Package 'goxygen' reference manual

Title:	In-Code Documentation for 'GAMS'
Description:	A collection of tools which extract a model documentation from 'GAMS' code and comments. In order to use the package you need to install 'pandoc' and 'pandoc-citeproc' first (<https://pandoc.org/>).
Authors:	Jan Philipp Dietrich [aut, cre], Kristine Karstens [aut], David Klein [aut], Lavinia Baumstark [aut], Falk Benke [aut]
Maintainer:	Jan Philipp Dietrich <[email protected]>
License:	BSD_2_clause + file LICENSE
Version:	1.4.4
Built:	2024-09-11 05:08:04 UTC
Source:	https://github.com/pik-piam/goxygen

A helper to merge two nested lists describing extra page blocks. The lists have the page name on the first level and flattened documentation blocks on the second level. It is ensured that elements for the same page are grouped in the same list.

Usage

appendExtraPageBlocks(blocks, add)
appendExtraPageBlocks(blocks, add)

Arguments

`blocks`	a nested list for extra page blocks per page
`add`	a seccond nested list for extra page blocks per page to be appended to the first one

Author(s)

Falk Benke

buildHTML

Description

Converts a folder with markdown files and a corresponding literature library (if available) to HTML files and creates cross-links between them.

Usage

buildHTML(
  style = "classic",
  folder = "html",
  mdfolder = "markdown",
  literature = "literature.bib",
  citation = "../CITATION.cff",
  supplementary = "images",
  debug = FALSE,
  templatefolder = ".."
)
buildHTML(
  style = "classic",
  folder = "html",
  mdfolder = "markdown",
  literature = "literature.bib",
  citation = "../CITATION.cff",
  supplementary = "images",
  debug = FALSE,
  templatefolder = ".."
)

Arguments

`style`	visualization style to be used for the creation. Currently available styles are "classic" and "ming"
`folder`	location the HTML files should be written to
`mdfolder`	path to the markdown folder to be used as source
`literature`	path to a bibliography, if available (will be ignored if file does not exist)
`citation`	Citation information in citation file format (optional)
`supplementary`	a vector of files and/or folders required for the conversion (e.g. an images subdirectory with figures to be shown in the documents)
`debug`	logical which switches on/off a debug mode which will return additional status updates and keep build files
`templatefolder`	Folder in which goxygen will search for template files in addition to the pre-installed ones.

Details

Pandoc (https://pandoc.org/) together with pandoc-citeproc need to be installed on the system.

Author(s)

Jan Philipp Dietrich

buildMarkdown

Description

Creates a folder filled with markdown files from a list object with markdown code

Usage

buildMarkdown(x, folder = "markdown")
buildMarkdown(x, folder = "markdown")

Arguments

`x`	a named list of markdown codes which should be written as markdown files. The name of each entry will become the file name.
`folder`	folder the markdown files should be written to

Author(s)

Jan Philipp Dietrich

buildTEX

Description

Converts a folder with markdown files and a corresponding literature library (if available) to a tex file

Usage

buildTEX(
  file = "documentation.tex",
  mdfolder = "markdown",
  literature = "literature.bib",
  citation = "../CITATION.cff",
  supplementary = NULL,
  pdf = TRUE,
  style = "classic",
  templatefolder = ".."
)
buildTEX(
  file = "documentation.tex",
  mdfolder = "markdown",
  literature = "literature.bib",
  citation = "../CITATION.cff",
  supplementary = NULL,
  pdf = TRUE,
  style = "classic",
  templatefolder = ".."
)

Arguments

`file`	name of the tex file to be written
`mdfolder`	path to the markdown folder to be used as source
`literature`	path to a bibliography, if available (will be ignored if file does not exist)
`citation`	Citation information in citation file format (optional)
`supplementary`	a vector of files and/or folders required for the conversion (e.g. an images subdirectory with figures to be shown in the documents)
`pdf`	boolean which specifies whether pdf file should be generated from tex
`style`	visualization style to be used for the Latex/PDF creation. Currently only "classic" style is available. Ignored for outputs other than Latex/PDF. Can be extended by additional templates stored in the `templatefolder` in the format `<style>.latex`. Classic template `system.file("templates","classic.latex",package="goxygen")` can serve as a starting point for own templates.
`templatefolder`	Folder in which goxygen will search for template files in addition to the pre-installed ones.

