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

Author: effigies

.dockerignore

@@ -34,4 +34,4 @@ Vagrantfile
 .mailmap
 
 # Previous coverage results
-.coverage
+.coverage

.zenodo.json

@@ -563,6 +563,16 @@
       "affiliation": "MIT, HMS",
       "name": "Ghosh, Satrajit",
       "orcid": "0000-0002-5312-6729"
+    },
+    {
+      "affiliation": "University College London",
+      "name": "Mancini, Matteo",
+      "orcid": "0000-0001-7194-4568"
+    },
+    {
+      "affiliation": "Donders Institute for Brain, Cognition and Behavior, Center for Cognitive Neuroimaging",
+      "name": "Chetverikov, Andrey",
+      "orcid": "0000-0003-2767-6310"
     }
   ],
   "keywords": [

CHANGES

@@ -1,6 +1,13 @@
 Upcoming release (0.14.1)
-================
-
+=========================
+
+* ENH: Add AFNI interface for 3dConvertDset (https://github.com/nipy/nipype/pull/2337)
+* MAINT: Cleanup EngineBase (https://github.com/nipy/nipype/pull/2376)
+* FIX: Robustly handled outputs of 3dFWHMx across different versions of AFNI (https://github.com/nipy/nipype/pull/2373)
+* FIX: Cluster threshold in randomise + change default prefix (https://github.com/nipy/nipype/pull/2369)
+* MAINT: Cleaning / simplify ``Node`` (https://github.com/nipy/nipype/pull/2325)
+* STY: Cleanup of PEP8 violations (https://github.com/nipy/nipype/pull/2358)
+* STY: Cleanup of trailing spaces and adding of missing newlines at end of files (https://github.com/nipy/nipype/pull/2355)
 
 0.14.0 (November 29, 2017)
 ==========================

CONTRIBUTING.md

@@ -16,8 +16,8 @@
 * The person who accepts/merges your PR will include an update to the CHANGES file: prefix: description (URL of pull request)
 * Run `make check-before-commit` before submitting the PR.
   This will require you to either install or be in developer mode with: `python setup.py install/develop`.
-* In general, do not catch exceptions without good reason. 
-  * catching non-fatal exceptions. 
+* In general, do not catch exceptions without good reason.
+  * catching non-fatal exceptions.
     Log the exception as a warning.
   * adding more information about what may have caused the error.
     Raise a new exception using ``raise_from(NewException("message"), oldException)`` from ``future``.

build_docs.py

@@ -8,7 +8,8 @@
 
     python setup.py build_sphinx
 """
-from __future__ import print_function, division, unicode_literals, absolute_import
+from __future__ import (print_function, division, unicode_literals,
+                        absolute_import)
 from builtins import open, str
 
 # Standard library imports
@@ -28,7 +29,7 @@
 DOC_BUILD_DIR = os.path.join('doc', '_build', 'html')
 DOC_DOCTREES_DIR = os.path.join('doc', '_build', 'doctrees')
 
-################################################################################
+###############################################################################
 # Distutils Command class for installing nipype to a temporary location.
 
 
@@ -63,7 +64,7 @@ def finalize_options(self):
         pass
 
 
-################################################################################
+###############################################################################
 # Distutils Command class for API generation
 class APIDocs(TempInstall):
     description = \
@@ -93,7 +94,7 @@ def run(self):
             os.chdir('..')
 
 
-################################################################################
+###############################################################################
 # Code to copy the sphinx-generated html docs in the distribution.
 def relative_path(filename):
     """ Return the relative path to the file, assuming the file is
@@ -103,7 +104,7 @@ def relative_path(filename):
     return os.path.abspath(filename)[length:]
 
 
-################################################################################
+###############################################################################
 # Distutils Command class build the docs
 # Sphinx import.
 try:
@@ -165,7 +166,7 @@ def finalize_options(self):
             self.build_dir = os.path.join(*DOC_BUILD_DIR.split(os.sep)[:-1])
             BuildDoc.finalize_options(self)
 
-################################################################################
+###############################################################################
 # Distutils Command class to clean
 
 

codecov.yml

@@ -25,4 +25,4 @@ coverage:
   ignore:          # files and folders that will be removed during processing
     - "nipype/external/*"
     - "tools/*"
-    - "doc/*"
+    - "doc/*"

doc/_static/nipype.css

@@ -57,4 +57,4 @@ div.doc2.container ul{
 
 div.doc2 .reference.internal{
     font-size: 14px;
-}
+}

doc/devel/gitwash/git_links.inc

@@ -2,7 +2,7 @@
    and name substitutions.  It may be included in many files,
    therefore it should only contain link targets and name
    substitutions.  Try grepping for "^\.\. _" to find plausible
-   candidates for this list.  
+   candidates for this list.
 
