From 475ab49f82f88bd79a08ed3d0196ec0cca8b9180 Mon Sep 17 00:00:00 2001
From: Brett Randall <javabrett@gmail.com>
Date: Wed, 20 Feb 2019 14:46:51 +1100
Subject: [PATCH 1/5] Made variable reference PYTHONPATH safe in case of set
 -eu.

Signed-off-by: Brett Randall <javabrett@gmail.com>
---
 base-notebook/start.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/base-notebook/start.sh b/base-notebook/start.sh
index 799d08dd..b9067acd 100755
--- a/base-notebook/start.sh
+++ b/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

From caf8c5c2417b1f42373c9f6e23a846b0720f594f Mon Sep 17 00:00:00 2001
From: John Kirkham <kirkhamj@janelia.hhmi.org>
Date: Thu, 21 Feb 2019 22:47:03 -0500
Subject: [PATCH 2/5] Require Dask 1.1 in the scipy-notebook

---
 scipy-notebook/Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scipy-notebook/Dockerfile b/scipy-notebook/Dockerfile
index f935debb..ab1c8f15 100644
--- a/scipy-notebook/Dockerfile
+++ b/scipy-notebook/Dockerfile
@@ -33,6 +33,7 @@ RUN conda install --quiet --yes \
     'statsmodels=0.9*' \
     'cloudpickle=0.5*' \
     'dill=0.2*' \
+    'dask=1.1.*' \
     'numba=0.38*' \
     'bokeh=0.13*' \
     'sqlalchemy=1.2*' \

From dd03a7e5cd7e0635dc82b064a9d03e09d5e37a2c Mon Sep 17 00:00:00 2001
From: Min RK <benjaminrk@gmail.com>
Date: Wed, 6 Mar 2019 13:20:18 +0100
Subject: [PATCH 3/5] notebook 5.7.5

and conda to 4.6.7
---
 base-notebook/Dockerfile | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/base-notebook/Dockerfile b/base-notebook/Dockerfile
index 04fc63b8..82c929b3 100644
--- a/base-notebook/Dockerfile
+++ b/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 && \

From 313ceb794c1f4820ea4cac5df55ff1de959affcb Mon Sep 17 00:00:00 2001
From: Peter Parente <ParenteP@valassis.com>
Date: Thu, 7 Mar 2019 20:33:31 -0500
Subject: [PATCH 4/5] Update packages in scipy-notebook

---
 scipy-notebook/Dockerfile | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/scipy-notebook/Dockerfile b/scipy-notebook/Dockerfile
index ab1c8f15..72ee94fa 100644
--- a/scipy-notebook/Dockerfile
+++ b/scipy-notebook/Dockerfile
@@ -20,28 +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=3.3*' \
+    '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*' \
     'dask=1.1.*' \
-    'numba=0.38*' \
-    'bokeh=0.13*' \
-    'sqlalchemy=1.2*' \
+    '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 && \

From a772c9ab6bbd88610410ae070b49e314235db55f Mon Sep 17 00:00:00 2001
From: Peter Parente <ParenteP@valassis.com>
Date: Thu, 7 Mar 2019 21:09:54 -0500
Subject: [PATCH 5/5] Fix matplotlib version typo

Getting ahead of myself here ...
---
 scipy-notebook/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scipy-notebook/Dockerfile b/scipy-notebook/Dockerfile
index 72ee94fa..8756743a 100644
--- a/scipy-notebook/Dockerfile
+++ b/scipy-notebook/Dockerfile
@@ -22,7 +22,7 @@ RUN conda install --quiet --yes \
     'ipywidgets=7.4*' \
     'pandas=0.24*' \
     'numexpr=2.6*' \
-    'matplotlib=3.3*' \
+    'matplotlib=3.0*' \
     'scipy=1.2*' \
     'seaborn=0.9*' \
     'scikit-learn=0.20*' \