Merge branch 'master' into bugfix_fugue

Author: chrisgorgo

.gitignore

@@ -13,3 +13,4 @@
 .settings
 .pydevproject
 .idea/
+/documentation.zip

.travis.yml

@@ -2,7 +2,6 @@ cache:
   - apt
 language: python
 python:
-  - 2.6
   - 2.7
 env:
   - INSTALL_DEB_DEPENDECIES=true

CHANGES

@@ -1,27 +1,68 @@
 Next release
 ============
 
+* ENH: Improved FieldMap-Based (FMB) workflow for correction of susceptibility distortions in EPI seqs.
+       (https://github.com/nipy/nipype/pull/1019)
+* ENH: Dropped support for now 7 years old Python 2.6 (https://github.com/nipy/nipype/pull/1069)
+* FIX: terminal_output is not mandatory anymore (https://github.com/nipy/nipype/pull/1070)
+* ENH: Added "nipype_cmd" tool for running interfaces from the command line (https://github.com/nipy/nipype/pull/795)
+* FIX: Fixed Camino output naming (https://github.com/nipy/nipype/pull/1061)
+* ENH: Add the average distance to ErrorMap (https://github.com/nipy/nipype/pull/1039)
+* ENH: Inputs with name_source can be now chained in cascade (https://github.com/nipy/nipype/pull/938)
+* ENH: Improve JSON interfaces: default settings when reading and consistent output creation
+       when writing (https://github.com/nipy/nipype/pull/1047)
+* FIX: AddCSVRow problems when using infields (https://github.com/nipy/nipype/pull/1028)
+* FIX: Removed unused ANTS registration flag (https://github.com/nipy/nipype/pull/999)
+* FIX: Amend create_tbss_non_fa() workflow to match FSL's tbss_non_fa command. (https://github.com/nipy/nipype/pull/1033)
+* FIX: remove unused mandatory flag from spm normalize (https://github.com/nipy/nipype/pull/1048)
+* ENH: Update ANTSCorticalThickness interface (https://github.com/nipy/nipype/pull/1013)
+* FIX: Edge case with sparsemodels and PEP8 cleanup (https://github.com/nipy/nipype/pull/1046)
+* ENH: New io interfaces for JSON files reading/writing (https://github.com/nipy/nipype/pull/1020)
+* ENH: Enhanced openfmri script to support freesurfer linkage (https://github.com/nipy/nipype/pull/1037)
+* BUG: matplotlib is supposed to be optional (https://github.com/nipy/nipype/pull/1003)
+* FIX: Fix split_filename behaviour when path has no file component (https://github.com/nipy/nipype/pull/1035)
+* ENH: Updated FSL dtifit to include option for grad non-linearities (https://github.com/nipy/nipype/pull/1032)
+* ENH: Updated Camino tracking interfaces, which can now use FSL bedpostx output.
+       New options also include choice of tracker, interpolator, stepsize and
+       curveinterval for angle threshold (https://github.com/nipy/nipype/pull/1029)
+* FIX: Interfaces redirecting X crashed if $DISPLAY not defined (https://github.com/nipy/nipype/pull/1027)
+* FIX: Bug crashed 'make api' (https://github.com/nipy/nipype/pull/1026)
+* ENH: Updated antsIntroduction to handle RA and RI registrations (https://github.com/nipy/nipype/pull/1009)
+* 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)
+* FIX: Output prefix in SPM Normalize with modulation (https://github.com/nipy/nipype/pull/1023)
+* ENH: Usability improvements in cluster environments (https://github.com/nipy/nipype/pull/1025)
+* ENH: ANTs JointFusion() (https://github.com/nipy/nipype/pull/1042)
+* ENH: Added csvReader() utility (https://github.com/nipy/nipype/pull/1044)
 
 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 
+       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 
+* 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, 
+* 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
@@ -37,7 +78,7 @@ Release 0.10.0 (October 10, 2014)
 * 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: 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.

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.

bin/nipype_cmd

@@ -0,0 +1,8 @@
+#!/usr/bin/env python
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+import sys
+from nipype.utils.nipype_cmd import main
+
+if __name__ == '__main__':
+    main(sys.argv)

bin/nipype_display_crash

@@ -74,7 +74,6 @@ if __name__ == "__main__":
                         default=None,
                         help='Directory to run the node in' + defstr)
     args = parser.parse_args()
-    print args.debug, args.ipydebug
     debug = 'ipython' if args.ipydebug else args.debug
     if debug == 'ipython':
         import sys

doc/devel/interface_specs.rst

@@ -358,6 +358,9 @@ CommandLine
 ``name_source``
     Indicates the list of input fields from which the value of the current File
     output variable will be drawn. This input field must be the name of a File.
+    Chaining is allowed, meaning that an input field can point to another as
+    ``name_source``, which also points as ``name_source`` to a third field.
+    In this situation, the templates for substitutions are also accumulated.
 
 ``name_template``
     By default a ``%s_generated`` template is used to create the output

doc/devel/software_using_nipype.rst

@@ -23,6 +23,16 @@ BROCCOLI
 
 `BROCCOLI <https://github.com/wanderine/BROCCOLI/>`_ is a piece of software for fast fMRI analysis on many core CPUs and GPUs. It provides Nipype Interfaces.
 
+Forward
+-------
+
+`Forward <http://cyclotronresearchcentre.github.io/forward/>`_ is set of tools simplifying the preparation of accurate electromagnetic head models for EEG forward modeling. It uses Nipype Workflows and Interfaces.
+
+Limbo
+-----
+
+`Limbo <https://github.com/Gilles86/in_limbo>`_ is a toolbox for finding brain regions that are neither significantly active nor inactive, but rather “in limbo”. It was build using custom Nipype Interfaces and Workflows.
+
 Lyman
 -----
 
@@ -33,6 +43,11 @@ Medimsight
 
 `Medimsight <https://www.medimsight.com>`_ is a commercial service medical imaging cloud platform. It uses Nipype to interface with various neuroimaging software.
 
+MIA
+---
+
+`MIA <http://mia.sourceforge.net>`_ MIA is a a toolkit for gray scale medical image analysis. It provides Nipype interfaces for easy integration with other software.
+
 Mindboggle
 ----------
 

doc/users/config_file.rst

@@ -120,6 +120,11 @@ Execution
     characters will be replaced by their hash. (possible values: ``true`` and
 	``false``; default value: ``true``)
 
+*poll_sleep_duration*
+    This controls how long the job submission loop will sleep between submitting
+    all pending jobs and checking for job completion. To be nice to cluster
+    schedulers the default is set to 60 seconds.
+
 Example
 ~~~~~~~
 

doc/users/index.rst

@@ -37,6 +37,7 @@
    saving_workflows
    spmmcr
    mipav
+   nipypecmd