pandoc-pyplot

A Pandoc filter for generating figures with Matplotlib from code directly in documents

Inspired by sphinx's plot_directive, pandoc-pyplot helps turn Python code present in your documents to embedded Matplotlib figures.

Usage

The filter recognizes code blocks with the plot_target attribute present. It will run the script in the associated code block in a Python interpreter and capture the generated Matplotlib figure. This captured figure will be saved in the located specific by plot_target.

Basic example

Here is a basic example using the scripting matplotlib.pyplot API:

    ```{plot_target=my_figure.jpg}
    import matplotlib.pyplot as plt

    plt.figure()
    plt.plot([0,1,2,3,4], [1,2,3,4,5])
    plt.title('This is an example figure')
    ```

pandoc-pyplot will determine whether the plot_target is a relative or absolute path. In case of a relative path (like above), all paths will be considered relative to the current working directory.

We can control the format of the output file by changing the plot_target file extension. All formats supported by Matplotlib on your machine are available.

Putting the above in input.md, we can then generate the plot and embed it:

pandoc --filter pandoc-pyplot input.md --output output.html

or

pandoc --filter pandoc-pyplot input.md --output output.pdf

or any other output format you want. There are more examples in the source repository, in the \examples directory.

Link to source code

In case of an output format that supports links (e.g. HTML), the embedded image generated by pandoc-pyplot will be a link to the source code which was used to generate the file. Therefore, other people can see what Python code was used to create your figures.

Alternate text

You can also specify some alternate text for your image. This is done using the optional plot_alt parameter:

    ```{plot_target=my_figure.jpg, plot_alt="This is a simple figure"}
    import matplotlib.pyplot as plt

    plt.figure()
    plt.plot([0,1,2,3,4], [1,2,3,4,5])
    plt.title('This is an example figure')
    ```

Requirements

This filter only works with the Matplotlib plotting library. Therefore, you a Python interpreter and at least Matplotlib installed. The python interpreter is expected to be discoverable using the name "python" (as opposed to "python3", for example)

Running the filter

The filter program must be in your PATH. In case it is, you can use the filter with Pandoc as follows:

pandoc --filter pandoc-pyplot input.md output.html

Another example with PDF output:

pandoc --filter pandoc-pyplot input.md output.pdf

Python exceptions will be printed to screen in case of a problem.

pandoc-pyplot has a very limited command-line interface. Take a look at the help available using the -h or --help argument:

pandoc-pyplot --help

Usage as a Haskell library

To include the functionality of pandoc-pyplot in a Haskell package, you can use the makePlot function:

-- From pandoc-types
import Text.Pandoc.Walk         (walkM)
import Text.Pandoc.Definition   (Pandoc)
-- From pandoc-pyplot
import Text.Pandoc.Filter.Pyplot (makePlot)

transformDocument :: Pandoc -> IO Pandoc
transformDocument = walkM makePlot

Usage with Hakyll

This filter was originally designed to be used with Hakyll. In case you want to use the filter with your own Hakyll setup, you must create a transform function first:

-- From pandoc-types
import Text.Pandoc          (Pandoc)
import Text.Pandoc.Walk     (walkM)

-- from pandoc-pyplot
import Text.Pandoc.Filter.Pyplot (makePlot)

import Hakyll

plotTransform :: Pandoc -> IO Pandoc
plotTransform = walkM . makePlot

-- Unsafe compiler is required because of the interaction
-- in IO (i.e. running an external Python script).
makePlotPandocCompiler :: Compiler (Item String)
makePlotPandocCompiler =
  pandocCompilerWithTransformM
    defaultHakyllReaderOptions
    defaultHakyllWriterOptions
    (unsafeCompiler . plotTransform)

Warning

Do not run this filter on unknown documents. There is nothing in pandoc-pyplot that can stop a Python script from performing evil actions. This is the reason this package is deemed unsafe in the parlance of Safe Haskell.

Aknowledgements

This package is inspired from pandoc-include-code.