Merge branch 'slides' into new-ag

.github/workflows/check_on_branch.yml

@@ -17,4 +17,4 @@ jobs:
     permissions:
       contents: read
     steps:
-      - uses: inbo/actions/check_pkg@checklist-0.3.2
+      - uses: inbo/actions/check_pkg@checklist-0.3.6

.github/workflows/check_on_main.yml

@@ -16,4 +16,4 @@ jobs:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: inbo/actions/check_pkg@checklist-0.3.2
+      - uses: inbo/actions/check_pkg@checklist-0.3.6

.github/workflows/examples.yml

@@ -16,7 +16,7 @@ jobs:
       - name: checkout
         uses: actions/checkout@v2
       - name: build examples
-        uses: inbo/actions/render_inbomd@inbomd-0.6.0
+        uses: inbo/actions/render_inbomd@inbomd-0.6.1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           EXAMPLE_BRANCH: main

.github/workflows/release.yml

@@ -20,7 +20,7 @@ jobs:
       - name: Get tag message
         run: |
           TAG=$(git tag --contains $(git rev-parse HEAD))
-          TAG_BODY=$(git tag --contains {{ github.sha }} -n100 | awk '(NR>1)')
+          TAG_BODY=$(git tag --contains $(git rev-parse HEAD) -n100 | awk '(NR>2)')
           echo "TAG=$TAG" >> $GITHUB_OUTPUT
           echo "TAG_BODY=$TAG_BODY" >> $GITHUB_OUTPUT
         id: tag-body

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "INBOmd: Markdown Templates for INBO",
-  "version": "0.6.1",
+  "version": "0.6.2",
   "license": "GPL-3.0",
   "upload_type": "software",
   "description": "<p>Several templates to generate reports, presentations and posters.<\/p>",
@@ -15,16 +15,19 @@
   "contributors": [
     {
       "name": "Onkelinx, Thierry",
+      "affiliation": "Research Institute for Nature and Forest (INBO)",
       "orcid": "0000-0001-8804-4216",
       "type": "ContactPerson"
     },
     {
       "name": "Vanderhaeghe, Floris",
+      "affiliation": "Research Institute for Nature and Forest (INBO)",
       "orcid": "0000-0002-6378-6229",
       "type": "ProjectMember"
     },
     {
       "name": "Lommelen, Els",
+      "affiliation": "Research Institute for Nature and Forest (INBO)",
       "orcid": "0000-0002-3481-5684",
       "type": "ProjectMember"
     },
@@ -36,6 +39,7 @@
   "creators": [
     {
       "name": "Onkelinx, Thierry",
+      "affiliation": "Research Institute for Nature and Forest (INBO)",
       "orcid": "0000-0001-8804-4216"
     }
   ],

CITATION.cff

@@ -1,9 +1,10 @@
 cff-version: 1.2.0
 message: If you use this software, please cite it using these metadata.
-title: 'INBOmd: Markdown Templates for INBO'
+title: "INBOmd: Markdown Templates for INBO"
 authors:
 - given-names: Thierry
   family-names: Onkelinx
+  affiliation: Research Institute for Nature and Forest (INBO)
   orcid: 0000-0001-8804-4216
 keywords:
 - markdown
@@ -13,15 +14,16 @@ keywords:
 contact:
 - given-names: Thierry
   family-names: Onkelinx
+  affiliation: Research Institute for Nature and Forest (INBO)
   orcid: 0000-0001-8804-4216
 doi: 10.5281/zenodo.842223
 license: GPL-3.0
 repository-code: https://github.com/inbo/INBOmd/
 type: software
-abstract: Several templates to generate reports, presentations and posters.
+abstract: "Several templates to generate reports, presentations and posters."
 identifiers:
 - type: doi
   value: 10.5281/zenodo.842223
 - type: url
-  value: []
-version: 0.6.1
+  value: https://inbo.github.io/INBOmd/
+version: 0.6.2

