Merge remote-tracking branch 'nipy/master' into clean-afni

# Conflicts:
#	nipype/interfaces/afni/preprocess.py

Author: tsalo

.travis.yml

@@ -6,40 +6,41 @@ python:
 - 3.4
 - 3.5
 env:
-- INSTALL_DEB_DEPENDECIES=true
-- INSTALL_DEB_DEPENDECIES=false
-- INSTALL_DEB_DEPENDECIES=true DUECREDIT_ENABLE=yes
+- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler"
+- INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler"
+- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit"
 before_install:
-- wget http://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh
-  -O /home/travis/.cache/miniconda.sh
-- bash /home/travis/.cache/miniconda.sh -b -p /home/travis/miniconda
-- export PATH=/home/travis/miniconda/bin:$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
-- bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
-- sudo apt-get -y update
-- sudo apt-get -y install xvfb fusefat
-- if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -y -qq
-  fsl afni elastix fsl-atlases; fi
-- if $INSTALL_DEB_DEPENDECIES; then
-  source /etc/fsl/fsl.sh;
-  source /etc/afni/afni.sh; fi
-- export FSLOUTPUTTYPE=NIFTI_GZ
+- function bef_inst {
+  wget http://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh
+  -O /home/travis/.cache/miniconda.sh &&
+  bash /home/travis/.cache/miniconda.sh -b -p /home/travis/miniconda &&
+  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 &&
+  bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh) &&
+  sudo apt-get -y update &&
+  sudo apt-get -y install xvfb fusefat &&
+  if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -y -qq
+  fsl afni elastix fsl-atlases; fi &&
+  if $INSTALL_DEB_DEPENDECIES; then
+    source /etc/fsl/fsl.sh;
+    source /etc/afni/afni.sh; fi &&
+  export FSLOUTPUTTYPE=NIFTI_GZ; }
+- travis_retry bef_inst
 install:
-- conda config --add channels conda-forge
-- conda update --yes conda
-- conda update --all -y python=$TRAVIS_PYTHON_VERSION
-# - if [[ "${INSTALL_DEB_DEPENDECIES}" == "true" && ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]]; then
-#   conda install -y vtk mayavi; fi
-- conda install -y nipype matplotlib nitime
-- pip install python-coveralls coverage doctest-ignore-unicode
-- if [ ! -z "$DUECREDIT_ENABLE"]; then pip install duecredit; fi
-- rm -r /home/travis/miniconda/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype*
-- pip install -r requirements.txt
-- pip install -e .
-- export COVERAGE_PROCESS_START=$(pwd)/.coveragerc
-- export COVERAGE_DATA_FILE=$(pwd)/.coverage
-- echo "data_file = ${COVERAGE_DATA_FILE}" >> ${COVERAGE_PROCESS_START}
+#  Add install of vtk and mayavi to test mesh (disabled): conda install -y vtk mayavi &&
+- function inst {
+  conda config --add channels conda-forge &&
+  conda update --yes conda &&
+  conda update --all -y python=$TRAVIS_PYTHON_VERSION &&
+  conda install -y nipype &&
+  rm -r /home/travis/miniconda/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype* &&
+  pip install -r requirements.txt &&
+  pip install -e .[$NIPYPE_EXTRAS] &&
+  export COVERAGE_PROCESS_START=$(pwd)/.coveragerc &&
+  export COVERAGE_DATA_FILE=$(pwd)/.coverage &&
+  echo "data_file = ${COVERAGE_DATA_FILE}" >> ${COVERAGE_PROCESS_START}; }
+- travis_retry inst
 script:
 - python -W once:FSL:UserWarning:nipype `which nosetests` --with-doctest --with-doctest-ignore-unicode --with-cov --cover-package nipype --logging-level=DEBUG --verbosity=3
 after_success:

