Merge branch 'new_interfaces' of https://github.com/fcp-indi/nipype into new_interfaces

Author: pintohutch

.gitignore

@@ -21,3 +21,7 @@ nipype/testing/data/von_errmap.nii.gz
 crash*.pklz
 .coverage
 htmlcov/
+__pycache__/
+*~
+.ipynb_checkpoints/
+.ruby-version

.travis.yml

@@ -4,6 +4,7 @@ language: python
 python:
 - 2.7
 - 3.4
+- 3.5
 env:
 - INSTALL_DEB_DEPENDECIES=true
 - INSTALL_DEB_DEPENDECIES=false
@@ -39,7 +40,7 @@ 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 networkx dateutil
+- conda install --yes numpy scipy nose networkx python-dateutil
 - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then conda install --yes traits; else pip install traits; fi
 - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then conda install --yes vtk; fi
 - pip install python-coveralls

CHANGES

@@ -1,6 +1,9 @@
-Next release
+Release 0.12.0-rc1 (April 20, 2016)
 ============
 
+* 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)
 * 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)
@@ -25,6 +28,9 @@ 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)
 ============

CONTRIBUTING.md

@@ -19,7 +19,7 @@
 
 When opening a new Issue, please take the following steps:
 
-1. Search GitHub and/or [Neurostars](neurostars.org) for your issue to avoid duplicate reports.
+1. Search GitHub and/or [Neurostars](http://neurostars.org) for your issue to avoid duplicate reports.
    Keyword searches for your error messages are most helpful.
 2. If possible, try updating to master and reproducing your issue,
    because we may have already fixed it.

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

@@ -2,10 +2,10 @@
 <h3>{{ _('Links') }}</h3>
 
 <ul>
-    <li>Docs: <a href="http://nipy.org/nipype">Stable</a> · <a href="http://www.mit.edu/~satra/nipype-nightly/">Nightly</a></li>
+    <li>Docs: <a href="http://nipy.org/nipype">Stable</a> · <a href="http://nipype.readthedocs.org/en/latest/">Dev</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>