DESCRIPTION

@@ -1,21 +1,24 @@
 Type: Package
 Package: INBOmd
 Title: Markdown Templates for INBO
-Version: 0.6.1
+Version: 0.6.2
 Authors@R: c(
     person("Thierry", "Onkelinx", , "thierry.onkelinx@inbo.be", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0001-8804-4216")),
+           comment = c(ORCID = "0000-0001-8804-4216", affiliation = "Research Institute for Nature and Forest (INBO)")),
     person("Floris", "Vanderhaeghe", , "floris.vanderhaeghe@inbo.be", role = "ctb",
-           comment = c(ORCID = "0000-0002-6378-6229")),
+           comment = c(ORCID = "0000-0002-6378-6229", affiliation = "Research Institute for Nature and Forest (INBO)")),
     person("Els", "Lommelen", , "els.lommelen@inbo.be", role = "ctb",
-           comment = c(ORCID = "0000-0002-3481-5684")),
+           comment = c(ORCID = "0000-0002-3481-5684", affiliation = "Research Institute for Nature and Forest (INBO)")),
     person("Research Institute for Nature and Forest (INBO)", , , "info@inbo.be", role = c("cph", "fnd"))
   )
 Description: Several templates to generate reports, presentations and
     posters.
 License: GPL-3
-URL: https://github.com/inbo/inbomd, https://doi.org/10.5281/zenodo.842223
+URL: https://inbo.github.io/INBOmd/, https://github.com/inbo/inbomd,
+    https://doi.org/10.5281/zenodo.842223
 BugReports: https://github.com/inbo/inbomd/issues
+Depends:
+    R (>= 3.5.0)
 Imports:
     assertthat,
     bookdown (>= 0.23.4),

Dockerfile

@@ -200,6 +200,9 @@ RUN  mkdir ${HOME}/.fonts \
   && fc-cache -fv \
   && Rscript -e 'tinytex:::updmap()'
 
+## Install kableExtra
+RUN  Rscript -e 'remotes::install_cran("kableExtra")'
+
 ## Install current version of INBOmd
 COPY .Rbuildignore inbomd/.Rbuildignore
 COPY DESCRIPTION inbomd/DESCRIPTION

NAMESPACE

@@ -47,6 +47,7 @@ importFrom(bookdown,gitbook)
 importFrom(bookdown,pdf_book)
 importFrom(checklist,ask_yes_no)
 importFrom(checklist,menu_first)
+importFrom(checklist,organisation)
 importFrom(checklist,read_checklist)
 importFrom(checklist,use_author)
 importFrom(dplyr,"%>%")
@@ -72,7 +73,7 @@ importFrom(knitr,kable)
 importFrom(knitr,opts_current)
 importFrom(knitr,opts_knit)
 importFrom(pdftools,pdf_convert)
-importFrom(qrcode,qrcode_gen)
+importFrom(qrcode,qr_code)
 importFrom(rmarkdown,includes_to_pandoc_args)
 importFrom(rmarkdown,knitr_options)
 importFrom(rmarkdown,output_format)

NEWS.md

@@ -1,6 +1,16 @@
+# INBOmd 0.6.2
+
+* Bugfixes
+
 # INBOmd 0.6.1
 
+* INBO authors and reviewers now must use their `orcid` and a standardised
+  `affiliation`.
+  We infer INBO membership from the author's email address.
+* `create_report()` and `add_author()` will set the INBO author affiliation in
+  the language of the report.
 * `slides()` no longer requires a reviewer.
+* Install missing `TinyTeX` installation or packages.
 * Bugfixes in `create_report()`.
 
 # INBOmd 0.6.0

R/add_author.R

@@ -20,14 +20,21 @@ add_author <- function(path = ".") {
 
   path(path, "index.Rmd") |>
     readLines() -> index
+  lang <- grep("^lang:", index)
+  assert_that(length(lang) > 0, msg = "No `lang:` entry found in yaml header")
+  assert_that(
+    length(lang) == 1, msg = "Multiple `lang:` entries found in yaml header"
+  )
+  lang <- gsub("lang: ", "", index[lang])
+
   author <- grep("^author:", index)
   assert_that(
     length(author) > 0, msg = "No `author:` entry found in yaml header"
   )
   assert_that(
     length(author) == 1, msg = "Multiple `author:` entries found in yaml header"
   )
-  use_author() |>
+  check_author(lang = lang) |>
     author2yaml(corresponding = FALSE) -> extra
   top <- grep("^\\w+:", index) - 1
   insert <- head(top[top > author], 1)

R/create_report.R

@@ -14,7 +14,8 @@
 #' @family utils
 #' @export
 #' @importFrom assertthat assert_that is.string noNA
-#' @importFrom checklist ask_yes_no menu_first read_checklist use_author
+#' @importFrom checklist ask_yes_no menu_first organisation read_checklist
+#' use_author
 #' @importFrom fs dir_create file_copy is_dir is_file path
 #' @importFrom gert git_find
 create_report <- function(path = ".", shortname) {
@@ -37,6 +38,16 @@ msg = "The report name folder may only contain lower case letters, digits and _"
     msg = "The report name folder already exists."
   )
 
