Merge remote-tracking branch 'upstream/master' into enh/FSLstd2imgcoords

Author: oesteban

.dockerignore

@@ -0,0 +1,7 @@
+.git/
+*.pyc
+*.egg-info
+__pycache__
+docker/nipype_*
+docker/test-*
+.coverage

.gitignore

@@ -21,3 +21,7 @@ nipype/testing/data/von_errmap.nii.gz
 crash*.pklz
 .coverage
 htmlcov/
+__pycache__/
+*~
+.ipynb_checkpoints/
+.ruby-version

.noserc

@@ -1,11 +1,11 @@
 [nosetests]
 verbosity=3
+logging-level=DEBUG
+with-doctest=1
+with-doctest-ignore-unicode=1
 
+with-xunit=1
 with-coverage=1
 cover-branches=1
 cover-xml=1
-cover-xml-file=./coverage.xml
 cover-min-percentage=50
-
-
-with-xunit=1

.travis.yml

@@ -4,61 +4,46 @@ language: python
 python:
 - 2.7
 - 3.4
+- 3.5
 env:
 - INSTALL_DEB_DEPENDECIES=true
 - INSTALL_DEB_DEPENDECIES=false
+- INSTALL_DEB_DEPENDECIES=true DUECREDIT_ENABLE=yes
 before_install:
-- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
-  -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
-  -O miniconda.sh; fi
-- chmod +x miniconda.sh
-- "./miniconda.sh -b"
-- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then export PATH=/home/travis/miniconda2/bin:$PATH; else export PATH=/home/travis/miniconda3/bin:$PATH; fi
+- wget http://repo.continuum.io/miniconda/Miniconda${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 update
-- sudo apt-get install xvfb
-- 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
-- if $INSTALL_DEB_DEPENDECIES; then source /etc/afni/afni.sh; fi
+- 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
-# Install vtk and fix numpy installation problem
-# Fix numpy problem: https://github.com/enthought/enable/issues/34#issuecomment-2029381
-- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then travis_retry sudo apt-get install -qq libx11-dev swig;
-  echo '[x11]' >> $HOME/.numpy-site.cfg; 
-  echo 'library_dirs = /usr/lib64:/usr/lib:/usr/lib/x86_64-linux-gnu' >> $HOME/.numpy-site.cfg;
-  echo 'include_dirs = /usr/include:/usr/include/X11' >> $HOME/.numpy-site.cfg;
-  fi
 install:
+- conda config --add channels conda-forge
 - conda update --yes conda
-- conda create -n testenv --yes pip python=$TRAVIS_PYTHON_VERSION
-- source activate testenv
-- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then pip install ordereddict; fi
-- conda install --yes numpy scipy nose networkx dateutil
-- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then conda install --yes traits; else pip install traits; fi
-- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then conda install --yes vtk; fi
-- pip install python-coveralls
-- pip install nose-cov
-# Add tvtk (PIL is required by blockcanvas)
-# Install mayavi (see https://github.com/enthought/mayavi/issues/271)
-- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then
-  pip install http://effbot.org/downloads/Imaging-1.1.7.tar.gz;
-  pip install -e git+https://github.com/enthought/etsdevtools.git#egg=etsdevtools;
-  pip install -e git+https://github.com/enthought/blockcanvas.git#egg=blockcanvas;
-  pip install -e git+https://github.com/enthought/etsproxy.git#egg=etsproxy;
-  pip install https://github.com/dmsurti/mayavi/archive/4d4aaf315a29d6a86707dd95149e27d9ed2225bf.zip;
-  pip install -e git+https://github.com/enthought/ets.git#egg=ets;
-  fi
-- pip install -r requirements.txt  # finish remaining requirements
-- python setup.py install
+- conda update --all -y python=$TRAVIS_PYTHON_VERSION
+# - if [[ "${INSTALL_DEB_DEPENDECIES}" == "true" && ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]]; then
+#   conda install -y vtk mayavi; fi
+- conda install -y nipype
+- pip install python-coveralls coverage doctest-ignore-unicode
+- if [ ! -z "$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}
 script:
-- python -W once:FSL:UserWarning:nipype `which nosetests` --with-doctest --with-cov --cover-package nipype --cov-config .coveragerc --logging-level=INFO
+- 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:
-- coveralls --config_file .coveragerc
+- coveralls --config_file ${COVERAGE_PROCESS_START}
 deploy:
   provider: pypi
   user: satra
@@ -68,4 +53,4 @@ deploy:
     tags: true
     repo: nipy/nipype
     branch: master
-  distributions: "sdist bdist_wheel"
+  distributions: "sdist"

