Merge branch 'master' into enh/JSONFileSink

Author: oesteban

.travis.yml

@@ -1,20 +1,24 @@
+cache:
+  - apt
 language: python
 python:
   - 2.6
   - 2.7
+env:
+  - INSTALL_DEB_DEPENDECIES=true
+  - INSTALL_DEB_DEPENDECIES=false
 # Setup anaconda
 before_install:
-  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-3.0.0-Linux-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-3.0.0-Linux-x86_64.sh -O miniconda.sh; fi
+  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-3.6.0-Linux-x86_64.sh -O miniconda.sh; fi
   - chmod +x miniconda.sh
   - ./miniconda.sh -b
   - export PATH=/home/travis/miniconda/bin:$PATH
-  # The next couple lines fix a crash with multiprocessing on Travis
-  - sudo rm -rf /dev/shm
-  - sudo ln -s /run/shm /dev/shm
-  - bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
-  - travis_retry sudo apt-get install -qq --no-install-recommends fsl afni
-  - travis_retry sudo apt-get install -qq fsl-atlases
-  - source /etc/fsl/fsl.sh
+  - 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); fi
+  - if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -qq --no-install-recommends fsl afni elastix; fi
+  - if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -qq fsl-atlases; fi
+  - if $INSTALL_DEB_DEPENDECIES; then source /etc/fsl/fsl.sh; fi
 
 # Install packages
 install:

CHANGES

@@ -1,11 +1,60 @@
-Next Release
+Next release
 ============
 
-* API: Interfaces to external packages are no longer available in the top-level ``nipype`` namespace, and must be imported directly (e.g. ``from nipype.interfaces import fsl``).
-* ENH: New ANTs interface: ApplyTransformsToPoints
+* ENH: Updated N4BiasCorrection input spec to include weight image and spline order. Made 
+	   argument formatting consistent. Cleaned ants.segmentation according to PEP8.
+	   (https://github.com/nipy/nipype/pull/990/files)
+* ENH: SPM12 Normalize interface (https://github.com/nipy/nipype/pull/986)
+* FIX: Utility interface test dir (https://github.com/nipy/nipype/pull/986)
+* FIX: IPython engine directory reset after crash (https://github.com/nipy/nipype/pull/987)
+* ENH: Resting state fMRI example with NiPy realignment and no SPM (https://github.com/nipy/nipype/pull/992)
+* FIX: Corrected Freesurfer SegStats _list_outputs to avoid error if summary_file is 
+	   undefined (issue #994)(https://https://github.com/nipy/nipype/pull/996)
+* FIX: OpenfMRI support and FSL 5.0.7 changes (https://github.com/nipy/nipype/pull/1006)
+
+Release 0.10.0 (October 10, 2014)
+============
+
+* ENH: New miscelaneous interfaces: SplitROIs (mapper), MergeROIs (reducer)
+       to enable parallel processing of very large images.
+* ENH: Updated FSL interfaces: BEDPOSTX and XFibres, former interfaces are still
+       available with the version suffix: BEDPOSTX4 and XFibres4. Added gpu 
+       versions of BEDPOSTX: BEDPOSTXGPU, BEDPOSTX5GPU, and BEDPOSTX4GPU
+* ENH: Added experimental support for MIPAV algorithms thorugh JIST plugins
+* ENH: New dipy interfaces: Denoise, Resample
+* ENH: New Freesurfer interfaces: Tkregister2 (for conversion of fsl style matrices to freesurfer format), MRIPretess
+* ENH: New FSL interfaces: WarpPoints, WarpPointsToStd, EpiReg, ProbTrackX2, WarpUtils, ConvertWarp
+* ENH: New miscelaneous interfaces: AddCSVRow, NormalizeProbabilityMapSet, AddNoise
+* ENH: New AFNI interfaces:  Eval, Means, SVMTest, SVMTrain
+* ENH: FUGUE interface has been refactored to use the name_template system, 3 examples 
+       added to doctests, some bugs solved.
+* API: Interfaces to external packages are no longer available in the top-level
+       ``nipype`` namespace, and must be imported directly (e.g.
+       ``from nipype.interfaces import fsl``).
+* ENH: Support for elastix via a set of new interfaces: Registration, ApplyWarp, 
+       AnalyzeWarp, PointsWarp, and EditTransform
+* ENH: New ANTs interface: ApplyTransformsToPoints, LaplacianThickness
+* ENH: New Diffusion Toolkit interface: TrackMerge
+* ENH: New MRtrix interface: FilterTracks
+* ENH: New metrics group in algorithms. Now Distance, Overlap, and FuzzyOverlap
+       are found in nipype.algorithms.metrics instead of misc. Overlap interface
+       extended to allow files containing multiple ROIs and volume physical units.
+* ENH: New interface in algorithms.metrics: ErrorMap (a voxel-wise diff map).
 * ENH: New FreeSurfer workflow: create_skullstripped_recon_flow()
+* ENH: Deep revision of workflows for correction of dMRI artifacts. New dmri_preprocessing
+       example.
 * ENH: New data grabbing interface that works over SSH connections, SSHDataGrabber
+* ENH: New color mode for write_graph
+* ENH: You can now force MapNodes to be run serially
+* ENH: Added ANTS based openfmri workflow
+* ENH: MapNode now supports flattening of nested lists 
+* ENH: Support for headless mode using Xvfb
+* ENH: nipype_display_crash has a debugging mode
 * FIX: MRTrix tracking algorithms were ignoring mask parameters.
+* FIX: FNIRT registration pathway and associated OpenFMRI example script
+* FIX: spm12b compatibility for Model estimate
+* FIX: Batch scheduler controls the number of maximum jobs properly
+* FIX: Update for FSL 5.0.7 which deprecated Contrast Manager
 
