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By example, I wanted to replace all inline math $...$ with \( ... \). So I had to match the (escaped) dollar sign \$ then put the text inbetween in a group (this is achieved by the parentheses). The brackets, in usual regex style, form a category of symbols. In this case every symbol but the dollar sign in order to simulate non-greedy matching. This is like using .+? in normal regular expressions. So the search pattern is:

\$([^\$]+)\$

The group given by the parentheses can be referred to in the replacement by \1, so the replacement text is:

\\( \1 \\)

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def convert_argument(arg, new_type, default=None):
    """
    Convert an argument to a new type unless it is `None`.
    """
    return default if arg is None else new_type(arg)

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class MetaBase(type):
    """
    Metaclass for MutableBase.

    This metaclass is one of two possible solutions to having a per-class
    mutable class attribute. The per-class aspect is tricky because the
    attribute is a mutable object. It is thus shared among MutableBase and all
    its subclasses.

    Shared state of the mutable class attribute is avoided with this metaclass

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def __getattr__(self, attribute):
    """
    Defer any attribute access that was unsuccessful to a compound class.

    Introduce a safeguard, for example, when unpickling this class, by raising an AttributeError.
    """
    if "compound" in self.__dict__:
        self.compound.__getattribute__(attribute)
    raise AttributeError("'{0}' object has no attribute '{1}'".format(self.__class__.__name__, attribute))

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class ProgressPrinter(object):
    """
    Write a recurring message to a stream on the same line.

    Warning
    -------
    Only works properly if the message fits on a single line for the given
    stream.
    """

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{
 "metadata": {
  "name": "simple_tf_gene_network"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {

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{
 "metadata": {
  "name": ""
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {