Fixes for Docker build. Added explicit installs for major python3 package dependencies

Author: jmtyszka

Dockerfile

@@ -1,11 +1,11 @@
-# BIDSKIT v1.2.0
+# BIDSKIT 2019.12.20
 # MAINTAINER: jmt@caltech.edu
 
 # Install Ubuntu 18.04 LTS Bionic Beaver
 FROM ubuntu:bionic
 
-# Install Node.js version 8
-FROM node:8
+# Install Node.js version 12
+FROM node:12
 
 # Install updates, Python3 for BIDS conversion script, Pip3 for Python to pull the pydicom module
 # git and make for building DICOM convertor from source + related dependencies
@@ -32,7 +32,13 @@ RUN cd /tmp && \
     cmake .. && \
     make install
 
+# Install important python3 packages explicitly to avoid compilation errors from setup.py
+RUN pip3 install cython scipy numpy pandas
+
+# Install python DICOM and BIDS packages
+RUN pip3 install pydicom pybids
+
 # Install python3 bidskit in the container
 ADD . /myapp
 WORKDIR /myapp
-RUN python3 setup.py install
+RUN python3 setup.py install

README.md

@@ -1,5 +1,5 @@
 # BIDSKIT
-### Version 2019.8.16
+### Version 2019.12.20
 Python utilities for converting from DICOM to BIDS neuroimaging formats.
 
 The *bidskit* console command takes a directory tree containing imaging series from one or more subjects (eg T1w MPRAGE, BOLD EPI, Fieldmaps), converts the imaging data to Nifti-1 format with JSON metadata files (sidecars) and populates a directory tree according to the latest BIDS specification.

setup.py

@@ -45,7 +45,7 @@
     # For a discussion on single-sourcing the version across setup.py and the
     # project code, see
     # https://packaging.python.org/en/latest/single_source_version.html
-    version='2019.8.16',  # Required
+    version='2019.12.20',  # Required
 
     # This is a one-line description or tagline of what your project does. This
     # corresponds to the "Summary" metadata field:
@@ -145,7 +145,7 @@
     # https://packaging.python.org/en/latest/requirements.html
     install_requires=['pydicom>=1.2.2',
                       'pybids>=0.9.5',
-                      'numpy>=1.15.2'],  # Optional
+                      'numpy'],
 
     # List additional groups of dependencies here (e.g. development
     # dependencies). Users will be able to install these using the "extras"
@@ -203,4 +203,8 @@
         'Funding': 'http://conte.caltech.edu/',
         'Source': 'https://github.com/jmtyszka/bidskit/',
     },
-)
+
+    # Allow or forbid running this package directly from a zip file
+    # https://setuptools.readthedocs.io/en/latest/setuptools.html#setting-the-zip-safe-flag
+    zip_safe=False,
+)