Merge branch 'master' into ants-jacobian

Author: dalejn

.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 $INSTALL_DEB_DEPENDECIES; then
+    source /etc/fsl/fsl.sh;
+    source /etc/afni/afni.sh; 
+    export FSLOUTPUTTYPE=NIFTI_GZ; fi }
+- travis_retry bef_inst
 install:
-- conda config --add channels conda-forge
-- conda update --yes conda
-- conda update --all -y python=$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

@@ -1,8 +1,24 @@
 Upcoming release 0.13
 =====================
 
+* REF: Refactor AFNI interfaces (https://github.com/nipy/nipype/pull/1678)
+* ENH: Move nipype commands to group command using click (https://github.com/nipy/nipype/pull/1608)
+* FIX: AFNI Retroicor interface fixes (https://github.com/nipy/nipype/pull/1669)
+* FIX: Minor errors after migration to setuptools (https://github.com/nipy/nipype/pull/1671)
+* ENH: Add AFNI 3dNote interface (https://github.com/nipy/nipype/pull/1637)
+* ENH: Abandon distutils, only use setuptools (https://github.com/nipy/nipype/pull/1627)
+* FIX: Minor bugfixes related to unicode literals (https://github.com/nipy/nipype/pull/1656)
+* TST: Automatic retries in travis (https://github.com/nipy/nipype/pull/1659/files)
+* ENH: Add signal extraction interface (https://github.com/nipy/nipype/pull/1647)
 * 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: Add CompCor (https://github.com/nipy/nipype/pull/1599)
+* ENH: Add duecredit entries (https://github.com/nipy/nipype/pull/1466)
+* FIX: Python 3 compatibility fixes (https://github.com/nipy/nipype/pull/1572)
+* REF: Improved PEP8 compliance for fsl interfaces (https://github.com/nipy/nipype/pull/1597)
+* REF: Improved PEP8 compliance for spm interfaces (https://github.com/nipy/nipype/pull/1593)
+* TST: Replaced coveralls with codecov (https://github.com/nipy/nipype/pull/1609)
+* ENH: More BrainSuite interfaces (https://github.com/nipy/nipype/pull/1554)
 * 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)

Makefile

@@ -3,7 +3,7 @@
 # rsync -e ssh nipype-0.1-py2.5.egg cburns,nipy@frs.sourceforge.net:/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"

bin/nipype2boutiques

@@ -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

bin/nipype_cmd

@@ -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>