-
-
Notifications
You must be signed in to change notification settings - Fork 877
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
move combine_words() and write_bib() to xfun
- Loading branch information
Showing
11 changed files
with
20 additions
and
431 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,172 +1,8 @@ | ||
| #' Generate BibTeX bibliography databases for R packages | ||
| #' | ||
| #' This function uses \code{utils::\link{citation}()} and | ||
| #' \code{utils::\link{toBibtex}()} to create bib entries for R packages and | ||
| #' write them in a file. It can facilitate the auto-generation of bibliography | ||
| #' databases for R packages, and it is easy to regenerate all the citations | ||
| #' after updating R packages. | ||
| #' | ||
| #' For a package, the keyword \samp{R-pkgname} is used for its bib item, where | ||
| #' \samp{pkgname} is the name of the package. Citation entries specified in the | ||
| #' \file{CITATION} file of the package are also included. The main purpose of | ||
| #' this function is to automate the generation of the package citation | ||
| #' information because it often changes (e.g. author, year, package version, | ||
| #' ...). | ||
| #' | ||
| #' There are at least two different uses for the URL in a reference list. You | ||
| #' might want to tell users where to go for more information; in that case, use | ||
| #' the default \code{packageURL = TRUE}, and the first URL listed in the | ||
| #' \file{DESCRIPTION} file will be used. Be careful: some authors don't put the | ||
| #' most relevant URL first. Alternatively, you might want to identify exactly | ||
| #' which version of the package was used in the document. If it was installed | ||
| #' from CRAN or some other repositories, the version number identifies it, and | ||
| #' \code{packageURL = FALSE} will use the repository URL (as used by | ||
| #' \code{utils::\link{citation}()}). | ||
| #' | ||
| #' @param x Package names. Packages which are not installed are ignored. | ||
| #' @param file The (\file{.bib}) file to write. By default, or if \code{NULL}, | ||
| #' output is written to the R console. | ||
| #' @param tweak Whether to fix some known problems in the citations, especially | ||
| #' non-standard format of author names. | ||
| #' @param width Width of lines in bibliography entries. If \code{NULL}, lines | ||
| #' will not be wrapped. | ||
| #' @param prefix Prefix string for keys in BibTeX entries; by default, it is | ||
| #' \samp{R-} unless \code{\link{option}('knitr.bib.prefix')} has been set to | ||
| #' another string. | ||
| #' @param lib.loc A vector of path names of R libraries. | ||
| #' @param packageURL Use the \code{URL} field from the \file{DESCRIPTION} file. | ||
| #' See Details below. | ||
| #' @return A list containing the citations. Citations are also written to the | ||
| #' \code{file} as a side effect. | ||
| #' @note Some packages on CRAN do not have standard bib entries, which was once | ||
| #' reported by Michael Friendly at | ||
| #' \url{https://stat.ethz.ch/pipermail/r-devel/2010-November/058977.html}. I | ||
| #' find this a real pain, and there are no easy solutions except contacting | ||
| #' package authors to modify their DESCRIPTION files. Anyway, the argument | ||
| #' \code{tweak} has provided ugly hacks to deal with packages which are known | ||
| #' to be non-standard in terms of the format of citations; \code{tweak = TRUE} | ||
| #' is by no means intended to hide or modify the original citation | ||
| #' information. It is just due to the loose requirements on package authors | ||
| #' for the DESCRIPTION file. On one hand, I apologize if it really mangles the | ||
| #' information about certain packages; on the other, I strongly recommend | ||
| #' package authors to consider the \samp{Authors@@R} field (see the manual | ||
| #' \emph{Writing R Extensions}) to make it easier for other people to cite R | ||
| #' packages. See \code{knitr:::.tweak.bib} for details of tweaks. Also note | ||
| #' this is subject to future changes since R packages are being updated. If | ||
| #' you want to contribute more tweaks, please edit the file | ||
| #' \file{inst/misc/tweak_bib.csv} in the source package. | ||
| #' A wrapper function of \code{xfun::pkg_bib()}. | ||
| #' @param ...,prefix Arguments passed to \code{xfun::\link[xfun]{pkg_bib}()}. | ||
| #' @export | ||
| #' @author Yihui Xie and Michael Friendly | ||
| #' @examplesIf interactive() | ||
| #' write_bib(c('RGtk2', 'gWidgets'), file = 'R-GUI-pkgs.bib') | ||
| #' unlink('R-GUI-pkgs.bib') | ||
| #' | ||
| #' write_bib(c('animation', 'rgl', 'knitr', 'ggplot2')) | ||
| #' write_bib(c('base', 'parallel', 'MASS')) # base and parallel are identical | ||
| #' write_bib('cluster', prefix = '') # a empty prefix | ||
