Merge pull request #6 from nipy/master

Update my fork of nipype

Author: sgiavasis

.gitignore

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

.travis.yml

@@ -4,28 +4,24 @@ python:
   - 2.7
 # Setup anaconda
 before_install:
-  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-2.2.2-Linux-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-2.2.2-Linux-x86_64.sh -O miniconda.sh; fi
+  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-3.0.0-Linux-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-3.0.0-Linux-x86_64.sh -O miniconda.sh; fi
   - chmod +x miniconda.sh
   - ./miniconda.sh -b
-  - export PATH=/home/travis/anaconda/bin:$PATH
+  - 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
-  - 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 --no-install-recommends fsl afni
-  - sudo apt-get install -qq fsl-atlases
+  - 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
 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

CHANGES

@@ -1,13 +1,31 @@
-Next release
+Release 0.9.2 (January 31, 2014)
+===========
+
+* ENH: New ANTs interface: ApplyTransformsToPoints
+
+* 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 interfaces: spm.ResliceToReference, FuzzyOverlap, afni.AFNItoNIFTI
-       spm.DicomImport, P2PDistance
+* 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)
-* ENHL 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
+* ENH: New AFNI interfaces:
+		- afni.AFNItoNIFTI
+		- afni.TCorr1D
 * ENH: Several new interfaces related to Camino were added:
         - camino.SFPICOCalibData
         - camino.Conmat
@@ -16,7 +34,31 @@ Next release
         - 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
@@ -25,29 +67,12 @@ Next release
         - 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
-
-* API: 'name' is now a positional argument for Workflow, Node, and MapNode constructors
-* API: SPM now defaults to SPM8 or SPM12b job format
-
-* ENH: New FSL interfaces: fsl.PrepareFieldmap, fsl.TOPUP, fsl.ApplyTOPUP, fsl.Eddy
-* ENH: New workflows: nipype.workflows.dmri.fsl.epi.[fieldmap_correction&topup_correction]
-
-* ENH: Added simplified outputname generation for command line interfaces.
 * FIX: Cleaned up input and output spec metadata
-
-* 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 (this is a WIP i hope to finish in a day or two)
-
 * 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)
@@ -77,7 +102,7 @@ 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
@@ -139,11 +164,11 @@ 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.
@@ -163,7 +188,7 @@ 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
@@ -196,8 +221,8 @@ 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
@@ -232,7 +257,7 @@ 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
@@ -268,15 +293,15 @@ 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
@@ -291,7 +316,7 @@ 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

README.rst

@@ -103,5 +103,5 @@ There are interfaces to some GNU code but these are entirely optional.
 All trademarks referenced herein are property of their respective
 holders.
 
-Copyright (c) 2009-2013, NIPY Developers
+Copyright (c) 2009-2014, NIPY Developers
 All rights reserved.

Vagrantfile

@@ -0,0 +1,62 @@
+VAGRANTFILE_API_VERSION = "2"
+
+$script = <<SCRIPT
+
+# Following section commented out as gridengine requires interactive
+# components
+# # Install neurodebian repo
+# bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
+#
+# # Install grid engine
+# sudo apt-get install -qq gridengine-master gridengine-exec gridengine-client gridengine-qmon
+# # Configure: http://wiki.unixh4cks.com/index.php/Setting_up_Sun_Grid_Engine_on_Ubuntu
+# sudo -u sgeadmin qconf -am vagrant
+# qconf -au vagrant users
+# qconf -as neuro
+# qconf -ahgrp @allhosts
+# qconf -aattr hostgroup hostlist neuro @allhosts
+# qconf -aq main.q
+# qconf -aattr queue hostlist @allhosts main.q
+# qconf -aattr queue slots "2, [neuro=3]" main.q
+
+# install anaconda
+wget http://repo.continuum.io/miniconda/Miniconda-3.0.0-Linux-x86_64.sh -O miniconda.sh
+chmod +x miniconda.sh
+./miniconda.sh -b
+echo "export PATH=$HOME/miniconda/bin:\\$PATH" >> .bashrc
+
+# install nipype dependencies
+$HOME/anaconda/bin/conda update --yes conda
+$HOME/anaconda/bin/conda install --yes pip numpy scipy nose traits networkx
+$HOME/anaconda/bin/conda install --yes dateutil ipython-notebook matplotlib
+$HOME/anaconda/bin/pip install nibabel --use-mirrors
+$HOME/anaconda/bin/pip install https://github.com/RDFLib/rdflib/archive/master.zip
+$HOME/anaconda/bin/pip install https://github.com/satra/prov/archive/enh/rdf.zip
+$HOME/anaconda/bin/pip install https://github.com/nipy/nipype/archive/master.zip
+SCRIPT
+
+Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
+
+  config.vm.define :engine do |engine_config|
+
+    engine_config.vm.box = "gridneuro"
+    #engine_config.vm.box_url = "http://files.vagrantup.com/precise64.box"
+    engine_config.vm.box_url = "https://dl.dropboxusercontent.com/u/363467/precise64_neuro.box"
+    engine_config.vm.network :forwarded_port, guest: 80, host: 8080
+
+    #engine_config.vm.network :public_network, :bridge => 'en0: Wi-Fi (AirPort)'
+    engine_config.vm.network :private_network, ip: "192.168.100.20"
+    engine_config.vm.hostname = 'neuro'
+    #engine_config.vm.synced_folder "../software", "/software"
+    #engine_config.vm.synced_folder "../data", "/data"
+
+    engine_config.vm.provider :virtualbox do |vb|
+      vb.customize ["modifyvm", :id, "--cpuexecutioncap", "50"]
+      vb.customize ["modifyvm", :id, "--ioapic", "on"]
+      vb.customize ["modifyvm", :id, "--memory", "4096"]
+      vb.customize ["modifyvm", :id, "--cpus", "4"]
+    end
+
+    engine_config.vm.provision "shell", :privileged => false, inline: $script
+  end
+end

