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https://github.com/aaren/notedown

Markdown <=> IPython Notebook
https://github.com/aaren/notedown

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Markdown <=> IPython Notebook

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README 

        
*Python 2/3 and IPython 4 / Jupyter compatible!*  



Convert IPython Notebooks to markdown (and back)

------------------------------------------------



[notedown] is a simple tool to create [IPython notebooks][ipython]

from markdown (and r-markdown).



[ipython]: http://www.ipython.org/notebook

[notedown]: http://github.com/aaren/notedown



`notedown` separates your markdown into code and not code. Code

blocks (fenced or indented) go into input cells, everything else

goes into markdown cells.



Usage:



    notedown input.md > output.ipynb



Installation:



    pip install notedown



or the latest on github:



    pip install https://github.com/aaren/notedown/tarball/master



### Conversion to markdown



Convert a notebook into markdown, stripping all outputs:



    notedown input.ipynb --to markdown --strip > output.md



Convert a notebook into markdown, with output JSON intact:



    notedown input.ipynb --to markdown > output_with_outputs.md



The outputs are placed as JSON in a code-block immediately after the

corresponding input code-block. `notedown` understands this

convention as well, so it is possible to convert this

markdown-with-json back into a notebook.



This means it is possible to edit markdown, convert to notebook,

play around a bit and convert back to markdown.



NB: currently, notebook and cell metadata is not preserved in the

conversion.



Strip the output cells from markdown:



    notedown with_output_cells.md --to markdown --strip > no_output_cells.md



### Running an IPython Notebook



    notedown notebook.md --run > executed_notebook.ipynb



### Editing in the browser *(new!)*



You can configure IPython / Jupyter to seamlessly use markdown as its storage

format. Add the following to your config file:



    c.NotebookApp.contents_manager_class = 'notedown.NotedownContentsManager'



Now you can edit your markdown files in the browser, execute code,

create plots - all stored in markdown!



For Jupyter, your config file is `jupyter_notebook_config.py` in `~/.jupyter`.

For IPython your config is `ipython_notebook_config.py` in your ipython

profile (probably `~/.ipython/profile_default`):



### Editing in vim



There is a [vim plugin][vimplug] that allows editing notebooks (ipynb files)

directly in vim. They will be automatically converted to markdown on opening the

file, and converted back to the original json format on writing.



[vimplug]: https://github.com/goerz/ipynb_notedown.vim



### R-markdown



You can use `notedown` to convert r-markdown as well. We just need

to tell `notedown` to use [knitr] to convert the r-markdown.

This requires that you have R installed with [knitr].



Convert r-markdown into markdown:



    notedown input.Rmd --to markdown --knit > output.md



Convert r-markdown into an IPython notebook:



    notedown input.Rmd --knit > output.ipynb



- `--rmagic` will add `%load_ext rpy2.ipython` at the start of the

  notebook, allowing you to execute code cells using the rmagic

  extension (requires [rpy2]). notedown does the appropriate `%R`

  cell magic automatically.



[knitr]: yihui.name/knitr

[rpy2]: http://rpy.sourceforge.net/



### Magic



Fenced code blocks annotated with a language other than python are

read into cells using IPython's `%%` [cell magic][].



[cell magic]: http://nbviewer.ipython.org/github/ipython/ipython/blob/1.x/examples/notebooks/Cell%20Magics.ipynb



You can disable this with `--nomagic`.



- `--pre` lets you add arbitrary code to the start of the notebook.

  e.g. `notedown file.md --pre '%matplotlib inline' 'import numpy as np'`



### How do I put a literal code block in my markdown?



By using the `--match` argument. `notedown` defaults to converting

*all* code-blocks into code-cells. This behaviour can be changed by

giving a different argument to `--match`:



- `--match=all`: convert all code blocks (the default)

- `--match=fenced`: only convert fenced code blocks

- `--match=language`: only convert fenced code blocks with

  'language' as the syntax specifier (or any member of the block

  attributes)

- `--match=strict`: only convert code blocks with Pandoc style

  attributes containing 'python' and 'input' as classes. i.e. code

  blocks must look like



        ```{.python .input}

        code

        ```



### This isn't very interactive!



Try editing the markdown in the IPython Notebook using the

`NotedownContentsManager` (see above).



You can get an interactive ipython session in vim by using

[vim-ipython], which allows you to connect to a running ipython

kernel. You can send code from vim to ipython and get code

completion from the running kernel. Try it!



[vim-ipython]: http://www.github.com/ivanov/vim-ipython



### Where's my syntax highlighting?!



Try using either [vim-markdown] or [vim-pandoc]. Both are clever

enough to highlight code in markdown.



[vim-markdown]: https://github.com/tpope/vim-markdown

[vim-pandoc]: https://github.com/vim-pandoc/vim-pandoc



### Rendering outputs in markdown



This is experimental!



Convert a notebook into markdown, rendering cell outputs as native

markdown elements:



    notedown input.ipynb --render



This means that e.g. png outputs become `![](data-uri)` images and

that text is placed in the document.



Of course, you can use this in conjuntion with runipy to produce

markdown-with-code-and-figures from markdown-with-code:



    notedown input.md --run --render > output.md



Not a notebook in sight!



The `--render` flag forces the output format to markdown.



### TODO



- [x] Python 3 support

- [x] unicode support

- [x] IPython 3 support

- [x] IPython 4 (Jupyter) support

- [ ] Allow kernel specification