doc: catching up to changes

Author: mgxd

.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

@@ -7,4 +7,4 @@
 ### How to replicate the behavior
 
 ### Platform details:
-please paste the output of: `python -c "import nipype; print(nipype.get_info())"`
+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

@@ -1,5 +1,6 @@
 cache:
-- apt
+  apt: true
+
 language: python
 python:
 - 2.7
@@ -10,11 +11,7 @@ env:
 - 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 $INSTALL_DEB_DEPENDECIES; then sudo ln -s /run/shm /dev/shm; fi &&
   bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh) &&
@@ -26,18 +23,24 @@ before_install:
     source /etc/fsl/fsl.sh;
     source /etc/afni/afni.sh;
     export FSLOUTPUTTYPE=NIFTI_GZ; fi }
-- travis_retry bef_inst
-install:
-#  Add install of vtk and mayavi to test mesh (disabled): conda install -y vtk mayavi &&
-- function inst {
+- function conda_inst {
+  export CONDA_HOME=$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=$TRAVIS_PYTHON_VERSION &&
   conda install -y nipype icu &&
-  rm -r /home/travis/miniconda/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype* &&
-  pip install -r requirements.txt &&
-  pip install -e .[$NIPYPE_EXTRAS]; }
-- travis_retry inst
+  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:
 - py.test --doctest-modules nipype
 deploy:

CHANGES

@@ -1,11 +1,24 @@
 Upcoming Release
 =====================
+
+* ENH: Enable new BBRegister init options for FSv6+ (https://github.com/nipy/nipype/pull/1811)
+* REF: Splits nipype.interfaces.utility into base, csv, and wrappers (https://github.com/nipy/nipype/pull/1828)
+* FIX: Makespec now runs with nipype in current directory (https://github.com/nipy/nipype/pull/1813)
+* FIX: Flexible nifti opening with mmap if Numpy < 1.12.0 (https://github.com/nipy/nipype/pull/1796 + https://github.com/nipy/nipype/pull/1831)
+* 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)
 * ENH: Update ReconAll interface for FreeSurfer v6.0.0 (https://github.com/nipy/nipype/pull/1790)
 * FIX: Cast DVARS float outputs to avoid memmap error (https://github.com/nipy/nipype/pull/1777)
 * FIX: FSL FNIRT intensity mapping files (https://github.com/nipy/nipype/pull/1799)
 * ENH: Additional outputs generated by FSL EDDY (https://github.com/nipy/nipype/pull/1793)
 * TST: Parallelize CircleCI build across 4 containers (https://github.com/nipy/nipype/pull/1769)
 
+
 0.13.0-rc1 (January 4, 2017)
 ===============================
 

Dockerfile

@@ -26,49 +26,204 @@
 # 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 <crn.poldracklab@gmail.com>
 
-# Preparations
-RUN ln -snf /bin/bash /bin/sh
+#
+# Based on https://github.com/poldracklab/fmriprep/blob/9c92a3de9112f8ef1655b876de060a2ad336ffb0/Dockerfile
+#
+FROM ubuntu:xenial-20161213
+MAINTAINER The nipype developers https://github.com/nipy/nipype
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+# Pre-cache neurodebian key
+COPY docker/files/neurodebian.gpg /root/.neurodebian.gpg
+
+# Prepare environment
+RUN apt-key add /root/.neurodebian.gpg && \
+    apt-get update && \
+    apt-get install -y --no-install-recommends curl bzip2 ca-certificates xvfb && \
+    curl -sSL http://neuro.debian.net/lists/xenial.us-ca.full >> /etc/apt/sources.list.d/neurodebian.sources.list && \
+    apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true; \
+    apt-get update
+
+# Installing freesurfer
+RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz | tar zxv -C /opt \
+    --exclude='freesurfer/trctrain' \
+    --exclude='freesurfer/subjects/fsaverage_sym' \
+    --exclude='freesurfer/subjects/fsaverage3' \
+    --exclude='freesurfer/subjects/fsaverage4' \
+    --exclude='freesurfer/subjects/fsaverage5' \
+    --exclude='freesurfer/subjects/fsaverage6' \
+    --exclude='freesurfer/subjects/cvs_avg35' \
+    --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
+    --exclude='freesurfer/subjects/bert' \
+    --exclude='freesurfer/subjects/V1_average' \
+    --exclude='freesurfer/average/mult-comp-cor' \
+    --exclude='freesurfer/lib/cuda' \
+    --exclude='freesurfer/lib/qt'
+
+ENV FSL_DIR=/usr/share/fsl/5.0 \
+    OS=Linux \
+    FS_OVERRIDE=0 \
+    FIX_VERTEX_AREA= \
+    FSF_OUTPUT_FORMAT=nii.gz \
+    FREESURFER_HOME=/opt/freesurfer
+ENV SUBJECTS_DIR=$FREESURFER_HOME/subjects \
+    FUNCTIONALS_DIR=$FREESURFER_HOME/sessions \
+    MNI_DIR=$FREESURFER_HOME/mni \
+    LOCAL_DIR=$FREESURFER_HOME/local \
+    FSFAST_HOME=$FREESURFER_HOME/fsfast \
+    MINC_BIN_DIR=$FREESURFER_HOME/mni/bin \
+    MINC_LIB_DIR=$FREESURFER_HOME/mni/lib \
+    MNI_DATAPATH=$FREESURFER_HOME/mni/data \
+    FMRI_ANALYSIS_DIR=$FREESURFER_HOME/fsfast
+ENV PERL5LIB=$MINC_LIB_DIR/perl5/5.8.5 \
+    MNI_PERL5LIB=$MINC_LIB_DIR/perl5/5.8.5 \
+    PATH=$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH
+RUN echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh
+
+# Installing Neurodebian packages (FSL, AFNI, git)
+RUN apt-get install -y --no-install-recommends \
+                    fsl-core=5.0.9-1~nd+1+nd16.04+1 \
+                    fsl-mni152-templates=5.0.7-2 \
+                    afni=16.2.07~dfsg.1-2~nd16.04+1
+
+ENV FSLDIR=/usr/share/fsl/5.0 \
+    FSLOUTPUTTYPE=NIFTI_GZ \
+    FSLMULTIFILEQUIT=TRUE \
+    POSSUMDIR=/usr/share/fsl/5.0 \
+    LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH \
+    FSLTCLSH=/usr/bin/tclsh \
+    FSLWISH=/usr/bin/wish \
+    AFNI_MODELPATH=/usr/lib/afni/models \
+    AFNI_IMSAVE_WARNINGS=NO \
+    AFNI_TTATLAS_DATASET=/usr/share/afni/atlases \
+    AFNI_PLUGINPATH=/usr/lib/afni/plugins \
+    PATH=/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH
+
+# Installing and setting up ANTs
+RUN mkdir -p /opt/ants && \
+    curl -sSL "https://github.com/stnava/ANTs/releases/download/v2.1.0/Linux_Ubuntu14.04.tar.bz2" \
+    | tar -xjC /opt/ants --strip-components 1
+
+ENV ANTSPATH=/opt/ants \
+    PATH=$ANTSPATH:$PATH
+
+# Installing and setting up c3d
+RUN mkdir -p /opt/c3d && \
+    curl -sSL "http://downloads.sourceforge.net/project/c3d/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz" \
+    | tar -xzC /opt/c3d --strip-components 1
+
+ENV C3DPATH=/opt/c3d/ \
+    PATH=$C3DPATH/bin:$PATH
+
+# Install some other required tools
+RUN apt-get install -y --no-install-recommends \
+                    git=1:2.7.4-0ubuntu1 \
+                    graphviz=2.38.0-12ubuntu2 \
+                    unzip \
+                    apt-utils \
+                    fusefat \
+                    make \
+                    ruby=1:2.3.0+1 && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# Install fake-S3
+ENV GEM_HOME /usr/lib/ruby/gems/2.3
+ENV BUNDLE_PATH="$GEM_HOME" \
+    BUNDLE_BIN="$GEM_HOME/bin" \
+    BUNDLE_SILENCE_ROOT_WARNING=1 \
+    BUNDLE_APP_CONFIG="$GEM_HOME"
+ENV PATH $BUNDLE_BIN:$PATH
+RUN mkdir -p "$GEM_HOME" "$BUNDLE_BIN" && \
+    chmod 777 "$GEM_HOME" "$BUNDLE_BIN"
+
+RUN gem install fakes3
+
+# Install Matlab MCR: from the good old install_spm_mcr.sh of @chrisfilo
+WORKDIR /opt
+RUN echo "destinationFolder=/opt/mcr" > mcr_options.txt && \
+    echo "agreeToLicense=yes" >> mcr_options.txt && \
+    echo "outputFile=/tmp/matlabinstall_log" >> mcr_options.txt && \
+    echo "mode=silent" >> mcr_options.txt && \
+    mkdir -p matlab_installer && \
+    curl -sSL http://www.mathworks.com/supportfiles/downloads/R2015a/deployment_files/R2015a/installers/glnxa64/MCR_R2015a_glnxa64_installer.zip \
+         -o matlab_installer/installer.zip && \
+    unzip matlab_installer/installer.zip -d matlab_installer/ && \
+    matlab_installer/install -inputFile mcr_options.txt && \
+    rm -rf matlab_installer mcr_options.txt
+
+# Install SPM
+RUN curl -sSL http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/spm12_r6472_Linux_R2015a.zip -o spm12.zip && \
+    unzip spm12.zip && \
+    rm -rf spm12.zip
+
+ENV MATLABCMD="/opt/mcr/v85/toolbox/matlab" \
+    SPMMCRCMD="/opt/spm12/run_spm12.sh /opt/mcr/v85/ script" \
+    FORCE_SPMMCR=1
 
-# 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
+# Installing and setting up miniconda
+RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.2.12-Linux-x86_64.sh && \
+    bash Miniconda3-4.2.12-Linux-x86_64.sh -b -p /usr/local/miniconda && \
+    rm Miniconda3-4.2.12-Linux-x86_64.sh
 
-ADD . nipype/
+ENV PATH=/usr/local/miniconda/bin:$PATH \
+    LANG=C.UTF-8 \
+    LC_ALL=C.UTF-8 \
+    ACCEPT_INTEL_PYTHON_EULA=yes
 
-# 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 .
+# Installing precomputed python packages
+RUN conda config --add channels conda-forge --add channels intel && \
+    chmod +x /usr/local/miniconda/bin/* && \
+    conda config --set always_yes yes --set changeps1 no && \
+    conda update -q conda && \
+    chmod +x /usr/local/miniconda/bin/*; sync && \
+    conda install -y mkl=2017.0.1 \
+                     numpy=1.11.2 \
+                     scipy=0.18.1 \
+                     scikit-learn=0.17.1 \
+                     matplotlib=1.5.3 \
+                     pandas=0.19.0 \
+                     libxml2=2.9.4 \
+                     libxslt=1.1.29 \
+                     traits=4.6.0 \
+                     psutil=5.0.1 \
+                     icu=58.1 && \
+    find /usr/local/miniconda/ -exec chmod 775 {} +
 
-RUN cd nipype/ && \
-    source activate nipypetests-3.4 && \
-    pip install -r requirements.txt && \
-    pip install -e .
+# matplotlib cleanups: set default backend, precaching fonts
+RUN sed -i 's/\(backend *: \).*$/\1Agg/g' /usr/local/miniconda/lib/python3.5/site-packages/matplotlib/mpl-data/matplotlibrc && \
+    python -c "from matplotlib import font_manager"
 
-RUN cd nipype/ && \
-    source activate nipypetests-3.5 && \
-    pip install -r requirements.txt && \
-    pip install -e .
+# Unless otherwise specified each process should only use one thread - nipype
+# will handle parallelization
+ENV MKL_NUM_THREADS=1 \
+    OMP_NUM_THREADS=1
 
-WORKDIR /scratch
+# Installing dev requirements (packages that are not in pypi)
+WORKDIR /root/
+COPY requirements.txt requirements.txt
+RUN pip install -r requirements.txt && \
+    rm -rf ~/.cache/pip
 
-# Install entrypoints
-ADD docker/circleci/run_* /usr/bin/
-RUN chmod +x /usr/bin/run_*
+# Installing nipype
+COPY . /root/src/nipype
+RUN cd /root/src/nipype && \
+    pip install -e .[all] && \
+    rm -rf ~/.cache/pip
 
-# RUN echo 'source /etc/profile.d/nipype_tests.sh' >> /etc/bash.bashrc
-ENTRYPOINT ["/usr/bin/run_examples.sh"]
+WORKDIR /root/
 
+ARG BUILD_DATE
+ARG VCS_REF
+ARG VERSION
+LABEL org.label-schema.build-date=$BUILD_DATE \
+      org.label-schema.name="NIPYPE" \
+      org.label-schema.description="NIPYPE - Neuroimaging in Python: Pipelines and Interfaces" \
+      org.label-schema.url="http://nipype.readthedocs.io" \
+      org.label-schema.vcs-ref=$VCS_REF \
+      org.label-schema.vcs-url="https://github.com/nipy/nipype" \
+      org.label-schema.version=$VERSION \
+      org.label-schema.schema-version="1.0"