Merge branch 'fix/Py3UseBuiltinOpen' into enh/FSLb0calc

Author: oesteban

.dockerignore

@@ -2,4 +2,6 @@
 *.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

@@ -9,57 +9,39 @@ env:
 - INSTALL_DEB_DEPENDECIES=true
 - INSTALL_DEB_DEPENDECIES=false
 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" && ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]]; then
+#   conda install -y vtk mayavi; fi
+- conda install -y nipype
+- pip install python-coveralls coverage doctest-ignore-unicode
+- rm -r /home/travis/miniconda/lib/python${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

@@ -2,8 +2,11 @@ Upcoming release 0.13
 =====================
 
 * ENH: New interface to b0calc of FSL-POSSUM (https://github.com/nipy/nipype/pull/1399)
+* 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)

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

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

@@ -9,38 +9,38 @@ dependencies:
     - "~/.apt-cache"
 
   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
+    - 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 -f docker/nipype_test_py27/Dockerfile -t nipype/nipype_test:py27 . :
+    - docker build -f docker/nipype_test/Dockerfile_py35 -t nipype/nipype_test:py35 . :
         timeout: 1600
-    - mkdir -p ~/docker; docker save nipype/nipype_test:py27 > ~/docker/image.tar :
+    - mkdir -p ~/docker; docker save nipype/nipype_test:py35 > ~/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:
-    - 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 :
+    - 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 :
+        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 -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 :
+    - 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 -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 :
+    - 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 -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 :
+    - 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 -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
+    - 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 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /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 ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested Linear /root/examples/ l2pipeline
   post:
     - bash docker/circleci/teardown.sh
 
@@ -50,5 +50,4 @@ general:
     - "~/logs"
     - "~/coverage.xml"
     - "~/nosetests.xml"
-    - "~/builddocs.log"
     - "~/scratch"

doc/sphinxext/autosummary_generate.py

@@ -16,9 +16,9 @@
             ./ext/autosummary_generate.py -o source/generated source/*.rst
 
 """
+from __future__ import print_function, unicode_literals
+from builtins import open
 
-from __future__ import print_function
-import glob
 import re
 import inspect
 import os

doc/sphinxext/numpy_ext/__init__.py

@@ -0,0 +1 @@
+# -*- coding: utf-8 -*-

doc/sphinxext/numpy_ext/docscrape.py

@@ -1,7 +1,7 @@
+# -*- coding: utf-8 -*-
 """Extract reference documentation from the NumPy source tree.
 
 """
-
 from __future__ import print_function
 from future import standard_library
 standard_library.install_aliases()
@@ -13,7 +13,7 @@
 import pydoc
 from warnings import warn
 
-from nipype.external.six import StringIO
+from io import StringIO
 
 
 class Reader(object):