upstream merge

Author: mgxd

CHANGES

@@ -1,7 +1,12 @@
 Next release
 ============
 
+<<<<<<< HEAD
 * ENH: Added dcm2niix interface (https://github.com/nipy/nipype/pull/1435)
+=======
+* ENH: Add nipype_crash_search command (https://github.com/nipy/nipype/pull/1422)
+* ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (https://github.com/nipy/nipype/pull/1305)
+>>>>>>> c389d5d4c0f1eb5ff321de5553f815d1fb6fcc47
 * FIX: job execution on systems/approaches where locale is undefined (https://github.com/nipy/nipype/pull/1401)
 * FIX: Clean up byte/unicode issues using subprocess (https://github.com/nipy/nipype/pull/1394)
 * FIX: Prevent crash when tvtk is loaded - ETS_TOOLKIT=null (https://github.com/nipy/nipype/pull/973)
@@ -26,6 +31,9 @@ Next release
 * ENH: Interfaces for MINC tools (https://github.com/nipy/nipype/pull/1304)
 * FIX: Use realpath to determine hard link source (https://github.com/nipy/nipype/pull/1388)
 * FIX: Correct linking/copying fallback behavior (https://github.com/nipy/nipype/pull/1391)
+* ENH: Nipype workflow and interfaces for FreeSurfer's recon-all (https://github.com/nipy/nipype/pull/1326)
+* FIX: Permit relative path for concatenated_file input to Concatenate() (https://github.com/nipy/nipype/pull/1411)
+* ENH: Makes ReconAll workflow backwards compatible with FreeSurfer 5.3.0 (https://github.com/nipy/nipype/pull/1434)
 
 Release 0.11.0 (September 15, 2015)
 ============

Makefile

@@ -66,7 +66,7 @@ test: clean test-code
 
 html:
 	@echo "building docs"
-	make -C doc clean html
+	make -C doc clean htmlonly
 
 specs:
 	@echo "Checking specs and autogenerating spec tests"

THANKS.rst

@@ -1,102 +1,22 @@
 .. -*- mode: rst -*-
 
-
 Code contributors
 -----------------
-Contributors to Nipype include but are not limited to:
-
-.. hlist::
 
-  * Aimi Watanabe
-  * Alexander Schaefer
-  * Alexandre Gramfort
-  * Alexandre Savio
-  * Anisha Keshavan
-  * Ariel Rokem
-  * Ben Acland
-  * Ben Cipollini
-  * Basile Pinsard
-  * Brendan Moloney
-  * Brian Cheung
-  * Charl Linssen
-  * Chris Filo Gorgolewski
-  * Chris Steele
-  * Christian Haselgrove
-  * Christopher Burns
-  * Cindee Madison
-  * Claire Tarbert
-  * Colin Buchanan
-  * Daniel Ginsburg
-  * Daniel Haehn
-  * Daniel Margulies
-  * Dav Clark
-  * David Welch
-  * Drew Erickson
-  * Erik Kastman
-  * Félix C. Morency
-  * Gael Varoquaux
-  * Hans Johnson
-  * Janosch Linkersdörfer
-  * Januzz
-  * Jarrod Millman
-  * Jeff Lai
-  * Jessica Forbes
-  * John Salvatore
-  * Lijie Huang
-  * Michael Hallquist
-  * Michael Hanke
-  * Michael Notter
-  * Michael Waskom
-  * Nolan Nichols
-  * Oliver Hinds
-  * Oscar Esteban
-  * Rosalia Tungaraza
-  * Satrajit Ghosh
-  * Sharad Sikka
-  * Stephan Gerhard
-  * Erik Ziegler
-  * Valentin Haenel
-  * Xiangzhen Kong
-  * Xu Wang
-  * Yannick Schwartz
-  * Yaroslav O. Halchenko
+See `Github contributors list <https://github.com/nipy/nipype/graphs/contributors>`__.
 
-For full most up to date list see `Ohloh <https://www.ohloh.net/p/nipype/contributors>`__.
+Funding
+-------
 
-Other contributors
-------------------
+Nipype is currently supported by `1R01EB020740-01A1 Nipype: Dataflows for Reproducible Biomedical Research <https://projectreporter.nih.gov/project_info_description.cfm?aid=9053094>`__.
 