doc/_templates/layout.html

@@ -6,21 +6,13 @@
 {{ super() }}
 <meta name="keywords" content="nipype, neuroimaging, pipeline, workflow, parallel, python, neuroscience">
 <script type="text/javascript">
+  (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
+  (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
+  m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
+  })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
 
-  var _gaq = _gaq || [];
-  var pluginUrl = '//www.google-analytics.com/plugins/ga/inpage_linkid.js';
-  _gaq.push(['_require', 'inpage_linkid', pluginUrl]);
-  _gaq.push(['_setAccount', 'UA-339450-7']);
-  _gaq.push(['_setDomainName', 'none']);
-  _gaq.push(['_setAllowLinker', true]);
-  _gaq.push(['_trackPageview']);
-
-  (function() {
-    var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
-    ga.src = ('https:' == document.location.protocol ? 'https://' : 'http://') + 'stats.g.doubleclick.net/dc.js';
-    var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
-  })();
-
+  ga('create', 'UA-339450-7', 'nipy.org/nipype');
+  ga('send', 'pageview');
 </script>
 {% 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">0.8.0</td><td align="right">pre-0.9</td>
+                <td align="left">0.9.2</td><td align="right">1.0-dev</td>
             </tr>
             <tr>
                 <td align="left"><a href="{{pathto('users/install')}}">Download</a></td>

doc/documentation.rst

@@ -9,7 +9,7 @@ Documentation
    :Release: |version|
    :Date: |today|
 
-Previous versions: `0.7 <http://nipy.org/nipype/0.7>`_ `0.6 <http://nipy.org/nipype/0.6>`_
+Previous versions:  `0.8 <http://nipy.org/nipype/0.8>`_ `0.7 <http://nipy.org/nipype/0.7>`_
 
 .. container:: doc2
 

doc/links_names.txt

@@ -15,6 +15,7 @@
 .. _nibabel: http://nipy.org/nibabel/
 .. _nipype: http://nipy.org/nipype/
 .. _ConnectomeViewer: http://www.connectomeviewer.org/viewer/
+.. _NeuroDebian: http://neuro.debian.net/
 
 .. Documentation tools
 .. _graphviz: http://www.graphviz.org/
@@ -73,6 +74,8 @@
 .. _pythonxy: http://www.pythonxy.com/
 .. _EPD: http://www.enthought.com/products/epd.php
 .. _Traits: http://code.enthought.com/projects/traits/
+.. _Anaconda: https://store.continuum.io/cshop/anaconda/
+.. _Canopy: https://www.enthought.com/products/canopy/
 
 .. Python imaging projects
 .. _PyMVPA: http://www.pymvpa.org
@@ -98,6 +101,9 @@
 .. _xcode: http://developer.apple.com/TOOLS/xcode
 .. _mingw: http://www.mingw.org
 .. _macports: http://www.macports.org/
+.. _Vagrant: http://www.vagrantup.com/
+.. _Docker: http://www.docker.io/
+.. _Virtualbox: https://www.virtualbox.org/
 
 .. Functional imaging labs
 .. _`functional imaging laboratory`: http://www.fil.ion.ucl.ac.uk

doc/quickstart.rst

@@ -11,6 +11,7 @@ Downloading and installing
    :maxdepth: 1
 
    users/install
+   users/vagrant
 
 Beginner's guide
 ================

doc/users/debug.rst

@@ -58,4 +58,11 @@ performance issues.
    you will get a `ConcurrentLogHandler` error. Simply remove the pypeline.lock
    file in your home directory and continue.
 
+#. One many clusters with shared NFS mounts synchronization of files across 
+   clusters may not happen before the typical NFS cache timeouts. When using 
+   PBS/LSF/SGE/Condor plugins in such cases the workflow may crash because it 
+   cannot retrieve the node result. Setting the `job_finished_timeout` can help::
+   
+   workflow.config['execution']['job_finished_timeout'] = 65
+
 .. include:: ../links_names.txt

doc/users/index.rst

@@ -11,6 +11,7 @@
    :maxdepth: 2
 
    install
+   vagrant
 
    interface_tutorial
    caching_tutorial