| #' write_bib('digest', prefix = 'R-pkg-') # a new prefix | ||
| #' write_bib('digest', tweak = FALSE) # original version | ||
| #' | ||
| #' # what tweak=TRUE does | ||
| #' str(knitr:::.tweak.bib) | ||
| write_bib = function( | ||
| x = .packages(), file = '', tweak = TRUE, width = NULL, | ||
| prefix = getOption('knitr.bib.prefix', 'R-'), lib.loc = NULL, | ||
| packageURL = TRUE | ||
| ) { | ||
| system.file = function(...) base::system.file(..., lib.loc = lib.loc) | ||
| citation = function(...) utils::citation(..., lib.loc = lib.loc) | ||
| x = x[nzchar(x)] # remove possible empty string | ||
| idx = mapply(system.file, package = x) == '' | ||
| if (any(idx)) { | ||
| warning('package(s) ', paste(x[idx], collapse = ', '), ' not found') | ||
| x = x[!idx] | ||
| } | ||
| # no need to write bib for packages in base R other than `base` itself | ||
| x = setdiff(x, setdiff(xfun::base_pkgs(), 'base')) | ||
| x = sort(x) | ||
| bib = sapply(x, function(pkg) { | ||
| meta = packageDescription(pkg, lib.loc = lib.loc) | ||
| # don't use the citation() URL if the package has provided its own URL | ||
| cite = citation(pkg, auto = if (is.null(meta$URL)) meta else { | ||
| if (packageURL) meta$Repository = meta$RemoteType = NULL | ||
| # use the first URL in case the package provided multiple URLs | ||
| meta$URL = sub('[, \t\n].*', '', meta$URL) | ||
| meta | ||
| }) | ||
| if (tweak) { | ||
| # e.g. gpairs has "gpairs: " in the title | ||
| cite$title = gsub(sprintf('^(%s: )(\\1)', pkg), '\\1', cite$title) | ||
| } | ||
| entry = toBibtex(cite) | ||
| entry[1] = sub('\\{,$', sprintf('{%s%s,', prefix, pkg), entry[1]) | ||
| entry | ||
| }, simplify = FALSE) | ||
| if (tweak) { | ||
| for (i in intersect(names(.tweak.bib), x)) { | ||
| message('tweaking ', i) | ||
| bib[[i]] = merge_list(bib[[i]], .tweak.bib[[i]]) | ||
| } | ||
| bib = lapply(bib, function(b) { | ||
| b['author'] = sub('Duncan Temple Lang', 'Duncan {Temple Lang}', b['author']) | ||
| # remove the ugly single quotes required by CRAN policy | ||
| b['title'] = gsub("(^|\\W)'([^']+)'(\\W|$)", '\\1\\2\\3', b['title']) | ||
| # keep the first URL if multiple are provided | ||
| if (!is.na(b['note'])) b['note'] = gsub( | ||
| '(^.*?https?://.*?),\\s+https?://.*?(},\\s*)$', '\\1\\2', b['note'] | ||
| ) | ||
| if (!('year' %in% names(b))) b['year'] = .this.year | ||
| b | ||
| }) | ||
| } | ||
| # also read citation entries from the CITATION file if provided | ||
| bib2 = lapply(x, function(pkg) { | ||
| if (pkg == 'base') return() | ||
| if (system.file('CITATION', package = pkg) == '') return() | ||
| cites = citation(pkg, auto = FALSE) | ||
| cites = Filter(x = cites, function(cite) { | ||
| # exclude entries identical to citation(pkg, auto = TRUE) | ||
| !isTRUE(grepl('R package version', cite$note)) | ||
| }) | ||
| s = make_unique(unlist(lapply(cites, function(cite) { | ||
| if (is.null(cite$year)) format(Sys.Date(), '%Y') else cite$year | ||
| }))) | ||
| mapply(cites, s, FUN = function(cite, suffix) { | ||
| # the entry is likely to be the same as citation(pkg, auto = TRUE) | ||
| if (isTRUE(grepl('R package version', cite$note))) return() | ||
| entry = toBibtex(cite) | ||
| entry[1] = sub('\\{,$', sprintf('{%s%s,', pkg, suffix), entry[1]) | ||
| entry | ||
| }, SIMPLIFY = FALSE) | ||
| }) | ||
| bib = c(bib, unlist(bib2, recursive = FALSE)) | ||
| bib = lapply(bib, function(b) { | ||
| idx = which(names(b) == '') | ||
| if (!is.null(width)) b[-idx] = str_wrap(b[-idx], width, 2, 4) | ||
| lines = c(b[idx[1L]], b[-idx], b[idx[2L]], '') | ||
| if (tweak) { | ||
| # e.g. KernSmooth and spam has & in the title and the journal, respectively | ||
| lines = gsub('(?<!\\\\)&', '\\\\&', lines, perl = TRUE) | ||
| } | ||
| structure(lines, class = 'Bibtex') | ||
| }) | ||
| if (!is.null(file) && length(x)) write_utf8(unlist(bib), file) | ||
| invisible(bib) | ||
| write_bib = function(..., prefix = getOption('knitr.bib.prefix', 'R-')) { | ||
| xfun::pkg_bib(..., prefix = prefix) | ||
| } | ||
|
|
||
| .this.year = sprintf(' year = {%s},', format(Sys.Date(), '%Y')) | ||
|
|
||
| #' @include utils.R | ||
|
|
||
| # hack non-standard author fields | ||
| .tweak.bib = local({ | ||
| x = read.csv(inst_dir('misc/tweak_bib.csv'), stringsAsFactors = FALSE) | ||
| if (Sys.getlocale('LC_COLLATE') == 'en_US.UTF-8') { | ||
| x = x[order(xtfrm(x$package)), , drop = FALSE] # reorder entries by package names | ||
| try_silent(write.csv(x, inst_dir('misc/tweak_bib.csv'), row.names = FALSE)) | ||
| } | ||
| setNames( | ||
| lapply(x$author, function(a) c(author = sprintf(' author = {%s},', a))), | ||
| x$package | ||
| ) | ||
| }) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file was deleted.
Oops, something went wrong.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Oops, something went wrong.
Oops, something went wrong.