 .. NOTE: reST targets are
    __not_case_sensitive__, so only one target definition is needed for
@@ -42,7 +42,7 @@
 .. _git config: http://www.kernel.org/pub/software/scm/git/docs/git-config.html
 .. _why the -a flag?: http://www.gitready.com/beginner/2009/01/18/the-staging-area.html
 .. _git staging area: http://www.gitready.com/beginner/2009/01/18/the-staging-area.html
-.. _tangled working copy problem: http://tomayko.com/writings/the-thing-about-git 
+.. _tangled working copy problem: http://tomayko.com/writings/the-thing-about-git
 .. _git management: http://kerneltrap.org/Linux/Git_Management
 .. _linux git workflow: http://www.mail-archive.com/[email protected]/msg39091.html
 .. _git parable: http://tom.preston-werner.com/2009/05/19/the-git-parable.html

doc/searchresults.rst

@@ -170,4 +170,4 @@ Search results
       .gsc-resultsHeader {
          clear: none;
       }
-    </style>
+    </style>

doc/sphinxext/autosummary_generate.py

@@ -39,9 +39,9 @@ def main():
                  help="Phantom import modules from a file")
     p.add_option("-o", "--output-dir", action="store", type="string",
                  dest="output_dir", default=None,
-                 help=("Write all output files to the given directory (instead "
-                       "of writing them as specified in the autosummary:: "
-                       "directives)"))
+                 help=("Write all output files to the given directory "
+                       "(instead of writing them as specified in the "
+                       "autosummary:: directives)"))
     options, args = p.parse_args()
 
     if len(args) == 0:
@@ -161,9 +161,12 @@ def get_documented_in_lines(lines, module=None, filename=None):
 
     """
     title_underline_re = re.compile("^[-=*_^#]{3,}\s*$")
-    autodoc_re = re.compile(".. auto(function|method|attribute|class|exception|module)::\s*([A-Za-z0-9_.]+)\s*$")
+    autodoc_re = re.compile(
+        ".. auto(function|method|attribute|class|exception|module)::"
+        "\s*([A-Za-z0-9_.]+)\s*$")
     autosummary_re = re.compile(r'^\.\.\s+autosummary::\s*')
-    module_re = re.compile(r'^\.\.\s+(current)?module::\s*([a-zA-Z0-9_.]+)\s*$')
+    module_re = re.compile(
+        r'^\.\.\s+(current)?module::\s*([a-zA-Z0-9_.]+)\s*$')
     autosummary_item_re = re.compile(r'^\s+([_a-zA-Z][a-zA-Z0-9_.]*)\s*.*?')
     toctree_arg_re = re.compile(r'^\s+:toctree:\s*(.*?)\s*$')
 
@@ -189,7 +192,8 @@ def get_documented_in_lines(lines, module=None, filename=None):
                 m = autosummary_item_re.match(line)
                 if m:
                     name = m.group(1).strip()
-                    if current_module and not name.startswith(current_module + '.'):
+                    if current_module and not name.startswith(
+                            current_module + '.'):
                         name = "%s.%s" % (current_module, name)
                     documented.setdefault(name, []).append(
                         (filename, current_title, 'autosummary', toctree))
@@ -210,7 +214,8 @@ def get_documented_in_lines(lines, module=None, filename=None):
                     current_module = name
                     documented.update(get_documented_in_docstring(
                         name, filename=filename))
-                elif current_module and not name.startswith(current_module + '.'):
+                elif current_module and not name.startswith(
+                        current_module + '.'):
                     name = "%s.%s" % (current_module, name)
                 documented.setdefault(name, []).append(
                     (filename, current_title, "auto" + m.group(1), None))
@@ -230,5 +235,6 @@ def get_documented_in_lines(lines, module=None, filename=None):
 
     return documented
 
+
 if __name__ == "__main__":
     main()

doc/sphinxext/ipython_console_highlighting.py

@@ -59,7 +59,6 @@ class IPythonConsoleLexer(Lexer):
 
     def get_tokens_unprocessed(self, text):
         pylexer = PythonLexer(**self.options)
-        tblexer = PythonTracebackLexer(**self.options)
 
