Merge pull request #1 from nipy/master

Update tsalo/nipype from nipy/nipype

Author: tsalo

.coveragerc

@@ -4,6 +4,5 @@ source = nipype
 include = */nipype/*
 omit =
     */nipype/external/*
-    */nipype/workflows/*
     */nipype/fixes/*
     */setup.py

.dockerignore

@@ -1,7 +1,34 @@
-.git/
-*.pyc
-*.egg-info
+# python cache
+__pycache__/**/*
 __pycache__
-docker/nipype_*
-docker/test-*
-.coverage
+*.pyc
+
+# python distribution
+build/**/*
+build
+dist/**/*
+dist
+nipype.egg-info/**/*
+nipype.egg-info
+.eggs/**/*
+.eggs
+src/**/*
+src/
+
+# git
+.gitignore
+.git/**/*
+.git
+
+# other
+docs/**/*
+docs/
+.coverage
+.coveragerc
+codecov.yml
+rtd_requirements.txt
+circle.yml
+Vagrantfile
+.travis.yml
+.noserc
+

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,10 @@
+### Summary
+
+### Actual behavior
+
+### Expected behavior
+
+### How to replicate the behavior
+
+### Platform details:
+please paste the output of: `python -c "import nipype; print(nipype.get_info()); print(nipype.__version__)"`

.gitignore

@@ -13,6 +13,7 @@
 .project
 .settings
 .pydevproject
+.eggs
 .idea/
 /documentation.zip
 .DS_Store
@@ -24,4 +25,4 @@ htmlcov/
 __pycache__/
 *~
 .ipynb_checkpoints/
-.ruby-version
+.ruby-version

.travis.yml

@@ -1,51 +1,48 @@
 cache:
-- apt
+  apt: true
+
 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
+- 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:
-- 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 &&
+- function apt_inst {
   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 &&
+  sudo apt-get -y install xvfb fusefat graphviz &&
   if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -y -qq
   fsl afni elastix fsl-atlases; fi &&
   if $INSTALL_DEB_DEPENDECIES; then
     source /etc/fsl/fsl.sh;
-    source /etc/afni/afni.sh; fi &&
-  export FSLOUTPUTTYPE=NIFTI_GZ; }
-- travis_retry bef_inst
-install:
-- function inst {
+    source /etc/afni/afni.sh;
+    export FSLOUTPUTTYPE=NIFTI_GZ; fi }
+- function conda_inst {
+  export CONDA_HOME=$HOME/conda &&
+  wget https://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh
+    -O /home/travis/.cache/conda.sh &&
+  bash /home/travis/.cache/conda.sh -b -p ${CONDA_HOME} &&
+  export PATH=${CONDA_HOME}/bin:$PATH &&
+  hash -r &&
+  conda config --set always_yes yes --set changeps1 no &&
+  conda update -q conda &&
+  conda install python=${TRAVIS_PYTHON_VERSION} &&
   conda config --add channels conda-forge &&
-  conda update --yes conda &&
-  conda update --all -y python=$TRAVIS_PYTHON_VERSION &&
-  conda install -y nipype matplotlib nitime &&
-  pip install python-coveralls coverage doctest-ignore-unicode &&
-  if [ ! -z "$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}; }
-- travis_retry inst
+  conda install -y nipype icu &&
+  rm -r ${CONDA_HOME}/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype*; }
+#  Add install of vtk and mayavi to test mesh (disabled): conda install -y vtk mayavi
+- travis_retry apt_inst
+- travis_retry conda_inst
+install:
+- travis_retry pip install -e .[$NIPYPE_EXTRAS]
 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:
-- bash <(curl -s https://codecov.io/bash) -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF unittests
+- py.test --doctest-modules nipype
 deploy:
   provider: pypi
   user: satra

CHANGES

@@ -1,17 +1,42 @@
 Upcoming release 0.13
 =====================
 
+* ENH: DVARS includes intensity normalization feature - turned on by default (https://github.com/nipy/nipype/pull/1827)
+* FIX: DVARS is correctly using sum of squares instead of standard deviation (https://github.com/nipy/nipype/pull/1827)
+* ENH: Refactoring of nipype.interfaces.utility (https://github.com/nipy/nipype/pull/1828)
+* FIX: CircleCI were failing silently. Some fixes to tests (https://github.com/nipy/nipype/pull/1833)
+* FIX: Issues in Docker image permissions, and docker documentation (https://github.com/nipy/nipype/pull/1825)
+* ENH: Revised all Dockerfiles and automated deployment to Docker Hub
+       from CircleCI (https://github.com/nipy/nipype/pull/1815)
+* FIX: Semaphore capture using MultiProc plugin (https://github.com/nipy/nipype/pull/1689)
+* REF: Refactor AFNI interfaces (https://github.com/nipy/nipype/pull/1678, https://github.com/nipy/nipype/pull/1680)
+* 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)
 * 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)
-
+* ENH: Added ANTs interface CreateJacobianDeterminantImage; replaces deprecated JacobianDeterminant
+       (https://github.com/nipy/nipype/pull/1654)
+* ENH: Update ReconAll interface for FreeSurfer v6.0.0 (https://github.com/nipy/nipype/pull/1790)
 
 Release 0.12.1 (August 3, 2016)
 ===============================