Details

Pandoc (https://pandoc.org/) together with pandoc-citeproc need to be installed on the system.

Author(s)

Jan Philipp Dietrich, Kristine Karstens

check_pandoc

Description

Support function which checks pandoc availability and stops with an error in case that pandoc cannot be found

Usage

check_pandoc(error = FALSE)
check_pandoc(error = FALSE)

Arguments

error

boolean indicating whether function should throw an error in case of missing pandoc or return a boolean FALSE.

Value

boolean indicating whether pandoc is available or not.

Author(s)

Jan Philipp Dietrich

chooseTemplate

Description

Support function helping to choose the selected template

Usage

chooseTemplate(style, templatefolder, ftype = NULL)
chooseTemplate(style, templatefolder, ftype = NULL)

Arguments

`style`	visualization style to be used for the creation.
`templatefolder`	Folder in which goxygen will search for template files in addition to the pre-installed ones.
`ftype`	template file type / file ending, or NULL if looking for a whole directory

Author(s)

Jan Philipp Dietrich

createIndexPage

Description

Creates markdown code from a supplied data list

Usage

createIndexPage(data)
createIndexPage(data)

Arguments

data

a list of data entries for the resulting markdown page. Following entries can be provided:

title: Page title
description: General description
citation: A read in citation in Citation File Format (CFF)

Value

a character vector containing the produced markdown text

Author(s)

Jan Philipp Dietrich

createListModularCode

Description

support function to create documentation of modular GAMS code.

Usage

createListModularCode(
  cc,
  interfaces,
  path = ".",
  citation = NULL,
  unitPattern = c("\\(", "\\)"),
  includeCore = FALSE,
  mainfile = "main.gms",
  docfolder = "doc",
  startType = "equations"
)
createListModularCode(
  cc,
  interfaces,
  path = ".",
  citation = NULL,
  unitPattern = c("\\(", "\\)"),
  includeCore = FALSE,
  mainfile = "main.gms",
  docfolder = "doc",
  startType = "equations"
)

Arguments

`cc`	codeCheck information
`interfaces`	interface information
`path`	path to the model to be documented
`citation`	citation data read from a CFF file
`unitPattern`	pattern that is usedto identify the unit in the description, default =c("\(","\)")
`includeCore`	Boolean whether core should be included or not, default=FALSE
`mainfile`	main file of the model
`docfolder`	folder the documentation should be written to relative to model folder
`startType`	input parameter for `extractDocumentation` to be passed when extracting documentation from realizations. Defaults to "equations", meaning that documentation in realizations should be interpreted as equations documentation, if no identifier is set.

Author(s)

Jan Philipp Dietrich

createListSimpleCode

Description

support function to create documentation of non-modular GAMS code.

Usage

createListSimpleCode(path = ".", citation = NULL, mainfile = "main.gms")
createListSimpleCode(path = ".", citation = NULL, mainfile = "main.gms")

Arguments

`path`	path to the model to be documented
`citation`	citation data read from a CFF file
`mainfile`	main file of the model

Author(s)

Jan Philipp Dietrich

createModulePage

Description

Creates markdown code from a supplied data list

Usage

createModulePage(data, docfolder)
createModulePage(data, docfolder)

Arguments

data

a list of data entries for the resulting markdown page. Following entries can be provided:

name: Name of the module
title: Page title
description: General description
input: Table containing inputs to the module
output: Table containing outputs from the module
realizations: A list of realizations with entries "description" and "limitations" for each of them
declarations: Table of declarations for internal objects
stes: Table containing sets used in the module
authors: Module authors
seealso: A vector with names of relevant other documentation pages.

