notedown 1.2.0

Convert markdown to IPython notebook.

notedown is a simple tool to create IPython notebooks from markdown and r-markdown.

It is really simple and 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

Why?

Save yourself from the indignity of writing text in the browser!

There might be more reasons, but that was the main one for me.

Conversion to markdown

Convert a notebook into markdown, with outputs intact:

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

Convert a notebook into markdown, stripping all outputs:

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

The outputs are placed as JSON in a code-block immediately after the corresponding input code-block. notedown understands this format as well, so it is possible to roundtrip notebooks through json and markdown formats.

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

You can run notebooks non-interactively from the command line using runipy:

pip install runipy
runipy your_notebook.ipynb

runipy can be used with notedown to turn markdown into an executed notebook:

notedown notebook.md --execute > executed_notebook.ipynb

Magic

Fenced code blocks annotated with a language other than python are read into cells using IPython’s %% cell magic.

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'

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 rmagic at the start of the notebook, allowing you to execute code cells using the rmagic extension. notedown does the appropriate %R cell magic automatically.

I can’t put a literal code block in my markdown!

Not right now, no. Notedown isn’t very clever.

This isn’t very interactive!

No, it isn’t. Notedown takes markdown and turns it into an IPython notebook.

You can set up a pseudo-interactive loop in Vim by calling

:!notedown % > out.ipynb

and viewing the result in the browser with

ipython notebook out.ipynb

You’ll get far better interactivity 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!

Here are some mappings for your vimrc to make this pleasant:

" Very useful mappings to be used with markdown and ipython
" search and select contents of fenced code blocks using <leader>f
nnoremap <leader>f /\v(\_^```python\n)@<=(\_.{-})(\n`{3}\_$)@=<CR>v//e<CR>
" goto the start of the current fenced code block with [b
" (see :help search)
nnoremap [b :call search('\n```python', 'b')<CR>
" select current code block with <leader>b
" TODO: assumes <leader>==, use <leader>f instead of ,f
" TODO: cancel search highlighting
nmap <leader>b [b,f
" (or could do [b0v/\n```)
" send current code block to ipython with <leader>p
nmap <leader>p ,b<C-s>

Where’s my syntax highlighting?!

You can syntax highlight python code contained in fenced code blocks with this command (put it in your vimrc):

function! HiPy ()
    let b:current_syntax=''
    unlet b:current_syntax
    syntax include @py syntax/python.vim
    " github flavoured markdown (code blocks fenced with ```)
    syntax region gfmpythoncode keepend start="^```py.*$" end=/^\s*```$\n/ contains=@py
endfunction

" enable highlighting of fenced python code with <leader>h
map <leader>h :call HiPy ()<CR>

BONUS! Of course you can do the same for latex display and inline maths:

syntax include syntax/tex.vim
" display maths with $$ ... $$
syn region texdisplaymaths start="\$\$" end="\$\$" skip="\\\$" contains=@texMathZoneGroup
" inline maths with $ ... $
" start is a $ not preceded by another $        - \(\$\)\@<!\$
" and not preceded by a \ (concat)              - \(\$\)\@<!\&\(\\\)\@<!\$
" and not followed by another $                 - \$\(\$\)\@!
" ending in a $ not preceded by a \             - \((\$\)\@<!\$
" skipping any \$                               - \\\$
" see :help \@<! for more
syn region texinlinemaths start="\(\$\)\@<!\&\(\\\)\@<!\$\(\$\)\@!" end="\(\$\)\@<!\$" skip="\\\$" contains=@texMathZoneGroup
" restriction is that you can't have something like \$$maths$ - there
" has to be a space after all of the \$ (literal $)

TODO

• [x] support more markdowns

• [ ] allow other cell types?

• [x] allow different language code cells (using %%lang magic)

• [x] allow code attributes? pass to cell creator?

• [x] code block format agnostic (fenced / indented)