CHANGES

@@ -1,7 +1,11 @@
 Upcoming release 0.13
 =====================
 
+* FIX: AFNI Retroicor interface fixes (https://github.com/nipy/nipype/pull/1669)
+* ENH: Add AFNI 3dNote interface (https://github.com/nipy/nipype/pull/1637)
+* FIX: Minor bugfixes related to unicode literals (https://github.com/nipy/nipype/pull/1656)
 * ENH: Add a DVARS calculation interface (https://github.com/nipy/nipype/pull/1606)
+* ENH: New interface to b0calc of FSL-POSSUM (https://github.com/nipy/nipype/pull/1399)
 * ENH: Convenient load/save of interface inputs (https://github.com/nipy/nipype/pull/1591)
 * ENH: Add a Framewise Displacement calculation interface (https://github.com/nipy/nipype/pull/1604)
 * FIX: Use builtins open and unicode literals for py3 compatibility (https://github.com/nipy/nipype/pull/1572)
@@ -124,14 +128,14 @@ Release 0.11.0 (September 15, 2015)
 * 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)
+     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)
+     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)
@@ -213,11 +217,11 @@ Release 0.9.0 (December 20, 2013)
 * ENH: AFNI interfaces refactor, prefix, suffix are replaced by
        "flexible_%s_templates"
 * ENH: New SPM interfaces:
-		- spm.ResliceToReference,
-		- spm.DicomImport
+    - spm.ResliceToReference,
+    - spm.DicomImport
 * ENH: New AFNI interfaces:
-		- afni.AFNItoNIFTI
-		- afni.TCorr1D
+    - afni.AFNItoNIFTI
+    - afni.TCorr1D
 * ENH: Several new interfaces related to Camino were added:
         - camino.SFPICOCalibData
         - camino.Conmat
@@ -231,13 +235,13 @@ Release 0.9.0 (December 20, 2013)
         - mrtrix.FindShPeaks
         - mrtrix.Directions2Amplitude
 * ENH: New FSL interfaces:
-		- fsl.PrepareFieldmap
-		- fsl.TOPUP
-		- fsl.ApplyTOPUP
-		- fsl.Eddy
+    - fsl.PrepareFieldmap
+    - fsl.TOPUP
+    - fsl.ApplyTOPUP
+    - fsl.Eddy
 * ENH: New misc interfaces:
-		- FuzzyOverlap,
-		- P2PDistance
+    - 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
@@ -295,7 +299,7 @@ Release 0.7.0 (Dec 18, 2012)
        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),
-	  how to set SGE specific options (smri_ants_build_template_new)
+    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
 * ENH: added deprecation metadata to traits
@@ -357,9 +361,9 @@ Release 0.5 (Mar 10, 2012)
 * 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
-	   Node level)
+     Node level)
 * API: "stop_on_first_rerun" does not stop for DataGrabber (unless overwrite is
-	   set to True on Node level)
+     set to True on Node level)
 * API: Output prefix can be set for spm nodes (SliceTiming, Realign, Coregister,
        Normalize, Smooth)
 

Makefile

@@ -3,7 +3,7 @@
 # rsync -e ssh nipype-0.1-py2.5.egg cburns,[email protected]:/home/frs/project/n/ni/nipy/nipype/nipype-0.1/
 
 PYTHON ?= python
-NOSETESTS ?= nosetests
+NOSETESTS=`which 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
 
@@ -56,7 +56,7 @@ inplace:
 	$(PYTHON) setup.py build_ext -i
 
 test-code: in
-	$(NOSETESTS) -s nipype --with-doctest --with-doctest-ignore-unicode
+	python -W once:FSL:UserWarning:nipype $(NOSETESTS) --with-doctest --with-doctest-ignore-unicode --logging-level=DEBUG --verbosity=3 nipype
 
 test-doc:
 	$(NOSETESTS) -s --with-doctest --with-doctest-ignore-unicode --doctest-tests --doctest-extension=rst \
@@ -66,7 +66,8 @@ test-coverage: clean-tests in
 	$(NOSETESTS) -s --with-doctest --with-doctest-ignore-unicode --with-coverage --cover-package=nipype \
 	--config=.coveragerc
 