 Release 0.9.2 (January 31, 2014)
 ============
@@ -26,7 +75,8 @@ Release 0.9.0 (December 20, 2013)
 * ENH: new tools for defining workflows: JoinNode, synchronize and itersource
 * ENH: W3C PROV support with optional RDF export built into Nipype
 * ENH: Added support for Simple Linux Utility Resource Management (SLURM)
-* ENH: AFNI interfaces refactor, prefix, suffix are replaced by "flexible_%s_templates"
+* ENH: AFNI interfaces refactor, prefix, suffix are replaced by
+       "flexible_%s_templates"
 * ENH: New SPM interfaces:
 		- spm.ResliceToReference,
 		- spm.DicomImport

CONTRIBUTING.md

@@ -0,0 +1,31 @@
+## Contributing pull-requests (PRs)
+
+* All work is submitted via Pull Requests.
+* Pull Requests can be submitted as soon as there is code worth discussing.
+  Pull Requests track the branch, so you can continue to work after the PR is submitted.
+  Review and discussion can begin well before the work is complete,
+  and the more discussion the better.
+  The worst case is that the PR is closed.
+* Pull Requests should generally be made against master
+* Pull Requests should be tested, if feasible:
+    - bugfixes should include regression tests
+    - new behavior should at least get minimal exercise
+* Use a descriptive prefix for your PR: ENH, FIX, TST, DOC, STY, REF (refactor), WIP (Work in progress)
+* After submiting the PR, include an update to the CHANGES file: prefix: description (URL of pull request)
+* `make specs`
+* do: `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`.
+
+## Contributing issues
+
+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.
+   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.
+3. OS and version
+4. Nipype version
+5. Output of: `import nipype; nipype.get_info()`
+6. Versions of underlying tools (e.g., ANTS, FSL, SPM, etc.,.)
+7. Any script, or output log, in a gist (gist.github.com)
+8. When applicable, and where possible, pointers to relevant data files.

Makefile

@@ -70,7 +70,7 @@ specs:
 	@echo "Checking specs and autogenerating spec tests"
 	python tools/checkspecs.py
 
-check-before-commit: trailing-spaces html test specs
+check-before-commit: specs trailing-spaces html test
 	@echo "removed spaces"
 	@echo "built docs"
 	@echo "ran test"

README.rst

@@ -8,6 +8,25 @@ NIPYPE: Neuroimaging in Python: Pipelines and Interfaces
 .. image:: https://coveralls.io/repos/nipy/nipype/badge.png
   :target: https://coveralls.io/r/nipy/nipype
 
+.. image:: https://pypip.in/version/nipype/badge.png
+    :target: https://pypi.python.org/pypi/nipype/
+    :alt: Latest Version
+
+.. image:: https://pypip.in/download/nipype/badge.png
+    :target: https://pypi.python.org/pypi/nipype/
+    :alt: Downloads
+
+.. image:: https://pypip.in/py_versions/nipype/badge.png
+    :target: https://pypi.python.org/pypi/nipype/
+    :alt: Supported Python versions
+
+.. image:: https://pypip.in/status/nipype/badge.png
+    :target: https://pypi.python.org/pypi/nipype/
+    :alt: Development Status
+
+.. image:: https://pypip.in/license/nipype/badge.png
+    :target: https://pypi.python.org/pypi/nipype/
+    :alt: License
 
