Merge branch 'master' into fix_freesurfer_abspath

Author: bpinsard

.coveragerc

@@ -0,0 +1,9 @@
+[run]
+branch = True
+source = nipype
+include = */nipype/*
+omit =
+    */nipype/external/*
+    */nipype/workflows/*
+    */nipype/fixes/*
+    */setup.py

.gitignore

@@ -12,3 +12,4 @@
 .project
 .settings
 .pydevproject
+.idea/

.travis.yml

@@ -1,24 +1,43 @@
+cache:
+  - apt
 language: python
 python:
-    - "2.7"
+  - 2.6
+  - 2.7
+env:
+  - INSTALL_DEB_DEPENDECIES=true
+  - INSTALL_DEB_DEPENDECIES=false
+# Setup anaconda
 before_install:
-    - deactivate
-    - sudo rmdir /dev/shm
-    - sudo ln -Tsf /{run,dev}/shm
-    - sudo apt-get update -qq
-    - sudo apt-get install lsb-release
-    - source /etc/lsb-release
-    - echo ${DISTRIB_CODENAME}
-    - wget -O- http://neuro.debian.net/lists/${DISTRIB_CODENAME}.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
-    - sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9
-    - sudo apt-get update -qq
-    - sudo apt-get install -qq python-scipy python-nose
-    - sudo apt-get install -qq python-networkx python-traits python-setuptools
-    - sudo apt-get install -qq python-nibabel
-    - sudo apt-get install -qq --no-install-recommends fsl afni
-    - sudo apt-get install -qq fsl-atlases
-    - source /etc/fsl/fsl.sh
-    - virtualenv --system-site-packages ~/virtualenv/this
-    - source ~/virtualenv/this/bin/activate
-install: python setup.py build_ext --inplace
-script: make test
+  - 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
+  - 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 $INSTALL_DEB_DEPENDECIES; then source /etc/fsl/fsl.sh; fi
+
+# Install packages
+install:
+  - conda update --yes conda
+  - conda create -n testenv --yes pip python=$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/trungdong/prov/archive/rdf.zip
+  - python setup.py install
+
+# Run test
+script:
+  - nosetests --with-doctest --with-cov --cov nipype --cov-config .coveragerc --logging-level=INFO
+
+# Calculate coverage
+after_success:
+  - coveralls --config_file .coveragerc

CHANGES

@@ -2,6 +2,126 @@ Next release
 ============
 
 
+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)
+============
+
+* FIX: DataFinder was broken due to a typo
+* FIX: Order of DataFinder outputs was not guaranteed, it's human sorted now
+* ENH: New interfaces: Vnifti2Image, VtoMat
+
+Release 0.9.1 (December 25, 2013)
+============
+
+* FIX: installation issues
+
+Release 0.9.0 (December 20, 2013)
+============
+
+* ENH: SelectFiles: a streamlined version of DataGrabber
+* 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: New SPM interfaces:
+		- spm.ResliceToReference,
+		- spm.DicomImport
+* ENH: New AFNI interfaces:
+		- afni.AFNItoNIFTI
+		- afni.TCorr1D
+* ENH: Several new interfaces related to Camino were added:
+        - camino.SFPICOCalibData
+        - camino.Conmat
+        - camino.QBallMX
+        - camino.LinRecon
+        - camino.SFPeaks
+        One outdated interface no longer part of Camino was removed:
+        - camino.Conmap
+* ENH: Three new mrtrix interfaces were added:
+        - mrtrix.GenerateDirections
+        - mrtrix.FindShPeaks
+        - mrtrix.Directions2Amplitude
+* ENH: New FSL interfaces:
+		- fsl.PrepareFieldmap
+		- fsl.TOPUP
+		- fsl.ApplyTOPUP
+		- fsl.Eddy
+* ENH: New misc interfaces:
+		- FuzzyOverlap,
+		- P2PDistance
+* ENH: New workflows: nipype.workflows.dmri.fsl.epi.[fieldmap_correction&topup_correction]
+* ENH: Added simplified outputname generation for command line interfaces.
+* ENH: Allow ants use a single mask image
+* ENH: Create configuration option for parameterizing directories with hashes
+* ENH: arrange nodes by topological sort with disconnected subgraphs
+* ENH: uses the nidm iri namespace for uuids
+* ENH: remove old reporting webpage
+* ENH: Added support for Vagrant
+
+* API: 'name' is now a positional argument for Workflow, Node, and MapNode constructors
+* API: SPM now defaults to SPM8 or SPM12b job format
+* API: DataGrabber and SelectFiles use human (or natural) sort now
+
+* FIX: Several fixes related to Camino interfaces:
+        - ProcStreamlines would ignore many arguments silently (target, waypoint, exclusion ROIS, etc.)
+        - DTLUTGen would silently round the "step", "snr" and "trace" parameters to integers
+        - PicoPDFs would not accept more than one lookup table
+        - PicoPDFs default pdf did not correspond to Camino default
+        - Track input model names were outdated (and would generate an error)
+        - Track numpds parameter could not be set for deterministic tractography
+        - FA created output files with erroneous extension
+* FIX: Deals properly with 3d files in SPM Realign
+* FIX: SPM with MCR fixed
+* FIX: Cleaned up input and output spec metadata
+* FIX: example openfmri script now makes the contrast spec a hashed input
+* FIX: FILMGLS compatibility with FSL 5.0.5
+* FIX: Freesurfer recon-all resume now avoids setting inputs
+* FIX: File removal from node respects file associations img/hdr/mat, BRIK/HEAD
+
 Release 0.8.0 (May 8, 2013)
 ===========================
 
