| Branch | Status |
|---|---|
| main |   |
| develop |   |
Table of Contents
This is the repository for the KBase Narrative Interface. The KBase Narrative Interface builds on the Jupyter Notebook and contains elements to interact with various KBase tools and data stores.
This document contains links to various documentation in the docs directory, with a brief description of each.
If you want to use the KBase Narrative Interface, just point your browser at https://narrative.kbase.us, make a free account, and jump in. This repo is only for people who wish to contribute to the development of the interface.
Short version: Requires the following:
- Python 3.6+
- Anaconda/Miniconda as an environment manager (https://www.anaconda.com/)
- Node.js (16.x+, Latest LTS recommended)
This is the recommended method of installation!
git clone https://github.com/kbase/narrative
cd narrative
conda create -n my_narrative_environment
conda activate my_narrative_environment
./scripts/install_narrative.sh
kbase-narrative
If the previous instructions do not work, try
# source ~/anaconda3/bin/activate or wherever you have python installed
conda create -n my_narrative_environment
conda activate my_narrative_environment
sh scripts/install_narrative.sh
# scripts/install_narrative.sh
kbase-narrative
This process installs lots of requirements of specific versions and may clobber things on your PYTHONPATH.
git clone https://github.com/kbase/narrative
cd narrative
./scripts/install_narrative.sh
kbase-narrative
Long version: Local Narrative setup
In progress!
The Narrative sits on top of the Jupyter Notebook, so most of its architecture is a mirror of that. However, the Narrative's interaction with other KBase elements - namely the data stores and job running services - merits its own description. This will be ongoing (and evolving!), but a brief description of how a job gets run and registered is available here:
When deployed in production, the Narrative Interface is compiled into a Docker container. When a user logs in, they have their own instance provisioned for them through an Nginx proxy, which provides a temporary server-side Narrative environment only for that user. Any changes made to a Narrative get saved as part of KBase data stores, but any changes to the file system or the Narrative kernel (e.g. local variables) are lost when the user logs out and their Docker instance gets shut down.
For general testing instructions and guidance refer to docs/testing.md. For information about headless browser testing refer to docs/HeadlessTesting.md.
A number of commands are available to automate parts of the development process. See docs/developer/running_tasks.md for more information.
The narrative repo uses the NPM module Husky to install and execute git hooks. Please ensure that any other git hook packages (e.g. the python pre-commit package) have been fully uninstalled first. If you run npm install, or use the standard install process, husky and the husky git hooks will be installed. If you are adding the module to an existing npm installation, you will need to run
npx husky installto enable git hooks.
The .husky directory contains the hooks that are run. See the package.json file and docs/developer/running_tasks.md for more information on the npm scripts that are executed, and the Husky documentation for details on how to add or edit hooks.
Husky hooks can be skipped by setting the environment variable:
HUSKY=0
Follow the gitflow directions located at docs/git-workflow.md to submit code to this repository.