{
"cells": [
{
"cell_type": "code",
"execution_count": null,
"metadata": {
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},
"outputs": [],
"source": [
"%load_ext load_style\n",
"%load_style talk.css"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# [runipy](https://github.com/paulgb/runipy)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"
\n",
"ATTENTION: If you have an old installation of **Runipy**, it is very unlikely to work with the new (format v4) IPython notebook (latest version 3.0 of IPython). \n",
"\n",
"I recommend that you install the latest development version of **runipy** from the [github repository](https://github.com/paulgb/runipy) with the following: \n",
"\n",
"```\n",
"pip install https://github.com/paulgb/runipy/archive/master.zip\n",
"```\n",
"\n",
"Another solution (for IPython version 3) is to use **nbconvert**, which now comes with an option to run a notebook in place and save the outputs in the same notebook, the (rather verbose) syntax is: \n",
"\n",
"\n",
"```\n",
"ᐅ ipython nbconvert notebook_to_execute.ipynb --ExecutePreprocessor.enabled=True --to notebook --output notebook_to_execute.ipynb\n",
"```\n",
"\n",
"However it does not seem to handle passing environment variables as **runipy** does ... \n",
"\n",
"see [http://ipython.org/ipython-doc/dev/whatsnew/version3.html](http://ipython.org/ipython-doc/dev/whatsnew/version3.html) for the list of changes in the version 3.0 of IPython and the IPython notebook, see in particular the [backwards incompatible changes](http://ipython.org/ipython-doc/dev/whatsnew/version3.html#backwards-incompatible-changes) section.\n",
"\n",
"
"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The following comes from the doc of **Runipy** and goes through its major use cases"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The [IPython notebook](http://ipython.org/notebook.html) provides an interactive interface to a Python\n",
"interpreter.\n",
"\n",
"* **Literate programming**: the IPython notebook is an ideal format for\n",
" writing \"literate\" programs, in which the code is part of a larger\n",
" multi-media document. ``runipy`` lets you run such programs directly,\n",
" without first converting to a pure Python script.\n",
" \n",
"* **Report generation**: ``runipy`` can run the notebook and convert it\n",
" into HTML in one go, making it an easy way to automate reports.\n",
" \n",
"* **Data pipeline**: if you use IPython notebooks to create a data\n",
" pipeline, ``runipy`` lets you automate that pipeline without losing\n",
" the notebook formatting.\n",
"\n",
"### Requirements\n",
"\n",
"``runipy`` currently supports IPython versions 2.3.x and the current\n",
"development version of 3.x.\n",
"\n",
"### Installation\n",
"\n",
"\n",
"The easiest way to install ``runipy`` is with ``pip``:\n",
"\n",
" $ pip install runipy\n",
"\n",
"### Command-line use\n",
"\n",
"\n",
"To run a ``.ipynb`` file as a script, run:\n",
"\n",
" $ runipy MyNotebook.ipynb\n",
"\n",
"To save the output of each cell back to the notebook file, run:\n",
"\n",
" $ runipy -o MyNotebook.ipynb\n",
" \n",
"**NOTE**: *The notebook seems to be automatically converted back to version 3 if it was in version 4.*\n",
"\n",
"To save the notebook output as a *new* notebook, run:\n",
"\n",
" $ runipy MyNotebook.ipynb OutputNotebook.ipynb\n",
"\n",
"To run a ``.ipynb`` file and generate an ``HTML`` report, run:\n",
"\n",
" $ runipy MyNotebook.ipynb --html report.html\n",
"\n",
"### Passing Arguments\n",
"\n",
"\n",
"You can pass arguments to the notebook through environment variables.\n",
"The use of environment variables is OS- and shell- dependent, but in a\n",
"typical UNIX-like environment they can be passed on the command line\n",
"before the program name:\n",
"\n",
" $ myvar=value runipy MyNotebook.ipynb\n",
"\n",
"Then in the notebook, to access myvar:\n",
"\n",
" from os import environ\n",
" myvar = environ['myvar']\n",
"\n",
"``environ`` is just a ``dict``, so you can use ``.get()`` to fall back\n",
"on a default value:\n",
"\n",
" from os import environ\n",
" myvar = environ.get('myvar', 'default!')\n",
"\n",
"### Stdin / Stdout\n",
"\n",
"``runipy`` can read stdin and stdout and sit in a UNIX pipeline:\n",
"\n",
"::\n",
"\n",
" $ runipy --stdout < MyNotebook.ipynb > OutputNotebook.ipynb\n",
"\n",
" $ cat MyNotebook.ipynb | runipy --stdout > OutputNotebook.ipynb\n",
"\n",
"### Programmatic use\n",
"\n",
"It is also possible to run IPython notebooks from Python, using:\n",
"\n",
" from runipy.notebook_runner import NotebookRunner\n",
" from IPython.nbformat.current import read\n",
"\n",
" notebook = read(open(\"MyNotebook.ipynb\"), 'json')\n",
" r = NotebookRunner(notebook)\n",
" r.run_notebook()\n",
"\n",
"and you can enable ``pylab`` with:\n",
"\n",
" r = NotebookRunner(notebook, pylab=True)\n",
"\n",
"The notebook is stored in the object and can be saved using:\n",
"\n",
" from IPython.nbformat.current import write\n",
" write(r.nb, open(\"MyOtherNotebook.ipynb\", 'w'), 'json')\n",
"\n",
"run\\_notebook() takes two optional arguments. The first,\n",
"skip\\_exceptions, takes a boolean value (False by default). If True,\n",
"exceptions will be ignored and the notebook will continue to execute\n",
"cells after encountering an exception. The second argument is\n",
"progress\\_callback, which must be either None or a function that takes\n",
"one argument. This function is called after execution of each cell with\n",
"the 0-based index of the cell just evaluated. This can be useful for\n",
"tracking progress of long-running notebooks\n"
]
}
],
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"kernelspec": {
"display_name": "Python 2",
"language": "python",
"name": "python2"
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"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
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"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.9"
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"nbformat_minor": 0
}