CHANGES

@@ -1,7 +1,35 @@
-Next release
-============
+Upcoming release 0.13
+=====================
 
 * ENH: Simple interface to FSL std2imgcoords (https://github.com/nipy/nipype/pull/1398)
+* FIX: Use builtins open and unicode literals for py3 compatibility (https://github.com/nipy/nipype/pull/1572)
+* TST: reduce the size of docker images & use tags for images (https://github.com/nipy/nipype/pull/1564)
+* ENH: Implement missing inputs/outputs in FSL AvScale (https://github.com/nipy/nipype/pull/1563)
+* FIX: Fix symlink test in copyfile (https://github.com/nipy/nipype/pull/1570, https://github.com/nipy/nipype/pull/1586)
+* ENH: Added support for custom job submission check in SLURM (https://github.com/nipy/nipype/pull/1582)
+
+
+Release 0.12.1 (August 3, 2016)
+===============================
+
+* FIX: runtime profiling is optional and off by default (https://github.com/nipy/nipype/pull/1561)
+* TST: circle CI tests run with docker (https://github.com/nipy/nipype/pull/1541)
+* FIX: workflow export functions without import error (https://github.com/nipy/nipype/pull/1552)
+
+
+Release 0.12.0 (July 12, 2016)
+==============================
+
+* ENH: New interface for Bruker to Nifti converter (https://github.com/nipy/nipype/pull/1523)
+* FIX: output file naming for FIRST outputs (https://github.com/nipy/nipype/pull/1524)
+* ENH: Adds `fslmaths -Tstd` to maths interfaces (https://github.com/nipy/nipype/pull/1518)
+* FIX: Selecting "gamma" in FSL Level1Design now does what the name says (https://github.com/nipy/nipype/pull/1500)
+* ENH: Added grad_dev input to fsl.dti.bedpostx5 interface(https://github.com/nipy/nipype/pull/1493)
+* ENH: ResourceMultiProc plugin to support resource allocation (https://github.com/nipy/nipype/pull/1372)
+* ENH: Added dcm2niix interface (https://github.com/nipy/nipype/pull/1435)
+* ENH: Add nipype_crash_search command (https://github.com/nipy/nipype/pull/1422)
+* ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (https://github.com/nipy/nipype/pull/1305)
+* FIX: job execution on systems/approaches where locale is undefined (https://github.com/nipy/nipype/pull/1401)
 * FIX: Clean up byte/unicode issues using subprocess (https://github.com/nipy/nipype/pull/1394)
 * FIX: Prevent crash when tvtk is loaded - ETS_TOOLKIT=null (https://github.com/nipy/nipype/pull/973)
 * ENH: New interfaces in dipy: RESTORE, EstimateResponseSH, CSD and StreamlineTractography
@@ -24,9 +52,15 @@ Next release
 * ENH: New interfaces for interacting with AWS S3: S3DataSink and S3DataGrabber (https://github.com/nipy/nipype/pull/1201)
 * ENH: Interfaces for MINC tools (https://github.com/nipy/nipype/pull/1304)
 * FIX: Use realpath to determine hard link source (https://github.com/nipy/nipype/pull/1388)
+* FIX: Correct linking/copying fallback behavior (https://github.com/nipy/nipype/pull/1391)
+* ENH: Nipype workflow and interfaces for FreeSurfer's recon-all (https://github.com/nipy/nipype/pull/1326)
+* FIX: Permit relative path for concatenated_file input to Concatenate() (https://github.com/nipy/nipype/pull/1411)
+* ENH: Makes ReconAll workflow backwards compatible with FreeSurfer 5.3.0 (https://github.com/nipy/nipype/pull/1434)
+* ENH: Added interfaces for AFNI 3dDegreeCentrality, 3dECM, 3dLFCD, 3dClipLevel, 3dmask_tool, and 3dSeg
+       (https://github.com/nipy/nipype/pull/1460)
 
 Release 0.11.0 (September 15, 2015)
-============
+===================================
 
 * API: Change how hash values are computed (https://github.com/nipy/nipype/pull/1174)
 * ENH: New algorithm: mesh.WarpPoints applies displacements fields to point sets
@@ -112,7 +146,7 @@ Release 0.11.0 (September 15, 2015)
        (https://github.com/nipy/nipype/pull/1142)
 
 Release 0.10.0 (October 10, 2014)
-============
+=================================
 
 * ENH: New miscelaneous interfaces: SplitROIs (mapper), MergeROIs (reducer)
        to enable parallel processing of very large images.
@@ -156,19 +190,19 @@ Release 0.10.0 (October 10, 2014)
 * 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