-test: clean test-code
+test: tests # just another name
+tests: clean test-code
 
 html:
 	@echo "building docs"

circle.yml

@@ -1,4 +1,10 @@
 machine:
+  environment:
+    OSF_NIPYPE_URL: "https://files.osf.io/v1/resources/nefdp/providers/osfstorage"
+    DATA_NIPYPE_TUTORIAL_URL: "${OSF_NIPYPE_URL}/57f4739cb83f6901ed94bf21"
+    DATA_NIPYPE_FSL_COURSE: "${OSF_NIPYPE_URL}/57f472cf9ad5a101f977ecfe"
+    DATA_NIPYPE_FSL_FEEDS: "${OSF_NIPYPE_URL}/57f473066c613b01f113e7af"
+
   services:
     - docker
 
@@ -15,9 +21,9 @@ dependencies:
 
   override:
     - mkdir -p ~/examples ~/scratch/nose ~/scratch/logs
-    - if [[ ! -d ~/examples/nipype-tutorial ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O nipype-tutorial.tar.bz2 https://dl.dropbox.com/s/jzgq2nupxyz36bp/nipype-tutorial.tar.bz2 && tar xjf nipype-tutorial.tar.bz2 -C ~/examples/; fi
-    - if [[ ! -d ~/examples/nipype-fsl_course_data ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q https://3552243d5be815c1b09152da6525cb8fe7b900a6.googledrive.com/host/0BxI12kyv2olZVUswazA3NkFvOXM/nipype-fsl_course_data.tar.gz && tar xzf nipype-fsl_course_data.tar.gz -C ~/examples/; fi
-    - if [[ ! -d ~/examples/feeds ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q https://3552243d5be815c1b09152da6525cb8fe7b900a6.googledrive.com/host/0BxI12kyv2olZVUswazA3NkFvOXM/fsl-5.0.9-feeds.tar.gz && tar xzf fsl-5.0.9-feeds.tar.gz -C ~/examples/; fi
+    - if [[ ! -d ~/examples/nipype-tutorial ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O nipype-tutorial.tar.bz2 "${DATA_NIPYPE_TUTORIAL_URL}" && tar xjf nipype-tutorial.tar.bz2 -C ~/examples/; fi
+    - if [[ ! -d ~/examples/nipype-fsl_course_data ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O nipype-fsl_course_data.tar.gz "${DATA_NIPYPE_FSL_COURSE}" && tar xzf nipype-fsl_course_data.tar.gz -C ~/examples/; fi
+    - if [[ ! -d ~/examples/feeds ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O fsl-5.0.9-feeds.tar.gz "${DATA_NIPYPE_FSL_FEEDS}" && tar xzf fsl-5.0.9-feeds.tar.gz -C ~/examples/; fi
     - if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi
     - docker build -f docker/nipype_test/Dockerfile_py35 -t nipype/nipype_test:py35 . :
         timeout: 1600

codecov.yml

@@ -1,6 +1,10 @@
 coverage:
   range: "0...100"
   status:
+    patch:
+      default:
+        target: 0
+        threshold: 100
     project:
       default:
         target: 0

doc/_templates/indexsidebar.html

@@ -6,7 +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://neurostars.org/t/nipype">User</a> · <a href="http://projects.scipy.org/mailman/listinfo/nipy-devel">Developer</a></li>
     <li><a href="about.html#funding">Funding</a> · <a href="http://nipy.org/software/license/index.html"><img src="https://img.shields.io/pypi/l/nipype.svg" alt="License"></a></li>
-    <li><a href="https://travis-ci.org/nipy/nipype"><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>
+    <li><a href="https://travis-ci.org/nipy/nipype"><img src="https://travis-ci.org/nipy/nipype.png?branch=master" alt="travis"></a> · <a href='https://codecov.io/gh/nipy/nipype'><img src='https://codecov.io/gh/nipy/nipype/branch/master/graph/badge.svg' alt='Coverage Status' /></a></li>
     <a href='https://pypi.python.org/pypi/nipype/'><img src='https://img.shields.io/pypi/pyversions/nipype.svg' alt='Python Versions' /></a></li>
 </ul>
 

doc/devel/testing_nipype.rst

@@ -1,3 +1,5 @@
+.. _dev_testing_nipype:
+
 ==============
 Testing nipype
 ==============
@@ -14,37 +16,91 @@ If both batteries of tests are passing, the following badges should be shown in
   :target: https://circleci.com/gh/nipy/nipype/tree/master
 
