory = os.path.abspath('data')