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codebraid

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Live code in Pandoc Markdown

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- - __init__.py
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- - gap.bespon
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- __init__.py
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- err.py
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.gitattributes
.gitignore
CHANGELOG.md
LICENSE.txt
pyproject.toml
README.md

# Installation Guide

1. Get the code

git clone https://github.com/gpoore/codebraid

Downloads the entire project code from GitHub to your computer.

cd codebraid

Moves into the project folder you just downloaded.

2. Python

Easy Recommended

Prerequisites

Git Needed to download the project code from GitHub.
Python 3 On Windows, be sure to check 'Add Python to PATH' during installation.

| | Codebraid | Jupyter Notebook | knitr | Pweave |

Type this command into your terminal and run it.

&ast; One primary language from the Jupyter kernel. The IPython kernel

Runs the Python script (or module).

The table above summarizes Codebraid features in comparison with Jupyter

Type this command into your terminal and run it.

*Jupyter notebooks* — Notebooks have a dedicated, browser-based graphical user

Type this command into your terminal and run it.

interface. Jupyter kernels typically allow the code in a cell to be executed

Type this command into your terminal and run it.

✅ If it runs without errors and prints output in the terminal, it worked.

Pulled directly from this repo's README.

// repository documentation

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# Codebraid – live code in Pandoc Markdown

Codebraid is a Python program that enables executable code in
[Pandoc](http://pandoc.org/) 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.  See
[Codebraid Preview for VS Code](https://marketplace.visualstudio.com/items?itemName=gpoore.codebraid-preview)
for editor support.  See the [Codebraid website](https://codebraid.org/) for
additional examples and documentation.

Codebraid provides two options for executing code.  It includes a built-in
code execution system that currently supports **Python 3.7+**, **Julia**,
**Rust**, **R**, **Bash**, **JavaScript**, **GAP** and **SageMath**.  Code can also be
executed using **Jupyter kernels**, with support for rich output like plots.

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

**Citing Codebraid:**
["Codebraid: Live Code in Pandoc Markdown"](http://conference.scipy.org/proceedings/scipy2019/geoffrey_poore.html),
Geoffrey M. Poore, *Proceedings of the 18th Python in Science Conference,* 2019, 54-61.

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

* [Python example](https://htmlpreview.github.io/?https://github.com/gpoore/codebraid/blob/master/examples/python.html)
    [[Pandoc Markdown source](https://github.com/gpoore/codebraid/blob/master/examples/python.cbmd)]
    [[raw HTML](https://github.com/gpoore/codebraid/blob/master/examples/python.html)]
  * [Jupyter example](https://htmlpreview.github.io/?https://github.com/gpoore/codebraid/blob/master/examples/jupyter.html)
    [[Pandoc Markdown source](https://github.com/gpoore/codebraid/blob/master/examples/jupyter.cbmd)]
    [[raw HTML](https://github.com/gpoore/codebraid/blob/master/examples/jupyter.html)]
  * [Rust example](https://htmlpreview.github.io/?https://github.com/gpoore/codebraid/blob/master/examples/rust.html)
    [[Pandoc Markdown source](https://github.com/gpoore/codebraid/blob/master/examples/rust.cbmd)]
    [[raw HTML](https://github.com/gpoore/codebraid/blob/master/examples/rust.html)]
  * [Julia example](https://htmlpreview.github.io/?https://github.com/gpoore/codebraid/blob/master/examples/julia.html)
    [[Pandoc Markdown source](https://github.com/gpoore/codebraid/blob/master/examples/julia.cbmd)]
    [[raw HTML](https://github.com/gpoore/codebraid/blob/master/examples/julia.html)]
  * [R example](https://htmlpreview.github.io/?https://github.com/gpoore/codebraid/blob/master/examples/R.html)
    [[Pandoc Markdown source](https://github.com/gpoore/codebraid/blob/master/examples/R.cbmd)]
    [[raw HTML](https://github.com/gpoore/codebraid/blob/master/examples/R.html)]
  * [Bash example](https://htmlpreview.github.io/?https://github.com/gpoore/codebraid/blob/master/examples/bash.html)
    [[Pandoc Markdown source](https://github.com/gpoore/codebraid/blob/master/examples/bash.cbmd)]
    [[raw HTML](https://github.com/gpoore/codebraid/blob/master/examples/bash.html)]
  * [JavaScript example](https://htmlpreview.github.io/?https://github.com/gpoore/codebraid/blob/master/examples/javascript.html)
    [[Pandoc Markdown source](https://github.com/gpoore/codebraid/blob/master/examples/javascript.cbmd)]
    [[raw HTML](https://github.com/gpoore/codebraid/blob/master/examples/javascript.html)]
  * [GAP example](https://htmlpreview.github.io/?https://github.com/gpoore/codebraid/blob/master/examples/gap.html)
    [[Pandoc Markdown source](https://github.com/gpoore/codebraid/blob/master/examples/gap.cbmd)]
    [[raw HTML](https://github.com/gpoore/codebraid/blob/master/examples/gap.html)]