CONTRIBUTING.md

@@ -10,16 +10,22 @@
 * Pull Requests should be tested, if feasible:
     - bugfixes should include regression tests
     - new behavior should at least get minimal exercise
-* Use a descriptive prefix for your PR: ENH, FIX, TST, DOC, STY, REF (refactor), WIP (Work in progress)
-* After submiting the PR, include an update to the CHANGES file: prefix: description (URL of pull request)
-* `make specs`
-* do: `make check-before-commit` before submitting the PR. This will require you to either install or be in developer mode with: `python setup.py install/develop`.
+* Use a descriptive prefix for your PR: ENH (enhancement), FIX, TST, DOC, STY, REF (refactor), WIP (Work in progress)
+* The person who accepts/merges your PR will include an update to the CHANGES file: prefix: description (URL of pull request)
+* Run `make check-before-commit` before submitting the PR.
+  This will require you to either install or be in developer mode with: `python setup.py install/develop`.
+* In general, do not catch exceptions without good reason. 
+  * catching non-fatal exceptions. 
+    Log the exception as a warning.
+  * adding more information about what may have caused the error.
+    Raise a new exception using ``raise_from(NewException("message"), oldException)`` from ``future``.
+    Do not log this, as it creates redundant/confusing logs.
 
 ## Contributing issues
 
 When opening a new Issue, please take the following steps:
 
-1. Search GitHub and/or [Neurostars](neurostars.org) for your issue to avoid duplicate reports.
+1. Search GitHub and/or [Neurostars](http://neurostars.org) for your issue to avoid duplicate reports.
    Keyword searches for your error messages are most helpful.
 2. If possible, try updating to master and reproducing your issue,
    because we may have already fixed it.

Dockerfile

@@ -0,0 +1,74 @@
+# Copyright (c) 2016, The developers of the Stanford CRN
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright notice, this
+#   list of conditions and the following disclaimer.
+#
+# * Redistributions in binary form must reproduce the above copyright notice,
+#   this list of conditions and the following disclaimer in the documentation
+#   and/or other materials provided with the distribution.
+#
+# * Neither the name of crn_base nor the names of its
+#   contributors may be used to endorse or promote products derived from
+#   this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+FROM nipype/testnipypedata:latest
+MAINTAINER Stanford Center for Reproducible Neuroscience <[email protected]>
+
+# Preparations
+RUN ln -snf /bin/bash /bin/sh
+
+# Install this branch's code
+WORKDIR /root/src
+
+# Install matplotlib, sphinx and coverage to build documentation
+# and run tests with coverage
+RUN source activate nipypetests-2.7 && \
+    pip install matplotlib sphinx coverage && \
+    source activate nipypetests-3.4 && \
+    pip install matplotlib sphinx coverage && \
+    source activate nipypetests-3.5 && \
+    pip install matplotlib sphinx coverage
+
+ADD . nipype/
+
+# Install the checked out version of nipype, check that requirements are
+# installed and install it for each of the three environments.
+RUN cd nipype/ && \
+    source activate nipypetests-2.7 && \
+    pip install -r requirements.txt && \
+    pip install -e .
+
+RUN cd nipype/ && \
+    source activate nipypetests-3.4 && \
+    pip install -r requirements.txt && \
+    pip install -e .
+
+RUN cd nipype/ && \
+    source activate nipypetests-3.5 && \
+    pip install -r requirements.txt && \
+    pip install -e .
+
+WORKDIR /scratch
+
+# Install entrypoints
+ADD docker/circleci/run_* /usr/bin/
+RUN chmod +x /usr/bin/run_*
+
+# RUN echo 'source /etc/profile.d/nipype_tests.sh' >> /etc/bash.bashrc
+ENTRYPOINT ["/usr/bin/run_examples.sh"]
+

LICENSE

@@ -1,30 +1,15 @@
-Copyright (c) 2009-2014, NIPY Developers
-All rights reserved.
+Copyright (c) 2009-2016, Nipype developers
 
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are
-met:
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
 
-    * Redistributions of source code must retain the above copyright
-       notice, this list of conditions and the following disclaimer.
+    http://www.apache.org/licenses/LICENSE-2.0
 
-    * Redistributions in binary form must reproduce the above
-       copyright notice, this list of conditions and the following
-       disclaimer in the documentation and/or other materials provided
-       with the distribution.
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
 
-    * Neither the name of the NIPY Developers nor the names of any
-       contributors may be used to endorse or promote products derived
-       from this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
-DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
-THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+Prior to release 0.12, Nipype was licensed under a BSD license.