fixed dockerfile install, added docker requirements file

.dockerignore

@@ -0,0 +1,28 @@
+# python cache
+__pycache__
+
+# python distribution
+fmrif_tools.egg-info
+src
+
+# git
+.git
+.gitignore
+
+# other
+docs
+
+# config req files
+requirements.in
+docker_requirements.in
+dev_requirements.in
+
+# Non-docker req files
+requirements.txt
+dev_requirements.txt
+
+# Mac files
+.DS_Store
+
+# IDE
+.idea

Dockerfile

@@ -1,30 +1,57 @@
-FROM neurodebian:wheezy
+FROM neurodebian:trusty
 
 # Add dcm2niix and lbgdcm (taken from scitran dcm2niix dockerfile)
 RUN apt-get update -qq \
     && apt-get install -y \
-    dcm2niix \
-    libgdcm-tools \
+    git \
     curl \
+    build-essential \
+    cmake \
+    pkg-config \
+    libgdcm-tools=2.2.4-1.1ubuntu4 \
+    bsdtar \
     unzip \
     pigz \
-    bzip2 \
     gzip \
-    wget
+    wget \
+    jq \
+    libgl1-mesa-glx
+
+# Compile DCM2NIIX from source (latest commit as of Sept. 1, 2017)
+ENV DCMCOMMIT=988d16b7327028d46ed7f45f00cc704254a91446
+RUN curl -#L  https://github.com/rordenlab/dcm2niix/archive/$DCMCOMMIT.zip | bsdtar -xf- -C /usr/local
+WORKDIR /usr/local/dcm2niix-${DCMCOMMIT}/build
+RUN cmake -DUSE_OPENJPEG=ON ../ && \
+    make && \
+    make install
+
 
 # Install and setup miniconda (taken from mriqc Dockerfile)
-RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.3.11-Linux-x86_64.sh && \
-    bash Miniconda3-4.3.11-Linux-x86_64.sh -b -p /usr/local/miniconda && \
-    rm Miniconda3-4.3.11-Linux-x86_64.sh
+RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.3.21-Linux-x86_64.sh && \
+    bash Miniconda3-4.3.21-Linux-x86_64.sh -b -p /usr/local/miniconda && \
+    rm Miniconda3-4.3.21-Linux-x86_64.sh
 
 ENV PATH=/usr/local/miniconda/bin:$PATH \
     LANG=C.UTF-8 \
     LC_ALL=C.UTF-8
 
-COPY . /root/src/fmrif_tools
-RUN cd /root/src/fmrif_tools && \
-    pip install -r requirements.txt && \
+RUN conda install -y \
+          numpy==1.13.1 \
+          matplotlib==2.0.2 \
+          pandas==0.20.3; \
+    sync &&  \
+    chmod +x /usr/local/miniconda/bin/* && \
+    conda clean --all -y; sync && \
+    python -c "from matplotlib import font_manager" && \
+    sed -i 's/\(backend *: \).*$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )
+
+WORKDIR /usr/local/src/fmrif_tools
+COPY . /usr/local/src/fmrif_tools
+RUN cd /usr/local/src/fmrif_tools && \
+    pip install -r docker_requirements.txt && \
     pip install . && \
     rm -rf ~/.cache/pip
 
-ENTRYPOINT["/usr/local/miniconda/bin/oxy2bids"]
+RUN ldconfig
+
+ENTRYPOINT ["/usr/local/miniconda/bin/oxy2bids"]

__about__.py

@@ -34,14 +34,15 @@
     'Intended Audience :: Science/Research',
     'Topic :: Scientific/Engineering :: Interface Engine/Protocol Translator',
     'License :: OSI Approved :: BSD License',
+    'Programming Language :: Python :: 3.6',
     'Programming Language :: Python :: 3.5',
     'Programming Language :: Python :: 2.7',
 ]
 
 REQUIRES = [
     'matplotlib == 2.0.2',
-    'pandas == 0.20.1',
+    'pandas == 0.20.3',
     'pydicom == 0.9.9',
-    'numpy == 1.13.0',
+    'numpy == 1.13.1',
     'bioread == 1.0.4',
 ]

dev_requirements.in

@@ -1,7 +1,7 @@
-pandas==0.20.1
+pandas==0.20.3
 matplotlib==2.0.2
 bioread==1.0.4
 pydicom==0.9.9
-numpy==1.13.0
+numpy==1.13.1
 jupyter
 notebook

dev_requirements.txt

@@ -28,8 +28,8 @@ mistune==0.7.4            # via nbconvert
 nbconvert==5.3.0          # via jupyter, notebook
 nbformat==4.4.0           # via ipywidgets, nbconvert, notebook
 notebook==5.0.0
-numpy==1.13.0
-pandas==0.20.1
+numpy==1.13.1
+pandas==0.20.3
 pandocfilters==1.4.2      # via nbconvert
 pexpect==4.2.1            # via ipython
 pickleshare==0.7.4        # via ipython

docker_requirements.in

@@ -0,0 +1,2 @@
+pydicom==0.9.9
+bioread==1.0.4

docker_requirements.txt

@@ -0,0 +1,9 @@
+#
+# This file is autogenerated by pip-compile
+# To update, run:
+#
+#    pip-compile --output-file docker_requirements.txt docker_requirements.in
+#
+bioread==1.0.4
+numpy==1.13.1             # via bioread
+pydicom==0.9.9

requirements.in

@@ -1,5 +1,5 @@
 matplotlib==2.0.2
-pandas==0.20.1
+pandas==0.20.3
 pydicom==0.9.9
-numpy==1.13.0
+numpy==1.13.1
 bioread==1.0.4

requirements.txt

@@ -7,8 +7,8 @@
 bioread==1.0.4
 cycler==0.10.0            # via matplotlib
 matplotlib==2.0.2
-numpy==1.13.0
-pandas==0.20.1
+numpy==1.13.1
+pandas==0.20.3
 pydicom==0.9.9
 pyparsing==2.2.0          # via matplotlib
 python-dateutil==2.6.1    # via matplotlib, pandas