From 7b0290f3dcc7fd99aabd050746a2342d66a7a553 Mon Sep 17 00:00:00 2001
From: David Perez-Suarez <d.perez-suarez@ucl.ac.uk>
Date: Tue, 1 Sep 2020 21:13:17 +0100
Subject: [PATCH 1/3] Adds a new buildscript for miniconda + jupyterhub

---
 miniconda-jupyterhub-4.8.3_install | 53 ++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)
 create mode 100644 miniconda-jupyterhub-4.8.3_install

diff --git a/miniconda-jupyterhub-4.8.3_install b/miniconda-jupyterhub-4.8.3_install
new file mode 100644
index 00000000..8e83ba57
--- /dev/null
+++ b/miniconda-jupyterhub-4.8.3_install
@@ -0,0 +1,53 @@
+#!/usr/bin/env bash
+
+###############################################
+# Installing miniconda and jupyterhub
+#
+# by Owain Kenway, 2018, David PS, 2020
+#
+set -e
+
+for i in ${includes_dir:=$(dirname $0 2>/dev/null)/includes}/{module_maker,require}_inc.sh; do . $i; done
+
+require gcc-libs/4.9.2
+
+NAME=${NAME:-miniconda-jhub}
+VERSION=${VERSION:-4.8.3}
+INSTALL_PREFIX=${INSTALL_PREFIX:-/shared/ucl/apps/$NAME/$VERSION/$COMPILER_TAG}
+SHA256=${SHA256:-879457af6a0bf5b34b48c12de31d4df0ee2f06a8e68768e5758c3293b2daf688}
+
+SRC_ARCHIVE=${SRC_ARCHIVE:-https://repo.anaconda.com/miniconda/Miniconda3-py38_${VERSION}-Linux-x86_64.sh}
+
+
+mkdir -p /dev/shm/$(whoami)/${NAME}
+
+temp_dir=$(mktemp -d -p /dev/shm/$(whoami)/${NAME})
+
+cd $temp_dir
+
+wget $SRC_ARCHIVE
+archive=$(basename "${SRC_ARCHIVE}")
+
+sha256sum -c <<< "$SHA256 $archive"
+
+bash "Miniconda3-py38_${VERSION}-Linux-x86_64.sh" -b -p ${INSTALL_PREFIX} -f
+
+
+# Basic conda installation, now to install JupyterHub
+# Load installed conda environment
+
+
+# Install jupyterhub
+oldpath=$PATH
+PATH=$INSTALL_PREFIX/bin:$PATH
+conda install -y -c conda-forge jupyterhub  # installs jupyterhub and proxy
+conda install -y jupyterlab notebook  # needed if running the notebook servers locally
+# Extensions - git for jupyterlab
+conda install -y -c conda-forge jupyterlab-git
+jupyter lab build
+
+
+PATH=$oldpath
+
+cd
+rm -rf $temp_dir

From 445f0a231433e8043766af8cff8cf607529f3bce Mon Sep 17 00:00:00 2001
From: David Perez-Suarez <d.perez-suarez@ucl.ac.uk>
Date: Tue, 1 Sep 2020 21:13:42 +0100
Subject: [PATCH 2/3] Adds VSCode to jupyterhub via a separate environment

---
 miniconda-jupyterhub-4.8.3_install | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/miniconda-jupyterhub-4.8.3_install b/miniconda-jupyterhub-4.8.3_install
index 8e83ba57..d4a2d4e3 100644
--- a/miniconda-jupyterhub-4.8.3_install
+++ b/miniconda-jupyterhub-4.8.3_install
@@ -46,6 +46,17 @@ conda install -y jupyterlab notebook  # needed if running the notebook servers l
 conda install -y -c conda-forge jupyterlab-git
 jupyter lab build
 
+# Extensions - VS Code via jupyter-lab
+conda install -y -c conda-forge jupyter-server-proxy jupyter-vscode-proxy # VS code interface
+jupyter labextension install @jupyterlab/server-proxy # It's not being installed from conda?
+jupyter lab build
+
+# creating it in its own environment:
+conda create -n jhubcode -c conda-forge code-server -y
+sed -i "2iCONDA_PREFIX=/shared/ucl/apps/miniconda-jhub/4.8.3/envs/jhubcode" /shared/ucl/apps/miniconda-jhub/4.8.3/envs/jhubcode/bin/code-server
+sed -i 's|node|${CONDA_PREFIX}/bin/node|' /shared/ucl/apps/miniconda-jhub/4.8.3/envs/jhubcode/bin/code-server
+ln -s  /shared/ucl/apps/miniconda-jhub/4.8.3/envs/jhubcode/bin/code-server /shared/ucl/apps/miniconda-jhub/4.8.3/bin/code-server
+code-server --install-extension ms-python.pythonnp
 
 PATH=$oldpath
 

From bf98b302ebffbded742dceb117d8bf84bc05731e Mon Sep 17 00:00:00 2001
From: David Perez-Suarez <d.perez-suarez@ucl.ac.uk>
Date: Wed, 2 Sep 2020 14:34:49 +0100
Subject: [PATCH 3/3] =?UTF-8?q?=F0=9F=93=A6=20Includes=20a=20list=20of=20p?=
 =?UTF-8?q?ackages=20that=20may=20be=20needed=20for=20teaching?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 miniconda-jupyterhub-4.8.3_install | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/miniconda-jupyterhub-4.8.3_install b/miniconda-jupyterhub-4.8.3_install
index d4a2d4e3..79394dd5 100644
--- a/miniconda-jupyterhub-4.8.3_install
+++ b/miniconda-jupyterhub-4.8.3_install
@@ -58,6 +58,34 @@ sed -i 's|node|${CONDA_PREFIX}/bin/node|' /shared/ucl/apps/miniconda-jhub/4.8.3/
 ln -s  /shared/ucl/apps/miniconda-jhub/4.8.3/envs/jhubcode/bin/code-server /shared/ucl/apps/miniconda-jhub/4.8.3/bin/code-server
 code-server --install-extension ms-python.pythonnp
 
+# package dependencies
+packages=(
+    # Scientific stack
+    numpy numpydoc scipy pandas pandas-datareader pandasql
+    # python tooling
+    pip setuptools sphinx requests
+    # plotting
+    matplotlib bokeh plotly
+    # domain libraries
+    astropy biopython nltk proj4 scikit-image scikit-learn statsmodels sympy pytorch tensorflow pywavelets gdal
+    # Performance and distribution
+    cython dask dask-core dask-glm dask-ml numba
+    # Files and db
+    dill h5py hdf5 pytables pyyaml xarray xlsxwriter sqlalchemy sqlalchemy-utils
+    # tooling
+    flake8 isort memory_profiler python-language-server rope typing typing_extensions yapf tox
+    # testing
+    pytest pytest-arraydiff pytest-astropy pytest-asyncio pytest-cov pytest-doctestplus pytest-mock
+    pytest-pep8 pytest-runner pytest-timeout pytest-xdist mock
+    # conda related and notebooks
+    nb_conda_kernels
+    # Teaching
+    nbgrader
+)
+
+conda install -y -c conda-forge "${packages[@]}"
+
+
 PATH=$oldpath
 
 cd