Merge remote-tracking branch 'upstream/master'

base-notebook/Dockerfile

@@ -60,16 +60,18 @@ RUN mkdir /home/$NB_USER/work && \
     fix-permissions /home/$NB_USER
 
 # Install conda as jovyan and check the md5 sum provided on the download site
-ENV MINICONDA_VERSION 4.5.11
+ENV MINICONDA_VERSION=4.5.12 \
+    CONDA_VERSION=4.6.7
+
 RUN cd /tmp && \
     wget --quiet https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \
-    echo "e1045ee415162f944b6aebfe560b8fee *Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" | md5sum -c - && \
+    echo "866ae9dff53ad0874e1d1a60b1ad1ef8 *Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" | md5sum -c - && \
     /bin/bash Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh -f -b -p $CONDA_DIR && \
     rm Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \
     $CONDA_DIR/bin/conda config --system --prepend channels conda-forge && \
     $CONDA_DIR/bin/conda config --system --set auto_update_conda false && \
     $CONDA_DIR/bin/conda config --system --set show_channel_urls true && \
-    $CONDA_DIR/bin/conda install --quiet --yes conda="${MINICONDA_VERSION%.*}.*" && \
+    $CONDA_DIR/bin/conda install --quiet --yes conda="${CONDA_VERSION%.*}.*" && \
     $CONDA_DIR/bin/conda update --all --quiet --yes && \
     conda clean -tipsy && \
     rm -rf /home/$NB_USER/.cache/yarn && \
@@ -90,7 +92,7 @@ RUN conda install --quiet --yes 'tini=0.18.0' && \
 # Do all this in a single RUN command to avoid duplicating all of the
 # files across image layers when the permissions change
 RUN conda install --quiet --yes \
-    'notebook=5.7.2' \
+    'notebook=5.7.5' \
     'jupyterhub=0.9.4' \
     'jupyterlab=0.35.4' && \
     conda clean -tipsy && \

base-notebook/start.sh

@@ -102,7 +102,7 @@ if [ $(id -u) == 0 ] ; then
     # the environment preserved
     run-hooks /usr/local/bin/before-notebook.d
     echo "Executing the command: ${cmd[@]}"
-    exec sudo -E -H -u $NB_USER PATH=$PATH XDG_CACHE_HOME=/home/$NB_USER/.cache PYTHONPATH=$PYTHONPATH "${cmd[@]}"
+    exec sudo -E -H -u $NB_USER PATH=$PATH XDG_CACHE_HOME=/home/$NB_USER/.cache PYTHONPATH=${PYTHONPATH:-} "${cmd[@]}"
 else
     if [[ "$NB_UID" == "$(id -u jovyan)" && "$NB_GID" == "$(id -g jovyan)" ]]; then
         # User is not attempting to override user/group via environment

scipy-notebook/Dockerfile

@@ -20,27 +20,28 @@ USER $NB_UID
 RUN conda install --quiet --yes \
     'conda-forge::blas=*=openblas' \
     'ipywidgets=7.4*' \
-    'pandas=0.23*' \
+    'pandas=0.24*' \
     'numexpr=2.6*' \
-    'matplotlib=2.2*' \
-    'scipy=1.1*' \
+    'matplotlib=3.0*' \
+    'scipy=1.2*' \
     'seaborn=0.9*' \
     'scikit-learn=0.20*' \
     'scikit-image=0.14*' \
-    'sympy=1.1*' \
-    'cython=0.28*' \
+    'sympy=1.3*' \
+    'cython=0.29*' \
     'patsy=0.5*' \
     'statsmodels=0.9*' \
-    'cloudpickle=0.5*' \
+    'cloudpickle=0.8*' \
     'dill=0.2*' \
-    'numba=0.38*' \
-    'bokeh=0.13*' \
-    'sqlalchemy=1.2*' \
+    'dask=1.1.*' \
+    'numba=0.42*' \
+    'bokeh=1.0*' \
+    'sqlalchemy=1.3*' \
     'hdf5=1.10*' \
-    'h5py=2.7*' \
+    'h5py=2.9*' \
     'vincent=0.4.*' \
-    'beautifulsoup4=4.6.*' \
-    'protobuf=3.*' \
+    'beautifulsoup4=4.7.*' \
+    'protobuf=3.7.*' \
     'xlrd'  && \
     conda remove --quiet --yes --force qt pyqt && \
     conda clean -tipsy && \