Merge pull request #93 from inbo/slides

bugfix in create_report()

.Rbuildignore

@@ -15,6 +15,7 @@ Dockerfile
 ^data-raw$
 ^docs$
 ^man-roxygen$
+^organisation.yml$
 ^pkgdown$
 create_docker.sh
 docker

.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_different_r_os.yml

@@ -42,10 +42,9 @@ jobs:
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r-dependencies@v2
-
-      - uses: r-lib/actions/check-r-package@v2
         with:
           extra-packages: any::rcmdcheck
+          needs: check
 
       - uses: r-lib/actions/check-r-package@v2
         with:

.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-0.6.2
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           EXAMPLE_BRANCH: main

.github/workflows/release.yml

@@ -5,27 +5,26 @@ on:
     tags:
       - v*
   workflow_run:
-    workflows: ["check package on main"]
+    workflows: ["check package on main with checklist"]
     types:
       - completed
 
 jobs:
-
-  build:
+  publish:
     runs-on: ubuntu-latest
     permissions:
       contents: write
     steps:
       - uses: actions/checkout@v3
-      - name: Get tag message
+      - name: Get tag
         run: |
+          git fetch --tags --force
           TAG=$(git tag --contains $(git rev-parse HEAD))
-          TAG_BODY=$(git tag --contains {{ github.sha }} -n100 | awk '(NR>1)')
-          echo "TAG=$TAG" >> $GITHUB_OUTPUT
-          echo "TAG_BODY=$TAG_BODY" >> $GITHUB_OUTPUT
-        id: tag-body
+          TAG_BODY=$(git tag --contains $(git rev-parse HEAD) --format='%(contents)')
+          echo "tag=$TAG" >> $GITHUB_ENV
+          echo "$TAG_BODY" > body.md
       - uses: ncipollo/release-action@v1
         with:
-          name: Release ${{ steps.tag-body.outputs.TAG }}
-          tag: ${{ steps.tag-body.outputs.TAG }}
-          body: ${{ steps.tag-body.outputs.TAG_BODY }}
+          name: Release ${{ env.tag }}
+          tag: ${{ env.tag }}
+          bodyFile: body.md

.gitignore

@@ -14,6 +14,7 @@
 *_files
 .DS_Store
 .RData
+.Renviron
 .Rhistory
 .Rproj.user
 .Ruserdata

.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

@@ -108,6 +108,13 @@ RUN apt-get update \
     r-cran-tinytex \
     r-cran-webshot
 
+## Install textshape
+RUN  apt-get update \
+  && apt-get install -y --no-install-recommends \
+    libfribidi-dev \
+    libharfbuzz-dev \
+  && Rscript -e 'remotes::install_cran("textshape")'
+
 ## Install ragg
 RUN  apt-get update \
   && apt-get install -y --no-install-recommends \
@@ -176,7 +183,11 @@ RUN  Rscript -e 'remotes::install_cran("lipsum")'
 RUN  Rscript -e 'remotes::install_cran("here")'
 
 ## Install gert
-RUN  Rscript -e 'remotes::install_cran("gert")'
+RUN  apt-get update \
+  && apt-get install -y  --no-install-recommends \
+    libcurl4-openssl-dev \
+    libssl-dev \
+  && Rscript -e 'remotes::install_cran("gert")'
 
 ## Install webshot dependency
 RUN  Rscript -e 'webshot::install_phantomjs()'
@@ -200,6 +211,9 @@ 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 +1,25 @@
+# INBOmd 0.6.2
+
+* `pdf_report()`, `gitbook()` and `epub_book()` gain an option to create 
+  internal reports with a different colophon.
+* `pdf_report()` and `gitbook()` gain a watermark argument.
+  It adds a text watermark in the margin of every page.
+  An automatic watermark appears when one of the required colophon fields is
+  missing.
+  Adding the information for all required colophon fields will remove this
+  automatic watermark.
+* All INBO personnel must display proper affiliation and ORCID.
+* 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")
+  }
+}