Merge remote-tracking branch 'upstream/master' into fix/1933

Author: oesteban

.circle/tests.sh

@@ -17,27 +17,27 @@ fi
 # They may need to be rebalanced in the future.
 case ${CIRCLE_NODE_INDEX} in
   0)
-    docker run --rm=false -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_pytests.sh && \
+    docker run --rm=false -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_pytests.sh && \
     docker run --rm=false -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_pytests.sh && \
-    docker run --rm=false -it -v $WORKDIR:/work -w /src/nipype/doc nipype/nipype:py35 /usr/bin/run_builddocs.sh && \
-    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow3d && \
-    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow4d
+    docker run --rm=false -it -v $WORKDIR:/work -w /src/nipype/doc --entrypoint=/usr/bin/run_builddocs.sh nipype/nipype:py36 /usr/bin/run_builddocs.sh && \
+    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow3d && \
+    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow4d
     exitcode=$?
     ;;
   1)
-    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /data/examples/ level1 && \
-    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /data/examples/ l2pipeline
+    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh fmri_spm_dartel Linear /data/examples/ level1 && \
+    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh fmri_spm_dartel Linear /data/examples/ l2pipeline
     exitcode=$?
     ;;
   2)
     docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \
-    docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline
+    docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline
     exitcode=$?
     ;;
   3)
-    docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \
-    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /data/examples/ l1pipeline && \
-    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /data/examples/ level1_workflow
+    docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \
+    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /data/examples/ l1pipeline && \
+    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /data/examples/ level1_workflow
     exitcode=$?
     ;;
 esac

.github/ISSUE_TEMPLATE.md

@@ -6,5 +6,17 @@
 
 ### How to replicate the behavior
 
+### Script/Workflow details
+
+Please put URL to code or code here (if not too long).
+
 ### Platform details:
-please paste the output of: `python -c "import nipype; print(nipype.get_info()); print(nipype.__version__)"`
+
+Please paste the output of: `python -c "import nipype; print(nipype.get_info()); print(nipype.__version__)"`
+
+### Execution environment
+
+Choose one
+- Container [Tag: ???]
+- My python environment inside container [Base Tag: ???]
+- My python environment outside container

.travis.yml

@@ -6,6 +6,7 @@ python:
 - 2.7
 - 3.4
 - 3.5
+- 3.6
 env:
 - INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler"
 - INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler"

CHANGES

@@ -2,6 +2,7 @@ Upcoming Release
 =====================
 
 * FIX: Ensure build fails in Circle when tests fail (https://github.com/nipy/nipype/pull/1981)
+* ENH: Add interface to antsAffineInitializer (https://github.com/nipy/nipype/pull/1980)
 * ENH: AFNI motion parameter support for FrameWiseDisplacement (https://github.com/nipy/nipype/pull/1840)
 * ENH: Add ANTs KellyKapowski interface (https://github.com/nipy/nipype/pull/1845)
 * FIX: AFNI interface bug setting OMP_NUM_THREADS to 1 (https://github.com/nipy/nipype/pull/1728)

Dockerfile

@@ -50,7 +50,7 @@ ENV PATH=/usr/local/miniconda/bin:$PATH \
 # only use one thread - nipype will handle parallelization
 
 # Installing precomputed python packages
-ARG PYTHON_VERSION_MINOR=5
+ARG PYTHON_VERSION_MINOR=6
 RUN conda config --add channels conda-forge; sync && \
     conda config --set always_yes yes --set changeps1 no; sync && \
     conda install -y python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR} \

circle.yml

@@ -38,11 +38,11 @@ dependencies:
     - if [ "$CIRCLE_TAG" != "" ]; then sed -i -E "s/(__version__ = )'[A-Za-z0-9.-]+'/\1'$CIRCLE_TAG'/" nipype/info.py; fi
 #     - e=1 && for i in {1..5}; do docker build -f docker/base.Dockerfile --rm=false -t nipype/base:latest . && e=0 && break || sleep 15; done && [ "$e" -eq "0" ] :
 #         timeout: 21600
-    - e=1 && for i in {1..5}; do docker build --rm=false -t nipype/nipype:latest -t nipype/nipype:py35 --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg VERSION=$CIRCLE_TAG . && e=0 && break || sleep 15; done && [ "$e" -eq "0" ] :
+    - e=1 && for i in {1..5}; do docker build --rm=false -t nipype/nipype:latest -t nipype/nipype:py36 --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg VERSION=$CIRCLE_TAG . && e=0 && break || sleep 15; done && [ "$e" -eq "0" ] :
         timeout: 6000
     - e=1 && for i in {1..5}; do docker build --rm=false -t nipype/nipype:py27 --build-arg PYTHON_VERSION_MAJOR=2 --build-arg PYTHON_VERSION_MINOR=7 --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg VERSION=$CIRCLE_TAG-py27 . && e=0 && break || sleep 15; done && [ "$e" -eq "0" ] :
         timeout: 6000
-    - docker save -o $HOME/docker/cache.tar nipype/base:latest nipype/nipype:py35 nipype/nipype:py27 :
+    - docker save -o $HOME/docker/cache.tar nipype/base:latest nipype/nipype:py36 nipype/nipype:py27 :
         timeout: 6000
 
 test:

doc/devel/testing_nipype.rst

@@ -109,16 +109,17 @@ Testing Nipype using Docker
 
 As of :code:`nipype-0.13`, Nipype is tested inside Docker containers. First, install the
 `Docker Engine <https://docs.docker.com/engine/installation/>`_.
-Nipype has one base docker image called nipype/nipype, and several additional test images
+Nipype has one base docker image called nipype/base:latest, and several additional test images
 for various Python versions.
 