docfolder

folder the documentation should be written to relative to model folder

Value

a character vector containing the produced markdown text

Author(s)

Jan Philipp Dietrich

createSimplePage

Description

Creates markdown code from a supplied data list

Usage

createSimplePage(data)
createSimplePage(data)

Arguments

data

a list of data entries for the resulting markdown page. Following entries can be provided:

title: Page title
description: General description
limitations: Limitations the implementation comes with
authors: Module authors

Value

a character vector containing the produced markdown text

Author(s)

Jan Philipp Dietrich

extractDocumentation

Description

Extracts doxygen-like GAMS documentation. Entries are introduced with an @type at the beginning of the line. In case of @realization also GAMS code is read and interpreted, in all other cases only the specific documentation comment is evaluated.

Usage

extractDocumentation(path, startType = NULL, comment = "*'")
extractDocumentation(path, startType = NULL, comment = "*'")

Arguments

`path`	path to the file(s) which should be evaluated
`startType`	set type for first line of code. This can be useful to extract documentation even if no documentation type has been set (e.g reading equations.gms as type realization)
`comment`	comment chars used for documentation comments

Value

a nested list of documentation pieces with type as name of each element. Each element contains two lists 'content' containing the actual documentation and 'cfg' containing optional attributes passed with the type.

Author(s)

Jan Philipp Dietrich

Examples

mainfile <- paste0(system.file("dummymodel", package = "gms"), "/main.gms")
calcfile <- paste0(system.file("dummymodel", package = "gms"),
                           "/modules/02_crazymodule/complex/calculations.gms")
# extracting information from the main file of the model
extractDocumentation(mainfile)
# extracting information from a file with some equations in it
extractDocumentation(calcfile)

mainfile <- paste0(system.file("dummymodel", package = "gms"), "/main.gms")
calcfile <- paste0(system.file("dummymodel", package = "gms"),
                           "/modules/02_crazymodule/complex/calculations.gms")
# extracting information from the main file of the model
extractDocumentation(mainfile)
# extracting information from a file with some equations in it
extractDocumentation(calcfile)

flattenPageBlockList

Description

A helper that processes additional attributes for a given list of code documentation blocks. Code documentation blocks are described as lists consisting of 'content' containing the documentation and a 'cfg' list containing attributes.

Usage

flattenPageBlockList(data)
flattenPageBlockList(data)

Arguments

data

a list of documentation pieces with type as name of each element

Details

If a block entry has the 'cgf' attribute 'extrapage', it is moved to a separate list 'extraPageBlocks' in the output, as these need to be rendered separately later.

Regular blocks without the 'extrapage' attribute are moved to a list 'blocks' and multiple blocks with the same name are merged into one block.

Cfg attributes other than 'extrapage' are currently not supported and therefore ignored, but a warning is thrown.

After processing the 'cfg' attributes, the code documentation blocks are flattened, i.e. a list consisting of a 'content' and 'cfg' entry is replaced by the data in 'cfg'.

This helper supports nesting of blocks in 'realizations' with code documentation per realization.

Value

a list with two element (1) 'blocks' containing the documentation elements with type as name of the element and (2) 'extraPageBlocks' containing lists for blocks to be put on an extra pages, sorted by page names.

Author(s)

Falk Benke

gamsequation2tex

Description

Convert a gams equation into latex code

Usage

gamsequation2tex(x)
gamsequation2tex(x)

Arguments

`x`	GAMS equation provided as character

Value

GAMS equation converted to latex code

Author(s)

Jan Philipp Dietrich

Examples


  x <- "eq_1 .. v_a =e= sum(j,v_b(j)*((1-s_c)+sum(cell(i,j),v_d(i)/f_d(i))));"
  cat(gamsequation2tex(x))
x <- "eq_1 .. v_a =e= sum(j,v_b(j)*((1-s_c)+sum(cell(i,j),v_d(i)/f_d(i))));"
  cat(gamsequation2tex(x))

goxygen

Description

Documentation function which extracts a full model documentation from a modularized gams model. The function extracts comments used as documentation, extracts code and can extract and convert GAMS equations as latex code. Output is returned in Markdown, HTML and PDF format.

