I ran into an issue when trying to get this to work with a NFS server which I did not have direct control over (EFS).  As part of the PersistentVolumeClaim, there is no easy way to set the UID and GID of the created directory.on the networked FS.

My only concern with this chown is that some user out there might be running jupyterhub in an odd configuration where $NB_USER is not supposed to have these exact permissions on the storage.  I think this is quite unlikely, but it is worth mentioning. 

I chronicled my experiences with working around this issue and setting up z2jh on EFS in https://github.com/jupyterhub/zero-to-jupyterhub-k8s/issues/421 with @yuvipanda.

Add /bin to sudo secure_path

Update Dockerfile to install r-hexbin

Fixes #532

Append /opt/conda/bin to the sudo secure_path

Retain behavior when su was used instead

 Fix for granting SUDO to jovyan user and run bash commands.

* Refactor to use sudo to become jovyna when the
  container starts as root
* Retain all environment variables when becoming
  jovyan
* Handle start.sh without additional commands when
  launching a container as NB_USER too

Please refer to alias, in bottom of commit.

> dbn
Execute the command: jupyter notebook

> dbn bash
jovyan@eedcc93a837d:~$

> dbn start.sh
Execute the command:
exit

> dbnr
Set username to: jovyan
usermod: no changes
Set jovyan GID to: 100
Execute the command: jupyter notebook
Running as root is not recommended. Use --allow-root to bypass.
exit

> dbnr bash
root@893cb78b8c9c:~#

> dbnr start.sh
Set username to: jovyan
usermod: no changes
Set jovyan GID to: 100
Execute the command:
No arguments supplied
HOSTNAME=d45c52e788b7
TERM=xterm
SHELL=/bin/bash
NB_USER=jovyan
LC_ALL=en_US.UTF-8
PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
_=/usr/bin/env
MINICONDA_VERSION=4.3.30
PWD=/home/jovyan
LANG=en_US.UTF-8
HOME=/home/jovyan
SHLVL=2
LANGUAGE=en_US.UTF-8
no_proxy=*.local, 169.254/16
DEBIAN_FRONTEND=noninteractive
CONDA_DIR=/opt/conda
NB_GID=100
NB_UID=1000
root@d45c52e788b7:~#

> dbnrs
Set username to: jovyan
usermod: no changes
Set jovyan GID to: 100
Granting jovyan sudo access
Execute the command: jupyter notebook
Copy/paste this URL into your browser when you connect for the first time, ....

> dbnrs bash
root@f293dce949db:~#

> dbnrs start.sh
Set username to: jovyan
usermod: no changes
Set jovyan GID to: 100
Granting jovyan sudo access
Execute the command:
No arguments supplied
HOSTNAME=d0cd57ea32e2
SHELL=/bin/bash
TERM=xterm
LC_ALL=en_US.UTF-8
USER=jovyan
SUDO_USER=root
SUDO_UID=0
USERNAME=jovyan
MAIL=/var/mail/jovyan
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin
PWD=/home/jovyan
LANG=en_US.UTF-8
SHLVL=1
SUDO_COMMAND=/bin/bash -c env; PATH=$PATH; bash
HOME=/home/jovyan
LANGUAGE=en_US.UTF-8
LOGNAME=jovyan
SUDO_GID=0
_=/usr/bin/env
jovyan@d0cd57ea32e2:~$

> dbns
Container must be run as root to grant sudo permissions
Execute the command: jupyter notebook
Copy/paste this URL in..

