diff --git a/.github/workflows/check_on_branch.yml b/.github/workflows/check_on_branch.yml deleted file mode 100644 index 1ee5f636..00000000 --- a/.github/workflows/check_on_branch.yml +++ /dev/null @@ -1,22 +0,0 @@ -on: - push: - branches-ignore: - - main - - master - - ghpages - -name: "check package with checklist" - -jobs: - check-package: - runs-on: ubuntu-latest - name: "check package" - env: - CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - permissions: - contents: read - steps: - - uses: inbo/actions/check_pkg@main - with: - aptget: libpoppler-cpp-dev diff --git a/.github/workflows/check_on_main.yml b/.github/workflows/check_on_main.yml deleted file mode 100644 index 8c32ec62..00000000 --- a/.github/workflows/check_on_main.yml +++ /dev/null @@ -1,21 +0,0 @@ -on: - push: - branches: - - main - - master -permissions: - contents: write - -name: "check package on main with checklist" - -jobs: - check-package: - runs-on: ubuntu-latest - name: "check package" - env: - CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - steps: - - uses: inbo/actions/check_pkg@main - with: - aptget: libpoppler-cpp-dev diff --git a/.github/workflows/check_package.yaml b/.github/workflows/check_package.yaml new file mode 100644 index 00000000..1beaf8ae --- /dev/null +++ b/.github/workflows/check_package.yaml @@ -0,0 +1,29 @@ +on: + push: + branches-ignore: + - ghpages + +name: "check package with checklist" + +jobs: + check-package: + runs-on: ubuntu-24.04 + name: check-package + env: + CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} + RSPM: "https://packagemanager.posit.co/cran/__linux__/noble/latest" + permissions: + contents: read + steps: + - name: "Check package with checklist" + uses: inbo/actions/check_pkg@composite + deploy-pages: + name: deploy-gh-pages + runs-on: ubuntu-24.04 + needs: check-package + if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master' + permissions: + contents: write + steps: + - name: "Tag and deploy gh-pages" + uses: inbo/actions/check_deploy@composite diff --git a/.github/workflows/examples.yml b/.github/workflows/examples.yml index 7fe04c0d..cb2481b2 100644 --- a/.github/workflows/examples.yml +++ b/.github/workflows/examples.yml @@ -19,7 +19,7 @@ jobs: uses: inbo/actions/render_inbomd@devel env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - EXAMPLE_BRANCH: main + EXAMPLE_BRANCH: citeme - name: push gh-pages if: ${{ github.event_name == 'push' }} diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml deleted file mode 100644 index 9b10b9f6..00000000 --- a/.github/workflows/release.yml +++ /dev/null @@ -1,30 +0,0 @@ -name: Releases - -on: - push: - tags: - - v* - workflow_run: - workflows: ["check package on main with checklist"] - types: - - completed - -jobs: - publish: - runs-on: ubuntu-latest - permissions: - contents: write - steps: - - uses: actions/checkout@v3 - - name: Get tag - run: | - git fetch --tags --force - TAG=$(git tag --contains $(git rev-parse HEAD)) - TAG_BODY=$(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 ${{ env.tag }} - tag: ${{ env.tag }} - bodyFile: body.md diff --git a/.github/workflows/remove_old_artifacts.yml b/.github/workflows/remove_old_artifacts.yml deleted file mode 100644 index 715b00d9..00000000 --- a/.github/workflows/remove_old_artifacts.yml +++ /dev/null @@ -1,18 +0,0 @@ -name: Remove old artifacts - -on: - schedule: - # Every day at 1am - - cron: '0 1 * * *' - -jobs: - remove-old-artifacts: - runs-on: ubuntu-latest - timeout-minutes: 10 - - steps: - - name: Remove old artifacts - uses: c-hive/gha-remove-artifacts@v1 - with: - age: '1 days' - skip-recent: 4 diff --git a/.zenodo.json b/.zenodo.json index b981f462..f46bfc92 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -1,6 +1,6 @@ { "title": "INBOmd: Markdown Templates for INBO", - "version": "0.6.4", + "version": "0.6.5", "license": "GPL-3.0", "upload_type": "software", "description": "

Several templates to generate reports, presentations and posters.<\/p>", @@ -8,7 +8,8 @@ "markdown", "bookdown", "corporate identity", - "template" + "template", + "inbo_version" ], "access_right": "open", "language": "eng", @@ -47,5 +48,6 @@ { "identifier": "inbo" } - ] + ], + "publisher": "Research Institute for Nature and Forest (INBO)" } diff --git a/CITATION.cff b/CITATION.cff index dc4f99ce..3702e7cf 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -11,6 +11,7 @@ keywords: - bookdown - corporate identity - template +- inbo_version contact: - given-names: Thierry family-names: Onkelinx @@ -26,4 +27,4 @@ identifiers: value: 10.5281/zenodo.842223 - type: url value: https://inbo.github.io/INBOmd/ -version: 0.6.4 +version: 0.6.5 diff --git a/DESCRIPTION b/DESCRIPTION index 55ea9a3d..09ddda9c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: INBOmd Title: Markdown Templates for INBO -Version: 0.6.4 +Version: 0.6.5 Authors@R: c( person("Thierry", "Onkelinx", , "thierry.onkelinx@inbo.be", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-8804-4216", affiliation = "Research Institute for Nature and Forest (INBO)")), @@ -9,7 +9,7 @@ Authors@R: c( 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", affiliation = "Research Institute for Nature and Forest (INBO)")), - person("Research Institute for Nature and Forest (INBO)", , , "info@inbo.be", role = c("cph", "fnd"), + person("Research Institute for Nature and Forest (INBO)", , , "info@inbo.be", role = c("cph", "fnd", "pbl"), comment = c(ROR = "00j54wy13")) ) Description: Several templates to generate reports, presentations and @@ -23,7 +23,7 @@ Depends: Imports: assertthat, bookdown (>= 0.23.4), - checklist (>= 0.5.3), + citeme (>= 0.1.4), dplyr, fs, gert, @@ -44,13 +44,13 @@ Suggests: quarto, rstudioapi, webshot -VignetteBuilder: +VignetteBuilder: knitr Additional_repositories: https://inbo.r-universe.dev -Config/checklist/communities: inbo -Config/checklist/keywords: markdown; bookdown; corporate identity; - template +Config/citeme/communities: inbo +Config/citeme/keywords: markdown; bookdown; corporate identity; template; + inbo_version +Config/roxygen2/version: 8.0.0 Encoding: UTF-8 Language: en-GB Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.3 diff --git a/NAMESPACE b/NAMESPACE index 59909967..6077b812 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -47,12 +47,9 @@ importFrom(assertthat,noNA) importFrom(bookdown,epub_book) importFrom(bookdown,gitbook) importFrom(bookdown,pdf_book) -importFrom(checklist,ask_yes_no) -importFrom(checklist,citation_meta) -importFrom(checklist,menu_first) -importFrom(checklist,organisation) -importFrom(checklist,read_checklist) -importFrom(checklist,use_author) +importFrom(citeme,citation_meta) +importFrom(citeme,inbo_org_list) +importFrom(citeme,select_individual) importFrom(dplyr,"%>%") importFrom(dplyr,mutate_all) importFrom(fs,dir_create) diff --git a/NEWS.md b/NEWS.md index d567a439..eac95ee9 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# INBOmd 0.6.5 + +* Use latest version of `citeme` and `checklist`. + # INBOmd 0.6.4 * Fix missing subtitle in citation in colophon of gitbook and epub. @@ -9,7 +13,7 @@ # INBOmd 0.6.2 -* `pdf_report()`, `gitbook()` and `epub_book()` gain an option to create +* `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. diff --git a/R/create_report.R b/R/create_report.R index 720a1815..39ce10b7 100644 --- a/R/create_report.R +++ b/R/create_report.R @@ -1,5 +1,8 @@ #' Create a template for an INBOmd bookdown report #' +#' This function is defunct. +#' Use `flandersqmd::create_report()` instead. +#' #' @param path The folder in which to create the folder containing the report. #' Defaults to the current working directory. #' @param shortname The name of the report project. @@ -13,298 +16,12 @@ #' Otherwise you will find the new report at `path/shortname`. #' @family utils #' @export -#' @importFrom assertthat assert_that is.string noNA -#' @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) { - assert_that(is.string(path), noNA(path), is_dir(path)) - assert_that(is.string(shortname), noNA(shortname)) - assert_that( - grepl("^[a-z0-9_]+$", shortname), - msg = paste( - "The report name folder may only contain lower case letters, digits and _" - ) - ) - root <- try(git_find(path), silent = TRUE) - path <- ifelse(inherits(root, "try-error"), path, root) - if (is_file(path(path, "checklist.yml"))) { - x <- read_checklist(path) - path <- path(path, ifelse(x$package, "inst", "source")) - dir_create(path) - } - - assert_that( - !is_dir(path(path, shortname)), - 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 = "") |> - sprintf(fmt = "title: \"%s\"") -> yaml - readline( - prompt = "Enter the optional subtitle (leave empty to omit): " - ) |> - gsub(pattern = "[\"|']", replacement = "") -> subtitle - yaml <- c(yaml, paste("subtitle:", subtitle)[subtitle != ""]) - cat("Please select the corresponding 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 <- check_author(lang = lang) - authors[, c("given", "family", "email")] |> - rbind(author[, c("given", "family", "email")]) |> - anyDuplicated() -> duplo - if (duplo > 0) { - cat( - paste(author$given, author$family, "is already listed as author") - ) - next - } - c(yaml, author2yaml(author, corresponding = FALSE)) -> yaml - authors <- rbind(authors, author) - } - cat("Please select the reviewer") - duplo <- 1 - while (duplo > 0) { - author <- check_author(lang = lang) - authors[, c("given", "family", "email")] |> - rbind(author[, c("given", "family", "email")]) |> - anyDuplicated() -> duplo - if (duplo > 0) { - cat( - paste(author$given, author$family, "is already listed as author") - ) - } - } - lang <- c(nl = "Dutch", en = "English", fr = "French") - lang <- names(lang)[ - menu_first(lang, title = "What is the main language of the report?") - ] - org <- organisation$new() - aff <- org$get_organisation[["inbo.be"]]$affiliation[lang] - style <- c("INBO", "Vlaanderen") - style <- ifelse( - lang != "nl", - "Flanders", - style[menu_first(style, title = "Which style to use?")] - ) - readline(prompt = "Enter one or more keywords separated by `;`") |> - gsub(pattern = "[\"|']", replacement = "") |> - strsplit(";") |> - unlist() |> - gsub(pattern = "^\\s+", replacement = "") |> - gsub(pattern = "\\s+$", replacement = "") |> - paste(collapse = "; ") |> - sprintf(fmt = "keywords: \"%s\"") -> keywords - c( - yaml, - "reviewer:", - author2yaml(author, corresponding = FALSE), - paste("lang:", lang), - paste("style:", style), - add_address("client"), - add_address("cooperation"), - "floatbarrier: subsubsection", - "geraardsbergen: true"[ - ask_yes_no( - "Do you want INBO Geraardsbergen as address instead of INBO Brussels?", - default = FALSE - ) - ], - "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", - 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", - "# Don't run the format below.", - paste( - "# Only required for RStudio to recognise the project as a bookdown", - "project." - ), - "# Hence don't use 'Build all formats'.", - " bookdown::dontrun: default" - ) -> yaml - - dir_create(path(path, shortname)) - writeLines( - text = c( - "Version: 1.0", - "", - "RestoreWorkspace: No", - "SaveWorkspace: No", - "AlwaysSaveHistory: No", - "", - "EnableCodeIndexing: Yes", - "UseSpacesForTab: Yes", - "NumSpacesForTab: 2", - "Encoding: UTF-8", - "", - "RnwWeave: knitr", - "LaTeX: XeLaTeX", - "", - "AutoAppendNewline: Yes", - "StripTrailingWhitespace: Yes", - "LineEndingConversion: Posix", - "", - "BuildType: Website", - "", - "MarkdownWrap: Sentence", - "MarkdownReferences: Document", - "MarkdownCanonical: Yes" - ), - con = path(path, shortname, shortname, ext = "Rproj") - ) - file_copy( - system.file( - "rmarkdown", - "templates", - "report", - "skeleton", - "skeleton.Rmd", - package = "INBOmd" - ), - path(path, shortname, "index.Rmd") + .Defunct( + "create_report", + package = "INBOmd", + msg = "Use `flandersqmd::create_report()` instead." ) - file_copy( - system.file( - "rmarkdown", - "templates", - "report", - "skeleton", - "000_abstract.Rmd", - package = "INBOmd" - ), - path(path, shortname, "000_abstract.Rmd") - ) - file_copy( - system.file( - "rmarkdown", - "templates", - "report", - "skeleton", - "01_inleiding.Rmd", - package = "INBOmd" - ), - path(path, shortname, "01_inleiding.Rmd") - ) - file_copy( - system.file( - "rmarkdown", - "templates", - "report", - "skeleton", - "001_resume.Rmd", - package = "INBOmd" - ), - path(path, shortname, "001_resume.Rmd") - ) - file_copy( - system.file( - "rmarkdown", - "templates", - "report", - "skeleton", - "_bookdown.yml", - package = "INBOmd" - ), - path(path, shortname, "_bookdown.yml") - ) - file_copy( - system.file( - "rmarkdown", - "templates", - "report", - "skeleton", - "references.bib", - package = "INBOmd" - ), - path(path, shortname, "references.bib") - ) - file_copy( - system.file( - "rmarkdown", - "templates", - "report", - "skeleton", - "zzz_references_and_appendix.Rmd", - package = "INBOmd" - ), - path(path, shortname, "zzz_references_and_appendix.Rmd") - ) - - path("generic_template", "cc_by_4_0.md") |> - system.file(package = "checklist") |> - file_copy(path(path, shortname, "LICENSE.md")) - - # read index template - path(path, shortname, "index.Rmd") |> - readLines() -> index - # remove existing yaml - index <- tail(index, -grep("---", index)[2]) - # add new yaml - index <- c("---", yaml, "---", index) - writeLines(index, path(path, shortname, "index.Rmd")) - - # update _bookdown.yml - path(path, shortname, "_bookdown.yml") |> - readLines() -> bookdown_yml - yaml[grep("^title", yaml)] |> - gsub(pattern = "title: \"(.