Merge pull request #8 from nipy/master

Update fork

Author: sgiavasis

.gitignore

@@ -5,6 +5,7 @@
 /nipype/build
 /nipype/nipype.egg-info
 /doc/_build
+/doc/preproc
 /doc/users/examples
 /doc/api/generated
 *.pyc
@@ -13,3 +14,10 @@
 .settings
 .pydevproject
 .idea/
+/documentation.zip
+.DS_Store
+nipype/testing/data/von-ray_errmap.nii.gz
+nipype/testing/data/von_errmap.nii.gz
+crash*.pklz
+.coverage
+htmlcov/

.mailmap

@@ -4,7 +4,7 @@ Cindee Madison <cindee@berkeley.edu> cindeem
 Chris Filo Gorgolewski <chris.gorgolewski@gmail.com> filo <filo@filo-Precision-M6500>
 Chris Filo Gorgolewski <chris.gorgolewski@gmail.com> Krzysztof Gorgolewski <krzysztof.gorgolewski@gmail.com>
 Erik Ziegler <erik.ziegler@ulg.ac.be> erikz <erik.ziegler@ulg.ac.be>
-Michael Waskom <mwaskom@stanford.edu> mwaskom <mwaskom@stanford.edu> Michael Waskom <mwaskom@mit.edu> mwaskom <mwaskom@mit.edu> 
+Michael Waskom <mwaskom@stanford.edu> mwaskom <mwaskom@stanford.edu> Michael Waskom <mwaskom@mit.edu> mwaskom <mwaskom@mit.edu>
 Gael Varoquaux <gael.varoquaux@normalesup.org> GaelVaroquaux
 Gael Varoquaux <gael.varoquaux@normalesup.org> GaelVaroquaux <gael.varoquaux@noramlesup.org>
 Daniel Ginsburg <daniel.ginsburg@childrens.harvard.edu> danginsburg <daniel.ginsburg@childrens.harvard.edu>

.travis.yml

@@ -1,39 +1,52 @@
+cache:
+- apt
 language: python
 python:
-  - 2.6
-  - 2.7
-# Setup anaconda
+- 2.7
+- 3.4
+env:
+- INSTALL_DEB_DEPENDECIES=true
+- INSTALL_DEB_DEPENDECIES=false
 before_install:
-  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-3.0.0-Linux-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-3.0.0-Linux-x86_64.sh -O miniconda.sh; fi
-  - chmod +x miniconda.sh
-  - ./miniconda.sh -b
-  - export PATH=/home/travis/miniconda/bin:$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
-
-# Install packages
+- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
+  -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+  -O miniconda.sh; fi
+- chmod +x miniconda.sh
+- "./miniconda.sh -b"
+- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then export PATH=/home/travis/miniconda2/bin:$PATH; else export PATH=/home/travis/miniconda3/bin:$PATH; fi
+- 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
+- if $INSTALL_DEB_DEPENDECIES; then source /etc/afni/afni.sh; fi
+- export FSLOUTPUTTYPE=NIFTI_GZ
 install:
-  - conda update --yes conda
-  - conda create -n testenv --yes pip python=$TRAVIS_PYTHON_VERSION
-  - source activate testenv
-  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then pip install ordereddict; fi
-  - conda install --yes numpy scipy nose traits networkx dateutil
-  - pip install nibabel --use-mirrors
-  - pip install python-coveralls --use-mirrors
-  - pip install nose-cov --use-mirrors
-  - pip install https://github.com/RDFLib/rdflib/archive/master.zip
-  - pip install https://github.com/satra/prov/archive/enh/rdf.zip
-  - python setup.py install
-
-# Run test
+- conda update --yes conda
+- conda create -n testenv --yes pip python=$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
+- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then conda install --yes traits; else pip install traits; fi
+- pip install python-coveralls
+- pip install nose-cov
+- pip install -r requirements.txt  # finish remaining requirements
+- python setup.py install
 script:
-  - nosetests --with-doctest --with-cov --cov nipype --cov-config .coveragerc --logging-level=INFO
-
-# Calculate coverage
+- python -W once:FSL:UserWarning:nipype `which nosetests` --with-doctest --with-cov --cover-package nipype --cov-config .coveragerc --logging-level=INFO
 after_success:
-  - coveralls --config_file .coveragerc
+- coveralls --config_file .coveragerc
+deploy:
+  provider: pypi
+  user: satra
+  password:
+    secure: OCO0FXb4f+pH4Uw7zWCIRp3qOJ1t7rhky4K8MjNU8tyVCJgd6O/Bv8GJgceS0LktPodlAAjB8SxAhTORPAQZ1D/44PJYy3NQIisvej1zjLpaA9TEGfl6W7MqhDpRyMHW+cnSi/n84SAmdr+Z4vOxScDHdwr13EPmGyOIlHMAGnE=
+  on:
+    tags: true
+    repo: nipy/nipype
+    branch: master
+  distributions: "sdist bdist_wheel"

