Merge pull request #98 from inbo/update

Version 0.6.3

Author: ThierryO

.github/workflows/examples.yml

@@ -14,9 +14,9 @@ jobs:
     name: "test Rmd"
     steps:
       - name: checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: build examples
-        uses: inbo/actions/[email protected].2
+        uses: inbo/actions/[email protected].3
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           EXAMPLE_BRANCH: main

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "INBOmd: Markdown Templates for INBO",
-  "version": "0.6.2",
+  "version": "0.6.3",
   "license": "GPL-3.0",
   "upload_type": "software",
   "description": "<p>Several templates to generate reports, presentations and posters.<\/p>",

CITATION.cff

@@ -26,4 +26,4 @@ identifiers:
   value: 10.5281/zenodo.842223
 - type: url
   value: https://inbo.github.io/INBOmd/
-version: 0.6.2
+version: 0.6.3

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: INBOmd
 Title: Markdown Templates for INBO
-Version: 0.6.2
+Version: 0.6.3
 Authors@R: c(
     person("Thierry", "Onkelinx", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8804-4216", affiliation = "Research Institute for Nature and Forest (INBO)")),
@@ -49,4 +49,4 @@ Config/checklist/keywords: markdown; bookdown; corporate identity;
 Encoding: UTF-8
 Language: en-GB
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0

Dockerfile

@@ -57,12 +57,6 @@ RUN  apt-get update \
   && apt-get install -y --no-install-recommends \
     git
 
-## Install pandoc
-RUN apt-get update \
-  && apt-get install -y --no-install-recommends \
-    pandoc \
-    pandoc-citeproc
-
 ## Install gpg
 RUN apt-get update \
   && apt-get install -y --no-install-recommends \
@@ -82,6 +76,11 @@ RUN apt-get update \
   && apt-get install -y  --no-install-recommends \
     r-base-dev
 
+## Install pandoc
+RUN  wget https://github.com/jgm/pandoc/releases/download/3.1.8/pandoc-3.1.8-1-amd64.deb \
+  && dpkg -i pandoc-3.1.8-1-amd64.deb \
+  && rm pandoc-3.1.8-1-amd64.deb
+
 COPY docker/.Rprofile /usr/lib/R/etc/Rprofile.site
 
 ## R packages

NAMESPACE

@@ -77,6 +77,7 @@ importFrom(qrcode,qr_code)
 importFrom(rmarkdown,includes_to_pandoc_args)
 importFrom(rmarkdown,knitr_options)
 importFrom(rmarkdown,output_format)
+importFrom(rmarkdown,pandoc_available)
 importFrom(rmarkdown,pandoc_options)
 importFrom(rmarkdown,pandoc_path_arg)
 importFrom(rmarkdown,pandoc_variable_arg)

NEWS.md

@@ -1,3 +1,8 @@
+# INBOmd 0.6.3
+
+* `pdf_report()` enforces pandoc >= 3.1.8
+* `create_report()` fixed (#97)
+
 # INBOmd 0.6.2
 
 * `pdf_report()`, `gitbook()` and `epub_book()` gain an option to create 

R/create_report.R

@@ -310,4 +310,5 @@ check_author <- function(lang = "nl") {
     )
     person <- check_author(lang = "nl")
   }
+  return(person)
 }

R/pdf_report.R

@@ -7,13 +7,13 @@
 #' @export
 #' @importFrom assertthat assert_that has_name is.string
 #' @importFrom fs path
-#' @importFrom rmarkdown output_format knitr_options pandoc_options
-#' pandoc_variable_arg includes_to_pandoc_args pandoc_version
-#' @importFrom utils compareVersion
+#' @importFrom rmarkdown output_format knitr_options pandoc_available
+#' pandoc_options pandoc_variable_arg includes_to_pandoc_args
 #' @family output
 pdf_report <- function(
   fig_crop = "auto", includes = NULL, pandoc_args = NULL, ...
 ) {
+  pandoc_available(version = "3.1.8", error = TRUE)
   dots <- list(...)
   assert_that(
     !has_name(dots, "number_sections"), msg =
@@ -97,12 +97,8 @@ pdf_report <- function(
   )
 
   args <- c(
-    "--template", template,
-    ifelse(
-      compareVersion(as.character(pandoc_version()), "2") < 0,
-      "--latex-engine", "--pdf-engine"
-    ),
-    "xelatex", pandoc_args, c("--csl", pandoc_path_arg(csl)),
+    "--template", template, "--pdf-engine",
+    "xelatex", pandoc_args, "--csl", pandoc_path_arg(csl),
     includes_to_pandoc_args(includes)
   )
   args <- args[args != ""]
@@ -195,11 +191,11 @@ pdf_report <- function(
 
     # move appendix after bibliography
     appendix <- grep("\\\\appendix", text)
-    startbib <- grep("\\\\hypertarget\\{refs\\}\\{\\}", text) # nolint: absolute_path_linter, line_length_linter.
+    startbib <- grep("\\\\phantomsection\\\\label\\{refs\\}", text) # nolint: absolute_path_linter, line_length_linter.
     if (length(startbib)) {
       if (length(appendix)) {
         text <- c(
-          text[1:(appendix - 1)],              # mainmatter
+          head(text, appendix - 1),            # mainmatter
           "\\chapter*{\\bibname}",
           "\\addcontentsline{toc}{chapter}{\\bibname}",
           text[startbib],                      # bibliography
@@ -208,18 +204,18 @@ pdf_report <- function(
           "",
           text[(startbib + 2):(length(text) - 1)],
           text[(appendix):(startbib - 1)],     # appendix
-          text[length(text)]                   # backmatter
+          tail(text, 1)                        # backmatter
         )
       } else {
         text <- c(
-          text[1:(startbib - 1)],              # mainmatter
+          head(text, startbib - 1),            # mainmatter
           "\\chapter*{\\bibname}",
           "\\addcontentsline{toc}{chapter}{\\bibname}",
           text[startbib],                      # bibliography
           "",
           text[startbib + 1],
           "",
-          text[(startbib + 2):length(text)]
+          tail(text, -startbib - 1)
         )
       }
     }

inst/CITATION

@@ -2,12 +2,12 @@ citHeader("To cite `INBOmd` in publications please use:")
 # begin checklist entry
 bibentry(
   bibtype = "Manual",
-  title = "INBOmd: Markdown Templates for INBO. Version 0.6.2",
+  title = "INBOmd: Markdown Templates for INBO. Version 0.6.3",
   author = c( author = c(person(given = "Thierry", family = "Onkelinx"))),
-  year = 2023,
+  year = 2024,
   url = "https://inbo.github.io/INBOmd/",
   abstract = "Several templates to generate reports, presentations and posters.",
-  textVersion = "Onkelinx, Thierry (2023) INBOmd: Markdown Templates for INBO. Version 0.6.2. https://inbo.github.io/INBOmd/",
+  textVersion = "Onkelinx, Thierry (2024) INBOmd: Markdown Templates for INBO. Version 0.6.3. https://inbo.github.io/INBOmd/",
   keywords = "markdown; bookdown; corporate identity; template",
   doi = "10.5281/zenodo.842223",
 )