Merged with master, fixed simple conflicts. Left changes from oesteba…

…n regarding encoding comment and imports for Python 3 compatability.

.dockerignore

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

.noserc

@@ -1,8 +1,9 @@
 [nosetests]
 verbosity=3
-
 logging-level=DEBUG
 with-doctest=1
+with-doctest-ignore-unicode=1
+
 with-xunit=1
 with-coverage=1
 cover-branches=1

.travis.yml

@@ -8,58 +8,42 @@ python:
 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' >> $HOME/.numpy-site.cfg;
-  fi
 install:
-- sudo apt-get install fusefat
+- conda config --add channels conda-forge
 - conda update --yes conda
-- conda create -n testenv --yes pip python=$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 python-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 [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then
-  pip install http://effbot.org/downloads/Imaging-1.1.7.tar.gz;
-  pip install -e git+https://github.com/enthought/etsdevtools.git#egg=etsdevtools;
-  pip install -e git+https://github.com/enthought/blockcanvas.git#egg=blockcanvas;
-  pip install -e git+https://github.com/enthought/etsproxy.git#egg=etsproxy;
-  pip install https://github.com/dmsurti/mayavi/archive/4d4aaf315a29d6a86707dd95149e27d9ed2225bf.zip;
-  pip install -e git+https://github.com/enthought/ets.git#egg=ets;
-  fi
+- conda update --all -y python=$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=DEBUG --verbosity=3
+- 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

CHANGES

@@ -1,6 +1,20 @@
 Upcoming release 0.13
 =====================
 
+* 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)
 ==============================

Makefile

@@ -46,21 +46,24 @@ clean-ctags:
 clean-doc:
 	rm -rf doc/_build
 
-clean: clean-build clean-pyc clean-so clean-ctags clean-doc
+clean-tests:
+	rm -f .coverage
+
+clean: clean-build clean-pyc clean-so clean-ctags clean-doc clean-tests
 
 in: inplace # just a shortcut
 inplace:
 	$(PYTHON) setup.py build_ext -i
 
 test-code: in
-	$(NOSETESTS) -s nipype --with-doctest
+	$(NOSETESTS) -s nipype --with-doctest --with-doctest-ignore-unicode
 
 test-doc:
-	$(NOSETESTS) -s --with-doctest --doctest-tests --doctest-extension=rst \
+	$(NOSETESTS) -s --with-doctest --with-doctest-ignore-unicode --doctest-tests --doctest-extension=rst \
 	--doctest-fixtures=_fixture doc/
 
-test-coverage:
-	$(NOSETESTS) -s --with-doctest --with-coverage --cover-package=nipype \
+test-coverage: clean-tests in
+	$(NOSETESTS) -s --with-doctest --with-doctest-ignore-unicode --with-coverage --cover-package=nipype \
 	--config=.coveragerc
 
 test: clean test-code

bin/nipype_crash_search

@@ -1,11 +1,12 @@
-#!/usr/bin/env python
+#!python
 """Search for tracebacks inside a folder of nipype crash
 log files that match a given regular expression.
 
 Examples:
 nipype_crash_search -d nipype/wd/log -r '.*subject123.*'
 """
 import re
+import sys
 import os.path as op
 from glob import glob
 
@@ -60,6 +61,7 @@ def display_crash_search(logdir, regex):
 
 if __name__ == "__main__":
     from argparse import ArgumentParser, RawTextHelpFormatter
+
     defstr = ' (default %(default)s)'
     parser = ArgumentParser(prog='nipype_crash_search',
                             description=__doc__,
@@ -71,6 +73,10 @@ if __name__ == "__main__":
                         default='*',
                         help='Regular expression to be searched in each traceback.' + defstr)
 
-    args = parser.parse_args()
+    if len(sys.argv) == 1:
+        parser.print_help()
+        exit(0)
 
