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Live code in Pandoc Markdown

Project description

Codebraid – live code in Pandoc Markdown

Codebraid is a Python program that enables executable code in Pandoc Markdown documents. Using Codebraid can be as simple as adding a class to your code blocks' attributes, and then running codebraid rather than pandoc to convert your document from Markdown to another format. codebraid supports almost all of pandoc's options and passes them to pandoc internally.

Codebraid currently can run Python 3.5+, Julia, Rust, R, and Bash code. Support for additional languages is coming soon.

Development: https://github.com/gpoore/codebraid

View example HTML output, or see the Markdown source or raw HTML (the Python and Rust examples demonstrate more advanced features at the end):

Simple example

Markdown source test.md:

```{.python .cb.run}
var = 'Hello from Python!'
var += ' $2^8 = {}$'.format(2**8)
```

```{.python .cb.run}
print(var)
```

Run codebraid (to save the output, add something like -o test_out.md, and add --overwrite if it already exists):

codebraid pandoc --from markdown --to markdown test.md

Output:

Hello from Python! $2^8 = 256$

As this example illustrates, variables persist between code blocks; by default, code is executed within a single session. Code output is also cached by default so that code is only re-executed when modified.

Features

Comparison with Jupyter, knitr, and Pweave

Codebraid Jupyter Notebook knitr Pweave
multiple programming languages per document ✓* ✓†
multiple independent sessions per language
inline code execution within paragraphs
no out-of-order code execution ✓‡
no markdown preprocessor or custom syntax
minimal diffs for easy version control
hide or display code in final document
insert code output anywhere in a document
can divide code into incomplete snippets
support for literate programming
compatible with any text editor

* One primary language per notebook, plus additional languages via %%script magic. There is no continuity between %%script cells, because each cell is executed in a separate process.
† knitr only provides continuity between code chunks for R, and more recently Python and Julia. Code chunks in other languages are executed individually in separate processes.
‡ Out-of-order execution is possible with R Markdown notebooks.


The table above summarizes Codebraid features in comparison with Jupyter notebooks, knitr (R Markdown), and Pweave, emphasizing Codebraid's unique features. Here are some additional points to consider:

Jupyter notebooks — Notebooks have a dedicated, browser-based graphical user interface. Jupyter kernels typically allow the code in a cell to be executed without re-executing any preceding code, providing superior interactivity. Codebraid has advantages for projects that are more focused on creating a document than on exploratory programming.

knitr — R Markdown documents have a dedicated user interface in R Studio. knitr provides superior support for R, as well as significant Python and Julia support that includes R integration. Codebraid offers continuity between code chunks for all supported languages, as well as multiple independent sessions per language. It also provides unique options for displaying code and its output.

More about key features

Easy debugging — By default, stderr is shown automatically in the document whenever there is an error, right next to the code that caused it. Even though user code is typically inserted into a template for execution, line numbers in error messages will correctly correspond with line numbers in code blocks, because Codebraid tracks the origin of each line of code and synchronizes error messages.

Simple language support — Adding support for a new language can take only a few minutes. Codebraid's default system for executing code is based on writing delimiters to stdout and stderr that allow it to associate code output with individual code chunks. Adding a language is as simple as creating a config file that tells Codebraid which program to run, which file extension to use, and how to write to stdout and stderr. See languages/ for examples.

No preprocessor — Unlike many approaches to making code in Markdown executable, Codebraid is not a preprocessor. Rather, Codebraid acts on the abstract syntax tree (AST) that Pandoc generates when parsing a document. Preprocessors often fail to disable commented-out code blocks because the preprocessor doesn't recognize Markdown comments. Preprocessors can also fail due to the finer points of Markdown parsing. None of this is an issue for Codebraid, because Pandoc does the Markdown parsing.

No custom syntax — Codebraid introduces no additional Markdown syntax. Making a code block or inline code executable uses Pandoc's existing syntax for defining code attributes.

Installation and requirements

Installation: pip3 install codebraid or pip install codebraid

Manual installation: python3 setup.py install or python setup.py install

Requirements:

  • Pandoc 2.4+ (2.7.2+ recommended)
  • Python 3.5+ with setuptools, and bespon 0.3 (bespon installation is typically managed by pip/setup.py)

By default, the python3 executable will be used to execute code. If it does not exist, python will be tried to account for Windows and Arch Linux. Future releases will allow specifying the executable on systems with multiple Python 3 installations.

Converting a document

Simply run codebraid pandoc <normal pandoc options>. Note that --overwrite is required for existing files.

codebraid should typically be run in the same directory as the document, so that the default working directory for code is the document directory. Future releases will allow customization of the working directory.

Caching

By default, code output is cached, and code is only re-executed when it is modified. The default cache location is a _codebraid directory in the directory with your markdown document. This can be modified using --cache-dir. Sharing a single cache location between multiple documents is not yet supported.

If you are working with external data that changes, you should run codebraid with --no-cache to prevent the cache from becoming out of sync with your data. Future releases will allow external dependencies to be specified so that caching will work correctly in these situations.

