Merge pull request #48 from Pakillo/latex

0.2.10 add LaTeX as output format

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: grateful
 Title: Facilitate Citation of R Packages
-Version: 0.2.9
+Version: 0.2.10
 Authors@R: c(
     person("Francisco", "Rodriguez-Sanchez", 
             email = "[email protected]", 

NEWS.md

@@ -1,3 +1,7 @@
+# grateful 0.2.10
+
+* Add support for LaTeX output (thanks @patrick-weiss for the suggestion). Use `out.format = "tex-document"` to obtain a full LaTeX document, or `out.format = "tex-fragment"` to produce just a fragment citing packages to be copied into another existing LaTeX document.
+
 # grateful 0.2.9
 
 * Match package names with citation keys explicitly, rather than relying on sorting.

R/cite_packages.R

@@ -64,7 +64,9 @@
 #'   the references. It is recommended to set `out.dir = getwd()`.
 #'
 #' @param out.format Output format when `output = "file"`:
-#' either "html" (the default), "docx" (Word), "pdf", "Rmd", or "md" (markdown).
+#' either "html" (the default), "docx" (Word), "pdf",
+#' "tex-fragment" (LaTeX fragment to be inserted into another LaTeX document),
+#' "tex-document" (full LaTeX document), "Rmd", or "md" (markdown).
 #' (Note that choosing "pdf" requires a working installation of LaTeX,
 #' see <https://yihui.org/tinytex/>).
 #'
@@ -158,7 +160,8 @@
 
 cite_packages <- function(output = c("file", "paragraph", "table", "citekeys"),
                           out.dir = NULL,
-                          out.format = c("html", "docx", "pdf", "Rmd", "md"),
+                          out.format = c("html", "docx", "pdf", "Rmd", "md",
+                                         "tex-fragment", "tex-document"),
                           citation.style = NULL,
                           pkgs = "All",
                           omit = c("grateful"),

R/create_rmd.R

@@ -7,7 +7,9 @@
 #' as produced by [get_pkgs_info()].
 #' @param csl Optional. Citation style to format references.
 #' See <https://www.zotero.org/styles>.
-#' @param out.format Output format. One of: "html", docx" (Word), "pdf", "Rmd", or "md" (markdown).
+#' @param out.format Output format, either "html", docx" (Word), "pdf",
+#' "tex-fragment" (LaTeX fragment to be inserted into another LaTeX document),
+#' "tex-document" (full LaTeX document), "Rmd"(Rmarkdown), or "md" (markdown).
 #' @param Rmd.file Name of the Rmarkdown file to be created.
 #' @param include.RStudio Include RStudio?
 #' @param passive.voice Logical. If `TRUE`, uses passive voice in any paragraph
@@ -23,7 +25,8 @@ create_rmd <- function(pkgs.df = NULL,
                        bib.file = "grateful-refs",
                        csl = NULL,
                        Rmd.file = "grateful-report",
-                       out.format = c("html", "docx", "pdf", "Rmd", "md"),
+                       out.format = c("html", "docx", "pdf", "Rmd", "md",
+                                      "tex-fragment", "tex-document"),
                        include.RStudio = FALSE,
                        passive.voice = FALSE,
                        ...) {

R/render_citations.R

@@ -2,7 +2,9 @@
 #'
 #' @param Rmd.file Path to Rmarkdown file generated by [create_rmd()].
 #' @param out.dir Directory to save the output document.
-#' @param out.format Output format, either "html", docx" (Word), "pdf", or "md" (markdown).
+#' @param out.format Output format, either "html", docx" (Word), "pdf",
+#' "tex-fragment" (LaTeX fragment to be inserted into another LaTeX document),
+#' "tex-document" (full LaTeX document), or "md" (markdown).
 #'
 #' @return A document in the format specified by `out.format`.
 #'
@@ -11,7 +13,8 @@
 
 render_citations <- function(Rmd.file = NULL,
                              out.dir = NULL,
-                             out.format = c("html", "docx", "pdf", "md")
+                             out.format = c("html", "docx", "pdf", "md",
+                                            "tex-fragment", "tex-document")
                              ) {
 