## Simple example

Markdown source `test.md`:

``````markdown
```{.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):

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

Output:

```markdown
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](https://jupyter.org/), [knitr](https://yihui.name/knitr/), and [Pweave](http://mpastell.com/pweave/)

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

&ast; One primary language from the Jupyter kernel.  The IPython kernel
supports additional languages via `%%script` magics.  There is no continuity
between `%%script` cells, because each cell is executed in a separate process.
Some magics, such as those provided by
[PyJulia](https://pyjulia.readthedocs.io) and
[rpy2](https://rpy2.readthedocs.io), provide more advanced capabilities.
<br>
† 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.
<br>
‡ Out-of-order execution is possible with R Markdown notebooks.

<hr>

The table above summarizes Codebraid features in comparison with Jupyter
notebooks (without extensions), 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.  It is also
possible to monitor code output in real time during execution via
`--live-output`.

*Simple language support* — Codebraid supports Jupyter kernels.  It also has a
built-in system for executing code.  Adding support for a new language with
this system can take only a few minutes.  Just create 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/`](https://github.com/gpoore/codebraid/tree/master/codebraid/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](http://pandoc.org/) 2.4+ (2.17.1.1+ recommended for `commonmark_x`).
  * Python 3.7+ with `setuptools`, and [`bespon`](https://bespon.org) 0.6
    (`bespon` installation is typically managed by `pip`/`setup.py`)

* For Jupyter support, [`jupyter_client`](https://pypi.org/project/jupyter-client/)
    and language kernels

* For YAML metadata support, [`ruamel.yaml`](https://pypi.org/project/ruamel.yaml/) (can be `ruamel_yaml` for Anaconda installations)

## Converting a document

Simply run `codebraid pandoc <normal pandoc options>`.  Codebraid currently
supports Pandoc Markdown (`--from markdown`) and CommonMark with Pandoc
extensions (`--from commonmark_x`) as input formats.

Note that `--overwrite` is required to overwrite existing files.  If you are
using a defaults file, `--from`, `--to`, and `--output` must be given
explicitly and cannot be inherited from the defaults file.  If you are using a
defaults file and converting to a standalone Pandoc Markdown document,
`--standalone` should be given explicitly rather than being inherited from the
defaults file.

`codebraid` should typically be run in the same directory as the document, so
that the default working directory for code is the document directory.

If you are converting from Pandoc Markdown to Pandoc Markdown with
`--standalone` (basically using `codebraid` to preprocess Markdown documents),
note that the following YAML metadata fields and command-line options are
ignored in that situation:
  * `header-includes` and `--include-in-header`
  * `include-before` and `--include-before-body`
  * `include-after` and `--include-after-body`
  * `toc`/`table-of-contents` and `--toc`/`--table-of-contents`

This is typically what you want.  Usually, "include" and a table of contents
are desired in a final output format like HTML or PDF, not in a Pandoc
Markdown file.  In the rare cases where "includes" and a table of contents are
needed in Markdown documents, this can be accomplished by piping the output of
`codebraid` through `pandoc`.

## Additional non-Pandoc command-line options

* `--live-output` — Show code output (stdout and stderr) live in the terminal
  during code execution.  For Jupyter kernels, also show  errors and a summary
  of rich output.  Output still appears in the document as normal.

Individual sessions can override this by setting `live_output=false` in the
  document.

* `--no-execute` — Disables code execution.  Only use available cached output.

* `--only-code-output`={format} — Write code output in JSON Lines format to
  stdout as soon as it is available, and do not create a document.

This is intended for use with Codebraid Preview, so that document previews
  can be updated during code execution.  Currently, the only supported format
  is `codebraid_preview`.  One JSON data object followed by a newline is
  written to stdout for each code chunk.  In some cases, the data for a chunk
  will be resent later if the data relevant for a chunk changes (for example,
  if code execution fails after the first chunk runs, but in such a way that
  an error message needs to be attached to the first chunk).  Data for a chunk
  is sent as soon as it is available from code processing, from cache, or from
  code execution (as soon as the chunk completes, typically before the session
  completes).  Additional JSON data may be sent to provide tracking of code
  execution progress or information such as metadata.  The JSON data provided
  for format `codebraid_preview` may change between minor versions.

## 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
working directory (directory where `codebraid` is run, typically the document
directory).  This can be modified using `--cache-dir`.  Multiple documents can
share a single cache location.  A cache directory can be synced between
different operating systems (such as Windows and Linux) while retaining full
functionality so long as documents are in equivalent locations under the
user's home directory (as resolved by
[`os.path.expanduser()`](https://docs.python.org/3/library/os.path.html#os.path.expanduser)).

When multiple documents share the same cache location, each document will
automatically clean up its own unused, outdated files.  However, if a document
is deleted or renamed, it may leave behind unused files in the cache, so it
may be worth manually deleting and regenerating the cache in those
circumstances.  Future cache enhancements should be able to detect all unused
files, making this unnecessary.

If you are working with external data that changes, you should run `codebraid`
with `--no-cache` or delete the cache as necessary 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.

## YAML metadata

Some document-wide settings can be given in the Markdown YAML metadata.
Codebraid settings must be under either a `codebraid` or `codebraid_` key in
the metadata.  Pandoc will ignore `codebraid_` so it will not be available to
filters; this distinction should not typically be important.

To use Jupyter kernels automatically for all sessions, simply set
`jupyter: true`.  For example,

