The runcode package

runcode is a LaTeX package that executes programming source codes (including all command line tools) from LaTeX, and embeds the results in the resulting pdf file. Many programming languages can be easily used and any command-line executable can be invoked when preparing the pdf file from a tex file. runcode is also available on CTAN.

It is recommended to use this package in the server mode together with the Python talk2stat package. Currently, the server mode supports Julia, MatLab, Python, and R. More languages will be added.

Installation

You can simply put the runcode.sty file in the LaTeX project folder.

The server mode requires the talk2stat package. To install it from the command line, use:

pip3 install talk2stat

Note: runcode requires to enable the shell-escape option when compiling a LaTeX document.

Usage

Load the package:

\usepackage[options]{runcode}

Available options are:

cache: use cached results.
fvextra: use the fvextra package to show code.
julia: start server for Julia (requires talk2stat).
listings: use the listings package to show code.
matlab: start server for MatLab (requires talk2stat).
minted: use the minted package to show code (requires the pygments package). This is the default option.
nominted: use the fvextra package instead of the minted package to show code (this does not require the pygments package, but it does not provide syntax highlights).
nohup: use the nohup command when starting a server. When using the server-mode, some editors terminate all child processes after LaTeX compiling such as Emacs with Auctex. This option set the variable notnohup to be false, and the server will not be terminated by the parent process. This option has to be declared before declaring any language, e.g., [nohup, R] works but [R, nohup] does not work.
python: start server for Python (requires talk2stat).
run: run source code.
R: start server for R (requires talk2stat).
stopserver: stop the server(s) when the pdf compilation is done.

Note: If minted is used, the style of the code block is controlled through the minted package, e.g.:

\setminted[julia]{linenos, frame=single, bgcolor=bg, breaklines=true}
\setminted[R]{linenos, frame=single, bgcolor=lightgray, breaklines=true}

Similarly, fvextra and listings packages can be customized through the \fvset and \lstset commands, respectively, e.g.:

\fvset{fontsize=\small, linenos=true, frame=single}
\lstset{basicstyle=\large, frame=single}

The outputs from executing codes are displayed in tcolorbox, so the style can be customized with \tcbset, e.g.:

\tcbset{breakable,colback=red!5!white,colframe=red!75!black}

Basic commands:

\runExtCode{Arg1}{Arg2}{Arg3}[Arg4] runs an external code.
- Arg1 is the executable program.
- Arg2 is the source file name.
- Arg3 is the output file name (with an empty value, the counter codeOutput is used).
- Arg4 controls whether to run the code. Arg4 is optional with three possible values.
  - empty value or skipped: the value of the global Boolean variable runcode is used;
  - run: the code will be executed;
  - cache (or anything else): use cached results; if the output file does not exist, the cache option will be overridden and the code will run.
\showCode{Arg1}{Arg2}[Arg3][Arg4] shows the source code, using minted (requires pygments), fvextra, or listings.
- Arg1 is the programming language.
- Arg2 is the source file name.
- Arg3 is the first line to show (optional with a default value 1).
- Arg4 is the last line to show (optional with a default value of the last line).
\includeOutput{Arg1}[Arg2] is used to embed the output from executed code.
- Arg1 is the output file name, and it needs to have the same value as that of Arg3 in \runExtCode. If an empty value is given to Arg1, the counter codeOutput is used.
- Arg2 is optional and it controls the type of output with a default value vbox.
  - vbox (or skipped) = verbatim in a box;
  - tex = pure latex;
  - inline = embed result in text.
\inln{Arg1}{Arg2}[Arg3][Arg4] is designed for simple calculations; it runs one command (or a short batch) and displays the output within the text.
- Arg1 is the executable program or programming language.
- Arg2 is the source code.
- Arg3 is the output file name (optional);
- Arg4 is the output type and controls whether to run the code.
  - inline (or skipped or with empty value): embed result in text;
  - vbox: verbatim in a box;
  - cache or appending .cache to the argument (e.g., vbox.cache) AND the output file in Arg3 exists: the cached result will be used and the code will not run.
\showChunk{Arg1}{Arg2}[Arg3][Arg4] prints a selected chunk from source code. The chunk is identified in the source code by two strings that define the beginning and end of the chunk. The default beginning is label===<name> where <name> should be a unique user-defined chunk ID. The default end marker is ===end. In the code, these markers should appear after a comment character, so that the code will run.
- Arg1 is the programming language.
- Arg2 is the source file name.
- Arg3 is is the chunk identifier.
- Arg4 and Arg5 are the beginning and end markings of a chunk (optional with default label== and ===end.

Extended commands:

\runCodeIncOut{Arg1}{Arg2}[Arg3][Arg4][Arg5] runs an external code and embeds the output. This is a combination of \runExtCode and \includeOutput.
- Arg1 is the executable program.
- Arg2 is the source file name.
- Arg3 (optional) controls whether to run the code. Its functionality is the same as that of Arg4 of \runExtCode.
- Arg4 (optional) is the output file name. Its functionality is the same as that of Arg3 of \runExtCode.
- Arg5 (optional) controls the type of output with a default value vbox. Its functionality is the same as that of Arg3 of \includeOutput.

Language specific shortcuts:

Replace LANG with Julia, MatLab, Python, or R, for the Julia, MatLab, Python, R language, respectively, for the following commands.

\runLANG[Arg1]{Arg2}{Arg3}[Arg4] runs an external LANG code file.
- Arg1 is optional and uses talk2stat’s LANG server by default.
- Arg2, Arg3, and Arg4 have the same effects as those of the basic command \runExtCode.
\runLANGIncOut[Arg1]{Arg2}[Arg3][Arg4][Arg5] runs an external LANG code file and embeds the output.
- Arg1 is optional and uses talk2stat’s LANG server by default.
- Arg2, Arg3, Arg4, and Arg5 have the same effects as those of the command \runCodeIncOut.
\inlnLANG[Arg1]{Arg2}[Arg3][Arg4] runs LANG source code (Arg2) and displays the output in line.
- Arg1 is optional and uses the LANG server by default.
- Arg2 is the LANG source code to run. If the LANG source code is wrapped between ”```” on both sides (as in the markdown grammar), then it will be implemented directly; otherwise the code will be written to a file on the disk and then be called.
- Arg3 and Arg4 have the same effects as those of the basic command \inln.
\runLANGChunk[Arg1]{Arg2}{Arg3}[Arg4][Arg5][Arg6] runs a selected chunk from an external LANG code file and embeds the output.
- Arg1 (optional ) uses talk2stat’s LANG server by default.
- Arg2 is the source file name.
- Arg3 is is the chunk identifier.
- Arg4 (optional) controls whether to run the code.
- Arg5 (optional) is the output file name.
- Arg6 (optional) controls the type of output with a default value vbox.

For example,

\runR{code/MontyHall_1.R}{montyhall-R1}
\runRIncOut{code/MontyHall_1.R}[][montyhall-R1]

Specifically for Python,

\runPythonBatch[Arg1][Arg2] runs an external Python code file in batch mode (without a server running). Python (at least currently), unlike the other languages we use, does not have an option to save and restore a session, which means that once a Python session ends, the working environement (variable, functions) is deleted. In order to allow a batch-mode in Python, we implemented such capability. It requires the dill module, which has to be installed via pip3 install dill.
- Arg1 is the Python source file name,
- Arg2 is the output file name.

Revisions

v2.3, January 12, 2024: two bug fixes (1. removed an extra space after \inlnX; 2. when an underscore appeared inside R code, the tex file would compile with an error).
v2.2, September 8, 2023: add \showChunk basic command and \runLANGChunk commands for multiple languages.
v2.1, June 30, 2023: detokenize code which is passed to \inln. This is necessary when the code contains special latex characters like backslash. These characters are escaped by latex when they are passed to macros as arguments, which, in the case of \inln, alters the correct syntax and causes execution errors. Detokenizing ensures that the code is passed as-is to R/Julia/MatLab/Python. We thank kiryph for reporting the issue.
v2.0, June 23, 2023: add \runCodeIncOut command that runs an external code and embeds the output and andd some language specific shortcuts; update \runExtCode so that if the output file does not exist, the cache option will be overridden and the code will run; update \inln so that its Arg4 accept cache or appending .cache to use the cached result. We thank kiryph for suggesting these features.
v1.9, June 13, 2023: update \inln command; the optional Arg3 is the output file name and the optional Arg4 is the output type.
v1.8, January 18, 2023, add support to listings.
v1.7, August 20, 2022: changed the tmp/ folder to generated/ in order to conform with CTAN suggestions; renamed the troubleshooting file.
v1.6, August 10, 2022: stop only configured/running servers; a new reducedspace option - some document classes put more space after the code box; changed the default timeout of servers to 60 seconds; expanded the troubleshooting document. New examples are now available on GitHub, including how to collaborate with people who use Overleaf.
v1.5, July 23, 2022: Removed the utf8x option when loading inputenc due to a conflict with hyperref.
v1.4, July 18, 2022: Fixed a bug in the cache mode.
v1.3, May 14, 2022: Removed the hard-coded minted options.
v1.2, May 3, 2022: Added python options (server and batch).
v1.1, April 17, 2021: Added a nohup option; improved error handling (missing code files, zero bytes in output files.)

Contributing

We welcome your contributions to this package by opening issues on GitHub and/or making a pull request. We also appreciate more example documents written using runcode.

Citing runcode: Haim Bar and HaiYing Wang (2021). Reproducible Science with LaTeX, Journal of Data Science 2021; 19, no. 1, 111-125, DOI 10.6339/21-JDS998

Ossifragus / runcode