Merge branch 'master' into enh/FSLb0calc

Author: oesteban

.dockerignore

@@ -0,0 +1,5 @@
+.git/
+*.pyc
+*.egg-info
+__pycache__
+

.noserc

@@ -1,11 +1,10 @@
 [nosetests]
 verbosity=3
 
+logging-level=DEBUG
+with-doctest=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

@@ -55,8 +55,7 @@ install:
   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
+- pip install -e .
 script:
 - python -W once:FSL:UserWarning:nipype `which nosetests` --with-doctest --with-cov --cover-package nipype --cov-config .coveragerc --logging-level=DEBUG --verbosity=3
 after_success:
@@ -70,4 +69,4 @@ deploy:
     tags: true
     repo: nipy/nipype
     branch: master
-  distributions: "sdist bdist_wheel"
+  distributions: "sdist"

CHANGES

@@ -1,7 +1,27 @@
-Release 0.12.0-rc1 (April 20, 2016)
-============
+Upcoming release 0.13
+=====================
 
 * ENH: New interface to b0calc of FSL-POSSUM (https://github.com/nipy/nipype/pull/1399)
+* 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)
+
+
+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)
@@ -33,9 +53,11 @@ Release 0.12.0-rc1 (April 20, 2016)
 * 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
@@ -121,7 +143,7 @@ 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.
@@ -165,19 +187,19 @@ 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

@@ -10,10 +10,16 @@
 * 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
 

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"]
+

Makefile

@@ -15,8 +15,6 @@ sdist: zipdoc
 	python setup.py sdist
 	@echo "Done building source distribution."
 	# XXX copy documentation.zip to dist directory.
-	# XXX Somewhere the doc/_build directory is removed and causes
-	# this script to fail.
 
 egg: zipdoc
 	@echo "Building egg..."
@@ -45,7 +43,10 @@ clean-build:
 clean-ctags:
 	rm -f tags
 
-clean: clean-build clean-pyc clean-so clean-ctags
+clean-doc:
+	rm -rf doc/_build
+
+clean: clean-build clean-pyc clean-so clean-ctags clean-doc
 
 in: inplace # just a shortcut
 inplace:

README.rst

@@ -18,10 +18,6 @@ NIPYPE: Neuroimaging in Python: Pipelines and Interfaces
     :target: https://pypi.python.org/pypi/nipype/
     :alt: Latest Version
 
-.. image:: https://img.shields.io/pypi/dm/nipype.svg
-    :target: https://pypi.python.org/pypi/nipype/
-    :alt: Downloads
-
 .. image:: https://img.shields.io/pypi/pyversions/nipype.svg
     :target: https://pypi.python.org/pypi/nipype/
     :alt: Supported Python versions