```
---
codebraid:
  jupyter: true
---
```

It is also possible to set a default kernel and/or default timeout.  For example,

```
---
codebraid:
  jupyter:
    kernel: python3
    timeout: 120
---
```

A Jupyter kernel and/or timeout can still be set in the first code chunk
for a given session, and will override the document-wide default.

It is also possible to set `live_output: <bool>` in the metadata.
Additional metadata settings will be added in future releases.

## Code options

### Commands (Classes)

Code is made executable by adding a Codebraid class to its
[Pandoc attributes](http://pandoc.org/MANUAL.html#fenced-code-blocks).
For example, `` `code`{.python} `` becomes
`` `code`{.python .cb-run} ``.

When code is executed, the output will depend on whether the built-in code
execution system or a Jupyter kernel is used.

When code is executed with the built-in system, the output is equivalent to
collecting all code for each session of each language, saving it to a file,
and then executing it (with an added compile step for some languages).  For
example, running Python code is equivalent to saving it to `file.py` and then
running `python file.py`, while running R code is equivalent to saving it to
`file.R` and then running `Rscript file.R`.  Code is not executed as it would
be in an interactive session (like running `python` or `R` at the command
prompt).  As a result, some output that would be present in an interactive
session is absent.  For example, in interactive sessions for some languages,
simply entering a variable returns a string representation without explicit
printing, and plotting opens a separate image window or displays an image
inline.  Such output is absent in Codebraid unless it is also produced when
code is executed as a script rather than in an interactive session.  The
`.cb-expr` command is provided for when an inline string representation of a
variable is desired.

An option for interactive-style code execution with the built-in system is
planned for a future release.  In the meantime, many interactive-style
features are available between the `.cb-expr` command and Jupyter kernels.

When code is executed with a Jupyter kernel, the default output will be
equivalent to executing it in a Jupyter notebook.  Rich output such plots,
images, and LaTeX math will be displayed automatically by default.  This can
be customized by using the `show` and `hide` options.

All classes for making code executable are listed below.  These all have the
form `.cb-<command>`.  Classes with the form `.cb.<command>` (period rather
than hyphen) are supported for Pandoc Markdown (`--from markdown`), but not
for `commonmark_x` since it has a more restricted class syntax.  The forms
shown below (`.cb-<command>`) should be preferred for compatibility across
Markdown variants supported by Pandoc.

* `.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.  This is not currently compatible with Jupyter
  kernels.

* `.cb-nb` — Execute code in notebook mode.  For inline code, this is
  equivalent to `.cb-expr` with verbatim output unless a Jupyter kernel is
  used, in which case rich output like plots or LaTeX will be displayed.  For
  code blocks, this inserts the code verbatim, followed by any printed output
  (stdout) verbatim.  If stderr exists, it is also inserted verbatim.  When a
  Jupyter kernel is used, rich output like plots or LaTeX is also displayed.

* `.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.  Unless `show` is specified, display options are
  inherited from the first copied code chunk.

If content is copied from multiple code chunks that are executed, all code
  chunks must be in the same session and must be in sequential order without
  any omitted chunks.  This ensures that what is displayed is always
  consistent with what was executed.

If content is copied from another `cb-paste` code chunk, only a single code
  chunk can be copied.  This reduces the indirection that is possible when
  displaying the output of code that has been executed.  This restriction may
  be removed in the future.

* `.cb-run` — Run code and interpret any printed content (stdout) as Markdown.
  Also insert stderr verbatim if it exists.  When a Jupyter kernel is used,
  rich output like plots or LaTeX is also displayed.

### 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.

#### First chunk settings

These are only permitted for the first code chunk in a session (or the first
chunk for a language, if a session is not specified and thus the default
session is in use).

* `executable`={string} — Executable to use for running or compiling code,
  instead of the default.  This only applies to Codebraid's built-in code
  execution system.

* `executable_opts`={string} — Command-line options passed to `executable`.
  This only applies to Codebraid's built-in code execution system.

* `args`={string} — Command-line arguments passed to code during execution.
