nbsrc 0.4.5
Jupyter notebooks from/to python and R scripts
License: MIT

# Jupyter notebooks from/to Python or R scripts

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Jupyter notebooks are complex files, that contain source code, metadata, and
rich outputs. Here we offer a simple and complementary format for Jupyter
notebooks, as pure python (or R) companion scripts.

The resulting python scripts are perfect candidates for
keeping notebooks under version control. They can be
edited outside of Jupyter, using
your favorite text editor, or even standard merge tools if you wish to merge
multiple contributions to a notebook.

With the `nbsrc` package, any python or R script can be loaded as a notebook
in Jupyter. If a classical `ipynb` notebook with a matching name exists,
outputs for matching inputs are reconstructed. And, if you associate python
and jupyter files as recommended below, when a `ipynb` notebook opens, the
corresponding inputs are taken from the `py` file, which you may have updated
outside of Jupyter.

## Can I have a demo?

Sure. Try our package on [binder](https://mybinder.org/v2/gh/mwouts/nbrmd/master?filepath=demo)!
There, you will be able
- to open and execute arbitrary python files as notebooks (give a try to
the matplotlib demo named `filled_step.py`)
- to open a notebook, then edit the companion python script, and reload the notebook,
to find up-to-date inputs in Jupyter.

## How does the python version look like?

Below is an example of a Jupyter notebook, together with its python representation.

We have hundreds of tests that ensure that
- Round trip conversion: python to notebook to python, is identity
- Round trip conversion, starting from a Jupyter notebook, preserves source
and metadata, not outputs. In some occasions (consecutive blank lines in
code cells), cells may be splitted into smaller ones.

Python [notebook](https://mybinder.org/v2/gh/mwouts/nbrmd/master?filepath=tests/python_notebook_sample.py) in Jupyter  | Python [script](https://github.com/mwouts/nbrmd/blob/master/tests/python_notebook_sample.py)
:--------------------------:|:-----------------------:
![](https://raw.githubusercontent.com/mwouts/nbsrc/master/img/python_notebook.png)   | ![](https://raw.githubusercontent.com/mwouts/nbsrc/master/img/python_source.png)

The representation of notebooks as R scripts follows the [standard](https://rmarkdown.rstudio.com/articles_report_from_r_script.html) for that language.

## How do I activate the companion script?

- generate a jupyter config, if you don't have one yet, with `jupyter notebook --generate-config`
- edit the config and include the below:
```python
c.NotebookApp.contents_manager_class = 'nbrmd.RmdFileContentsManager'
c.ContentsManager.default_nbrmd_formats = 'ipynb,py'
```

Then, make sure you have the [`nbrmd`](https://github.com/mwouts/nbrmd)
package up-to-date, and re-start jupyter, i.e. run
```bash
pip install nbrmd --upgrade
jupyter notebook
```

With the above configuration, every Jupyter notebook will have a companion
`.py` script. And every `.py` script that you edit in Jupyter
will have a companion `.ipynb` notebook.

If you prefer the `.ipynb` notebook not to be created by Jupyter when a `.py`
script is edited, set
```
c.ContentsManager.default_nbrmd_formats = ''
```
(as the default value is `ipynb`). Outputs for scripts, however,
will not be saved any more.

## Per notebook configuration

With the above configuration, every notebook will have a companion `.py` file.

If you prefer that the companion script be generated only for a few notebooks,
then remove the `c.ContentsManager.default_nbrmd_formats` line from Jupyter's
configuration, and instead edit the notebook metadata as follows:
```
{
  "kernelspec": {
    "name": "python3",
    (...)
  },
  "language_info": {
    (...)
  },
  "nbrmd_formats": "ipynb,py"
}
```

Accepted formats are: `.ipynb`, `.Rmd`, `.py` and `.R`.

In case you want both `.py` and `.Rmd`, please note that the
order matters: the first non-`.ipynb` extension
is the one used as the reference source for notebook inputs.

## What is the difference between `nbsrc` and `nbrmd`?

[`nbrmd`](https://github.com/mwouts/nbrmd)
is a python package that represents Jupyter notebooks as R markdown
files. It is also where notebooks as python scripts are implemented. But
I felt notebooks as scripts deserved a standalone documentation, and
that's the main reason for having the `nbsrc` package.

You don't actually need the `nbsrc` package unless you want the command line
conversion tools.

## Command line conversion

The `nbsrc` package provides a `nbsrc` script that converts Jupyter notebooks
 to R or python scripts, and vice-versa.
 
Install it with 
```
pip install nbsrc --upgrade
```

and then use it as:
```bash
nbsrc jupyter.ipynb         # this prints the `.py` or `.R` alternative
nbsrc jupyter.ipynb -i      # this creates a jupyter.py or jupyter.R file
nbsrc jupyter.py    -i      # and this, a jupyter.ipynb file
nbsrc jupyter.py    -i -p   # update the jupyter.ipynb file and preserve outputs that correspond to unchanged inputs
```

Alternatively, the `nbsrc` package provides two `nbconvert` exporters that you can use with
```bash
nbconvert jupyter.ipynb --to pynotebook
nbconvert jupyter.ipynb --to rnotebook
```