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. See
Codebraid Preview for VS Code
for editor support. See the Codebraid website 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", 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):
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.
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 | ✓ | ✓ | ✓ | |
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 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 and
rpy2, provide more advanced capabilities.
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 (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.
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/
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: pip3 install codebraid
or pip install codebraid
Manual installation: python3 setup.py install
or python setup.py install
Requirements:
Pandoc 2.4+ (2.17.1.1+ recommended for commonmark_x
).
Python 3.7+ with setuptools
, and bespon
0.6
(bespon
installation is typically managed by pip
/setup.py
)
For Jupyter support, jupyter_client
and language kernels
For YAML metadata support, ruamel.yaml
(can be ruamel_yaml
for Anaconda installations)
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
.
--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.
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()
).
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.
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 is made executable by adding a Codebraid class to its
Pandoc attributes.
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.
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.
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.
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.
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.verbatim_or_empty
produces inline code containing a singleFor 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.
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.
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.