Source of allencellmodeling.github.io

To add and display a new notebook as a page on the site:

Things that you do to the notebook

• Make sure you have the figures sized as you want them to appear
• Add 'raw nbconvert' cell at the start of the notebook declaring the layout as post and the title of the post. This YAML front matter will be used to render the notebook's information on the index page, e.g.

---
title: Publishing a Jupyter-notebook
summary: A short explanation to appear on the index page. 
---

• Title the .ipynb file in the format YEAR-MONTH-DAY-title so that it becomes, e.g., 2017-08-17-test_notebook.ipynb
• Set the $NOTEBOOKNAME bash variable as in NOTEBOOKNAME=2017-08-17-test_notebook.ipynb

Things you do to the repo

• Pull from master
• Put the .ipynb file in the _posts directory
• Convert the notebook to a markdown file using

jupyter nbconvert --to markdown --NbConvertApp.output_files_dir='../assets/nbfiles/{notebook_name}' --FilesWriter.relpath='({{ site.url }}/assets/nbfiles/' $NOTEBOOKNAME

• This creates a markdown file like 2017-07-17-test_notebook.md and the related images in ../assets/nbfiles/2017-07-17-test_notebook_files
• Move the .ipynb to ../assets/notebooks

The conversion and moving processes are scriptable for future improvement.