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A workflow for creating and editing publication ready scientific reports, from one or more Jupyter Notebooks

Project description

Project: https://github.com/chrisjsewell/ipypublish

Webpage: https://chrisjsewell.github.io/ipypublish

https://travis-ci.org/chrisjsewell/ipypublish.svg?branch=master

A workflow for creating and editing publication ready scientific reports and presentations, from one or more Jupyter Notebooks, without leaving the browser!

https://github.com/chrisjsewell/ipypublish/raw/master/example_workflow.gif

For an example of the potential input/output, see Example.ipynb , Example.pdf, Example.html and Example.slides.html.

Design Philosophy

In essence, the dream is to have the ultimate hybrid of Jupyter Notebook, WYSIWYG editor (e.g. MS Word) and document preparation system (e.g. TexMaker), being able to:

  • Dynamically (and reproducibly) explore data, run code and output the results
  • Dynamically edit and visualise the basic components of the document (text, math, figures, tables, references, citations, etc).
  • Have precise control over what elements are output to the final document and how they are layed out and typeset.
    • Also be able to output the same source document to different layouts and formats (pdf, html, presentation slides, etc).

Workflow

  1. Create a notebook with some content!
  2. optionally create a .bib file and logo image
  3. Adjust the notebook and cell metadata.
  4. Clone the ipypublish GitHub repository and run the nbpublish.py script for either the specific notebook, or a folder containing multiple notebooks.
  5. A converted folder will be created, into which final .tex .pdf and _viewpdf.html files will be output, named by the notebook or folder input

The default latex template outputs all markdown cells (unless tagged latex_ignore), and then only code and output cells with latex metadata tags. See Example.ipynb, Example.pdf and Example.slides.html for an example of the potential input and output.

See the project site for more info!

Acknowledgements

I took strong influence from:

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