TST: Depend paramiko so SSHDataGrabber tests run

Author: ashgillman

.travis.yml

@@ -12,7 +12,7 @@ python:
 env:
 - INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" CI_SKIP_TEST=1
 - INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler" CI_SKIP_TEST=1
-- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit" CI_SKIP_TEST=1
+- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit,ssh" CI_SKIP_TEST=1
 - INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" PIP_FLAGS="--pre" CI_SKIP_TEST=1
 
 addons:

Dockerfile

@@ -0,0 +1,109 @@
+# Copyright (c) 2016, The developers of the Stanford CRN
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright notice, this
+#   list of conditions and the following disclaimer.
+#
+# * Redistributions in binary form must reproduce the above copyright notice,
+#   this list of conditions and the following disclaimer in the documentation
+#   and/or other materials provided with the distribution.
+#
+# * Neither the name of crn_base nor the names of its
+#   contributors may be used to endorse or promote products derived from
+#   this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+# 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.
+
+
+#
+# Based on https://github.com/poldracklab/fmriprep/blob/9c92a3de9112f8ef1655b876de060a2ad336ffb0/Dockerfile
+#
+FROM nipype/base:latest
+MAINTAINER The nipype developers https://github.com/nipy/nipype
+
+ARG PYTHON_VERSION_MAJOR=3
+
+# Installing and setting up miniconda
+RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda${PYTHON_VERSION_MAJOR}-4.2.12-Linux-x86_64.sh && \
+    bash Miniconda${PYTHON_VERSION_MAJOR}-4.2.12-Linux-x86_64.sh -b -p /usr/local/miniconda && \
+    rm Miniconda${PYTHON_VERSION_MAJOR}-4.2.12-Linux-x86_64.sh
+
+ENV PATH=/usr/local/miniconda/bin:$PATH \
+    LANG=C.UTF-8 \
+    LC_ALL=C.UTF-8 \
+    ACCEPT_INTEL_PYTHON_EULA=yes \
+    MKL_NUM_THREADS=1 \
+    OMP_NUM_THREADS=1
+# MKL/OMP_NUM_THREADS: unless otherwise specified, each process should
+# only use one thread - nipype will handle parallelization
+
+# Installing precomputed python packages
+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} \
+                     mkl \
+                     numpy \
+                     scipy \
+                     scikit-learn \
+                     matplotlib \
+                     pandas \
+                     libxml2 \
+                     libxslt \
+                     traits=4.6.0 \
+                     psutil \
+                     paramiko \
+                     icu=58.1 && \
+    sync;
+
+# matplotlib cleanups: set default backend, precaching fonts
+RUN sed -i 's/\(backend *: \).*$/\1Agg/g' /usr/local/miniconda/lib/python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}/site-packages/matplotlib/mpl-data/matplotlibrc && \
+    python -c "from matplotlib import font_manager"
+
+# Install CI scripts
+COPY docker/files/run_* /usr/bin/
+RUN chmod +x /usr/bin/run_*
+
+# Replace imglob with a Python3 compatible version
+COPY nipype/external/fsl_imglob.py /usr/bin/fsl_imglob.py
+RUN rm -rf ${FSLDIR}/bin/imglob && \
+    chmod +x /usr/bin/fsl_imglob.py && \
+    ln -s /usr/bin/fsl_imglob.py ${FSLDIR}/bin/imglob
+
+# Installing dev requirements (packages that are not in pypi)
+WORKDIR /src/
+COPY requirements.txt requirements.txt
+RUN pip install -r requirements.txt && \
+    rm -rf ~/.cache/pip
+
+# Installing nipype
+COPY . /src/nipype
+RUN cd /src/nipype && \
+    pip install -e .[all] && \
+    rm -rf ~/.cache/pip
+
+WORKDIR /work/
+
+ARG BUILD_DATE
+ARG VCS_REF
+ARG VERSION
+LABEL org.label-schema.build-date=$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"

nipype/info.py

@@ -163,7 +163,8 @@ def get_nipype_gitversion():
     'profiler': ['psutil>=5.0'],
     'duecredit': ['duecredit'],
     'xvfbwrapper': ['xvfbwrapper'],
-    'pybids': ['pybids']
+    'pybids': ['pybids'],
+    'ssh': ['paramiko'],
     # 'mesh': ['mayavi']  # Enable when it works
 }