circle.yml

@@ -1,78 +1,54 @@
+machine:
+  services:
+    - docker
+
 dependencies:
   cache_directories:
+    - "~/docker"
+    - "~/examples"
     - "~/.apt-cache"
-    - "~/examples/data"
-    - "~/examples/fsdata"
-    - "~/mcr"
-    - "~/spm12"
-    - "~/examples/fsl_course_data"
+
   pre:
+    - mkdir -p "~/scratch/nose"
+    - mkdir -p "~/examples"
     # Let CircleCI cache the apt archive
     - sudo rm -rf /var/cache/apt/archives && sudo ln -s ~/.apt-cache /var/cache/apt/archives && mkdir -p ~/.apt-cache/partial
-    - bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
+    - sudo apt-get -y update && sudo apt-get install -y wget bzip2
+
   override:
-    # Install apt packages
-    - sudo apt-get install -y fsl-core fsl-atlases fsl-mni152-templates fsl-feeds afni swig python-vtk xvfb fusefat
-    - echo 'source /etc/fsl/fsl.sh' >> $HOME/.profile
-    - echo 'source /etc/afni/afni.sh' >> $HOME/.profile
-    - mkdir -p ~/examples/ && ln -sf /usr/share/fsl-feeds/ ~/examples/feeds
-    # Enable system-wide vtk
-    - ln -sf /usr/lib/pymodules/python2.7/vtk ~/virtualenvs/venv-system/lib/python2.7/site-packages/
-    # Set up python environment
-    - pip install --upgrade pip
-    - pip install -e .
-    - pip install matplotlib sphinx ipython boto coverage dipy
-    # Add tvtk
-    - 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 -e git+https://github.com/enthought/ets.git#egg=ets
-    - pip install https://github.com/rtfd/readthedocs-sphinx-ext/archive/master.zip
-    - gem install fakes3
-    - if [[ ! -d ~/examples/data ]]; then wget "https://dl.dropbox.com/s/jzgq2nupxyz36bp/nipype-tutorial.tar.bz2" && tar jxvf nipype-tutorial.tar.bz2 && mv nipype-tutorial/* ~/examples/; fi
-    - if [[ ! -d ~/examples/fsl_course_data ]]; then wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt1.tar.gz" && wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt2.tar.gz" && wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/tbss.tar.gz" && mkdir ~/examples/fsl_course_data && tar zxvf fdt1.tar.gz -C ~/examples/fsl_course_data && tar zxvf fdt2.tar.gz -C ~/examples/fsl_course_data && tar zxvf tbss.tar.gz -C ~/examples/fsl_course_data; fi
-    - bash ~/nipype/tools/install_spm_mcr.sh
-    - mkdir -p ~/.nipype && echo '[logging]' > ~/.nipype/nipype.cfg && echo 'workflow_level = DEBUG' >> ~/.nipype/nipype.cfg && echo 'interface_level = DEBUG' >> ~/.nipype/nipype.cfg && echo 'filemanip_level = DEBUG' >> ~/.nipype/nipype.cfg
-machine:
-  environment:
-    FSLOUTPUTTYPE: NIFTI_GZ
+    - if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi
+    - docker build -f docker/nipype_test_py27/Dockerfile -t nipype/nipype_test:py27 . :
+        timeout: 1600
+    - mkdir -p ~/docker; docker save nipype/nipype_test:py27 > ~/docker/image.tar :
+        timeout: 1600
+    - if [[ ! -d ~/examples/nipype-tutorial ]]; then wget -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/feeds ]]; then wget -q -O fsl-feeds.tar.gz https://googledrive.com/host/0BxI12kyv2olZNXBONlJKV0Y1Tm8 && tar xzf fsl-feeds.tar.gz -C ~/examples/; fi
+
 test:
   override:
-    - mkdir -p ${CIRCLE_TEST_REPORTS}/nose
-    - source $HOME/.profile; nosetests --with-doctest --xunit-file="${CIRCLE_TEST_REPORTS}/nose/${CIRCLE_PROJECT_REPONAME}.xml" -c ./.noserc --logging-level=DEBUG --verbosity=3:
-        environment:
-          SPMMCRCMD: "$HOME/spm12/run_spm12.sh $HOME/mcr/v85/ script"
-          FORCE_SPMMCR: 1
-          FSL_COURSE_DATA: "$HOME/examples/fsl_course_data"
-        timeout: 2600
-    - set -o pipefail && cd doc && make html 2>&1 | tee ~/log.txt
-    - cat ~/log.txt && if grep -q "ERROR" ~/log.txt; then false; else true; fi
-    - source $HOME/.profile; python ~/nipype/tools/run_examples.py test_spm Linear workflow3d workflow4d:
-        pwd: ../examples
-        environment:
-          SPMMCRCMD: "$HOME/spm12/run_spm12.sh $HOME/mcr/v85/ script"
-          FORCE_SPMMCR: 1
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py27 /usr/bin/run_builddocs.sh
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v $(pwd)/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d :
         timeout: 1600
-    - source $HOME/.profile; python ~/nipype/tools/run_examples.py fmri_fsl_feeds Linear l1pipeline:
-        pwd: ../examples
-    - source $HOME/.profile; python ~/nipype/tools/run_examples.py fmri_spm_dartel Linear level1 l2pipeline:
-        pwd: ../examples
-        environment:
-          SPMMCRCMD: "$HOME/spm12/run_spm12.sh $HOME/mcr/v85/ script"
-          FORCE_SPMMCR: 1
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v $(pwd)/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d :
         timeout: 1600
-    - source $HOME/.profile; python ~/nipype/tools/run_examples.py fmri_fsl_reuse Linear level1_workflow:
-        pwd: ../examples
-    - source $HOME/.profile; python ~/nipype/tools/run_examples.py fmri_spm_nested Linear level1 l2pipeline:
-        pwd: ../examples
-        environment:
-          SPMMCRCMD: "$HOME/spm12/run_spm12.sh $HOME/mcr/v85/ script"
-          FORCE_SPMMCR: 1
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v $(pwd)/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /root/examples/ l1pipeline
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v $(pwd)/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ level1 :
+        timeout: 1600
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v $(pwd)/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ l2pipeline :
+        timeout: 1600
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v $(pwd)/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v $(pwd)/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested Linear /root/examples/ level1
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v $(pwd)/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested Linear /root/examples/ l2pipeline
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_nosetests.sh :
+        timeout: 2600
+  post:
+    - bash docker/circleci/teardown.sh
 
 general:
   artifacts:
-    - "doc/_build/html"
-    - "~/log.txt"
-    - "nosetests.xml"
-    - "coverage.xml"
+    - "~/docs"
+    - "~/logs"
+    - "~/coverage.xml"
+    - "~/nosetests.xml"
+    - "~/builddocs.log"
+    - "~/scratch"

doc/Makefile

@@ -35,9 +35,9 @@ htmlonly:
 
 api:
 	rm -rf api/generated
-	python ../tools/build_modref_templates.py
+	python -u ../tools/build_modref_templates.py
 	rm -rf interfaces/generated
-	python ../tools/build_interface_docs.py
+	python -u ../tools/build_interface_docs.py
 	@echo "Build API docs finished."
 
 html: clean examples2rst api htmlonly
@@ -76,7 +76,7 @@ doctest:
 	      "results in _build/doctest/output.txt."
 
 gitwash-update:
-	python ../tools/gitwash_dumper.py devel nipype \
+	python -u ../tools/gitwash_dumper.py devel nipype \
             --repo-name=nipype \
             --github-user=nipy \
             --project-url=http://nipy.org/nipype \