  For example, this could be used to add values to `sys.argv` for Python.
  This only applies to Codebraid's built-in code execution system.

* `jupyter_kernel`={string} — Jupyter kernel to use for executing code instead
  of Codebraid's built-in code execution system.  Multiple Jupyter kernels can
  be used within a single document, and multiple sessions are possible per
  kernel.  Except when otherwise specified, Jupyter kernels should be usable
  just like the built-in code execution system.

* `jupyter_timeout`={int} — Jupyter kernel timeout per code chunk in seconds.
  The default is 60.

* `live_output`={`true`, `false`} — Show code output (stdout and stderr) live
  in the terminal during code execution.  For Jupyter kernels, also show
  errors and a summary of rich output.  Output still appears in the document
  as normal.  Showing output can also be enabled via the command-line option
  `--live-output`.

When `live_output=false` is set for a session, this setting takes precedence
  over the command-line option `--live-output`, and output will not be shown
  for that session.

All output is written to stderr, so stdout only contains the document when
  `--output` is not specified.  Output is interspersed with delimiters marking
  the start of each session and the start of each code chunk.  The delimiters
  for the start of each code chunk include source names and line numbers.

With Codebraid's built-in code execution system, the output for a code chunk
  may be delayed until all code in the chunk has finished executing, unless
  code output is line buffered or code manually flushes stdout and stderr.
  For example, with Python you may want to use print functions like
  `print("text", flush=True)`.  Another option is to use Python in
  line-buffered mode by setting `executable_opts="-u"` in the first code chunk
  of a session.

With Jupyter kernels, the output for a code chunk will be delayed until all
  code in the chunk has finished executing.

#### 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 when code is executed with Codebraid's built-in code
  execution system.  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 option 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`, `copied_markup`, `code`, `stdout`, `stderr`, `expr`,
  `rich_output`, `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
  using Codebraid's built-in code execution system, since only these evaluate
  an expression.  `rich_output` is currently only relevant for Jupyter
  kernels.

* `hide_markup_keys`={key(s)} — Hide the specified code chunk attribute key(s)
  in the Markdown source displayed via `markup` or `copied_markup`.  Multiple
  keys can be specified via `hide_markup_keys=key1+key2`.

`hide_markup_keys` only applies to the code chunk in which it is used, to
  determined the `markup` for that code chunk.  Thus, it only affects
  `copied_markup` indirectly.

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

* `show`={`markup`, `copied_markup`, `code`, `stdout`, `stderr`, `expr`,
  `rich_output`, `none`} — Override the elements that are displayed by
  default.  `expr` only applies to `.cb-expr` and to `.cb-nb` with inline code
  using Codebraid's built-in code execution system, since only these evaluate
  an expression.  Elements can be combined.  For example, `show=code+stdout`.

Each element except `rich_output` 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.

For `rich_output`, the format is specified as one or more abbreviations for
  the mime types of the output to be displayed.  For example,
  `rich_output:plain` will display `text/plain` output if it exists, and
  otherwise nothing.  `rich_output:png|plain` will display a PNG image if it
  exists, or otherwise will fall back to plain text if available.  The
  following formats are currently supported:

- `latex` (corresponds to `text/latex`)
    - `html` (`text/html`)
    - `markdown` (`text/markdown`)
    - `plain` (`text/plain`)
    - `png` (`image/png`)
    - `jpg` and `jpeg` (`image/jpeg`)
    - `svg` (`image/svg+xml`)
    - `pdf` (`application/pdf`)

For `rich_output` formats with a `text/*` mime type (`latex`, `html`,
  `markdown`, `plain`), it is possible to specify whether they are displayed
  `raw`, `verbatim`, or `verbatim_or_empty`.  For example,
  `show=rich_output:latex:raw` and `show=rich_output:latex:verbatim`.  `raw`
  treats `latex` and `html` as raw content with those formats embedded within
  Markdown.  `raw` treats `markdown` and `plain` as Markdown.  When a display
  style is not specified, all `rich_output` formats with a `text/*` mime type
  are displayed `raw` by default, except for `plain` which is displayed
  `verbatim`.

`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.

`copied_markup` displays the Markdown source for code chunks copied via
  `copy`.

`expr` defaults to `raw` if a format is not specified.  `rich_output`
  defaults to `latex|markdown|png|jpg|svg|plain`.  All others default to