-.. hlist::
+Satrajit Ghosh work on this project was partially funded by NIBIB `R03EB008673 <https://projectreporter.nih.gov/project_info_description.cfm?aid=7501200>`__ and by the `INCF <http://www.incf.org>`__ through a contract with TankThink Labs, LLC.
+Chris Burns was supported by NIMH grant `5R01MH081909-02  Continued Development and Maintenance of the Neuroimaging in Python Project <https://projectreporter.nih.gov/project_info_description.cfm?aid=7288112>`__. Hans Jonson was supported by
+`2 U54 EB005149 - 06	 Core 2b Huntington's Disease - Driving Biological Project <http://projectreporter.nih.gov/project_info_description.cfm?aid=8153616>`__,
+`S10 RR023392	 Enterprise Storage In A Collaborative Neuroimaging Environment	 <http://projectreporter.nih.gov/project_info_description.cfm?aid=7209718>`__,
+`R01 NS040068	 Neurobiological Predictors of Huntington's Disease	 <http://projectreporter.nih.gov/project_info_description.cfm?aid=6266377>`__,
+and `UL1 TR000442	University of Iowa Clinical and Translational Science Program <http://projectreporter.nih.gov/project_info_description.cfm?aid=8467220>`__.
 
-  * Matthew Brett
-  * Michael Castelle
-  * Philippe Ciuciu
-  * Yann Cointepas
-  * Mark D'Esposito
-  * Susan Gabrieli
-  * Brian Hawthorne
-  * Tim Leslie
-  * Fernando Perez
-  * Tyler Perrachione
-  * Jean-Baptiste Poline
-  * Alexis Roche
-  * Denis Riviere
-  * Gretchen Reynolds
-  * Jonathan Taylor
-  * Bertrand Thirion
-  * Bernjamin Thyreau
-  * Mike Trumpis
-  * Karl Young
-  * Tom Waite
 
 We would also like to thank `JetBrains <http://www.jetbrains.com/>`__ for providing `Pycharm <http://www.jetbrains.com/pycharm/>`__ licenses.
 
-Funding
--------
-Satrajit Ghosh work on this project was partially funded by NIBIB R03 EB008673 (PI: Ghosh and Whitfield-Gabrieli) and by the `INCF <http://www.incf.org>`__ through a contract with TankThink Labs, LLC.
-Chris Burns was supported by NIMH grant 5R01MH081909-02 (PI: Desposito). Hans Jonson was supported by
-`2 U54 EB005149 - 06	 Core 2b Huntington's Disease - Driving Biological Project <http://projectreporter.nih.gov/project_info_description.cfm?aid=8153616&icde=16158743&ddparam=&ddvalue=&ddsub=&cr=18&csb=PT&cs=ASC>`__,
-`S10 RR023392	 Enterprise Storage In A Collaborative Neuroimaging Environment	 <http://projectreporter.nih.gov/project_info_description.cfm?aid=7209718&icde=16158552&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC>`__,
-`R01 NS040068	 Neurobiological Predictors of Huntington's Disease	 <http://projectreporter.nih.gov/project_info_description.cfm?aid=6266377&icde=16158103>`__,
-and `UL1 TR000442	University of Iowa Clinical and Translational Science Program <http://projectreporter.nih.gov/project_info_description.cfm?aid=8467220&icde=16159156&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC>`__.
-

Vagrantfile

@@ -20,19 +20,20 @@ $script = <<SCRIPT
 # qconf -aattr queue slots "2, [neuro=3]" main.q
 
 # install anaconda
-wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
+wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
 chmod +x miniconda.sh
 ./miniconda.sh -b
-echo "export PATH=$HOME/miniconda/bin:\\$PATH" >> .bashrc
+echo "export PATH=$HOME/miniconda3/bin:\\$PATH" >> .bashrc
 
 # install nipype dependencies
-$HOME/miniconda/bin/conda update --yes conda
-$HOME/miniconda/bin/conda install --yes pip numpy scipy nose traits networkx
-$HOME/miniconda/bin/conda install --yes dateutil ipython-notebook matplotlib
-$HOME/miniconda/bin/pip install nibabel --use-mirrors
-$HOME/miniconda/bin/pip install https://github.com/RDFLib/rdflib/archive/master.zip
-$HOME/miniconda/bin/pip install https://github.com/trungdong/prov/archive/rdf.zip
-$HOME/miniconda/bin/pip install https://github.com/nipy/nipype/archive/master.zip
+$HOME/miniconda3/bin/conda update --yes conda
+$HOME/miniconda3/bin/conda install --yes pip scipy nose networkx lxml future simplejson
+$HOME/miniconda3/bin/conda install --yes python-dateutil jupyter matplotlib
+$HOME/miniconda3/bin/pip install nibabel
+$HOME/miniconda3/bin/pip install prov
+$HOME/miniconda3/bin/pip install xvfbwrapper
+$HOME/miniconda3/bin/pip install traits
+$HOME/miniconda3/bin/pip install https://github.com/nipy/nipype/archive/master.zip
 SCRIPT
 
 Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|

bin/nipype_crash_search

@@ -0,0 +1,76 @@
+#!/usr/bin/env python
+"""Search for tracebacks inside a folder of nipype crash
+log files that match a given regular expression.
+
+Examples:
+nipype_crash_search -d nipype/wd/log -r '.*subject123.*'
+"""
+import re
+import os.path as op
+from glob import glob
+
+from traits.trait_errors import TraitError
+from nipype.utils.filemanip import loadcrash
+
+
+def load_pklz_traceback(crash_filepath):
+    """ Return the traceback message in the given crash file."""
+    try:
+        data = loadcrash(crash_filepath)
+    except TraitError as te:
+        return str(te)
+    except:
+        raise
+    else:
+        return '\n'.join(data['traceback'])
+
+
+def iter_tracebacks(logdir):
+    """ Return an iterator over each file path and
+    traceback field inside `logdir`.
+    Parameters
+    ----------
+    logdir: str
+        Path to the log folder.
+
+    field: str
+        Field name to be read from the crash file.
+
+    Yields
+    ------
+    path_file: str
+
+    traceback: str
+    """
+    crash_files = sorted(glob(op.join(logdir, '*.pkl*')))
+
+    for cf in crash_files:
+        yield cf, load_pklz_traceback(cf)
+
+
+def display_crash_search(logdir, regex):
+    rex = re.compile(regex, re.IGNORECASE)
+    for file, trace in iter_tracebacks(logdir):
+        if rex.search(trace):
+            print("-" * len(file))
+            print(file)
+            print("-" * len(file))
+            print(trace)
+
+
+if __name__ == "__main__":
+    from argparse import ArgumentParser, RawTextHelpFormatter
+    defstr = ' (default %(default)s)'
+    parser = ArgumentParser(prog='nipype_crash_search',
+                            description=__doc__,
+                            formatter_class=RawTextHelpFormatter)
+    parser.add_argument('-l','--logdir', type=str, dest='logdir',
+                        action="store", default=None,
+                        help='The working directory log file.' + defstr)
+    parser.add_argument('-r', '--regex', dest='regex',
+                        default='*',
+                        help='Regular expression to be searched in each traceback.' + defstr)
+
+    args = parser.parse_args()
+
+    display_crash_search(args.logdir, args.regex)

circle.yml

@@ -28,6 +28,7 @@ dependencies:
     - pip install -e git+https://github.com/enthought/blockcanvas.git#egg=blockcanvas
     - pip install -e git+https://github.com/enthought/etsproxy.git#egg=etsproxy
     - pip install -e git+https://github.com/enthought/ets.git#egg=ets
+    - pip install https://github.com/rtfd/readthedocs-sphinx-ext/archive/master.zip
     - gem install fakes3
     - if [[ ! -d ~/examples/data ]]; then wget "https://dl.dropbox.com/s/jzgq2nupxyz36bp/nipype-tutorial.tar.bz2" && tar jxvf nipype-tutorial.tar.bz2 && mv nipype-tutorial/* ~/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

doc/_templates/indexsidebar.html

@@ -5,7 +5,7 @@ <h3>{{ _('Links') }}</h3>
     <li>Docs: <a href="http://nipy.org/nipype">Stable</a> · <a href="http://www.mit.edu/~satra/nipype-nightly/">Nightly</a></li>
     <li>Code: <a href="http://github.com/nipy/nipype">Github</a> · <a href="http://github.com/nipy/nipype/issues">Bugs-Requests</a></li>
     <li>Forum: <a href="http://neurostars.org/t/nipype">User</a> · <a href="http://projects.scipy.org/mailman/listinfo/nipy-devel">Developer</a></li>
-    <li><a href="http://nipy.org/software/license/index.html"><img src="https://img.shields.io/pypi/l/nipype.svg" alt="License"></a> · <a href="http://nipy.org/about/funding.html">Funding</a></li>
+    <li><a href="http://nipy.org/software/license/index.html"><img src="https://img.shields.io/pypi/l/nipype.svg" alt="License"></a> · <a href="about.html#funding">Funding</a></li>
     <li><a href="https://travis-ci.org/nipy/nipype"><img src="https://travis-ci.org/nipy/nipype.png?branch=master" alt="travis"></a> · <a href='https://coveralls.io/r/nipy/nipype'><img src='https://coveralls.io/repos/nipy/nipype/badge.png' alt='Coverage Status' /></a></li>
     <li><a href="https://pypi.python.org/pypi/nipype/"><img src="https://img.shields.io/pypi/dm/nipype.svg" alt="Downloads"></a> · <a href='https://pypi.python.org/pypi/nipype/'><img src='https://img.shields.io/pypi/pyversions/nipype.svg' alt='Python Versions' /></a></li>
 </ul>

doc/_templates/layout.html

@@ -14,6 +14,12 @@
   ga('create', 'UA-339450-7', 'nipy.org/nipype');
   ga('send', 'pageview');
 </script>
+<script>
+  ((window.gitter = {}).chat = {}).options = {
+    room: 'nipy/nipype'
+  };
+</script>
+<script src="https://sidecar.gitter.im/dist/sidecar.v1.js" async defer></script>
 {% endblock %}
 