-The base nipype/nipype image is built as follows::
+The base nipype image is built as follows::
 
   cd path/to/nipype/
-  docker build -t nipype/nipype .
+  docker build -t nipype/base:latest -f docker/base.Dockerfile .
+
+This base image contains several useful tools (FreeSurfer, AFNI, FSL, ANTs, etc.),
+but not nipype.
 
-This base image contains several useful tools (FreeSurfer, AFNI, FSL, ANTs, etc.) and
-a nipype installation, all in Python 3.5.
 It is possible to fetch a built image from the latest master branch of nipype
 using::
 
@@ -128,26 +129,15 @@ using::
 The docker run command will then open the container and offer a bash shell for the
 developer.
 
-The additional test images have several test scripts installed. For instance,
-to build and run all tests on Python 2.7::
-
-  cd path/to/nipype/
-  docker build -f docker/Dockerfile_py27 -t nipype/nipype_test:py27 .
-  docker run -it --rm -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_pytests.sh
-
-For running nipype in Python 3.5::
+For building a continer for running nipype in Python 3.6::
 
   cd path/to/nipype/
-  docker build -f docker/Dockerfile_py35 -t nipype/nipype_test:py35 .
+  docker build -f Dockerfile -t nipype/nipype_test:py36 .
   docker run -it --rm -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_pytests.sh
+                      nipype/nipype_test:py36 /usr/bin/run_pytests.sh
 
-The last two examples assume that the example data is downladed into ~/examples and
+The last examples assume that the example data is downladed into ~/examples and
 the ~/scratch folder will be created if it does not exist previously.

doc/documentation.rst

@@ -11,8 +11,13 @@ Documentation
 
 Previous versions:  `0.12.0 <http://nipype.readthedocs.io/en/0.12.0/>`_ `0.11.0 <http://nipy.org/nipype/0.11.0>`_
 
+
 .. container:: doc2
 
+  .. admonition:: Michael Notter's Nipype guide
+
+    Be sure to read `Michael's excellent tutorials <https://miykael.github.io/nipype_tutorial/>`_.
+
   .. admonition:: Guides
 
     .. hlist::

doc/links_names.txt

@@ -74,8 +74,7 @@
 .. _pythonxy: https://python-xy.github.io/
 .. _EPD: http://www.enthought.com/products/epd.php
 .. _Traits: http://code.enthought.com/projects/traits/
-.. _Anaconda: https://www.continuum.io/downloads
-.. _Canopy: https://www.enthought.com/products/canopy/
+.. _Miniconda: https://conda.io/miniconda.html
 
 .. Python imaging projects
 .. _PyMVPA: http://www.pymvpa.org

doc/quickstart.rst

@@ -11,34 +11,30 @@ Downloading and installing
    :maxdepth: 1
 
    users/install
-   users/vagrant
 
 Beginner's guide
 ================
 
-Beginner's tutorials (IPython Notebooks). `Available here`__
+Michael Notter's Nipype tutorial. `Available here`__
 
-Michael Notter's Nipype guide. `Available here`__
+__ https://miykael.github.io/nipype_tutorial/
 
-Dissecting Nipype Workflows. `Available here`__
+Nipype workshop materials
+=========================
 
-Introductory slides [older]. `Available here`__
+Self-assessment questionnaire with links to learning about each piece. `Available here`__
 
-__ https://github.com/mwaskom/nipype_concepts
-__ http://miykael.github.com/nipype-beginner-s-guide/index.html
-__ http://slideviewer.herokuapp.com/url/raw.github.com/nipy/nipype/master/examples/nipype_tutorial.ipynb?theme=sky
-__ http://satra.github.com/intro2nipype
+Lecture slides `Available here`__
 
-User guides
-===========
+__ http://nipy.org/workshops/2017-03-boston/review.html
+__ http://nipy.org/workshops/2017-03-boston/index.html
 
-.. toctree::
-   :maxdepth: 1
+`Docker containers <https://hub.docker.com/r/nipype/workshops/tags/>`_
+
+`Github project for lectures <https://github.com/nipy/workshops/tree/gh-pages/2017-03-boston>`_
+`Github project for dockerfiles + notebooks <https://github.com/nipy/workshops/tree/master/170327-nipype>`_
 
-   users/interface_tutorial
-   users/pipeline_tutorial
-   users/plugins
-   users/debug
+`All notebooks visualized <http://nbviewer.jupyter.org/github/nipy/workshops/tree/master/170327-nipype/notebooks/>`_
 
 Developer guides
 ================
@@ -47,16 +43,6 @@ Developer guides
    :maxdepth: 1
 
    devel/writing_custom_interfaces
-   devel/gitwash/index
 
 .. include:: links_names.txt
 
-Useful links for beginners
-===========================
-
-Getting started with Python - Tutorials. `Available here`__
-
-Python for Beginners `Available here`__
-
-   __ http://www.codecademy.com/en/tracks/python
-   __ https://www.python.org/about/gettingstarted/

doc/users/index.rst

@@ -11,15 +11,12 @@
    :maxdepth: 2
 
    install
-   vagrant
 
-   interface_tutorial
    caching_tutorial
 
 .. toctree::
    :maxdepth: 1
 
-   pipeline_tutorial
    plugins
    config_file
    debug

doc/users/install.rst

@@ -9,18 +9,17 @@ This page covers the necessary steps to install Nipype.
 Nipype for users
 ----------------
 
-Using conda
-~~~~~~~~~~~
-
-Installing nipype from the conda-forge channel can be achieved by adding conda-forge to your channels with::
-
-  conda config --add channels conda-forge
+Using docker
+~~~~~~~~~~~~
 
+You can follow the `Nipype tutorial <https://miykael.github.io/nipype_tutorial/>`_
 
-Once the conda-forge channel has been enabled, nipype can be installed with::
+Using conda
+~~~~~~~~~~~
 
-  conda install nipype
+Installing nipype from the conda-forge channel can be achieved by::
 
+  conda install --channel conda-forge nipype
 
 It is possible to list all of the versions of nipype available on your platform with::
 
@@ -36,18 +35,23 @@ The installation process is similar to other Python packages.
 
 If you already have a Python environment set up, you can do::
 
-  easy_install nipype
-
-or::
-
   pip install nipype
 
-
 If you want to install all the optional features of ``nipype``,
-use the following command (only for ``nipype>=0.13``)::
+use the following command::
 
   pip install nipype[all]
 
+While `all` installs everything, one can also install select components as
+listed below::
+
+    'doc': ['Sphinx>=1.4', 'matplotlib', 'pydotplus'],
+    'tests': ['pytest-cov', 'codecov'],
+    'nipy': ['nitime', 'nilearn', 'dipy', 'nipy', 'matplotlib'],
+    'profiler': ['psutil'],
+    'duecredit': ['duecredit'],
+    'xvfbwrapper': ['xvfbwrapper'],
+
 
 Debian and Ubuntu
 ~~~~~~~~~~~~~~~~~
@@ -59,11 +63,14 @@ manager.
 Mac OS X
 ~~~~~~~~
 
-The easiest way to get nipype running on Mac OS X is to install Anaconda_ or
-Canopy_ and then add nipype by executing::
+The easiest way to get nipype running on Mac OS X is to install Miniconda_ and
+follow the instructions above. If you have a non-conda environment you can
+install nipype by typing::
 
-  easy_install nipype
+  pip install nipype
 
+Note that the above procedure may require availability of gcc on your system
+path to compile the traits package.
 
 From source
 ~~~~~~~~~~~
@@ -79,47 +86,42 @@ If you downloaded the source distribution named something
 like ``nipype-x.y.tar.gz``, then unpack the tarball, change into the
 ``nipype-x.y`` directory and install nipype using::
 
-    python setup.py install
+    pip install .
 
 **Note:** Depending on permissions you may need to use ``sudo``.
 
 
 Testing the install
 -------------------
 
-The best way to test the install is checking nipype's version ::
+The best way to test the install is checking nipype's version and then running
+the tests::
 
     python -c "import nipype; print(nipype.__version__)"
-
+    python -c "import nipype; nipype.test()"
 
 Installation for developers
 ---------------------------
 
 Developers should start `here <../devel/testing_nipype.html>`_.
 
-
 Recommended Software
-------------
+--------------------
 
 Strong Recommendations
 ~~~~~~~~~~~~~~~~~~~~~~
 
-IPython_ 0.10.2 - 1.0.0
-  Interactive python environment. This is necessary for some parallel
-  components of the pipeline engine.
+IPython_
+  Interactive python environment.
 
-Matplotlib_ 1.0 - 1.2
+Matplotlib_
   Plotting library
 
-`RDFLib <http://rdflib.readthedocs.org/en/latest/>`_ 4.1
-  RDFLibrary required for provenance export as RDF
-
 Sphinx_ 1.1
   Required for building the documentation
 
 `Graphviz <http://www.graphviz.org/>`_
-  Required for building the documentation. The python wrapper package (``graphviz``)
-  and the program itself both need to be installed.
+  Required for building the documentation.
 
 Interface Dependencies
 ~~~~~~~~~~~~~~~~~~~~~~
@@ -148,7 +150,7 @@ Slicer_
   3.6 or later
 
 Nipy_
-  0.1.2+20110404 or later
+  0.4 or later
 
 Nitime_
   (optional)