+  lang <- c(nl = "Dutch", en = "English", fr = "French")
+  lang <- names(lang)[
+    menu_first(lang, title = "What is the main language of the report?")
+  ]
+  style <- c("INBO", "Vlaanderen")
+  style <- ifelse(
+    lang != "nl", "Flanders",
+    style[menu_first(style, title = "Which style to use?")]
+  )
+
   # build new yaml
   readline(prompt = "Enter the title: ") |>
     gsub(pattern = "[\"|']", replacement = "") |>
@@ -47,10 +58,10 @@ msg = "The report name folder may only contain lower case letters, digits and _"
     gsub(pattern = "[\"|']", replacement = "") -> subtitle
   yaml <- c(yaml, paste("subtitle:", subtitle)[subtitle != ""])
   cat("Please select the corresponding author")
-  authors <- use_author()
+  authors <- check_author(lang = lang)
   c(yaml, "author:", author2yaml(authors, corresponding = TRUE)) -> yaml
   while (isTRUE(ask_yes_no("Add another author?", default = FALSE))) {
-    author <- use_author()
+    author <- check_author(lang = lang)
     authors[, c("given", "family", "email")] |>
       rbind(author[, c("given", "family", "email")]) |>
       anyDuplicated() -> duplo
@@ -66,7 +77,7 @@ msg = "The report name folder may only contain lower case letters, digits and _"
   cat("Please select the reviewer")
   duplo <- 1
   while (duplo > 0) {
-    author <- use_author()
+    author <- check_author(lang = lang)
     authors[, c("given", "family", "email")] |>
       rbind(author[, c("given", "family", "email")]) |>
       anyDuplicated() -> duplo
@@ -80,6 +91,8 @@ msg = "The report name folder may only contain lower case letters, digits and _"
   lang <- names(lang)[
     menu_first(lang, title = "What is the main language of the report?")
   ]
+  org <- organisation$new()
+  aff <- org$get_organisation[["inbo.be"]]$affiliation[lang]
   style <- c("INBO", "Vlaanderen")
   style <- ifelse(
     lang != "nl", "Flanders",
@@ -106,8 +119,7 @@ msg = "The report name folder may only contain lower case letters, digits and _"
     "lof: TRUE"[ask_yes_no("Do you want a list of figures?", default = FALSE)],
     "lot: TRUE"[ask_yes_no("Do you want a list of tables?", default = FALSE)],
     keywords, "community: \"inbo\"", "publication_type: report",
-    "funder: Research Institute for Nature and Forest (INBO)",
-    "rightsholder: Research Institute for Nature and Forest (INBO)",
+    paste("funder:", aff), paste("rightsholder:", aff),
     "bibliography: references.bib", "link-citations: TRUE",
     "site: bookdown::bookdown_site", "output:", "  INBOmd::gitbook: default",
     "  INBOmd::pdf_report: default", "  INBOmd::epub_book: default",
@@ -245,7 +257,7 @@ author2yaml <- function(author, corresponding = FALSE) {
     yaml <- c(yaml, sprintf("    orcid: \"%s\"", author$orcid))
   }
   if (!is.na(author$affiliation) && author$affiliation != "") {
-    yaml <- c(yaml, paste("    affiliation: \"%s\"", author$affiliation))
+    yaml <- c(yaml, sprintf("    affiliation: \"%s\"", author$affiliation))
   }
   if (!corresponding) {
     return(paste(yaml, collapse = "\n"))
@@ -280,3 +292,22 @@ add_address <- function(type = "client") {
     sprintf("%s_logo: %s", type, logo)[logo != ""]
   )
 }
+
+#' @importFrom checklist use_author
+check_author <- function(lang = "nl") {
+  person <- use_author()
+  if (is_inbo(person) && !person$affiliation %in% inbo_affiliation) {
+    paste0("`", inbo_affiliation, "`", collapse = "; ") |>
+      sprintf(fmt = "INBO staff must use one of %s as affiliation.") |>
+      cat("Please update the author information.", "\n", sep = " ")
+    person <- check_author(lang = "nl")
+    person$affiliation <- inbo_affiliation[lang]
+  }
+  if (is_inbo(person) && is.na(person$orcid)) {
+    cat(
+      "INBO staff must provide an ORCID.",
+      "Please update the author information.", "\n", sep = " "
+    )
+    person <- check_author(lang = "nl")
+  }
+}

R/ebook.R

@@ -15,6 +15,10 @@ epub_book <- function() {
     yaml_front_matter() |>
     validate_persons(reviewer = TRUE) |>
     validate_rightsholder() -> fm
+  assert_that(
+    !has_name(fm, "nocolophon"), msg = "Legacy option `nocolophon` detected.
+    Please use the `public_report` option."
+  )
   style <- ifelse(has_name(fm, "style"), fm$style, "INBO")
   assert_that(length(style) == 1)
   assert_that(style %in% c("INBO", "Vlaanderen", "Flanders"),
@@ -40,7 +44,6 @@ epub_book <- function() {
     style == "Flanders" || lang == "nl",
     msg = "Use style: Flanders when the language is not nl"
   )
-  validate_doi(ifelse(has_name(fm, "doi"), fm$doi, "1.1/1"))
 
   pandoc_args <- c(
     "--csl",
@@ -50,6 +53,23 @@ epub_book <- function() {
     "--lua-filter",
     system.file(file.path("pandoc", "translations.lua"), package = "INBOmd")
   )
+  validate_doi(ifelse(has_name(fm, "doi"), fm$doi, "1.1/1"))
+  if (
+    !has_name(fm, "doi") && has_name(fm, "public_report") && !fm$public_report
+  ) {
+    Sys.time() |>
+      format("%Y-%m-%d %H:%M:%S") |>
+      c(fm$reportnr) |>
+      tail(1) |>
+      pandoc_variable_arg(name = "pagefootmessage") |>
+      c(pandoc_variable_arg("internal", "true")) |>
+      c(pandoc_args) -> pandoc_args
+  } else {
+    c(fm$doi, "!!! missing DOI !!!") |>
+      head(1) |>
+      pandoc_variable_arg(name = "doi") |>
+      c(pandoc_args) -> pandoc_args
+  }
   file.path("css_styles", c("fonts", "img")) |>
     system.file(package = "INBOmd") |>
     list.files(full.names = TRUE) -> fonts

R/gitbook.R

@@ -53,7 +53,6 @@ gitbook <- function(code_folding = c("none", "show", "hide")) {
     split_by %in% c("chapter+number", "section+number"),
     msg = "`split_by` must be either 'chapter+number' or `section+number`"
   )
-  validate_doi(ifelse(has_name(fm, "doi"), fm$doi, "1.1/1"))
 
   pandoc_args <- c(
     "--csl",
@@ -63,6 +62,24 @@ gitbook <- function(code_folding = c("none", "show", "hide")) {
     "--lua-filter",
     system.file(file.path("pandoc", "translations.lua"), package = "INBOmd")
   )
+  validate_doi(ifelse(has_name(fm, "doi"), fm$doi, "1.1/1"))
+  if (
+    !has_name(fm, "doi") && has_name(fm, "public_report") && !fm$public_report
+  ) {
+    Sys.time() |>
+      format("%Y-%m-%d %H:%M:%S") |>
+      c(fm$reportnr) |>
+      tail(1) |>
+      pandoc_variable_arg(name = "pagefootmessage") |>
+      c(pandoc_variable_arg("internal", "true")) |>
+      c(pandoc_args) -> pandoc_args
+  } else {
+    c(fm$doi, "!!! missing DOI !!!") |>
+      head(1) |>
+      pandoc_variable_arg(name = "doi") |>
+      c(pandoc_args) -> pandoc_args
+  }
+
   assert_that(
     getwd() |>
       path("index.Rmd") |>
@@ -110,7 +127,7 @@ gitbook <- function(code_folding = c("none", "show", "hide")) {
     template = template, extra_dependencies = list(inbomd_dep),
     code_folding = code_folding
   )
-  post <- config$post_processor  # in case a post processor have been defined
+  op <- config$post_processor  # in case a post processor have been defined
   config$post_processor <- function(metadata, input, output, clean, verbose) {
     file(output, encoding = "UTF-8") |>
       readLines() -> x
@@ -119,7 +136,7 @@ gitbook <- function(code_folding = c("none", "show", "hide")) {
       x <- c(head(x, i - 1), "", tail(x, -i + 1))
     }
     writeLines(x, output)
-    post(metadata, input, output, clean, verbose)
+    op(metadata, input, output, clean, verbose)
   }
   config$clean_supporting <- TRUE
   return(config)