Usage

goxygen(
  path = ".",
  docfolder = "doc",
  cache = FALSE,
  output = c("html", "tex", "pdf"),
  htmlStyle = "ming",
  texStyle = "classic",
  templatefolder = ".",
  cff = "CITATION.cff",
  modularCode = is.modularGAMS(),
  unitPattern = c("\\(", "\\)"),
  includeCore = FALSE,
  mainfile = "main.gms",
  startType = "equations",
  ...
)
goxygen(
  path = ".",
  docfolder = "doc",
  cache = FALSE,
  output = c("html", "tex", "pdf"),
  htmlStyle = "ming",
  texStyle = "classic",
  templatefolder = ".",
  cff = "CITATION.cff",
  modularCode = is.modularGAMS(),
  unitPattern = c("\\(", "\\)"),
  includeCore = FALSE,
  mainfile = "main.gms",
  startType = "equations",
  ...
)

Arguments

`path`	path to the model to be documented
`docfolder`	folder the documentation should be written to relative to model folder
`cache`	Boolean to allow read data from existing cache file
`output`	List of output to be written, available are "html","pdf" and "tex"
`htmlStyle`	visualization style to be used for the HTML creation. Currently available styles are "classic" and "ming". Ignored for outputs other than HTML. Can be extended by additional templates stored in the `templatefolder` in the form `<style>.html5` together with a subfolder with supplementary files and the name of the style `<style>` (both need to be provided). The preinstalled ming template `system.file("templates","ming.css",package="goxygen")` and `system.file("templates","ming.html5",package="goxygen")` can serve as a starting point for own templates.
`texStyle`	visualization style to be used for the Latex/PDF creation. Currently only "classic" style is available. Ignored for outputs other than Latex/PDF. Can be extended by additional templates stored in the `templatefolder` in the format `<style>.latex`. Classic template `system.file("templates","classic.latex",package="goxygen")` can serve as a starting point for own templates.
`templatefolder`	Folder in which goxygen will search for template files in addition to the pre-installed ones.
`cff`	path to a citation file in citation-file-format (ignored if not existing)
`modularCode`	Boolean deciding whether code should be interpreted as modular GAMS code (only av)
`unitPattern`	pattern that is usedto identify the unit in the description, default =c("\(","\)")
`includeCore`	boolean whether core should be included or not, default=FALSE
`mainfile`	main file of the model
`startType`	input parameter for `createListModularCode`, default = "equations"
`...`	optional arguments to `interfaceplot`, passed via `modules_interfaceplot`.

Note

Documentation lines in the code must start with *' to be detected as documentation. Identifier at the beginning of each block describe what kind of documentation is given. All identifiers start with @ followed by the name of the identifier. Currently, following identifiers are available

@title Title
@authors List of authors
@description Model description (only the documentation text will be interpreted)
@equations Equation description (documentation text will be extracted and gams equations will be converted to latex code)
@code Code description (documentation text and code will be extracted)
@limitations details about limitations of an implementation
@stop everything following will be ignored until the next identifier is mentioned again. Useful to stop a section

In addition you can store a model logo (100px height, 100px weight) as logo.png in the main folder of the model which then will be used in the HTML version of the documentation. If you want to add citations to your documentation you can do so by adding a bibtex file with the name literature.bib in the main folder of the model. To link these references in the text you can use the syntax @<id> in which "<id>" stands for the identifier given to the corresponding bibtex entry.

