Big upgrade

- Bump root container version
- Bump  packages of
  - scipy-notebook
  - r-notebook
  - datascience-notebook
- add -y flag to jupyter lab commands in scipy-notebook
- Fix a bug in check outdated packages when packages installed through pip

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*' \
     && \

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

@@ -89,7 +89,9 @@ class CondaPackageHelper:
         """Extract packages and versions from the lines returned by the list of specifications"""
         dependencies = json.loads(env_export).get("dependencies")
         packages_dict = dict()
-        for split in map(lambda x: x.split("=", 1), dependencies):
+        for split in map(lambda x: x.split("=", 1) if isinstance(x, str) else None, dependencies):
+            if split is None:
+                break
             # default values
             package = split[0]
             version = set()