*)\"", replacement = "\\1") |> - tolower() |> - abbreviate(minlength = 20) |> - gsub(pattern = " ", replacement = "_") |> - sprintf( - fmt = "book_filename: \"%2$s_%1$s.Rmd\"", - ifelse( - nrow(authors) > 2, - gsub("[ -]", "_", authors$family[1]) |> - sprintf(fmt = "%s_et_al"), - gsub("[ -]", "_", authors$family) |> - paste(collapse = "_") - ) |> - tolower() - ) |> - gsub(pattern = "book_filename: \"(.*)\"", x = bookdown_yml) |> - gsub( - pattern = "delete_merged_file: FALSE", - replacement = "delete_merged_file: TRUE" - ) -> bookdown_yml - ifelse(basename(path) == "source", "../..", "..") |> - path("output", shortname) |> - sprintf(fmt = "output_dir: \"%s\"") |> - gsub(pattern = "output_dir: \"../output\"", bookdown_yml) |> - writeLines(path(path, shortname, "_bookdown.yml")) - - if ( - !requireNamespace("rstudioapi", quietly = TRUE) || - !rstudioapi::isAvailable() - ) { - return(invisible(NULL)) - } - rstudioapi::openProject(path(path, shortname), newSession = TRUE) } #' @importFrom assertthat assert_that @@ -335,35 +52,9 @@ author2yaml <- function(author, corresponding = FALSE) { paste(c(yaml, " corresponding: true"), collapse = "\n") } -add_address <- function(type = "client") { - address <- character(0) - while (TRUE) { - sprintf( - "Add line %i of the %s name and address (leave empty to stop): ", - length(address) + 1, - type - ) |> - readline() -> extra - if (extra == "") { - break - } - address <- c(address, extra) - } - if (length(address) == 0) { - return(address) - } - sprintf("optional filename of the %s logo: ", type) |> - readline() -> logo - c( - sprintf("%s:", type), - sprintf(" - %s", address), - sprintf("%s_logo: %s", type, logo)[logo != ""] - ) -} - -#' @importFrom checklist use_author +#' @importFrom citeme select_individual check_author <- function(lang = "nl") { - person <- use_author() + person <- select_individual(lang = lang) if (is_inbo(person) && !person$affiliation %in% inbo_affiliation) { paste0("`", inbo_affiliation, "`", collapse = "; ") |> sprintf(fmt = "INBO staff must use one of %s as affiliation.") |> diff --git a/R/ebook.R b/R/ebook.R index 174a1acb..c21ed5d1 100644 --- a/R/ebook.R +++ b/R/ebook.R @@ -151,6 +151,11 @@ epub_book <- function() { cover_image = cover_image ) config$clean_supporting <- TRUE + paste( + "`INBOmd` is deprecated and will be no longer maintained after 2027.", + "Switch to `flandersqmd` for longer support." + ) |> + warning(call. = FALSE) return(config) } diff --git a/R/gitbook.R b/R/gitbook.R index e1773d85..f62b7a94 100644 --- a/R/gitbook.R +++ b/R/gitbook.R @@ -8,7 +8,7 @@ #' @export #' @importFrom assertthat assert_that has_name #' @importFrom bookdown gitbook -#' @importFrom checklist citation_meta +#' @importFrom citeme citation_meta #' @importFrom fs file_exists path #' @importFrom htmltools htmlDependency #' @importFrom pdftools pdf_convert @@ -161,6 +161,11 @@ gitbook <- function(code_folding = c("none", "show", "hide")) { op(metadata, input, output, clean, verbose) } config$clean_supporting <- TRUE + paste( + "`INBOmd` is deprecated and will be no longer maintained after 2027.", + "Switch to `flandersqmd` for longer support." + ) |> + warning(call. = FALSE) return(config) } @@ -200,7 +205,7 @@ gitbook_edit_button <- function(path) { } #' @importFrom assertthat has_name -#' @importFrom checklist citation_meta +#' @importFrom citeme citation_meta #' @importFrom stats setNames check_zenodo <- function(fm) { list( diff --git a/R/inbo_website.R b/R/inbo_website.R index 5d251c98..dfe1fd5a 100644 --- a/R/inbo_website.R +++ b/R/inbo_website.R @@ -8,70 +8,25 @@ inbo_website <- function(path = ".") { assert_that(is.string(path), noNA(path)) path <- normalizePath(path, mustWork = FALSE) assert_that(is_dir(path), msg = "`path` is not an existing directory") + paste( + "`INBOmd` is deprecated and will be no longer maintained after 2027.", + "Switch to `flandersqmd` for longer support." + ) |> + warning(call. = FALSE) if (is_file(path(path, "_bookdown.yml"))) { return(inbo_website_bookdown(path)) } - if (is_file(path(path, "_quarto.yml"))) { - return(inbo_website_quarto(path)) - } - stop("no `_bookdown.yml` or `_bookdown.yml` found in `path`") -} - - -#' @importFrom checklist citation_meta -#' @importFrom fs path -inbo_website_quarto <- function(path) { - assert_that(requireNamespace("quarto", quietly = TRUE)) - system.file("generic_template/cc_by_4_0.md", package = "checklist") |> - file.copy("LICENSE.md", overwrite = FALSE) - cit <- citation_meta$new(path) - if ( - !is.null(cit$get_errors) && - !all(grepl("\\.zenodo.json is modified", cit$get_errors)) - ) { - return(cit) - } - yml <- quarto::quarto_inspect(path) - assert_that( - has_name(yml$config$project, "output-dir"), - has_name(yml$config, "flandersqmd"), - has_name(yml$config$flandersqmd, "shorttitle") + stopifnot( + "Use `flandersqmd` to render quarto reports." = !is_file( + path(path, "_quarto.yml") + ) ) - output_dir <- yml$config$project$`output-dir` - - oldwd <- getwd() - on.exit(setwd(oldwd), add = TRUE) - setwd(path) - quarto::quarto_render(".", as_job = FALSE) - - # copy .zenodo.json to output directory - list.files(path, pattern = ".zenodo.json", all.files = TRUE) |> - file.copy(output_dir, overwrite = TRUE) - - # pack report into a zip archive - dir_ls( - output_dir, - recurse = TRUE, - regexp = "\\.zip", - invert = TRUE, - all = TRUE - ) |> - path_rel(output_dir) -> files - - setwd(output_dir) - path(output_dir, tolower(yml$config$flandersqmd$shorttitle), ext = "zip") |> - zip(files = files, flags = "-r9XqT") - # remove output except zip archive - dir_ls(output_dir, type = "dir") |> - dir_delete() - dir_ls(output_dir, type = "file", regexp = "\\.zip", invert = TRUE) |> - file_delete() - return(invisible(NULL)) + stop("no `_bookdown.yml` or `_bookdown.yml` found in `path`") } #' @importFrom assertthat assert_that #' @importFrom fs dir_create dir_delete dir_ls file_delete is_dir is_file path -#' path_abs path_ext_remove path_rel +#' @importFrom fs path_abs path_ext_remove path_rel #' @importFrom rmarkdown clean_site render_site #' @importFrom utils zip #' @importFrom withr defer diff --git a/R/minutes.R b/R/minutes.R index 735a5ff1..1c28c47c 100644 --- a/R/minutes.R +++ b/R/minutes.R @@ -13,7 +13,7 @@ #' } #' @export #' @importFrom rmarkdown output_format knitr_options pandoc_options -#' pandoc_variable_arg pandoc_version +#' @importFrom rmarkdown pandoc_variable_arg pandoc_version #' @importFrom utils compareVersion #' @family output minutes <- function( diff --git a/R/mission.R b/R/mission.R index 56127bd5..104b5eba 100644 --- a/R/mission.R +++ b/R/mission.R @@ -18,7 +18,7 @@ #' } #' @export #' @importFrom rmarkdown output_format knitr_options pandoc_options -#' pandoc_variable_arg pandoc_version +#' @importFrom rmarkdown pandoc_variable_arg pandoc_version #' @importFrom utils compareVersion #' @family output mission <- function( diff --git a/R/on_attach.R b/R/on_attach.R index e8420af4..47705b10 100644 --- a/R/on_attach.R +++ b/R/on_attach.R @@ -2,7 +2,10 @@ paste( "WARNING: INBOmd requires some additional configuration steps after", "install or upgrade. Please visit", - "https://github.com/inbo/INBOmd/blob/main/README.md for instructions." + "https://github.com/inbo/INBOmd/blob/main/README.md for instructions.", + "\n\nCAUTION: `INBOmd` is now deprecated and will be no longer maintained", + "after 2027.", + "Switch to `flandersqmd` for longer support." ) |> packageStartupMessage() } diff --git a/R/pdf_report.R b/R/pdf_report.R index 421a8ce7..26a4ee18 100644 --- a/R/pdf_report.R +++ b/R/pdf_report.R @@ -7,10 +7,11 @@ #' @template yaml_pdf #' @export #' @importFrom assertthat assert_that has_name is.string -#' @importFrom checklist citation_meta +#' @importFrom citeme citation_meta #' @importFrom fs path #' @importFrom rmarkdown output_format knitr_options pandoc_available -#' pandoc_options pandoc_variable_arg includes_to_pandoc_args +#' @importFrom rmarkdown pandoc_options pandoc_variable_arg +#' @importFrom rmarkdown includes_to_pandoc_args #' @family output pdf_report <- function( fig_crop = "auto", @@ -296,6 +297,11 @@ pdf_report <- function( of } ) + paste( + "`INBOmd` is deprecated and will be no longer maintained after 2027.", + "Switch to `flandersqmd` for longer support." + ) |> + warning(call. = FALSE) return(config) } @@ -427,9 +433,9 @@ contact_person <- function(person) { } #' @importFrom assertthat assert_that has_name is.string noNA -#' @importFrom checklist organisation +#' @importFrom citeme inbo_org_list validate_rightsholder <- function(yaml) { - org <- organisation$new() + org <- inbo_org_list() aff <- org$get_organisation[["inbo.be"]]$affiliation stopifnot( "no `funder` found" = has_name(yaml, "funder"), diff --git a/R/poster.R b/R/poster.R index 8cdbc225..d78c4caf 100644 --- a/R/poster.R +++ b/R/poster.R @@ -28,7 +28,8 @@ #' poster. #' @export #' @importFrom rmarkdown output_format knitr_options pandoc_options -#' pandoc_variable_arg includes_to_pandoc_args pandoc_version +#' @importFrom rmarkdown pandoc_variable_arg includes_to_pandoc_args +#' @importFrom rmarkdown pandoc_version #' @importFrom utils compareVersion #' @importFrom grDevices pdf dev.off #' @importFrom graphics par image @@ -184,6 +185,11 @@ poster <- function( writeLines(enc2utf8(text), output, useBytes = FALSE) output } + paste( + "`INBOmd` is deprecated and will be no longer maintained after 2027.", + "Switch to `flandersqmd` for longer support." + ) |> + warning(call. = FALSE) output_format( knitr = knitr_options( diff --git a/R/references.R b/R/references.R index cda27aeb..f8f85c07 100644 --- a/R/references.R +++ b/R/references.R @@ -12,19 +12,18 @@ references <- function(appendix = FALSE, part = FALSE) { assert_that(is.flag(appendix), noNA(appendix)) if (is_html_output()) { fm <- yaml_front_matter(file.path(getwd(), "index.Rmd")) - style <- ifelse(has_name(fm, "style"), fm$style, "INBO") - lang <- ifelse( - has_name(fm, "lang"), - fm$lang, - ifelse(style == "Flanders", "en", "nl") - ) + lang <- fm$lang ref_title <- sprintf( "# %s {-}", - c(nl = "Referenties", en = "Bibliography", fr = "Bibliographie")[lang] + c( + `nl-BE` = "Referenties", + `en-GB` = "Bibliography", + `fr-FR` = "Bibliographie" + )[lang] ) app_title <- sprintf( "# (APPENDIX) %s {-}", - c(nl = "Bijlagen", en = "Appendices", fr = "Annexes")[lang] + c(`nl-BE` = "Bijlagen", `en-GB` = "Appendices", `fr-FR` = "Annexes")[lang] ) output <- c(ref_title, "

", app_title[appendix]) } else { diff --git a/R/slides.R b/R/slides.R index baeb0363..872e017f 100644 --- a/R/slides.R +++ b/R/slides.R @@ -11,7 +11,7 @@ #' @importFrom bookdown pdf_book #' @importFrom fs path #' @importFrom rmarkdown output_format knitr_options pandoc_options -#' pandoc_variable_arg pandoc_path_arg pandoc_version +#' @importFrom rmarkdown pandoc_variable_arg pandoc_path_arg pandoc_version #' @importFrom utils compareVersion #' @family output slides <- function(toc = TRUE, ...) { diff --git a/README.md b/README.md index de4b67e9..eb8d3361 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ [![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) [![Lifecycle: stable](https://lifecycle.r-lib.org/articles/figures/lifecycle-stable.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable) ![License](https://img.shields.io/github/license/inbo/INBOmd) -[![R build status](https://github.com/inbo/INBOmd/actions/workflows/check_on_main.yml/badge.svg)](https://github.com/inbo/INBOmd/actions) +[![R build status](https://github.com/inbo/INBOmd/actions/workflows/check_package.yml/badge.svg)](https://github.com/inbo/INBOmd/actions) [![Codecov test coverage](https://app.codecov.io/gh/inbo/inbomd/branch/main/graph/badge.svg)](https://app.codecov.io/gh/inbo/inbomd?branch=main) ![GitHub code size in bytes](https://img.shields.io/github/languages/code-size/inbo/inbomd.svg) ![GitHub repo size](https://img.shields.io/github/repo-size/inbo/inbomd.svg) @@ -21,7 +21,7 @@ The current package has following Rmarkdown templates: The templates are available in RStudio using `File` > `New file` > `R Markdown` > `From template`. -More details, including instructions for installation and usage are available at the [INBOmd website](https://inbo.github.io/INBOmd/articles/introduction.html). +More details, including instructions for installation and usage are available at the [INBOmd website](https://inbo.github.io/INBOmd/articles/inbomd.html). ## In the wild @@ -73,12 +73,12 @@ install.packages("INBOmd", repos = "https://inbo.r-universe.dev") #} #pak::pkg_install("inbo/INBOmd", dependencies = TRUE) -# add the local latex package contained in INBOmd to the TinyTeX install +# add the local latex package contained in INBOmd to the TinyTeX install tinytex::tlmgr_conf( c("auxtrees", "add", system.file("local_tex", package = "INBOmd")) ) -# install some other needed latex packages +# install some other needed latex packages