 {% block header %}

doc/_templates/navbar.html

@@ -10,6 +10,6 @@
 <a class="navbar" href="{{pathto('index')}}">Home</a> ·
 <a class="navbar" href="{{pathto('quickstart')}}">Quickstart</a> ·
 <a class="navbar" href="{{pathto('documentation')}}">Documentation</a> ·
-<a class="navbar" href="{{pathto('about')}}">Citation</a> ·
-<a class="navbar" href="http://nipy.org">NiPy</a>
+<a class="navbar" href="{{pathto('about')}}">About</a> ·
+<a class="navbar" href="http://nipy.org">Nipy</a>
 

doc/_templates/sidebar_versions.html

@@ -17,24 +17,14 @@ <h3>{{ _('Versions') }}</h3>
                 <td align="left">Release</td><td align="right">Devel</td>
             </tr>
             <tr>
-                <td align="left">0.11.0</td><td align="right">{{ version }}</td>
+                <td align="left">{{ release }}</td><td align="right">{{ version }}</td>
             </tr>
             <tr>
                 <td align="left"><a href="{{pathto('users/install')}}">Download</a></td>
                 <td align="right"><a href="https://github.com/nipy/nipype">Github</a></td>
             </tr>
         </table>
     </div>
-
-    <div id="buttons">
-        <div id="ohloh-use" style="margin-right: 25px; margin-top: -2px; float: left;">
-            <script type="text/javascript"
-                    src="https://www.openhub.net/p/480871/widgets/project_users_logo.js">
-            </script>
-        </div><!-- use -->
-        <g:plusone size="medium" annotation="none"></g:plusone>
-        <div class="clear"></div>
-    </div><!-- buttons container -->
 </div>
 
 

doc/about.rst

@@ -14,7 +14,7 @@ Citation
    Ghosh SS. (2011). Nipype: a flexible, lightweight and extensible neuroimaging
    data processing framework in Python. Front. Neuroimform. 5:13.
 
-   `Download`__
+   `Download Paper`__
 
    __ paper_
 

doc/conf.py

@@ -14,12 +14,24 @@
 
 import sys
 import os
+from shutil import rmtree
 
 nipypepath = os.path.abspath('..')
 sys.path.insert(1, nipypepath)
 
 import nipype
 
+if not os.path.exists('users/examples'):
+    os.mkdir('users/examples')
+os.system('python ../tools/make_examples.py --no-exec')
+
+if os.path.exists('api/generated'):
+    rmtree('api/generated')
+os.system('python ../tools/build_modref_templates.py')
+if os.path.exists('interfaces/generated'):
+    rmtree('interfaces/generated')
+os.system('python ../tools/build_interface_docs.py')
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
@@ -29,7 +41,8 @@
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.todo',
+extensions = ['readthedocs_ext.readthedocs',
+              'sphinx.ext.todo',
               'sphinx.ext.pngmath',
               'sphinx.ext.inheritance_diagram',
               'sphinx.ext.graphviz',
@@ -40,8 +53,8 @@
               'numpy_ext.numpydoc',
               'matplotlib.sphinxext.plot_directive',
               'matplotlib.sphinxext.only_directives',
-              'IPython.sphinxext.ipython_directive',
-              'IPython.sphinxext.ipython_console_highlighting'
+              #'IPython.sphinxext.ipython_directive',
+              #'IPython.sphinxext.ipython_console_highlighting'
               ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -58,7 +71,7 @@
 
 # General information about the project.
 project = u'nipype'
-copyright = u'2009-15, Neuroimaging in Python team'
+copyright = u'2009-16, Neuroimaging in Python team'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -67,7 +80,7 @@
 # The short X.Y version.
 version = nipype.__version__
 # The full version, including alpha/beta/rc tags.
-release = version
+release = "0.11.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/users/debug.rst

@@ -42,6 +42,9 @@ performance issues.
 #. All Nipype crashfiles can be inspected with the `nipype_display_crash`
    utility.
 
+#. The `nipype_crash_search` command allows you to search for regular expressions
+in the tracebacks of the Nipype crashfiles within a log folder.
+
 #. Nipype determines the hash of the input state of a node. If any input
    contains strings that represent files on the system path, the hash evaluation
    mechanism will determine the timestamp or content hash of each of those