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