 
-Tests implementation
---------------------
+Installation for developers
+---------------------------
+
+To check out the latest development version::
+
+    git clone https://github.com/nipy/nipype.git
+
+After cloning::
+
+    cd nipype
+    pip install -r requirements.txt
+    python setup.py develop
+
+or::
+
+    cd nipype
+    pip install -r requirements.txt
+    pip install -e .[tests]
+
+
+
+Test implementation
+-------------------
 
 Nipype testing framework is built upon `nose <http://nose.readthedocs.io/en/latest/>`_.
 By the time these guidelines are written, Nipype implements 17638 tests.
 
-To run the tests locally, first get nose installed::
+After installation in developer mode, the tests can be run with the
+following simple command at the root folder of the project ::
+
+    make tests
 
-  pip install nose
+If ``make`` is not installed in the system, it is possible to run the tests using::
 
+    python -W once:FSL:UserWarning:nipype `which nosetests` --with-doctest \
+           --with-doctest-ignore-unicode --logging-level=DEBUG --verbosity=3 nipype
 
-Then, after nipype is `installed in developer mode <../users/install.html#nipype-for-developers>`_,
-the tests can be run with the following simple command::
 
-  make tests
+A successful test run should complete in a few minutes and end with
+something like::
 
+    ----------------------------------------------------------------------
+    Ran 17922 tests in 107.254s
+
+    OK (SKIP=27)
+
+
+All tests should pass (unless you're missing a dependency). If the ``SUBJECTS_DIR```
+environment variable is not set, some FreeSurfer related tests will fail.
+If any of the tests failed, please report them on our `bug tracker
+<http://github.com/nipy/nipype/issues>`_.
+
+On Debian systems, set the following environment variable before running
+tests::
+
+       export MATLABCMD=$pathtomatlabdir/bin/$platform/MATLAB
+
+where ``$pathtomatlabdir`` is the path to your matlab installation and
+``$platform`` is the directory referring to x86 or x64 installations
+(typically ``glnxa64`` on 64-bit installations).
 
 Skip tests
-----------
+~~~~~~~~~~
 
 Nipype will skip some tests depending on the currently available software and data
 dependencies. Installing software dependencies and downloading the necessary data
 will reduce the number of skip tests.
 
 Some tests in Nipype make use of some images distributed within the `FSL course data
 <http://fsl.fmrib.ox.ac.uk/fslcourse/>`_. This reduced version of the package can be downloaded `here
-<https://3552243d5be815c1b09152da6525cb8fe7b900a6.googledrive.com/host/0BxI12kyv2olZVUswazA3NkFvOXM/nipype-fsl_course_data.tar.gz>`_.
+<https://files.osf.io/v1/resources/nefdp/providers/osfstorage/57f472cf9ad5a101f977ecfe>`_.
 To enable the tests depending on these data, just unpack the targz file and set the :code:`FSL_COURSE_DATA` environment
 variable to point to that folder.
 
 
+Avoiding any MATLAB calls from testing
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+On unix systems, set an empty environment variable::
+
+    export NIPYPE_NO_MATLAB=
+
+This will skip any tests that require matlab.
+
+
 Testing Nipype using Docker
 ---------------------------
 

doc/users/grabbing_and_sinking.rst

@@ -235,7 +235,7 @@ when using multiple nested iterables.
 Substitutions
 -------------
 
-The `substitutions` and `substitutions_regexp` inputs allow users to modify the
+The ``substitutions`` and ``regexp_substitutions`` inputs allow users to modify the
 output destination path and name of a file. Substitutions are a list of 2-tuples
 and are carried out in the order in which they were entered. Assuming that the
 output path of a file is: