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Replace .ipynb with .md in the IPython Notebook

The goal of ipymd is to replace .ipynb notebook files like:

{
 "cells": [
  {
   "cell_type": "markdown",
   "source": [
    "Here is some Python code:"
   ]
  },
  {
   "cell_type": "code",
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Hello world!\n"
     ]
    }
   ],
   "source": [
    "print(\"Hello world!\")"
   ]
  }
  ...
  ]
}

with:

Here is some Python code:

```python
>>> print("Hello world!")
Hello world!
```

The JSON .ipynb are removed from the equation, and the conversion happens on the fly. The IPython Notebook becomes an interactive Markdown text editor!

A drawback is that you lose prompt numbers and images (for now).

This is useful when you write technical documents, blog posts, books, etc.

image

Installation

  1. Install ipymd:

    To install the latest release version:

    pip install ipymd

    Alternatively, to install the development version:

    pip install git+https://github.com/rossant/ipymd

  2. Optional: To interact with .ipynb files:

    pip install jupyter ipython

    To interact with .odt files:

    pip install git+https://github.com/eea/odfpy

  3. Open your jupyter_notebook_config.py. Here's how to find it:

    jupyter notebook --generate-config  # generate a default config file
jupyter --config-dir  # find out the path to the config file

  4. Add the following in jupyter_notebook_config.py:

    c.NotebookApp.contents_manager_class = 'ipymd.IPymdContentsManager'

  5. Now, you can open .md files in the Notebook.

Why?

IPython Notebook

Pros:

  • Excellent UI for executing code interactively and writing text

Cons:

  • .ipynb not git-friendly
  • Cannot easily edit in a text editor
  • Cannot easily edit on GitHub's web interface

Markdown

Pros:

  • Simple ASCII/Unicode format to write code and text
  • Can easily edit in a text editor
  • Can easily edit on GitHub's web interface
  • Git-friendly

Cons:

  • No UI to execute code interactively

ipymd

All pros of IPython Notebook and Markdown, no cons!

How it works

  • Write in Markdown in document.md

    • Either in a text editor (convenient when working on text)
    • Or in the Notebook (convenient when writing code examples)

  • Markdown cells, code cells and (optionally) notebook metadata are saved in the file

  • Collaborators can work on the Markdown document using GitHub's web interface.

  • By convention, a notebook code cell is equivalent to a Markdown code block with explicit python syntax highlighting:

    >>> print("Hello world")
Hello world

  • Notebook metadata can be specified in YAML inside Jekyll-style front-matter dashes at the beginning of a document:

    ---
kernelspec:
  name: some-non-native-kernel
---

First cell content

    Native kernel metadata will be elided by default: non-python kernels haven't been tested yet, but support is planned.

  • Cell metadata is specified with YAML stream documents with dashes and periods, such as to create slides:

    # Previous slide

---
slideshow:
  slide_type: slide
...

# Some Slide Content

    NOTE: You probably shouldn't use --- to mean an <hr/>: *** could be a suitable substitute.

  • Null metadata (i.e. splitting a markdown cell) can be created with just three dashes. This is useful when adding slideshow notes or skipped cells.

    A cell

---

Another cell

  • The back-and-forth conversion is not strictly the identity function:

    • Extra line breaks in Markdown are discarded
    • Text output and standard output are combined into a single text output (stdout lines first, output lines last)

Caveats

WARNING: use this library at your own risks, backup your data, and version-control your notebooks and Markdown files!

  • Renaming doesn't work yet (issue #4)
  • New notebook doesn't work yet (issue #5)
  • Only nbformat v4 is supported currently (IPython 3.0)

Formats

ipymd uses a modular architecture that lets you define new formats. The following formats are currently implemented, and can be selected by modifying ~/.ipython/profile_<whichever>/ipython_notebook_config.py:

  • IPython notebook (.ipynb)
  • Markdown (.md)
    • c.IPymdContentsManager.format = 'markdown'
  • O'Reilly Atlas (.md with special HTML tags for code and mathematical equations)
    • c.IPymdContentsManager.format = 'atlas'
  • Python (.py): code cells are delimited by double line breaks. Markdown cells = Python comments. [TODO: this doesn't work well, see #28 and #31]
  • Opendocument (.odt). You need to install the development version of odfpy.

You can convert from any supported format to any supported format. This works by converting to an intermediate format that is basically a list of notebook cells.

ipymd cells

An ipymd cell is a Python dictionary with the following fields:

  • cell_type: markdown, code or notebok_metadata (if implemented)
  • input: a string with the code input (code cell only)
  • output: a string with the text output and stdout (code cell only)
  • source: a string containing Markdown markup (markdown cell only)
  • metadata: a dictionary containing cell (or notebook) metadata

Kernel Metadata

By default, notebook metadata for the native kernel (usually python2 or python3) won't be written to markdown. Since ipymd doesn't yet support other kernels, this doesn't matter much, but if you would like to pick a non-native python kernel to be interpreted as the default for ipymd, and store kernelspec and language_info for the other, you can add this to your ipython_notebook_config.py file:

  • c.IPymdContentsManager.default_kernel_name = 'python2'

Or, to always remember all notebook-level metadata:

  • c.IPymdContentsManager.verbose_metadata = True

Customize the Markdown format

You can customize the exact way the notebook is converted from/to Markdown by deriving from BaseMarkdownReader or MarkdownReader (idem with writers). Look at ipymd/formats/markdown.py.

Implement your own format

You can also implement your own format by following these instructions:

  • Create a MyFormatReader class that implements:

    • self.read(contents): yields ipymd cells from a contents string

  • Create a MyFormatWriter class that implements:

    • self.write(cell): append an ipymd cell
      • (optional) self.write_notebook_metadata(cell): write the notebook metadata dictionary
    • self.contents: return the contents as a string

  • To activate this format, call this at Notebook launch time (not in a kernel!), perhaps in your ipython_notebook_config.py:

  from ipymd import format_manager
  format_manager().register(
      name='my_format',
      reader=MyFormatReader,
      writer=MyFormatWriter,
      file_extension='.md',  # or anything else
      file_type='text',  # or JSON
  )
  • Now you can convert contents: ipymd.convert(contents, from_='notebook', to='my_format') or any other combination.

Contributing a new ipymd format

  • To further integrate your format in ipymd, create a ipymd/formats/my_format.py file.
  • Put your reader and writer class in there, as well as a top-level variable:
  MY_FORMAT = dict(
      reader=MyFormatReader,
      writer=MyFormatWriter,
      file_extension='.md',
      file_type='text',
  )
  • In setup.py, add this to entry_points:
      ...
      entry_points={
          'ipymd.format': [
              ...
              'my_format=myformat:MY_FORMAT',
              ...
          ]
      }

Note that the entry_point name will be used by default. you may override it, if you like, but Don't Repeat Yourself.

  • Add some unit tests in ipymd/formats/tests.
  • Propose a PR!

Look at the existing format implementations for more details.

Packaging a format

  • If you want to be able to redistribute your format without adding it to ipymd proper (i.e. in-house or experimental), implement all your code in a real python module.
  • Someplace easy to import, e.g. myformat.py or myformat/__init__.py, add:
  MY_FORMAT = dict(
      reader=MyFormatReader,
      writer=MyFormatWriter,
      file_extension='.md',  # or anything else
      file_type='text',  # or JSON
  )

and this to your setup.py:

  ...
      entry_points={
          'ipymd.format': [
              'my_format=myformat:MY_FORMAT',
              ],
          },
  ...
  • Publish on pypi!
  • Your users will now be able to pip install myformat, then configure their Notebook to use your format with the name my_format.