         curcode = ''
         insertions = []
@@ -72,21 +71,22 @@ def get_tokens_unprocessed(self, text):
                 insertions.append((len(curcode),
                                    [(0, Comment, line)]))
             elif input_prompt is not None:
-                insertions.append((len(curcode),
-                                   [(0, Generic.Prompt, input_prompt.group())]))
+                insertions.append((len(
+                    curcode), [(0, Generic.Prompt, input_prompt.group())]))
                 curcode += line[input_prompt.end():]
             elif continue_prompt is not None:
-                insertions.append((len(curcode),
-                                   [(0, Generic.Prompt, continue_prompt.group())]))
+                insertions.append((len(
+                    curcode), [(0, Generic.Prompt, continue_prompt.group())]))
                 curcode += line[continue_prompt.end():]
             elif output_prompt is not None:
-                insertions.append((len(curcode),
-                                   [(0, Generic.Output, output_prompt.group())]))
+                insertions.append((len(
+                    curcode), [(0, Generic.Output, output_prompt.group())]))
                 curcode += line[output_prompt.end():]
             else:
                 if curcode:
                     for item in do_insertions(insertions,
-                                              pylexer.get_tokens_unprocessed(curcode)):
+                                              pylexer.get_tokens_unprocessed(
+                                                  curcode)):
                         yield item
                         curcode = ''
                         insertions = []

doc/sphinxext/numpy_ext/docscrape.py

@@ -295,7 +295,8 @@ def _parse(self):
 
         for (section, content) in self._read_sections():
             if not section.startswith('..'):
-                section = ' '.join([s.capitalize() for s in section.split(' ')])
+                section = ' '.join([s.capitalize()
+                                    for s in section.split(' ')])
             if section in ('Parameters', 'Returns', 'Raises', 'Warns',
                            'Other Parameters', 'Attributes', 'Methods'):
                 self[section] = self._parse_param_list(content)
@@ -443,7 +444,7 @@ def __init__(self, func, role='func', doc=None, config={}):
                 argspec = inspect.formatargspec(*argspec)
                 argspec = argspec.replace('*', '\*')
                 signature = '%s%s' % (func_name, argspec)
-            except TypeError as e:
+            except TypeError:
                 signature = '%s()' % func_name
             self['Signature'] = signature
 
@@ -459,7 +460,6 @@ def __str__(self):
         out = ''
 
         func, func_name = self.get_func()
-        signature = self['Signature'].replace('*', '\*')
 
         roles = {'func': 'function',
                  'meth': 'method'}

doc/sphinxext/numpy_ext/numpydoc.py

@@ -11,7 +11,7 @@
 - Convert Parameters etc. sections to field lists.
 - Convert See Also section to a See also entry.
 - Renumber references.
-- Extract the signature from the docstring, if it can't be determined otherwise.
+- Extract signature from docstring, if it can't be determined otherwise.
 
 .. [1] https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt
 

doc/users/aws.rst

@@ -99,4 +99,4 @@ s3://mybucket/path/to/output/dir/sub001/motion/realigned_file1.nii.gz
 
 Using S3DataGrabber
 ======================
-Coming soon...
+Coming soon...

doc/users/caching_tutorial.rst

@@ -1,4 +1,3 @@
-
 .. _caching:
 
 ===========================

doc/users/config_file.rst

@@ -170,7 +170,7 @@ Resource Monitor
     Indicates where the summary file collecting all profiling information from the
     resource monitor should be stored after execution of a workflow.
     The ``summary_file`` does not apply to interfaces run independently.
-    (unset by default, in which case the summary file will be written out to 
+    (unset by default, in which case the summary file will be written out to
     ``<base_dir>/resource_monitor.json`` of the top-level workflow).
 
 *summary_append*

doc/users/install.rst

@@ -117,4 +117,4 @@ Developers should start `here <../devel/testing_nipype.html>`_.
 
 Developers can also use this docker container: `docker pull nipype/nipype:master`
 
-.. include:: ../links_names.txt
+.. include:: ../links_names.txt

doc/users/plugins.rst

@@ -82,9 +82,9 @@ Optional arguments::
   exceed the total amount of resources available (memory and threads), when
   ``False`` (default), only a warning will be issued.
 
-  maxtasksperchild : number of nodes to run on each process before refreshing 
+  maxtasksperchild : number of nodes to run on each process before refreshing
   the worker (default: 10).
-  
+
 
 To distribute processing on a multicore machine, simply call::
 

doc/users/sphinx_ext.rst

@@ -1,4 +1,3 @@
-
 .. _sphinx_ext:
 
 Sphinx extensions
@@ -11,4 +10,4 @@ and simplify the generation process.
 
 .. automodule:: nipype.sphinxext.plot_workflow
     :undoc-members:
-    :noindex:
+    :noindex: