add(infrastructure): Dockerfile, and miscellaneous amends

.docker/files/neurodebian.gpg

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Dockerfile

@@ -0,0 +1,131 @@
+# Use Ubuntu 16.04 LTS
+FROM ubuntu:xenial-20161213
+
+# Pre-cache neurodebian key
+COPY .docker/files/neurodebian.gpg /usr/local/etc/neurodebian.gpg
+
+# Prepare environment
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+                    lsb-release \
+                    curl \
+                    bzip2 \
+                    ca-certificates \
+                    xvfb \
+                    build-essential \
+                    autoconf \
+                    libtool \
+                    pkg-config \
+                    git && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# Installing Neurodebian packages (FSL, AFNI, git)
+RUN curl -sSL "http://neuro.debian.net/lists/$( lsb_release -c | cut -f2 ).us-ca.full" >> /etc/apt/sources.list.d/neurodebian.sources.list && \
+    apt-key add /usr/local/etc/neurodebian.gpg && \
+    (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true)
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+                    fsl-core=5.0.9-5~nd16.04+1 \
+                    afni=16.2.07~dfsg.1-5~nd16.04+1 \
+                    convert3d \
+                    git-annex-standalone && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+ENV FSL_DIR="/usr/share/fsl/5.0" \
+    FSLDIR="/usr/share/fsl/5.0" \
+    FSLOUTPUTTYPE="NIFTI_GZ" \
+    FSLMULTIFILEQUIT="TRUE" \
+    POSSUMDIR="/usr/share/fsl/5.0" \
+    LD_LIBRARY_PATH="/usr/lib/fsl/5.0:$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"
+ENV PATH="/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH"
+
+# Installing ANTs 2.2.0 (NeuroDocker build)
+ENV ANTSPATH=/usr/lib/ants
+RUN mkdir -p $ANTSPATH && \
+    curl -sSL "https://dl.dropbox.com/s/2f4sui1z6lcgyek/ANTs-Linux-centos5_x86_64-v2.2.0-0740f91.tar.gz" \
+    | tar -xzC $ANTSPATH --strip-components 1
+ENV PATH=$ANTSPATH:$PATH
+
+# Installing and setting up miniconda
+RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh && \
+    bash Miniconda3-4.5.11-Linux-x86_64.sh -b -p /usr/local/miniconda && \
+    rm Miniconda3-4.5.11-Linux-x86_64.sh
+
+# Set CPATH for packages relying on compiled libs (e.g. indexed_gzip)
+ENV PATH="/usr/local/miniconda/bin:$PATH" \
+    CPATH="/usr/local/miniconda/include/:$CPATH" \
+    LANG="C.UTF-8" \
+    LC_ALL="C.UTF-8" \
+    PYTHONNOUSERSITE=1
+
+# Installing precomputed python packages
+RUN conda install -y python=3.7.1 \
+                     mkl=2018.0.3 \
+                     mkl-service \
+                     numpy=1.15.4 \
+                     scipy=1.1.0 \
+                     scikit-learn=0.19.1 \
+                     matplotlib=2.2.2 \
+                     pandas=0.23.4 \
+                     libxml2=2.9.8 \
+                     libxslt=1.1.32 \
+                     graphviz=2.40.1 \
+                     traits=4.6.0 \
+                     zlib; sync && \
+    chmod -R a+rX /usr/local/miniconda; sync && \
+    chmod +x /usr/local/miniconda/bin/*; sync && \
+    conda clean --all -y; sync && \
+    conda clean -tipsy && sync
+
+# Precaching fonts, set 'Agg' as default backend for matplotlib
+RUN python -c "from matplotlib import font_manager" && \
+    sed -i 's/\(backend *: \).*$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )
+
+# Unless otherwise specified each process should only use one thread - nipype
+# will handle parallelization
+ENV MKL_NUM_THREADS=1 \
+    OMP_NUM_THREADS=1
+
+# Create a shared $HOME directory
+RUN useradd -m -s /bin/bash -G users sdcflows
+WORKDIR /home/sdcflows
+ENV HOME="/home/sdcflows"
+
+# Installing dev requirements (packages that are not in pypi)
+WORKDIR /src/sdcflows
+
+# Installing sMRIPREP
+COPY . /src/sdcflows
+ARG VERSION
+# Force static versioning within container
+RUN echo "${VERSION}" > /src/sdcflows/sdcflows/VERSION && \
+    echo "include sdcflows/VERSION" >> /src/sdcflows/MANIFEST.in && \
+    pip install --no-cache-dir .[all] && \
+    rm -rf $HOME/.cache/pip
+
+RUN find $HOME -type d -exec chmod go=u {} + && \
+    find $HOME -type f -exec chmod go=u {} +
+
+ENV IS_DOCKER_8395080871=1
+
+RUN ldconfig
+WORKDIR /tmp/
+ENTRYPOINT ["/usr/local/miniconda/bin/sdcflows"]
+
+ARG BUILD_DATE
+ARG VCS_REF
+LABEL org.label-schema.build-date=$BUILD_DATE \
+      org.label-schema.name="SDCflows" \
+      org.label-schema.description="SDCflows - Susceptibility Distortion Correction (SDC) workflows for EPI MR schemes" \
+      org.label-schema.url="http://sdcflows.readthedocs.io" \
+      org.label-schema.vcs-ref=$VCS_REF \
+      org.label-schema.vcs-url="https://github.com/poldracklab/sdcflows" \
+      org.label-schema.version=$VERSION \
+      org.label-schema.schema-version="1.0"

sdcflows/interfaces/fmap.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- 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:

setup.cfg

@@ -10,7 +10,7 @@ long_description = file:long_description.rst
 long_description_content_type = text/x-rst; charset=UTF-8
 license = Apache-2.0
 classifiers =
-    Development Status :: 4 - Beta
+    Development Status :: 2 - Pre-Alpha
     Intended Audience :: Science/Research
     Topic :: Scientific/Engineering :: Image Recognition
     License :: OSI Approved :: BSD License
@@ -25,15 +25,15 @@ setup_requires =
     numpy
     cython
 install_requires =
-    niworkflows >=0.9.3,<0.10.0a0
-    templateflow >=0.1.3,<0.2.0a0
     nibabel >=2.2.1
     nipype >=1.2.0
-    pybids >=0.7.1,<0.8.0a0
+    niworkflows >=0.9.3,<0.10.0a0
     numpy
+    pybids >=0.7.1,<0.8.0a0
+    templateflow >=0.1.3,<0.2.0a0
 test_requires =
-    coverage
     codecov
+    coverage
     pytest
 packages = find:
 include_package_data = True
@@ -58,7 +58,7 @@ tests =
     pytest
 all =
     %(doc)s
-    %(tests)
+    %(tests)s
 
 [options.package_data]
 sdcflows =