Code options

Classes

Code is made executable by adding a Codebraid class to its Pandoc attributes. For example, `code`{.python}` becomes `code`{.python .cb.run}`.

  • .cb.code — Insert code verbatim, but do not run it. This is primarily useful when combined with other features like naming and then copying code chunks.

  • .cb.expr — Evaluate an expression and interpret the result as Markdown. Only works with inline code.

  • .cb.nb — Execute code in notebook mode. For inline code, this is equivalent to .cb.expr. For code blocks, this inserts the code verbatim, followed by any printed output (stdout) verbatim. If stderr exists, it is also inserted verbatim.

  • .cb.paste — Insert code and/or output copied from one or more named code chunks. The copy keyword is used to specify chunks to be copied. This does not execute any code. If content is copied from multiple code chunks, all code chunks must be in the same session and must be in sequential order. Unless show is specified, display options are inherited from the first copied code chunk.

  • .cb.run — Run code and interpret any printed content (stdout) as Markdown. Also insert stderr verbatim if it exists.

Keyword arguments

Pandoc code attribute syntax allows keyword arguments of the form key=value, with spaces (not commas) separating subsequent keys. value can be unquoted if it contains only letters and some symbols; otherwise, double quotation marks "value" are required. For example,

{.python key1=value1 key2=value2}

Codebraid adds support for additional keyword arguments. In some cases, multiple keywords can be used for the same option. This is primarily for Pandoc compatibility.

Execution

  • complete={true, false} — By default, code chunks must contain complete units of code (function definitions, loops, expressions, and so forth). With complete=false, this is not required. Any stdout from code chunks with complete=false is accumulated until the next code chunk with complete=true (the default value), or until the end of the session, whichever comes first.

    Setting complete is incompatible with outside_main=true, since the complete status of code chunks with outside_main=true is inferred automatically.

  • outside_main={true, false} — This allows code chunks to overwrite the Codebraid template code. It is primarily useful for languages like Rust, in which code is inserted by default into a main() template. In that case, if a session starts with one or more code chunks with outside_main=true, these are used instead of the beginning of the main() template. Similarly, if a session ends with one or more code chunks with outside_main=true, these are used instead of the end of the main() template. If there are any code chunks in between that lack outside_main (that is, default outside_main=false), then these will have their stdout collected on a per-chunk basis like normal. Having code chunks that lack outside_main is not required; if there are none, the total accumulated stdout for a session belongs to the last code chunk in the session.

    outside_main=true is incompatible with explicitly setting complete. The complete status of code chunks with outside_main=true is inferred automatically.

  • session={identifier-style string} — By default, all code for a given language is executed in a single, shared session so that data and variables persist between code chunks. This allows code to be separated into multiple independent sessions. Session names must be Python-style identifiers.

Display

  • first_number/startFrom/start-from/start_from={integer or next} — Specify the first line number for code when line numbers are displayed. next means continue from the last code in the current session.

  • hide={markup, code, stdout, stderr, expr, all} — Hide some or all of the elements that are displayed by default. Elements can be combined. For example, hide=stdout+stderr. Note that expr only applies to .cb.expr or .cb.nb with inline code, since only these evaluate an expression.

  • line_numbers/numberLines/number-lines/number_lines={true, false} — Number code lines in code blocks.

  • show={markup, code, stdout, stderr, expr, none} — Override the elements that are displayed by default. expr only applies to .cb.expr and to .cb.nb with inline code, since only these evaluate an expression. Elements can be combined. For example, show=code+stdout. Each element displayed can optionally specify a format from raw, verbatim, or verbatim_or_empty. For example, show=code:verbatim+stdout:raw.

    • raw means interpreted as Markdown.
    • verbatim produces inline code or a code block, depending on context. Nothing is produced if there is no content (for example, nothing in stdout.)
    • verbatim_or_empty produces inline code containing a single non-breaking space or a code block containing a single empty line in the event that there is no content. It is useful when a placeholder is desired, or a visual confirmation that there is indeed no output.

    markup displays the Markdown source for the inline code or code block. Because the Markdown source is not available in the Pandoc AST but rather must be recreated from it, the Markdown source displayed with markup may use a different number of backticks, quote attribute values slightly differently, or contain other insignificant differences from the original document.

    expr defaults to raw if a format is not specified. All others default to verbatim.

Copying

  • copy={chunk name(s)} — Copy one or more named code chunks. When copy is used with a command like .cb.run that executes code, only the code is copied, and it is executed as if it had been entered directly. When copy is used with .cb.code, only the code is copied and nothing is executed. When copy is used with .cb.paste, both code and output are copied, and nothing is executed. Multiple code chunks may be copied; for example, copy=name1+name2. In that case, the code from all chunks is concatenated, as is any output that is copied. Because copy brings in code from other code chunks, the actual content of a code block or inline code using copy is discarded. As a result, this must be empty, or a space or underscore can be used as a placeholder.

  • name={identifier-style string} — Name a code chunk so that it can later be copied by name. Names must be Python-style identifiers.

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