 Current neuroimaging software offer users an incredible opportunity to
 analyze data using a variety of different algorithms. However, this has
@@ -19,7 +38,7 @@ umbrella of NiPy, is a Python project that provides a uniform interface
 to existing neuroimaging software and facilitates interaction between
 these packages within a single workflow. Nipype provides an environment
 that encourages interactive exploration of algorithms from different
-packages (e.g., SPM, FSL, FreeSurfer, AFNI, Slicer), eases the
+packages (e.g., SPM, FSL, FreeSurfer, AFNI, Slicer, ANTS), eases the
 design of workflows within and between packages, and reduces the
 learning curve necessary to use different packages. Nipype is creating a
 collaborative platform for neuroimaging software development in a
@@ -44,29 +63,31 @@ documentation.
 Website
 -------
 
-Information specific to NIPYPE is located here::
+Information specific to Nipype is located here::
 	    
     http://nipy.org/nipype
 
 
-Mailing Lists
--------------
-
-For core NIPYPE related issues, please see the developer's list here::
-       
-       http://projects.scipy.org/mailman/listinfo/nipy-devel
+Support and Communication
+-------------------------
 
-For user NIPYPE related issues, please see the user's list here::
+If you have a problem or would like to ask a question about how to do something in Nipype please submit a question
+to `NeuroStars.org <http://neurostars.org>`_ with a *nipype* tag. `NeuroStars.org <http://neurostars.org>`_  is a platform similar to StackOverflow but dedicated to neuroinformatics. All previous Nipype questions are available here::
 
-       http://groups.google.com/group/nipy-user
+       http://neurostars.org/t/nipype/
+	   
 
-For NIPYPE related issues, please add *NIPYPE* to the subject line
+To participate in the Nipype development related discussion please use the following mailing list::
+       
+       http://projects.scipy.org/mailman/listinfo/nipy-devel
+	   
+Please add *[nipype]* to the subject line when posting on the mailing list.
 
 
-NIPYPE structure
+Nipype structure
 ----------------
 
-Currently NIPYPE consists of the following files and directories:
+Currently Nipype consists of the following files and directories:
 
   INSTALL
     NIPYPE prerequisites, installation, development, testing, and 

bin/nipype_display_crash

@@ -1,53 +1,85 @@
 #!/usr/bin/env python
 """Displays crash information from Nipype crash files. For certain crash files,
 one can rerun a failed node in a temp directory.
-"""
 
-import argparse
-from nipype.utils.filemanip import loadcrash
+Examples:
+
+nipype_display_crash crashfile.pklz
+nipype_display_crash crashfile.pklz -r -i
+nipype_display_crash crashfile.pklz -r -i
+
+"""
 
-def display_crash_files(crashfile, rerun):
+def display_crash_files(crashfile, rerun, debug, directory):
     """display crash file content and rerun if required"""
 
+    from nipype.utils.filemanip import loadcrash
     crash_data = loadcrash(crashfile)
     node = None
     if 'node' in crash_data:
         node = crash_data['node']
     tb = crash_data['traceback']
-    print "\n"
-    print "File: %s"%crashfile
+    print("\n")
+    print("File: %s" % crashfile)
     if node:
-        print "Node: %s"%node
+        print("Node: %s" % node)
         if node.base_dir:
-            print "Working directory: %s"%node.output_dir()
+            print("Working directory: %s" % node.output_dir())
         else:
-            print "Node crashed before execution"
-        print "\n"
-        print "Node inputs:"
-        print node.inputs
-        print "\n"
-    print "Traceback: "
-    print ''.join(tb)
-    print "\n"
+            print("Node crashed before execution")
+        print("\n")
+        print("Node inputs:")
+        print(node.inputs)
+        print("\n")
+    print("Traceback: ")
+    print(''.join(tb))
+    print ("\n")
 
     if rerun:
         if node is None:
-            print "No node in crashfile. Cannot rerun"
+            print("No node in crashfile. Cannot rerun")
             return
-        print "Rerunning node"
-        node.base_dir = None
+        print("Rerunning node")
+        node.base_dir = directory
         node.config = {'execution': {'crashdump_dir': '/tmp'}}
-        node.run()
-        print "\n"
+        try:
+            node.run()
+        except:
+            if debug and debug != 'ipython':
+                import pdb
+                pdb.post_mortem()
+            else:
+                raise
+        print("\n")
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(prog='nipype_display_crash',
-                                     description=__doc__)
+    from argparse import ArgumentParser, RawTextHelpFormatter
+    defstr = ' (default %(default)s)'
+    parser = ArgumentParser(prog='nipype_display_crash',
+                            description=__doc__,
+                            formatter_class=RawTextHelpFormatter)
     parser.add_argument('crashfile', metavar='f', type=str,
-                   help='crash file to display')
+                        help='crash file to display')
     parser.add_argument('-r','--rerun', dest='rerun',
                         default=False, action="store_true",
-                        help='rerun crashed node')
+                        help='rerun crashed node' + defstr)
+    group = parser.add_mutually_exclusive_group()
+    group.add_argument('-d','--debug', dest='debug',
+                        default=False, action="store_true",
+                        help='enable python debugger when re-executing' + defstr)
+    group.add_argument('-i','--ipydebug', dest='ipydebug',
+                        default=False, action="store_true",
+                        help='enable ipython debugger when re-executing' + defstr)
+    parser.add_argument('--dir', dest='directory',
+                        default=None,
+                        help='Directory to run the node in' + defstr)
     args = parser.parse_args()
-
-    display_crash_files(args.crashfile, args.rerun)
+    debug = 'ipython' if args.ipydebug else args.debug
+    if debug == 'ipython':
+        import sys
+        from IPython.core import ultratb
+        sys.excepthook = ultratb.FormattedTB(mode='Verbose',
+                                             color_scheme='Linux',
+                                             call_pdb=1)
+    display_crash_files(args.crashfile, args.rerun,
+                        debug, args.directory)

doc/_templates/indexsidebar.html

@@ -4,9 +4,10 @@ <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>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://groups.google.com/group/nipy-user">User</a> · <a href="http://projects.scipy.org/mailman/listinfo/nipy-devel">Developer</a></li>
-    <li>Info: <a href="http://nipy.org/software/license/index.html">License</a> · <a href="http://nipy.org/about/funding.html">Funding</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://pypip.in/license/nipype/badge.png" alt="License"></a> · <a href="http://nipy.org/about/funding.html">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://pypip.in/download/nipype/badge.png" alt="Downloads"></a> · <a href='https://pypi.python.org/pypi/nipype/'><img src='https://pypip.in/py_versions/nipype/badge.png' alt='Python Versions' /></a></li>
 </ul>
 
 {% endblock %}

doc/_templates/sidebar_versions.html

@@ -17,7 +17,7 @@ <h3>{{ _('Versions') }}</h3>
                 <td align="left">Release</td><td align="right">Devel</td>
             </tr>
             <tr>
-                <td align="left">0.9.2</td><td align="right">1.0-dev</td>
+                <td align="left">0.10.0</td><td align="right">1.0-dev</td>
             </tr>
             <tr>
                 <td align="left"><a href="{{pathto('users/install')}}">Download</a></td>

doc/conf.py

@@ -38,7 +38,9 @@
               'sphinx.ext.autosummary',
               'numpy_ext.numpydoc',
               'matplotlib.sphinxext.plot_directive',
-              'matplotlib.sphinxext.only_directives'
+              'matplotlib.sphinxext.only_directives',
+              'IPython.sphinxext.ipython_directive',
+              'IPython.sphinxext.ipython_console_highlighting'
               ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -55,7 +57,7 @@
 
 # General information about the project.
 project = u'nipype'
-copyright = u'2009-13, Neuroimaging in Python team'
+copyright = u'2009-14, 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

doc/devel/index.rst

@@ -18,6 +18,7 @@ conventions documented in the `NIPY Developers Guide
    gitwash/index   
    architecture
    provenance
+   software_using_nipype
 
 
 .. include:: ../links_names.txt

doc/devel/interface_specs.rst

@@ -404,6 +404,9 @@ If you used genfile:
 
 And optionally:
 
+* ``_redirect_x``: If set to True it will make Nipype start Xvfb before running the interface and redirect X output to it. This is useful for
+commandlines that spawn a graphical user interface.
+
 * ``_format_arg(name, spec, value)``: For extra formatting of the input values before passing them to generic ``_parse_inputs()`` method.
 
 For example this is the class definition for Flirt, minus the docstring::