CHANGES

@@ -1,8 +1,148 @@
-Next Release
+Next release
 ============
 
-* ENH: New ANTs interface: ApplyTransformsToPoints
+* TST: Cache APT in CircleCI (https://github.com/nipy/nipype/pull/1333)
+* ENH: Add new flags to the BRAINSABC for new features (https://github.com/nipy/nipype/pull/1322)
+* ENH: Provides a Nipype wrapper for ANTs DenoiseImage (https://github.com/nipy/nipype/pull/1291)
+* FIX: Minor bugfix logging hash differences (https://github.com/nipy/nipype/pull/1298)
+* FIX: Use released Prov python library (https://github.com/nipy/nipype/pull/1279)
+* ENH: Support for Python 3 (https://github.com/nipy/nipype/pull/1221)
+* FIX: VTK version check missing when using tvtk (https://github.com/nipy/nipype/pull/1219)
+* ENH: Added an OAR scheduler plugin (https://github.com/nipy/nipype/pull/1259)
+* ENH: New ANTs interface: antsBrainExtraction (https://github.com/nipy/nipype/pull/1231)
+* API: Default model level for the bedpostx workflow has been set to "2" following FSL 5.0.9 lead
+* ENH: New interfaces for interacting with AWS S3: S3DataSink and S3DataGrabber (https://github.com/nipy/nipype/pull/1201)
+* ENH: Interfaces for MINC tools (https://github.com/nipy/nipype/pull/1304)
+
+Release 0.11.0 (September 15, 2015)
+============
+
+* API: Change how hash values are computed (https://github.com/nipy/nipype/pull/1174)
+* ENH: New algorithm: mesh.WarpPoints applies displacements fields to point sets
+       (https://github.com/nipy/nipype/pull/889).
+* ENH: New interfaces for MRTrix3 (https://github.com/nipy/nipype/pull/1126)
+* ENH: New option in afni.3dRefit - zdel, ydel, zdel etc. (https://github.com/nipy/nipype/pull/1079)
+* FIX: ants.Registration composite transform outputs are no longer returned as lists (https://github.com/nipy/nipype/pull/1183)
+* BUG: ANTs Registration interface failed with multi-modal inputs
+    (https://github.com/nipy/nipype/pull/1176) (https://github.com/nipy/nipype/issues/1175)
+* ENH: dipy.TrackDensityMap interface now accepts a reference image (https://github.com/nipy/nipype/pull/1091)
+* FIX: Bug in XFibres5 (https://github.com/nipy/nipype/pull/1168)
+* ENH: Attempt to use hard links for data sink.
+    (https://github.com/nipy/nipype/pull/1161)
+* FIX: Updates to SGE Plugins
+    (https://github.com/nipy/nipype/pull/1129)
+* ENH: Add ants JointFusion() node with testing
+    (https://github.com/nipy/nipype/pull/1160)
+* ENH: Add --float option for antsRegistration calls
+    (https://github.com/nipy/nipype/pull/1159)
+* ENH: Added interface to simulate DWIs using the multi-tensor model
+       (https://github.com/nipy/nipype/pull/1085)
+* ENH: New interface for FSL fslcpgeom utility (https://github.com/nipy/nipype/pull/1152)
+* ENH: Added SLURMGraph plugin for submitting jobs to SLURM with dependencies (https://github.com/nipy/nipype/pull/1136)
+* FIX: Enable absolute path definitions in DCMStack (https://github.com/nipy/nipype/pull/1089,
+       replaced by https://github.com/nipy/nipype/pull/1093)
+* ENH: New mesh.MeshWarpMaths to operate on surface-defined warpings
+       (https://github.com/nipy/nipype/pull/1016)
+* FIX: Refactor P2PDistance, change name to ComputeMeshWarp, add regression tests,
+       fix bug in area weighted distance, and added optimizations
+       (https://github.com/nipy/nipype/pull/1016)
+* ENH: Add an option not to resubmit Nodes that finished running when using SGEGraph (https://github.com/nipy/nipype/pull/1002)
+* FIX: FUGUE is now properly listing outputs. (https://github.com/nipy/nipype/pull/978)
+* ENH: Improved FieldMap-Based (FMB) workflow for correction of susceptibility distortions in EPI seqs.
+       (https://github.com/nipy/nipype/pull/1019)
+* FIX: In the FSLXcommand _list_outputs function fixed for loop range (https://github.com/nipy/nipype/pull/1071)
+* 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)
+* FIX: typo in nipype.interfaces.freesurfer.utils.py Tkregister2 (https://github.com/nipy/nipype/pull/1083)
+* FIX: SSHDataGrabber outputs now return full path to the grabbed/downloaded files. (https://github.com/nipy/nipype/pull/1086)
+* FIX: Add QA output for TSNR to resting workflow (https://github.com/nipy/nipype/pull/1088)
+* FIX: Change N4BiasFieldCorrection to use short tag for dimensionality (backward compatible) (https://github.com/nipy/nipype/pull/1096)
+* ENH: Added -newgrid input to Warp in AFNI (3dWarp wrapper) (https://github.com/nipy/nipype/pull/1128)
+* FIX: Fixed AFNI Copy interface to use positional inputs as required (https://github.com/nipy/nipype/pull/1131)
+* ENH: Added a check in Dcm2nii to check if nipype created the config.ini file and remove if true (https://github.com/nipy/nipype/pull/1132)
+* ENH: Use a while loop to wait for Xvfb (up to a max wait time "xvfb_max_wait" in config file, default 10)
+       (https://github.com/nipy/nipype/pull/1142)
+
+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)
 ============
@@ -23,7 +163,8 @@ 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.

