Merge pull request #2 from nipy/master

Update nipype fork.

Author: sgiavasis

.coveragerc

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

.travis.yml

@@ -1,31 +1,40 @@
 language: python
 python:
-    - "2.7"
+  - 2.7
+# 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
-    - pip install https://github.com/RDFLib/rdflib/archive/master.zip
-    - pip install https://github.com/satra/prov/archive/enh/rdf.zip
+  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-2.0.3-Linux-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-2.0.3-Linux-x86_64.sh -O miniconda.sh; fi
+  - chmod +x miniconda.sh
+  - ./miniconda.sh -b
+  - export PATH=/home/travis/anaconda/bin:$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
+  - source /etc/fsl/fsl.sh
+
+# Install packages
 install:
-    - source ~/virtualenv/this/bin/activate
-    - python setup.py build_ext --inplace
+  - conda install --yes pip python=$TRAVIS_PYTHON_VERSION 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
 script:
-    - source ~/virtualenv/this/bin/activate
-    - make test
+  - nosetests --with-doctest --with-cov --cov nipype --cov-config .coveragerc --logging-level=INFO
 
+# Calculate coverage
+after_success:
+  - coveralls --config_file .coveragerc

CHANGES

@@ -3,11 +3,52 @@ Next release
 
 * ENH: SelectFiles: a streamlined version of DataGrabber
 * ENH: New interfaces: spm.ResliceToReference, FuzzyOverlap, afni.AFNItoNIFTI
+       spm.DicomImport, P2PDistance
 * 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: 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
+        
+* 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
 
 * 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)
 ===========================

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: trailing-spaces html test specs
 	@echo "removed spaces"
 	@echo "built docs"
 	@echo "ran test"
+	@echo "generated spec tests"

README.rst

@@ -2,6 +2,12 @@
 NIPYPE: Neuroimaging in Python: Pipelines and Interfaces
 ========================================================
 
+.. image:: https://travis-ci.org/nipy/nipype.png?branch=master
+  :target: https://travis-ci.org/nipy/nipype
+
+.. image:: https://coveralls.io/repos/nipy/nipype/badge.png
+  :target: https://coveralls.io/r/nipy/nipype
+
 
 Current neuroimaging software offer users an incredible opportunity to
 analyze data using a variety of different algorithms. However, this has

doc/_templates/indexsidebar.html

@@ -6,6 +6,7 @@ <h3>{{ _('Links') }}</h3>
     <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><a href="https://travis-ci.org/nipy/nipy"><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>
 </ul>
 
 {% endblock %}

doc/_templates/layout.html

@@ -8,14 +8,16 @@
 <script type="text/javascript">
 
   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://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+    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);
   })();
 

doc/conf.py

@@ -55,7 +55,7 @@
 
 # General information about the project.
 project = u'nipype'
-copyright = u'2009-12, Neuroimaging in Python team'
+copyright = u'2009-13, 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