toolstart-jupyter

Template repository for a nanoHUB tool that uses a Jupyter notebook frontend.

Getting Started

The following procedure describes how to get a basic jupyter notebook "tool" up and running on nanoHUB. It is assumed you are a registered user and developer on nanoHUB and intend to install and publish your notebook content there. Refer to the whypublish links below for details on why and how to publish content on nanoHUB.

1. Create a new GitHub repository and select toolsart-jupyter as a template.
   See: Creating a Repository From a Template
2. Create a new tool page on nanoHUB using the nanoHUB tool creation form

• Set the Repository Host Option to "Host GIT repository on GitHUB"
• Set the Repository Url to your GitHub repo:
  Public URL: https://github.com/yourgithubrepo
  Private URL: ssh://github.com/yourgithubrepo

3. Edit the /middleware/invoke file as follows:

• Determine whether the tool will run as an ordinary notebook or in app mode, adjust the start_jupyter option as needed. See App Mode vs Sequential Notebook below for more details.
• Edit the -T @tool mytool.ipynb part to match the actual name of your notebook.
• Edit the -t mytool \ part to match the "short name" of the tool as created on nanohub via the nanoHUB tool creation form.

App Mode vs Sequential Notebook

Notebooks that are published with the -A option to the start_jupyter command or will launch in in app mode which will cause them to execute in their entirety when launched. This is primarily intended for tools that deploy an ipywidjets/event-based user interface.

Notebooks published without the -A option to the start_jupyter command will deploy ad standard hosted jupyter notebooks that can be executed and edited by the user.

References

https://jupyter.org/
https://nanohub.org
https://nanohub.org/whypublish
https://nanohub.org/whypublish/whypublishhowtostart
https://nanohub.org/whypublish/whypublishdeployjupyter
https://ipywidgets.readthedocs.io/en/latest
https://github.com/hubzero/hublib

start_jupyter options

 $ start_jupyter --help
usage: usage: start_jupyter [-h] [-t] [-c] [-d] [-A] [-T dir] [name]

Start a Jupyter notebook-based tool

positional arguments:
  name        Name of notebook to run.  The terminal and
              dashboard (tree view of files) will de disabled.

              If no name is given, a notebook server will
              be started in the current directory.  Terminal
              and dashboard will be enabled.

optional arguments:
  -h, --help  show this help message and exit.
  -d          Show debug (verbose) output.
  -t          Run as a Tool with no notebook controls.
  -c          Copy instead of link notebook files.
  -A          Run in AppMode.
  -T dir      Search for notebook starting in dir.

invoke_app options*

-A tool arguments
 -c execute command in background
 -C command to execute for starting the tool
 -e environment variable (${VERSION} substituted with $TOOL_VERSION)
 -f No FULLSCREEN
 -p add to path          (${VERSION} substituted with $TOOL_VERSION)
 -r rappture version
 -t tool name
 -T tool root directory
 -u use envionment packages
 -v visualization server version
 -w specify alternate window manager

*source: https://help.hubzero.org/documentation/22/tooldevs/invoke