Merge branch 'master' into test_improvements

.travis.yml

-dist: xenial
+dist: bionic
 language: python
 python:
     - 3.7

all-spark-notebook/Dockerfile

@@ -23,8 +23,8 @@ USER $NB_UID
 
 # R packages
 RUN conda install --quiet --yes \
-    'r-base=3.6.2' \
-    'r-ggplot2=3.2*' \
+    'r-base=3.6.3' \
+    'r-ggplot2=3.3*' \
     'r-irkernel=1.1*' \
     'r-rcurl=1.98*' \
     'r-sparklyr=1.1*' \

base-notebook/Dockerfile

@@ -4,7 +4,7 @@
 # Ubuntu 18.04 (bionic)
 # https://hub.docker.com/_/ubuntu/?tab=tags&name=bionic
 # OS/ARCH: linux/amd64
-ARG ROOT_CONTAINER=ubuntu:bionic-20200219@sha256:0925d086715714114c1988f7c947db94064fd385e171a63c07730f1fa014e6f9
+ARG ROOT_CONTAINER=ubuntu:bionic-20200311@sha256:e5dd9dbb37df5b731a6688fa49f4003359f6f126958c9c928f937bec69836320
 ARG BASE_CONTAINER=$ROOT_CONTAINER
 FROM $BASE_CONTAINER
 

datascience-notebook/Dockerfile

@@ -45,11 +45,11 @@ USER $NB_UID
 
 # R packages including IRKernel which gets installed globally.
 RUN conda install --quiet --yes \
-    'r-base=3.6.2' \
+    'r-base=3.6.3' \
     'r-caret=6.0*' \
     'r-crayon=1.3*' \
     'r-devtools=2.2*' \
-    'r-forecast=8.10*' \
+    'r-forecast=8.11*' \
     'r-hexbin=1.28*' \
     'r-htmltools=0.4*' \
     'r-htmlwidgets=1.5*' \
@@ -60,8 +60,8 @@ RUN conda install --quiet --yes \
     'r-rcurl=1.98*' \
     'r-reshape2=1.4*' \
     'r-rmarkdown=2.1*' \
-    'r-rsqlite=2.1*' \
-    'r-shiny=1.3*' \
+    'r-rsqlite=2.2*' \
+    'r-shiny=1.4*' \
     'r-tidyverse=1.3*' \
     'rpy2=3.1*' \
     && \

docs/using/recipes.md

@@ -112,7 +112,7 @@ ARG conda_env=python36
 ARG py_ver=3.6
 
 # you can add additional libraries you want conda to install by listing them below the first line and ending with "&& \"
-RUN conda env create --quiet --yes -p $CONDA_DIR/envs/$conda_env python=$py_ver ipython ipykernel && \
+RUN conda create --quiet --yes -p $CONDA_DIR/envs/$conda_env python=$py_ver ipython ipykernel && \
     conda clean --all -f -y
 
 # alternatively, you can comment out the lines above and uncomment those below

r-notebook/Dockerfile

@@ -25,7 +25,7 @@ USER $NB_UID
 
 # R packages
 RUN conda install --quiet --yes \
-    'r-base=3.6.2' \
+    'r-base=3.6.3' \
     'r-caret=6.0*' \
     'r-crayon=1.3*' \
     'r-devtools=2.2*' \
@@ -41,7 +41,7 @@ RUN conda install --quiet --yes \
     'r-reshape2=1.4*' \
     'r-rmarkdown=2.1*' \
     'r-rodbc=1.3*' \
-    'r-rsqlite=2.1*' \
+    'r-rsqlite=2.2*' \
     'r-shiny=1.4*' \
     'r-tidyverse=1.3*' \
     'unixodbc=2.3.*' \

scipy-notebook/Dockerfile

@@ -18,16 +18,16 @@ USER $NB_UID
 RUN conda install --quiet --yes \
     'beautifulsoup4=4.8.*' \
     'conda-forge::blas=*=openblas' \
-    'bokeh=1.4.*' \
+    'bokeh=2.0.*' \
     'cloudpickle=1.3.*' \
     'cython=0.29.*' \
-    'dask=2.11.*' \
+    'dask=2.14.*' \
     'dill=0.3.*' \
     'h5py=2.10.*' \
     'hdf5=1.10.*' \
     'ipywidgets=7.5.*' \
     'ipympl=0.5.*'\
-    'matplotlib-base=3.1.*' \
+    'matplotlib-base=3.2.*' \
     'numba=0.48.*' \
     'numexpr=2.7.*' \
     'pandas=1.0.*' \
@@ -53,8 +53,8 @@ RUN conda install --quiet --yes \
     jupyter labextension install @jupyter-widgets/jupyterlab-manager@^2.0.0 --no-build && \
     jupyter labextension install @bokeh/jupyter_bokeh@^2.0.0 --no-build && \
     jupyter labextension install jupyter-matplotlib@^0.7.2 --no-build && \
-    jupyter lab build && \
-    jupyter lab clean && \
+    jupyter lab build -y && \
+    jupyter lab clean -y && \
     npm cache clean --force && \
     rm -rf /home/$NB_USER/.cache/yarn && \
     rm -rf /home/$NB_USER/.node-gyp && \

test/helpers.py

@@ -87,7 +87,11 @@ class CondaPackageHelper:
     @staticmethod
     def _packages_from_json(env_export):
         """Extract packages and versions from the lines returned by the list of specifications"""
+        #dependencies = filter(lambda x:  isinstance(x, str), json.loads(env_export).get("dependencies"))
         dependencies = json.loads(env_export).get("dependencies")
+        # Filtering packages installed through pip in this case it's a dict {'pip': ['toree==0.3.0']}
+        # Since we only manage packages installed through conda here
+        dependencies = filter(lambda x:  isinstance(x, str), dependencies)
         packages_dict = dict()
         for split in map(lambda x: x.split("=", 1), dependencies):
             # default values