   if (is.null(Rmd.file)) {
@@ -28,14 +31,23 @@ render_citations <- function(Rmd.file = NULL,
   if (out.format == "pdf") output <- "pdf_document"
   if (out.format == "html") output <- "html_document"
   if (out.format == "md") output <- "md_document"
+  if (out.format == "tex-fragment") output <- "latex_fragment"
+  if (out.format == "tex-document") output <- "latex_document"
+
+  output.options <- NULL
+  if (out.format == "tex-fragment" | out.format == "tex-document") {
+    out.format <- "tex"
+    output.options <- list(latex_engine = "xelatex", citation_package = "natbib")
+  }
 
   out.name <- gsub(pattern = ".Rmd", replacement = "", basename(Rmd.file))
 
   rmarkdown::render(
     input = Rmd.file,
     output_format = output,
     output_file = paste0(out.name, ".", out.format),
-    output_dir = out.dir
+    output_dir = out.dir,
+    output_options = output.options
   )
 
   out.file <- file.path(out.dir, paste0(out.name, ".", out.format))

README.Rmd

@@ -22,12 +22,14 @@ knitr::opts_chunk$set(
 [![Codecov test coverage](https://codecov.io/gh/Pakillo/grateful/branch/master/graph/badge.svg)](https://app.codecov.io/gh/Pakillo/grateful?branch=master)
 `r badger::badge_lifecycle("stable")`
 `r badger::badge_repostatus("Active")`
+[![HitCount since 2024-06-05](https://hits.dwyl.com/Pakillo/grateful.svg?style=flat-square)](https://hits.dwyl.com/Pakillo/grateful)
+[![HitCount since 2024-06-05](https://hits.dwyl.com/Pakillo/grateful.svg?style=flat-square&show=unique)](https://hits.dwyl.com/Pakillo/grateful)
 [![](https://cranlogs.r-pkg.org/badges/grand-total/grateful)](https://cran.r-project.org/package=grateful)
 <!-- badges: end -->
 
 The goal of **grateful** is to make it very easy to cite R and the R packages used in any analyses, so that package authors receive their deserved credit. By calling a single function, **grateful** will scan the project for R packages used and generate a BibTeX file containing all citations for those packages. 
 
-**grateful** can then generate a new document with citations in the desired output format (Word, PDF, HTML, Markdown). These references can be formatted for a specific journal, so that we can just paste them directly into our manuscript or report. 
+**grateful** can then generate a new document with citations in the desired output format (Word, PDF, LaTeX, HTML, Markdown). These references can be formatted for a specific journal, so that we can just paste them directly into our manuscript or report. 
 
 Alternatively, we can use **grateful** directly within an [Rmarkdown](https://rmarkdown.rstudio.com/) or [Quarto](https://quarto.org/) document. In this case, a paragraph containing in-text citations of all used R packages will (optionally) be inserted into the Rmarkdown/Quarto document, and these packages will be included in the reference list when rendering. 
 
@@ -75,7 +77,7 @@ cite_packages(out.dir = ".")            # save report to working directory
 