+    args = parser.parse_args()
     display_crash_search(args.logdir, args.regex)
+    exit(0)

bin/nipype_display_pklz

@@ -0,0 +1,36 @@
+#!python
+"""Prints the content of any .pklz file in your working directory.
+
+Examples:
+
+nipype_print_pklz _inputs.pklz
+nipype_print_pklz _node.pklz
+"""
+
+def pprint_pklz_file(pklz_file):
+    """ Print the content of the pklz_file. """
+    from pprint import pprint
+    from nipype.utils.filemanip import loadpkl
+
+    pkl_data = loadpkl(pklz_file)
+    pprint(pkl_data)
+
+
+if __name__ == "__main__":
+
+    import sys
+    from argparse import ArgumentParser, RawTextHelpFormatter
+
+    defstr = ' (default %(default)s)'
+    parser = ArgumentParser(prog='nipype_print_pklz',
+                            description=__doc__,
+                            formatter_class=RawTextHelpFormatter)
+    parser.add_argument('pklzfile', metavar='f', type=str,
+                        help='pklz file to display')
+
+    if len(sys.argv) == 1:
+        parser.print_help()
+        exit(0)
+
+    args = parser.parse_args()
+    pprint_pklz_file(args.pklzfile)

build_docs.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """
@@ -7,8 +8,8 @@
 
     python setup.py build_sphinx
 """
-
-from __future__ import print_function
+from __future__ import print_function, division, unicode_literals, absolute_import
+from builtins import open, str
 
 # Standard library imports
 import sys
@@ -22,7 +23,7 @@
 
 _info_fname = pjoin(os.path.dirname(__file__), 'nipype', 'info.py')
 INFO_VARS = {}
-exec(open(_info_fname, 'rt').read(), {}, INFO_VARS)
+exec(str(open(_info_fname, 'rt').read()), {}, INFO_VARS)
 
 DOC_BUILD_DIR = os.path.join('doc', '_build', 'html')
 DOC_DOCTREES_DIR = os.path.join('doc', '_build', 'doctrees')

circle.yml

@@ -5,42 +5,58 @@ machine:
 dependencies:
   cache_directories:
     - "~/docker"
+    - "~/examples"
+    - "~/.apt-cache"
 
   pre:
-    - mkdir -p "~/scratch/nose"
+    # Let CircleCI cache the apt archive
+    - mkdir -p ~/.apt-cache/partial && sudo rm -rf /var/cache/apt/archives && sudo ln -s ~/.apt-cache /var/cache/apt/archives
+    - sudo apt-get -y update && sudo apt-get install -y wget bzip2
 
   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 [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi
-    - docker build -t nipype/testbench:latest . :
+    - docker build -f docker/nipype_test/Dockerfile_py35 -t nipype/nipype_test:py35 . :
         timeout: 1600
-    - mkdir -p ~/docker; docker save nipype/testbench:latest > ~/docker/image.tar :
+    - docker build -f docker/nipype_test/Dockerfile_py27 -t nipype/nipype_test:py27 . :
         timeout: 1600
+    - mkdir -p ~/docker; docker save nipype/nipype_test:py27 > ~/docker/image.tar :
+        timeout: 1600
+    - pip install xunitmerge
 
 test:
   override:
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch --entrypoint="/usr/bin/run_builddocs.sh" nipype/testbench
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench test_spm Linear /root/examples/ workflow3d :
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
+    - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_nosetests.sh py35 :
+        timeout: 2600
+    - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_nosetests.sh py27 :
+        timeout: 2600
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d :
         timeout: 1600
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench test_spm Linear /root/examples/ workflow4d :
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d :
         timeout: 1600
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_fsl_feeds Linear /root/examples/ l1pipeline
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_spm_dartel Linear /root/examples/ level1 :
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /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 ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ level1 :
         timeout: 1600
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_spm_dartel Linear /root/examples/ l2pipeline :
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ l2pipeline :
         timeout: 1600
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_fsl_reuse Linear /root/examples/ level1_workflow
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_spm_nested Linear /root/examples/ level1
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_spm_nested Linear /root/examples/ l2pipeline
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch --entrypoint="/usr/bin/run_nosetests.sh" nipype/testbench :
-        timeout: 2600
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
+    - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
+    - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
+    - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ l2pipeline
+
   post:
     - bash docker/circleci/teardown.sh
 
 general:
   artifacts:
     - "~/docs"
     - "~/logs"
-    - "~/coverage.xml"
-    - "~/nosetests.xml"
-    - "~/builddocs.log"
+    - "~/coverage_py27.xml"
+    - "~/coverage_py35.xml"
+    - "~/nosetests_py27.xml"
+    - "~/nosetests_py35.xml"
     - "~/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 \

doc/devel/index.rst

@@ -19,6 +19,7 @@ conventions documented in the `NIPY Developers Guide
    architecture
    provenance
    software_using_nipype
+   testing_nipype
 
 
 .. include:: ../links_names.txt