  `verbatim`.

* `example`={bool} — Insert a code block containing the Markdown source of the
  code chunk, followed by the rest of the output as normal.  This is only
  valid for inline code if the code is in a paragraph by itself.  This option
  is currently not compatible with `--only-code-output` and Codebraid Preview.
  This option is intended primarily for documentation about Codebraid.

#### 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.

#### Including external files

* `include_file`={path} — Include the specified file.  A leading `~/` or
  `~<user>/` is expanded to the user's home directory under all operating
  systems, including under Windows with both slashes and backslashes.

When `include_file` is used with a command like `.cb-run` that executes
  code, the file is included and executed as part of the current session just
  as if the file contents had been entered directly.  When `include_file` is
  used with `.cb-code`, the file is included and displayed just as if it had
  been entered directly.  Because `include_file` brings in code from another
  file, the actual content of a code block or inline code using `include_file`
  is discarded.  As a result, this must be empty, or a space or underscore can
  be used as a placeholder.

* `include_encoding`={encoding} — Encoding for included file.  The default
  encoding is UTF-8.

* `include_lines`={lines/line ranges} — Include the specified lines or line
  ranges.  For example, `1-3,5,7-9,11-`.  Line numbers are one-indexed.  Line
  ranges are inclusive, so `1-3` is `1` up to and including `3`.  If a range
  ends with a hyphen, like `11-`, then everything is included from the line
  through the end of the file.

Cannot be combined with other `include` options that specify what is to
  be included.

* `include_regex`={regex} — Include the first segment of the file that matches
  the provided regular expression.

Keep in mind that Pandoc's key-value attributes evaluate backslash escapes
  in values whether or not the values are quoted with double quotation marks,
  so two levels of backslash-escaping are always necessary (one for Pandoc's
  strings, one for the regex itself; there are no raw strings).  Regular
  expressions use *multiline mode*, so `^`/`$` match the start/end of a line,
  and `\A`/`\Z` can be used to match the start/end of the file.  Regular
  expressions use *dotall mode*, so `.` matches anything including the newline
  `\n`; use `[^\n]` when this is not desired.

Cannot be combined with other `include` options that specify what is to
  be included.

* `include_start_string`={string} — Include everything from the first
  occurrence of this string onward.

Can only be combined with other `include` options that specify the end of
  what is to be included.

* `include_start_regex`={regex} — Include everything from the first
  match of this regex onward.

Can only be combined with other `include` options that specify the end of
  what is to be included.  See `include_regex` for notes on regex usage.

* `include_after_string`={string} — Include everything after the first
  occurrence of this string onward.

Can only be combined with other `include` options that specify the end of
  what is to be included.

* `include_after_regex`={regex} — Include everything after the first
  match of this regex onward.

Can only be combined with other `include` options that specify the end of
  what is to be included.  See `include_regex` for notes on regex usage.

* `include_before_string`={string} — Include everything before the first
  occurrence of this string.

Can only be combined with other `include` options that specify the start of
  what is to be included.  If the start is specified, then the first
  occurrence after this point is used, rather than the first occurrence in the
  overall file.

* `include_before_regex`={regex} — Include everything before the first
  match of this regex.

Can only be combined with other `include` options that specify the start of
  what is to be included.  If the start is specified, then the first match
  after this point is used, rather than the first match in the overall file.
  See `include_regex` for notes on regex usage.

* `include_end_string`={string} — Include everything through the first
  occurrence of this string.

Can only be combined with other `include` options that specify the start of
  what is to be included.  If the start is specified, then the first
  occurrence after this point is used, rather than the first occurrence in the
  overall file.

* `include_end_regex`={regex} — Include everything through the first
  match of this regex.

Can only be combined with other `include` options that specify the start of
  what is to be included.  If the start is specified, then the first match
  after this point is used, rather than the first match in the overall file.
  See `include_regex` for notes on regex usage.