MANIFEST.in

@@ -10,5 +10,4 @@ include doc/documentation.zip
 include nipype/COMMIT_INFO.txt
 
 recursive-include doc *
-recursive-include matlabscripts *
 recursive-include tools *

Makefile

@@ -5,6 +5,8 @@
 PYTHON ?= python
 NOSETESTS ?= nosetests
 
+.PHONY: zipdoc sdist egg upload_to_pypi trailing-spaces clean-pyc clean-so clean-build clean-ctags clean in inplace test-code test-doc test-coverage test html specs check-before-commit check
+
 zipdoc: html
 	zip documentation.zip doc/_build/html
 
@@ -26,7 +28,7 @@ upload_to_pypi: zipdoc
 	python setup.py sdist --formats=zip,gztar upload
 
 trailing-spaces:
-	find . -name "*.py" | xargs perl -pi -e 's/[ \t]*$$//'
+	find . -name "*[.py|.rst]" -type f | xargs perl -pi -e 's/[ \t]*$$//'
 	@echo "Reverting test_docparse"
 	git checkout nipype/utils/tests/test_docparse.py
 
@@ -70,7 +72,8 @@ specs:
 	@echo "Checking specs and autogenerating spec tests"
 	python tools/checkspecs.py
 
-check-before-commit: trailing-spaces html test specs
+check: check-before-commit # just a shortcut
+check-before-commit: specs trailing-spaces html test
 	@echo "removed spaces"
 	@echo "built docs"
 	@echo "ran test"