 <br>
 
-This document can also be a Word document, PDF file, markdown file, or left as the source Rmarkdown file using `out.format`:
+This document can also be a Word or LaTeX document, PDF file, markdown file, or left as the source Rmarkdown file using `out.format`:
 
 ```{r eval = FALSE}
 cite_packages(out.format = "docx", out.dir = ".")

README.md

@@ -15,6 +15,10 @@ coverage](https://codecov.io/gh/Pakillo/grateful/branch/master/graph/badge.svg)]
 [![Project Status: Active - The project has reached a stable, usable
 state and is being actively
 developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
+[![HitCount since
+2024-06-05](https://hits.dwyl.com/Pakillo/grateful.svg?style=flat-square)](https://hits.dwyl.com/Pakillo/grateful)
+[![HitCount since
+2024-06-05](https://hits.dwyl.com/Pakillo/grateful.svg?style=flat-square&show=unique)](https://hits.dwyl.com/Pakillo/grateful)
 [![](https://cranlogs.r-pkg.org/badges/grand-total/grateful)](https://cran.r-project.org/package=grateful)
 <!-- badges: end -->
 
@@ -25,9 +29,9 @@ the project for R packages used and generate a BibTeX file containing
 all citations for those packages.
 
 **grateful** can then generate a new document with citations in the
-desired output format (Word, PDF, HTML, Markdown). These references can
-be formatted for a specific journal, so that we can just paste them
-directly into our manuscript or report.
+desired output format (Word, PDF, LaTeX, HTML, Markdown). These
+references can be formatted for a specific journal, so that we can just
+paste them directly into our manuscript or report.
 
 Alternatively, we can use **grateful** directly within an
 [Rmarkdown](https://rmarkdown.rstudio.com/) or
@@ -85,8 +89,8 @@ cite_packages(out.dir = ".")            # save report to working directory
 
 <br>
 
-This document can also be a Word document, PDF file, markdown file, or
-left as the source Rmarkdown file using `out.format`:
+This document can also be a Word or LaTeX document, PDF file, markdown
+file, or left as the source Rmarkdown file using `out.format`:
 
 ``` r
 cite_packages(out.format = "docx", out.dir = ".")

tests/testthat/test-create_rmd.R

@@ -8,7 +8,7 @@ test_that("NULL arguments return error", {
 test_that("create_rmd produces correct Rmd", {
 
   skip_on_cran()
-  skip_on_ci()
+  # skip_on_ci()
 
   pkgs <- get_pkgs_info(pkgs = "grateful", out.dir = tempdir())
   rmd <- create_rmd(pkgs.df = pkgs, out.dir = tempdir(), out.format = "Rmd")
@@ -27,7 +27,7 @@ test_that("create_rmd produces correct Rmd", {
                  "",
                  "|Package  |Version |Citation  |",
                  "|:--------|:-------|:---------|",
-                 paste0("|grateful |", utils::packageVersion("grateful"),"   |@grateful |"),
+                 paste0("|grateful |", utils::packageVersion("grateful"),"  |@grateful |"),
                  "",
                  "**You can paste this paragraph directly in your report:**",
                  "",
@@ -39,3 +39,25 @@ test_that("create_rmd produces correct Rmd", {
 
 
 })
+
+
+
+test_that("csl is downloaded if needed", {
+  skip_on_cran()
+  pkgs <- get_pkgs_info(pkgs = "grateful", out.dir = tempdir())
+  rmd <- create_rmd(pkgs.df = pkgs, out.dir = tempdir(), out.format = "Rmd",
+                    csl = "peerj")
+  expect_true(file.exists(file.path(tempdir(), "peerj.csl")))
+
+})
+
+
+test_that("rendered report is produced", {
+  skip_on_cran()
+  skip_on_ci()
+  pkgs <- get_pkgs_info(pkgs = "grateful", out.dir = tempdir())
+  rmd <- create_rmd(pkgs.df = pkgs, out.dir = tempdir(), out.format = "html")
+  expect_true(file.exists(file.path(tempdir(), "grateful-report.html")))
+  expect_true(!file.exists(file.path(tempdir(), "grateful-report.Rmd")))
+
+})

tests/testthat/test-render_citations.R

@@ -33,4 +33,14 @@ test_that("render_citations returns a report", {
   expect_equal(rendcit, file.path(tempdir(), "grateful-report.md"))
   expect_true(file.exists(file.path(tempdir(), "grateful-report.md")))
 
+  # LaTeX fragment
+  rendcit <- render_citations(Rmd.file = rmd, out.dir = tempdir(), out.format = "tex-fragment")
+  expect_equal(rendcit, file.path(tempdir(), "grateful-report.tex"))
+  expect_true(file.exists(file.path(tempdir(), "grateful-report.tex")))
+
+  # LaTeX document
+  rendcit <- render_citations(Rmd.file = rmd, out.dir = tempdir(), out.format = "tex-document")
+  expect_equal(rendcit, file.path(tempdir(), "grateful-report.tex"))
+  expect_true(file.exists(file.path(tempdir(), "grateful-report.tex")))
+
 })