tinytex::tlmgr_install(c( "babel-dutch", "babel-english", "babel-french", "dvips", "helvetic", "hyphen-dutch", "hyphen-french", "inconsolata", "tex", "times" diff --git a/checklist.yml b/checklist.yml index d06e5317..a1bbe01a 100644 --- a/checklist.yml +++ b/checklist.yml @@ -2,19 +2,19 @@ description: Configuration file for checklist::check_pkg() package: yes allowed: warnings: - - motivation: package not intended for CRAN and requires INBO specific packages. + - motivation: Package not intended for CRAN value: |- checking CRAN incoming feasibility ... WARNING Maintainer: 'Thierry Onkelinx ' New submission - Strong dependencies not in mainstream repositories: - checklist + Strong dependencies not in the CRAN or BioC software repositories: + citeme Suggests or Enhances not in mainstream repositories: INBOtheme Availability using Additional_repositories specification: - checklist yes https://inbo.r-universe.dev + citeme yes https://inbo.r-universe.dev INBOtheme yes https://inbo.r-universe.dev notes: [] required: @@ -22,12 +22,12 @@ required: - DESCRIPTION - R CMD check - checklist -- codemeta - documentation - filename conventions - folder conventions - license - lintr +- organisation - repository secret - spelling spelling: @@ -45,3 +45,5 @@ spelling: - inst/rmarkdown/templates/report/skeleton/zzz_references_and_appendix.Rmd - inst/rmarkdown/templates/slides/skeleton/skeleton.Rmd fr-BE: inst/rmarkdown/templates/report/skeleton/001_resume.Rmd +pak: [] +gha_install: [] diff --git a/inst/CITATION b/inst/CITATION index 187e5160..2301c355 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -2,13 +2,13 @@ citHeader("To cite `INBOmd` in publications please use:") # begin checklist entry bibentry( bibtype = "Manual", - title = "INBOmd: Markdown Templates for INBO. Version 0.6.4", + title = "INBOmd: Markdown Templates for INBO. Version 0.6.5", author = c(person(given = "Thierry", family = "Onkelinx")), year = 2026, url = "https://inbo.github.io/INBOmd/", abstract = "Several templates to generate reports, presentations and posters.", - textVersion = "Onkelinx, Thierry (2026) INBOmd: Markdown Templates for INBO. Version 0.6.4. https://inbo.github.io/INBOmd/", - keywords = "markdown; bookdown; corporate identity; template", + textVersion = "Onkelinx, Thierry (2026) INBOmd: Markdown Templates for INBO. Version 0.6.5. https://inbo.github.io/INBOmd/", + keywords = "markdown; bookdown; corporate identity; template; inbo_version", doi = "10.5281/zenodo.842223", ) # end checklist entry diff --git a/inst/local_tex/tex/latex/inbogeneric_2015/inbogeneric_2015.sty b/inst/local_tex/tex/latex/inbogeneric_2015/inbogeneric_2015.sty index 54ff82c8..90e2ca19 100644 --- a/inst/local_tex/tex/latex/inbogeneric_2015/inbogeneric_2015.sty +++ b/inst/local_tex/tex/latex/inbogeneric_2015/inbogeneric_2015.sty @@ -5,6 +5,8 @@ \def\codesize#1{\def\@codesize{#1}} \codesize{\normalsize} +\newcounter{none} + % required for the Euro symbol \RequirePackage[gen]{eurosym} % allows more complex formula's and \eqref diff --git a/inst/rmarkdown/templates/report/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/report/skeleton/skeleton.Rmd index 4372cd96..03e928d4 100644 --- a/inst/rmarkdown/templates/report/skeleton/skeleton.Rmd +++ b/inst/rmarkdown/templates/report/skeleton/skeleton.Rmd @@ -2,7 +2,7 @@ # generic options. See ?INBOmd::pdf_report() for full list and more details. title: # subtitle: -author: +author: - name: given: Firstname1 family: Last name1 @@ -38,7 +38,7 @@ cover_photo: # doi: # reportnr: # ordernr: -# depotnr: +# depotnr: client: - Organisation (remove client section when not needed) - Street number @@ -102,7 +102,6 @@ opts_chunk$set( error = FALSE, message = TRUE ) -library(tidyverse) library(INBOtheme) if (interactive()) { theme_set(theme_inbo(base_size = 10)) diff --git a/inst/rmarkdown/templates/slides/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/slides/skeleton/skeleton.Rmd index ee32736d..2d662f90 100644 --- a/inst/rmarkdown/templates/slides/skeleton/skeleton.Rmd +++ b/inst/rmarkdown/templates/slides/skeleton/skeleton.Rmd @@ -1,8 +1,8 @@ ---- +--- # generic options. See ?INBOmd::slides() for full list and more details. title: subtitle: -author: +author: - name: given: Firstname1 family: "Last name1" @@ -42,7 +42,6 @@ library(knitr) opts_chunk$set( dev = "cairo_pdf" ) -library(tidyverse) library(INBOtheme) if (interactive()) { theme_set(theme_inbo(base_size = 12, transparent = "plot")) diff --git a/man/add_author.Rd b/man/add_author.Rd index 1ce197bf..e238d6e4 100644 --- a/man/add_author.Rd +++ b/man/add_author.Rd @@ -14,18 +14,18 @@ This function will interactively add the information of an author from the local authors database. } \seealso{ -Other utils: -\code{\link{add_report_numbers}()}, -\code{\link{check_dependencies}()}, -\code{\link{column_start}()}, -\code{\link{column_width}()}, -\code{\link{cover_info}()}, -\code{\link{create_report}()}, -\code{\link{dyn_table}()}, -\code{\link{inbo_website}()}, -\code{\link{prepare_cover}()}, -\code{\link{references}()}, -\code{\link{render_natbib}()}, -\code{\link{validate_doi}()} +Other utils: +\code{\link[=add_report_numbers]{add_report_numbers()}}, +\code{\link[=check_dependencies]{check_dependencies()}}, +\code{\link[=column_start]{column_start()}}, +\code{\link[=column_width]{column_width()}}, +\code{\link[=cover_info]{cover_info()}}, +\code{\link[=create_report]{create_report()}}, +\code{\link[=dyn_table]{dyn_table()}}, +\code{\link[=inbo_website]{inbo_website()}}, +\code{\link[=prepare_cover]{prepare_cover()}}, +\code{\link[=references]{references()}}, +\code{\link[=render_natbib]{render_natbib()}}, +\code{\link[=validate_doi]{validate_doi()}} } \concept{utils} diff --git a/man/add_report_numbers.Rd b/man/add_report_numbers.Rd index 60536832..f121e8ec 100644 --- a/man/add_report_numbers.Rd +++ b/man/add_report_numbers.Rd @@ -56,18 +56,18 @@ Only required in case \code{copies} is set to a non-zero number.