BUG: Fix missing python 2 environment

See also [#433](jupyter/docker-stacks#433) on jupyter/docker-stack.
Python 2 support is now removed from jupyter/datascience-notebook. Update dockerfile and config.yml to install python2 kernel manually.

.circleci/config.yml

@@ -17,6 +17,17 @@ jobs:
           command: |
             apt-get update
             apt-get install -y openssh-client openssh-server
+      - run:
+          # Jupyter datascience notebook does not support python 2 anymore, install it manually.
+          # See also https://github.com/jupyter/docker-stacks/issues/432
+          # Next, install python 2 kernel globally, so it can be found from the root
+          name: Install Python 2 Kernel
+          command: |
+            conda create -n python2 python=2 ipykernel
+            pip install kernda --no-cache
+            $CONDA_DIR/envs/python2/bin/python -m ipykernel install
+            kernda -o -y /usr/local/share/jupyter/kernels/python2/kernel.json
+            pip uninstall kernda -y
       - run:
           name: Install pyradiomics in Python 2 and 3
           command: |
@@ -44,6 +55,3 @@ jobs:
             jupyter nbconvert --ExecutePreprocessor.kernel_name=python2 --ExecutePreprocessor.timeout=-1 --to notebook --output-dir /tmp --execute notebooks/helloRadiomics.ipynb notebooks/helloFeatureClass.ipynb notebooks/PyRadiomicsExample.ipynb
 
             jupyter nbconvert --ExecutePreprocessor.kernel_name=python3 --ExecutePreprocessor.timeout=-1 --to notebook --output-dir /tmp --execute  notebooks/helloRadiomics.ipynb notebooks/helloFeatureClass.ipynb notebooks/PyRadiomicsExample.ipynb
-
-
-

Dockerfile

@@ -15,6 +15,19 @@ LABEL org.label-schema.build-data=$BUILD_DATE \
 
 USER root
 ADD . /root/pyradiomics
+
+# Jupyter datascience notebook does not support python 2 anymore, install it manually.
+# If using cache, it is possible python2 environment exists from previous install, therefore
+# only install if python2 environment does not exist
+# See also https://github.com/jupyter/docker-stacks/issues/432
+# Next, also install python 2 kernel globally, so it can be found from the root
+RUN /bin/bash -c "source activate python2 \
+    || (conda create -n python2 python=2 ipykernel \
+    && pip install kernda --no-cache \
+    && $CONDA_DIR/envs/python2/bin/python -m ipykernel install \
+    && kernda -o -y /usr/local/share/jupyter/kernels/python2/kernel.json \
+    && pip uninstall kernda -y)"
+
 # Install in Python 3
 RUN /bin/bash -c "source activate root \
     && cd /root/pyradiomics \