> dbns bash
jovyan@ce5c2491fa32:~$

> dbns start.sh
Container must be run as root to grant sudo permissions
Execute the command:
exit

###### Build user setup
docker build -t $USER/base-notebook -f Dockerfile .

# Normal, dbn: docker-base-notebook
alias dbn='docker run -ti --rm -p 8888:8888 -v "$PWD":/home/jovyan/work --name base-notebook $USER/base-notebook'
# Root, dbnr: dbn with root
alias dbnr='docker run -ti --rm -p 8888:8888 --user root -v "$PWD":/home/jovyan/work --name base-notebook $USER/base-notebook'
# Jovyan SUDO, dbnr: dbn with SUDO for jovyan
alias dbnrs='docker run -ti --rm -p 8888:8888 --user root -e GRANT_SUDO=yes -v "$PWD":/home/jovyan/work --name base-notebook $USER/base-notebook'
# Root, fail to sudo for jovyan.
alias dbns='docker run -ti --rm -p 8888:8888 -e GRANT_SUDO=yes -v "$PWD":/home/jovyan/work --name base-notebook $USER/base-notebook'

Test image builded with:
> docker build -t $USER/base-notebook -f Dockerfile .

> docker run -ti --rm -p 8888:8888 -e GRANT_SUDO=yes --user root jupyter/base-notebook:033056e6 bash
root@84db8819258d:~#

docker run -ti --rm -p 8888:8888 -e GRANT_SUDO=yes --user root $USER/base-notebook bash
> root@c23f1fd7d279:~#

> docker run -ti --rm -p 8888:8888 -e GRANT_SUDO=yes --user root jupyter/base-notebook:033056e6 start.sh
Set username to: jovyan
usermod: no changes
Set jovyan GID to: 100
Granting jovyan sudo access
Execute the command:
HOSTNAME=a231202e6d1a
TERM=xterm
SHELL=/bin/bash
NB_USER=jovyan
LC_ALL=en_US.UTF-8
USER=jovyan
MAIL=/var/mail/jovyan
PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
MINICONDA_VERSION=4.3.30
PWD=/home/jovyan
LANG=en_US.UTF-8
GRANT_SUDO=yes
HOME=/home/jovyan
SHLVL=1
LANGUAGE=en_US.UTF-8
no_proxy=*.local, 169.254/16
LOGNAME=jovyan
DEBIAN_FRONTEND=noninteractive
CONDA_DIR=/opt/conda
NB_GID=100
NB_UID=1000
_=/usr/bin/env
tlinnet@linmac:base-notebook$

> docker run -ti --rm -p 8888:8888 -e GRANT_SUDO=yes --user root $USER/base-notebook start.sh
Set username to: jovyan
usermod: no changes
Set jovyan GID to: 100
Granting jovyan sudo access
Execute the command:
No arguments supplied
HOSTNAME=364e5fc77224
SHELL=/bin/bash
TERM=xterm
LC_ALL=en_US.UTF-8
USER=jovyan
SUDO_USER=root
SUDO_UID=0
USERNAME=jovyan
MAIL=/var/mail/jovyan
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin
PWD=/home/jovyan
LANG=en_US.UTF-8
SHLVL=1
SUDO_COMMAND=/bin/bash -c env; PATH=$PATH; bash
HOME=/home/jovyan
LANGUAGE=en_US.UTF-8
LOGNAME=jovyan
SUDO_GID=0
_=/usr/bin/env
jovyan@364e5fc77224:~$

> docker run -ti --rm -p 8888:8888 -e GRANT_SUDO=yes --user root jupyter/base-notebook:033056e6 start.sh echo hello
tlinnet@linmac:base-notebook$ docker run -ti --rm -p 8888:8888 -e GRANT_SUDO=yes --user root jupyter/base-notebook:033056e6 start.sh echo hello
Set username to: jovyan
usermod: no changes
Set jovyan GID to: 100
Granting jovyan sudo access
Execute the command: echo hello
hello
tlinnet@linmac:base-notebook$

> docker run -ti --rm -p 8888:8888 -e GRANT_SUDO=yes --user root $USER/base-notebook start.sh echo hello
Set username to: jovyan
usermod: no changes
Set jovyan GID to: 100
Granting jovyan sudo access
Execute the command: echo hello
hello
tlinnet@linmac:base-notebook$

Update Julia version in README to match script

Julia v0.6.2

pytest integration tests

Make local test setup easier

Not really testing a docker-stacks feature, only
that docker host permissions work

julia 0.6.0