@@ -29,7 +149,7 @@ Release 0.7.0 (Dec 18, 2012)
 * ENH: New interfaces: ICC, Meshfix, ants.Register, C3dAffineTool, ants.JacobianDeterminant,
        afni.AutoTcorrelate, DcmStack
 * ENH: New workflows: ants template building (both using 'ANTS' and the new 'antsRegistration')
-* ENH: New examples: how to use ANTS template building workflows (smri_ants_build_tmeplate), 
+* ENH: New examples: how to use ANTS template building workflows (smri_ants_build_tmeplate),
 	  how to set SGE specific options (smri_ants_build_template_new)
 * ENH: added no_flatten option to Merge
 * ENH: added versioning option and checking to traits
@@ -91,11 +211,11 @@ Release 0.5 (Mar 10, 2012)
 * API: IPython plugin now invokes IPython 0.11 or greater
 * API: Canned workflows are now all under a different package structure
 * API: SpecifyModel event_info renamed to event_files
-* API: DataGrabber is always being rerun (unless overwrite is set to False on 
+* API: DataGrabber is always being rerun (unless overwrite is set to False on
 	   Node level)
-* API: "stop_on_first_rerun" does not stop for DataGrabber (unless overwrite is 
+* API: "stop_on_first_rerun" does not stop for DataGrabber (unless overwrite is
 	   set to True on Node level)
-* API: Output prefix can be set for spm nodes (SliceTiming, Realign, Coregister, 
+* API: Output prefix can be set for spm nodes (SliceTiming, Realign, Coregister,
        Normalize, Smooth)
 
 * ENH: Added fsl resting state workflow based on behzadi 2007 CompCorr method.
@@ -115,7 +235,7 @@ Release 0.5 (Mar 10, 2012)
 * ENH: IdentityNode with iterable expansion takes place after remaining Identity
        Node removal
 * ENH: Crashfile display script added
-* ENH: Added FmriRealign4d node wrapped from nipy 
+* ENH: Added FmriRealign4d node wrapped from nipy
 * ENH: Added TBSS workflows and examples
 * ENH: Support for openfmri data processing
 * ENH: Package version check
@@ -148,8 +268,8 @@ Release 0.4 (Jun 11, 2011)
 
 * API: Timestamp hashing does not use ctime anymore. Please update your hashes by
        running workflows with updatehash=True option
-       NOTE: THIS IS THE DEFAULT CONFIG NOW, so unless you updatehash, workflows will 
-       rerun 
+       NOTE: THIS IS THE DEFAULT CONFIG NOW, so unless you updatehash, workflows will
+       rerun
 * API: Workflow run function no longer supports (inseries, createdirsonly).
        Functions used in connect string must be pickleable
 * API: SPM EstimateContrast: ignore_derivs replaced by use_derivs
@@ -184,7 +304,7 @@ Release 0.4 (Jun 11, 2011)
     - ChangeDataType, Threshold, MeanImage, IsotropicSmooth, ApplyMask, TemporalFilter
       DilateImage, ErodeImage, SpatialFilter, UnaryMaths, BinaryMaths, MultiImageMaths
 * ENH: added support for networx 1.4 and improved iterable expansion
-* ENH: Replaced BEDPOSTX and EddyCurrent with nipype pipelines 
+* ENH: Replaced BEDPOSTX and EddyCurrent with nipype pipelines
 * ENH: Ability to create a hierarchical dot file
 * ENH: Improved debugging information for rerunning nodes
 * ENH: Added 'stop_on_first_rerun' option
@@ -220,15 +340,15 @@ Release 0.3.4 (Jan 12, 2011)
 * ENH: Added SPM node for calculating various threshold statistics
 * ENH: Added distance and dissimilarity measurements
 
-* BF: Diffusion toolkit gets installed 
+* BF: Diffusion toolkit gets installed
 * BF: Changed FNIRT interface to accept flexible lists (rather than 4-tuples)
       on all options specific to different subsampling levels
 
 Release 0.3.3 (Sep 16, 2010)
 ============================
 
 * API: subject_id in ModelSpec is now deprecated
-* API: spm.Threshold 
+* API: spm.Threshold
   - does not need mask, beta, RPV anymore
   - takes only one image (stat_image - mind the name change)
   - works with SPM2 SPM.mat
@@ -243,7 +363,7 @@ Release 0.3.3 (Sep 16, 2010)
 * BF: Traits logic for 'requires' metadata
 * BF: allows workflows to be relocatable
 * BF: nested workflows with connections don't raise connection not found error
-* BF: multiple workflows with identical nodenames and iterables do not create nestsed workflows  
+* BF: multiple workflows with identical nodenames and iterables do not create nestsed workflows
 
 Release 0.3.2 (Aug 03, 2010)
 ============================

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2009-2013, NIPY Developers
+Copyright (c) 2009-2014, NIPY Developers
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

Makefile

@@ -57,16 +57,21 @@ test-doc:
 	--doctest-fixtures=_fixture doc/
 
 test-coverage:
-	$(NOSETESTS) -s --with-doctest --with-coverage --cover-erase --cover-html \
-	--cover-html-dir=coverage --cover-package=nipype nipype
+	$(NOSETESTS) -s --with-doctest --with-coverage --cover-package=nipype \
+	--config=.coveragerc
 
 test: clean test-code
 
 html:
 	@echo "building docs"
 	make -C doc clean html
 
-check-before-commit: trailing-spaces html test
+specs:
+	@echo "Checking specs and autogenerating spec tests"
+	python tools/checkspecs.py
+
+check-before-commit: specs trailing-spaces html test
 	@echo "removed spaces"
 	@echo "built docs"
 	@echo "ran test"
+	@echo "generated spec tests"