Author(s)

Jan Philipp Dietrich

Examples

# make sure that pandoc is available
if (check_pandoc()) {
  # run goxygen for dummy model and store documentation as HTML in a temporary directory
  docfolder <- paste0(tempdir(), "/doc")
  goxygen(system.file("dummymodel", package = "gms"),  docfolder = docfolder, output = "html")
}
# make sure that pandoc is available
if (check_pandoc()) {
  # run goxygen for dummy model and store documentation as HTML in a temporary directory
  docfolder <- paste0(tempdir(), "/doc")
  goxygen(system.file("dummymodel", package = "gms"),  docfolder = docfolder, output = "html")
}

oldBuildHTML

Description

Converts a folder with markdown files and a corresponding literature library (if available) to HTML files and creates cross-links between them.

Usage

oldBuildHTML(
  folder = "html",
  mdfolder = "markdown",
  literature = "literature.bib",
  citation = "../CITATION.cff",
  supplementary = NULL,
  addHTML = NULL
)
oldBuildHTML(
  folder = "html",
  mdfolder = "markdown",
  literature = "literature.bib",
  citation = "../CITATION.cff",
  supplementary = NULL,
  addHTML = NULL
)

Arguments

`folder`	location the HTML files should be written to
`mdfolder`	path to the markdown folder to be used as source
`literature`	path to a bibliography, if available (will be ignored if file does not exist)
`citation`	Citation information in citation file format (optional)
`supplementary`	a vector of files and/or folders required for the conversion (e.g. an images subdirectory with figures to be shown in the documents)
`addHTML`	character vector with HTML code which should be added to the body of each HTML file.

Details

Pandoc (https://pandoc.org/) together with pandoc-citeproc need to be installed on the system.

Author(s)

Jan Philipp Dietrich

returnReferences

Description

Support function to create a reference file linking references with corresponding adresses.

Usage

returnReferences(names, targets, file, level = 2)
returnReferences(names, targets, file, level = 2)

Arguments

`names`	vector of reference names
`targets`	vector of reference adresses (same order and lengths as names)
`file`	name of the reference file to be written
`level`	level of the "References" title to be written

Author(s)

Jan Philipp Dietrich

`zz`	a connection object of class "textConnection" containing the markdown document
`title`	the title to be used (character vector of length 1)
`level`	level of the heading (1 means main header, higher numbers reflect lower levels)
`id`	ID given to the title (relevant for anchors)

`zz`	a connection object of class "textConnection" containing the markdown document
`name`	Name of the module for which the interfaceplot should be shown
`docfolder`	folder the documentation should be written to relative to model folder

`zz`	a connection object of class "textConnection" containing the markdown document
`limitations`	A character vector containing the given limitations
`emptyIfNULL`	switch which decides whether limitations section should be ignored, if limitations input is NULL or if it should state that there are no known limitations.

`data`	a character vector to be written to the markdown document
`zz`	a connection object of class "textConnection" containing the markdown document
`title`	the title to be used (character vector of length 1)
`level`	level of the heading (1 means main header, higher numbers reflect lower levels)
`id`	ID given to the title (relevant for anchors)

`zz`	a connection object of class "textConnection" containing the markdown document
`data`	a character vector to be written to the markdown document

Package 'goxygen'

Help Index

.empty

Description

Usage

Arguments

Author(s)

See Also

.header

Description

Usage

Arguments

Author(s)

See Also

.interfaceplot

Description

Usage

Arguments

Author(s)

See Also

.limitations

Description

Usage

Arguments

Author(s)

See Also

.section

Description

Usage

Arguments

Author(s)

See Also

.updateImagePaths

Description

Usage

Arguments

Author(s)

See Also

.write

Description

Usage

Arguments

Author(s)

See Also

appendExtraPageBlocks

Description

Usage

Arguments

Author(s)

buildHTML

Description

Usage

Arguments

Details

Author(s)

See Also

buildMarkdown

Description

Usage

Arguments

Author(s)

See Also

buildTEX

Description

Usage

Arguments

Details

Author(s)

See Also

check_pandoc

Description

Usage

Arguments

Value

Author(s)

chooseTemplate

Description

Usage

Arguments

Author(s)