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pystitch

Description

Write reproducible reports in Markdown

437 Stars 18 Forks MIT License 132 Commits 15 Opened issues

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Stitch

|Build Status|

A

knitr 
-
RMarkdown 
-like library, in Python.

Note: You might want to consider Jan Schulz's

knitpy 
__ instead. It's probably more mature at this point. However, I wanted to see if there was a simpler way of doing things.

The high-level goal of this type of library (knitr/RMarkdown, knitpy, and stitch) is to make writing reproducible reports easier.

Documentation is available

here 
__.

Examples

See the project's

examples page 
__ for a side-by-side comparison of input markdown and stitched HTML.

More complex examples are linked to from there as well.

Install

stitch
supports Python 3.5 and above. At the moment
stitch
can be installed from pip via

.. code-block:: sh

pip install knotr

I know, it's confusing. I've filed a claim for

stitch
on PyPI, but I think the people working that support queue are over-worked. Once that gets processed, I'll put it up on conda-forge as well. If you need a mnemonic, it's "I want knitr, but
not
the one written in
R
." Also I wanted to confuse R users. And knots are kind of like a buggy version of knits.

stitch
requires pandoc>=1.18. This can be installed using your system package manager, or
pypandoc 
__.

Design

The goal was to keep

stitch
itself extremely simple by reusing existing libraries. A high level overview of our tasks is
  1. Command-line Interface
  2. Parse markdown file
  3. Execute code chunks, capturing the output
  4. Collate execution output into the document
  5. Render to final output

Fortunately the building blocks are all there.

We reuse

  • pandoc 
    __ via
    pypandoc 
    __ for parsing markdown and rendering the final output
  • jupyter 
    __ for language kernels, executing code, and collecting the output
  • Use
    pandocfilters 
    __ to collate the execution output into the document

So all

stitch
has to do is to provide a command-line interface, scan the document for code chunks, manage some kernels, hand the code to the kernels, pass the output to an appropriate
pandocfilter
.

The biggest departure from

knitpy
is the use of pandoc's JSON AST. This is what you get from
pandoc -t json input.md

This saves us from having do any kind of custom parsing of the markdown. The only drawback so far is somewhat inscrutable Haskell exceptions if

stitch
happens to produce a bad document.

Documentation

Stitch's documentation has an odd build process, so standard tools like readthedocs weren't flexible enough. To make the docs, install stitch and all the extra dependencies. Clone https://github.com/pystitch/pystitch.github.io

Checkout the

src
branch.

Run

make html
.

.. |Build Status| image:: https://travis-ci.org/pystitch/stitch.svg?branch=master :target: https://travis-ci.org/pystitch/stitch

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