} Add the report numbers to a bookdown report } \seealso{ -Other utils: -\code{\link{add_author}()}, -\code{\link{check_dependencies}()}, -\code{\link{column_start}()}, -\code{\link{column_width}()}, -\code{\link{cover_info}()}, -\code{\link{create_report}()}, -\code{\link{dyn_table}()}, -\code{\link{inbo_website}()}, -\code{\link{prepare_cover}()}, -\code{\link{references}()}, -\code{\link{render_natbib}()}, -\code{\link{validate_doi}()} +Other utils: +\code{\link[=add_author]{add_author()}}, +\code{\link[=check_dependencies]{check_dependencies()}}, +\code{\link[=column_start]{column_start()}}, +\code{\link[=column_width]{column_width()}}, +\code{\link[=cover_info]{cover_info()}}, +\code{\link[=create_report]{create_report()}}, +\code{\link[=dyn_table]{dyn_table()}}, +\code{\link[=inbo_website]{inbo_website()}}, +\code{\link[=prepare_cover]{prepare_cover()}}, +\code{\link[=references]{references()}}, +\code{\link[=render_natbib]{render_natbib()}}, +\code{\link[=validate_doi]{validate_doi()}} } \concept{utils} diff --git a/man/check_dependencies.Rd b/man/check_dependencies.Rd index 21a187b4..0f9ecba3 100644 --- a/man/check_dependencies.Rd +++ b/man/check_dependencies.Rd @@ -12,18 +12,18 @@ Check if the required dependencies of INBOmd are installed Missing dependencies will be installed automatically } \seealso{ -Other utils: -\code{\link{add_author}()}, -\code{\link{add_report_numbers}()}, -\code{\link{column_start}()}, -\code{\link{column_width}()}, -\code{\link{cover_info}()}, -\code{\link{create_report}()}, -\code{\link{dyn_table}()}, -\code{\link{inbo_website}()}, -\code{\link{prepare_cover}()}, -\code{\link{references}()}, -\code{\link{render_natbib}()}, -\code{\link{validate_doi}()} +Other utils: +\code{\link[=add_author]{add_author()}}, +\code{\link[=add_report_numbers]{add_report_numbers()}}, +\code{\link[=column_start]{column_start()}}, +\code{\link[=column_width]{column_width()}}, +\code{\link[=cover_info]{cover_info()}}, +\code{\link[=create_report]{create_report()}}, +\code{\link[=dyn_table]{dyn_table()}}, +\code{\link[=inbo_website]{inbo_website()}}, +\code{\link[=prepare_cover]{prepare_cover()}}, +\code{\link[=references]{references()}}, +\code{\link[=render_natbib]{render_natbib()}}, +\code{\link[=validate_doi]{validate_doi()}} } \concept{utils} diff --git a/man/column_start.Rd b/man/column_start.Rd index a18f773a..64810385 100644 --- a/man/column_start.Rd +++ b/man/column_start.Rd @@ -19,18 +19,18 @@ column_start(number = 3, start = 1, margin = 20, edge = 10) Calculate the starting position of an A0 column } \seealso{ -Other utils: -\code{\link{add_author}()}, -\code{\link{add_report_numbers}()}, -\code{\link{check_dependencies}()}, -\code{\link{column_width}()}, -\code{\link{cover_info}()}, -\code{\link{create_report}()}, -\code{\link{dyn_table}()}, -\code{\link{inbo_website}()}, -\code{\link{prepare_cover}()}, -\code{\link{references}()}, -\code{\link{render_natbib}()}, -\code{\link{validate_doi}()} +Other utils: +\code{\link[=add_author]{add_author()}}, +\code{\link[=add_report_numbers]{add_report_numbers()}}, +\code{\link[=check_dependencies]{check_dependencies()}}, +\code{\link[=column_width]{column_width()}}, +\code{\link[=cover_info]{cover_info()}}, +\code{\link[=create_report]{create_report()}}, +\code{\link[=dyn_table]{dyn_table()}}, +\code{\link[=inbo_website]{inbo_website()}}, +\code{\link[=prepare_cover]{prepare_cover()}}, +\code{\link[=references]{references()}}, +\code{\link[=render_natbib]{render_natbib()}}, +\code{\link[=validate_doi]{validate_doi()}} } \concept{utils} diff --git a/man/column_width.Rd b/man/column_width.Rd index 15ff98a4..25bc25f2 100644 --- a/man/column_width.Rd +++ b/man/column_width.Rd @@ -17,18 +17,18 @@ column_width(number = 3, margin = 20, edge = 10) Calculate the width of an A0 column } \seealso{ -Other utils: -\code{\link{add_author}()}, -\code{\link{add_report_numbers}()}, -\code{\link{check_dependencies}()}, -\code{\link{column_start}()}, -\code{\link{cover_info}()}, -\code{\link{create_report}()}, -\code{\link{dyn_table}()}, -\code{\link{inbo_website}()}, -\code{\link{prepare_cover}()}, -\code{\link{references}()}, -\code{\link{render_natbib}()}, -\code{\link{validate_doi}()} +Other utils: +\code{\link[=add_author]{add_author()}}, +\code{\link[=add_report_numbers]{add_report_numbers()}}, +\code{\link[=check_dependencies]{check_dependencies()}}, +\code{\link[=column_start]{column_start()}}, +\code{\link[=cover_info]{cover_info()}}, +\code{\link[=create_report]{create_report()}}, +\code{\link[=dyn_table]{dyn_table()}}, +\code{\link[=inbo_website]{inbo_website()}}, +\code{\link[=prepare_cover]{prepare_cover()}}, +\code{\link[=references]{references()}}, +\code{\link[=render_natbib]{render_natbib()}}, +\code{\link[=validate_doi]{validate_doi()}} } \concept{utils} diff --git a/man/cover_info.Rd b/man/cover_info.Rd index 9ca81a02..7ab07115 100644 --- a/man/cover_info.Rd +++ b/man/cover_info.Rd @@ -17,18 +17,18 @@ Then run this function to covert the information into a \code{cover.txt} and send that file along the other files to the review process. } \seealso{ -Other utils: -\code{\link{add_author}()}, -\code{\link{add_report_numbers}()}, -\code{\link{check_dependencies}()}, -\code{\link{column_start}()}, -\code{\link{column_width}()}, -\code{\link{create_report}()}, -\code{\link{dyn_table}()}, -\code{\link{inbo_website}()}, -\code{\link{prepare_cover}()}, -\code{\link{references}()}, -\code{\link{render_natbib}()}, -\code{\link{validate_doi}()} +Other utils: +\code{\link[=add_author]{add_author()}}, +\code{\link[=add_report_numbers]{add_report_numbers()}}, +\code{\link[=check_dependencies]{check_dependencies()}}, +\code{\link[=column_start]{column_start()}}, +\code{\link[=column_width]{column_width()}}, +\code{\link[=create_report]{create_report()}}, +\code{\link[=dyn_table]{dyn_table()}}, +\code{\link[=inbo_website]{inbo_website()}}, +\code{\link[=prepare_cover]{prepare_cover()}}, +\code{\link[=references]{references()}}, +\code{\link[=render_natbib]{render_natbib()}}, +\code{\link[=validate_doi]{validate_doi()}} } \concept{utils} diff --git a/man/create_report.Rd b/man/create_report.Rd index 0c8ac13f..2a392b38 100644 --- a/man/create_report.Rd +++ b/man/create_report.Rd @@ -21,21 +21,22 @@ at \code{path/inst/shortname}. Otherwise you will find the new report at \code{path/shortname}.} } \description{ -Create a template for an INBOmd bookdown report +This function is defunct. +Use \code{flandersqmd::create_report()} instead. } \seealso{ -Other utils: -\code{\link{add_author}()}, -\code{\link{add_report_numbers}()}, -\code{\link{check_dependencies}()}, -\code{\link{column_start}()}, -\code{\link{column_width}()}, -\code{\link{cover_info}()}, -\code{\link{dyn_table}()}, -\code{\link{inbo_website}()}, -\code{\link{prepare_cover}()}, -\code{\link{references}()}, -\code{\link{render_natbib}()}, -\code{\link{validate_doi}()} +Other utils: +\code{\link[=add_author]{add_author()}}, +\code{\link[=add_report_numbers]{add_report_numbers()}}, +\code{\link[=check_dependencies]{check_dependencies()}}, +\code{\link[=column_start]{column_start()}}, +\code{\link[=column_width]{column_width()}}, +\code{\link[=cover_info]{cover_info()}}, +\code{\link[=dyn_table]{dyn_table()}}, +\code{\link[=inbo_website]{inbo_website()}}, +\code{\link[=prepare_cover]{prepare_cover()}}, +\code{\link[=references]{references()}}, +\code{\link[=render_natbib]{render_natbib()}}, +\code{\link[=validate_doi]{validate_doi()}} } \concept{utils} diff --git a/man/dyn_table.Rd b/man/dyn_table.Rd index 74a26d60..58c3946e 100644 --- a/man/dyn_table.Rd +++ b/man/dyn_table.Rd @@ -42,18 +42,18 @@ expanded to a vector of individual letters, e.g. \code{'clc'} becomes } } \seealso{ -Other utils: -\code{\link{add_author}()}, -\code{\link{add_report_numbers}()}, -\code{\link{check_dependencies}()}, -\code{\link{column_start}()}, -\code{\link{column_width}()}, -\code{\link{cover_info}()}, -\code{\link{create_report}()}, -\code{\link{inbo_website}()}, -\code{\link{prepare_cover}()}, -\code{\link{references}()}, -\code{\link{render_natbib}()}, -\code{\link{validate_doi}()} +Other utils: +\code{\link[=add_author]{add_author()}}, +\code{\link[=add_report_numbers]{add_report_numbers()}}, +\code{\link[=check_dependencies]{check_dependencies()}}, +\code{\link[=column_start]{column_start()}}, +\code{\link[=column_width]{column_width()}}, +\code{\link[=cover_info]{cover_info()}}, +\code{\link[=create_report]{create_report()}}, +\code{\link[=inbo_website]{inbo_website()}}, +\code{\link[=prepare_cover]{prepare_cover()}}, +\code{\link[=references]{references()}}, +\code{\link[=render_natbib]{render_natbib()}}, +\code{\link[=validate_doi]{validate_doi()}} } \concept{utils} diff --git a/man/epub_book.Rd b/man/epub_book.Rd index 6f9b9121..587a5f4a 100644 --- a/man/epub_book.Rd +++ b/man/epub_book.Rd @@ -113,13 +113,13 @@ Fill all required fields to get ride of this automatic watermark. } \seealso{ -Other output: -\code{\link{gitbook}()}, -\code{\link{handouts}()}, -\code{\link{minutes}()}, -\code{\link{mission}()}, -\code{\link{pdf_report}()}, -\code{\link{poster}()}, -\code{\link{slides}()} +Other output: +\code{\link[=gitbook]{gitbook()}}, +\code{\link[=handouts]{handouts()}}, +\code{\link[=minutes]{minutes()}}, +\code{\link[=mission]{mission()}}, +\code{\link[=pdf_report]{pdf_report()}}, +\code{\link[=poster]{poster()}}, +\code{\link[=slides]{slides()}} } \concept{output} diff --git a/man/gitbook.Rd b/man/gitbook.Rd index 64388dcb..2989250b 100644 --- a/man/gitbook.Rd +++ b/man/gitbook.Rd @@ -144,13 +144,13 @@ Otherwise you don't get an \code{index.html} file. } \seealso{ -Other output: -\code{\link{epub_book}()}, -\code{\link{handouts}()}, -\code{\link{minutes}()}, -\code{\link{mission}()}, -\code{\link{pdf_report}()}, -\code{\link{poster}()}, -\code{\link{slides}()} +Other output: +\code{\link[=epub_book]{epub_book()}}, +\code{\link[=handouts]{handouts()}}, +\code{\link[=minutes]{minutes()}}, +\code{\link[=mission]{mission()}}, +\code{\link[=pdf_report]{pdf_report()}}, +\code{\link[=poster]{poster()}}, +\code{\link[=slides]{slides()}} } \concept{output} diff --git a/man/handouts.Rd b/man/handouts.Rd index ada2a430..e8045497 100644 --- a/man/handouts.Rd +++ b/man/handouts.Rd @@ -130,13 +130,13 @@ E.g. an 11pt font on a slide is as readable as an 11pt font on a A4 paper.\tabul } \seealso{ -Other output: -\code{\link{epub_book}()}, -\code{\link{gitbook}()}, -\code{\link{minutes}()}, -\code{\link{mission}()}, -\code{\link{pdf_report}()}, -\code{\link{poster}()}, -\code{\link{slides}()} +Other output: +\code{\link[=epub_book]{epub_book()}}, +\code{\link[=gitbook]{gitbook()}}, +\code{\link[=minutes]{minutes()}}, +\code{\link[=mission]{mission()}}, +\code{\link[=pdf_report]{pdf_report()}}, +\code{\link[=poster]{poster()}}, +\code{\link[=slides]{slides()}} } \concept{output} diff --git a/man/inbo_website.Rd b/man/inbo_website.Rd index b5ebdade..bca5204b 100644 --- a/man/inbo_website.Rd +++ b/man/inbo_website.Rd @@ -13,18 +13,18 @@ inbo_website(path = ".") Render the report into a zip file for the INBO website } \seealso{ -Other utils: -\code{\link{add_author}()}, -\code{\link{add_report_numbers}()}, -\code{\link{check_dependencies}()}, -\code{\link{column_start}()}, -\code{\link{column_width}()}, -\code{\link{cover_info}()}, -\code{\link{create_report}()}, -\code{\link{dyn_table}()}, -\code{\link{prepare_cover}()}, -\code{\link{references}()}, -\code{\link{render_natbib}()}, -\code{\link{validate_doi}()} +Other utils: +\code{\link[=add_author]{add_author()}}, +\code{\link[=add_report_numbers]{add_report_numbers()}}, +\code{\link[=check_dependencies]{check_dependencies()}}, +\code{\link[=column_start]{column_start()}}, +\code{\link[=column_width]{column_width()}}, +\code{\link[=cover_info]{cover_info()}}, +\code{\link[=create_report]{create_report()}}, +\code{\link[=dyn_table]{dyn_table()}}, +\code{\link[=prepare_cover]{prepare_cover()}}, +\code{\link[=references]{references()}}, +\code{\link[=render_natbib]{render_natbib()}}, +\code{\link[=validate_doi]{validate_doi()}} } \concept{utils} diff --git a/man/minutes.Rd b/man/minutes.Rd index 94520167..d565bb62 100644 --- a/man/minutes.Rd +++ b/man/minutes.Rd @@ -59,13 +59,13 @@ Available extra parameters: } } \seealso{ -Other output: -\code{\link{epub_book}()}, -\code{\link{gitbook}()}, -\code{\link{handouts}()}, -\code{\link{mission}()}, -\code{\link{pdf_report}()}, -\code{\link{poster}()}, -\code{\link{slides}()} +Other output: +\code{\link[=epub_book]{epub_book()}}, +\code{\link[=gitbook]{gitbook()}}, +\code{\link[=handouts]{handouts()}}, +\code{\link[=mission]{mission()}}, +\code{\link[=pdf_report]{pdf_report()}}, +\code{\link[=poster]{poster()}}, +\code{\link[=slides]{slides()}} } \concept{output} diff --git a/man/mission.Rd b/man/mission.Rd index cfa81988..94f099ce 100644 --- a/man/mission.Rd +++ b/man/mission.Rd @@ -68,13 +68,13 @@ Available extra parameters: } } \seealso{ -Other output: -\code{\link{epub_book}()}, -\code{\link{gitbook}()}, -\code{\link{handouts}()}, -\code{\link{minutes}()}, -\code{\link{pdf_report}()}, -\code{\link{poster}()}, -\code{\link{slides}()} +Other output: +\code{\link[=epub_book]{epub_book()}}, +\code{\link[=gitbook]{gitbook()}}, +\code{\link[=handouts]{handouts()}}, +\code{\link[=minutes]{minutes()}}, +\code{\link[=pdf_report]{pdf_report()}}, +\code{\link[=poster]{poster()}}, +\code{\link[=slides]{slides()}} } \concept{output} diff --git a/man/pdf_report.Rd b/man/pdf_report.Rd index 17cc0380..49e308a2 100644 --- a/man/pdf_report.Rd +++ b/man/pdf_report.Rd @@ -211,13 +211,13 @@ references, page numbers, ... } \seealso{ -Other output: -\code{\link{epub_book}()}, -\code{\link{gitbook}()}, -\code{\link{handouts}()}, -\code{\link{minutes}()}, -\code{\link{mission}()}, -\code{\link{poster}()}, -\code{\link{slides}()} +Other output: +\code{\link[=epub_book]{epub_book()}}, +\code{\link[=gitbook]{gitbook()}}, +\code{\link[=handouts]{handouts()}}, +\code{\link[=minutes]{minutes()}}, +\code{\link[=mission]{mission()}}, +\code{\link[=poster]{poster()}}, +\code{\link[=slides]{slides()}} } \concept{output} diff --git a/man/poster.Rd b/man/poster.Rd index a48db19c..1bb0bac2 100644 --- a/man/poster.Rd +++ b/man/poster.Rd @@ -65,13 +65,13 @@ poster. } } \seealso{ -Other output: -\code{\link{epub_book}()}, -\code{\link{gitbook}()}, -\code{\link{handouts}()}, -\code{\link{minutes}()}, -\code{\link{mission}()}, -\code{\link{pdf_report}()}, -\code{\link{slides}()} +Other output: +\code{\link[=epub_book]{epub_book()}}, +\code{\link[=gitbook]{gitbook()}}, +\code{\link[=handouts]{handouts()}}, +\code{\link[=minutes]{minutes()}}, +\code{\link[=mission]{mission()}}, +\code{\link[=pdf_report]{pdf_report()}}, +\code{\link[=slides]{slides()}} } \concept{output} diff --git a/man/prepare_cover.Rd b/man/prepare_cover.Rd index a112a70c..ab56a31a 100644 --- a/man/prepare_cover.Rd +++ b/man/prepare_cover.Rd @@ -20,18 +20,18 @@ Store this page as \code{cover.pdf} at \code{path}. Also convert it to \code{cover.png}. } \seealso{ -Other utils: -\code{\link{add_author}()}, -\code{\link{add_report_numbers}()}, -\code{\link{check_dependencies}()}, -\code{\link{column_start}()}, -\code{\link{column_width}()}, -\code{\link{cover_info}()}, -\code{\link{create_report}()}, -\code{\link{dyn_table}()}, -\code{\link{inbo_website}()}, -\code{\link{references}()}, -\code{\link{render_natbib}()}, -\code{\link{validate_doi}()} +Other utils: +\code{\link[=add_author]{add_author()}}, +\code{\link[=add_report_numbers]{add_report_numbers()}}, +\code{\link[=check_dependencies]{check_dependencies()}}, +\code{\link[=column_start]{column_start()}}, +\code{\link[=column_width]{column_width()}}, +\code{\link[=cover_info]{cover_info()}}, +\code{\link[=create_report]{create_report()}}, +\code{\link[=dyn_table]{dyn_table()}}, +\code{\link[=inbo_website]{inbo_website()}}, +\code{\link[=references]{references()}}, +\code{\link[=render_natbib]{render_natbib()}}, +\code{\link[=validate_doi]{validate_doi()}} } \concept{utils} diff --git a/man/references.Rd b/man/references.Rd index 297c48e4..2e81e38f 100644 --- a/man/references.Rd +++ b/man/references.Rd @@ -16,18 +16,18 @@ Only relevant for pdf output.} Insert references at this position } \seealso{ -Other utils: -\code{\link{add_author}()}, -\code{\link{add_report_numbers}()}, -\code{\link{check_dependencies}()}, -\code{\link{column_start}()}, -\code{\link{column_width}()}, -\code{\link{cover_info}()}, -\code{\link{create_report}()}, -\code{\link{dyn_table}()}, -\code{\link{inbo_website}()}, -\code{\link{prepare_cover}()}, -\code{\link{render_natbib}()}, -\code{\link{validate_doi}()} +Other utils: +\code{\link[=add_author]{add_author()}}, +\code{\link[=add_report_numbers]{add_report_numbers()}}, +\code{\link[=check_dependencies]{check_dependencies()}}, +\code{\link[=column_start]{column_start()}}, +\code{\link[=column_width]{column_width()}}, +\code{\link[=cover_info]{cover_info()}}, +\code{\link[=create_report]{create_report()}}, +\code{\link[=dyn_table]{dyn_table()}}, +\code{\link[=inbo_website]{inbo_website()}}, +\code{\link[=prepare_cover]{prepare_cover()}}, +\code{\link[=render_natbib]{render_natbib()}}, +\code{\link[=validate_doi]{validate_doi()}} } \concept{utils} diff --git a/man/render_natbib.Rd b/man/render_natbib.Rd index 84783150..d300a12d 100644 --- a/man/render_natbib.Rd +++ b/man/render_natbib.Rd @@ -36,18 +36,18 @@ R markdown into \code{tex}.} Render a Markdown file with \code{natbib} bibliography } \seealso{ -Other utils: -\code{\link{add_author}()}, -\code{\link{add_report_numbers}()}, -\code{\link{check_dependencies}()}, -\code{\link{column_start}()}, -\code{\link{column_width}()}, -\code{\link{cover_info}()}, -\code{\link{create_report}()}, -\code{\link{dyn_table}()}, -\code{\link{inbo_website}()}, -\code{\link{prepare_cover}()}, -\code{\link{references}()}, -\code{\link{validate_doi}()} +Other utils: +\code{\link[=add_author]{add_author()}}, +\code{\link[=add_report_numbers]{add_report_numbers()}}, +\code{\link[=check_dependencies]{check_dependencies()}}, +\code{\link[=column_start]{column_start()}}, +\code{\link[=column_width]{column_width()}}, +\code{\link[=cover_info]{cover_info()}}, +\code{\link[=create_report]{create_report()}}, +\code{\link[=dyn_table]{dyn_table()}}, +\code{\link[=inbo_website]{inbo_website()}}, +\code{\link[=prepare_cover]{prepare_cover()}}, +\code{\link[=references]{references()}}, +\code{\link[=validate_doi]{validate_doi()}} } \concept{utils} diff --git a/man/slides.Rd b/man/slides.Rd index bf523414..8ad7b318 100644 --- a/man/slides.Rd +++ b/man/slides.Rd @@ -117,13 +117,13 @@ E.g. an 11pt font on a slide is as readable as an 11pt font on a A4 paper.\tabul } \seealso{ -Other output: -\code{\link{epub_book}()}, -\code{\link{gitbook}()}, -\code{\link{handouts}()}, -\code{\link{minutes}()}, -\code{\link{mission}()}, -\code{\link{pdf_report}()}, -\code{\link{poster}()} +Other output: +\code{\link[=epub_book]{epub_book()}}, +\code{\link[=gitbook]{gitbook()}}, +\code{\link[=handouts]{handouts()}}, +\code{\link[=minutes]{minutes()}}, +\code{\link[=mission]{mission()}}, +\code{\link[=pdf_report]{pdf_report()}}, +\code{\link[=poster]{poster()}} } \concept{output} diff --git a/man/validate_doi.Rd b/man/validate_doi.Rd index 03bbe4f2..0e2986bf 100644 --- a/man/validate_doi.Rd +++ b/man/validate_doi.Rd @@ -22,18 +22,18 @@ The part after the forward slash consists either of only digits or of two sets of any character separated by a dot. } \seealso{ -Other utils: -\code{\link{add_author}()}, -\code{\link{add_report_numbers}()}, -\code{\link{check_dependencies}()}, -\code{\link{column_start}()}, -\code{\link{column_width}()}, -\code{\link{cover_info}()}, -\code{\link{create_report}()}, -\code{\link{dyn_table}()}, -\code{\link{inbo_website}()}, -\code{\link{prepare_cover}()}, -\code{\link{references}()}, -\code{\link{render_natbib}()} +Other utils: +\code{\link[=add_author]{add_author()}}, +\code{\link[=add_report_numbers]{add_report_numbers()}}, +\code{\link[=check_dependencies]{check_dependencies()}}, +\code{\link[=column_start]{column_start()}}, +\code{\link[=column_width]{column_width()}}, +\code{\link[=cover_info]{cover_info()}}, +\code{\link[=create_report]{create_report()}}, +\code{\link[=dyn_table]{dyn_table()}}, +\code{\link[=inbo_website]{inbo_website()}}, +\code{\link[=prepare_cover]{prepare_cover()}}, +\code{\link[=references]{references()}}, +\code{\link[=render_natbib]{render_natbib()}} } \concept{utils} diff --git a/vignettes/inbomd.Rmd b/vignettes/inbomd.Rmd index 2aef70e0..360df26c 100644 --- a/vignettes/inbomd.Rmd +++ b/vignettes/inbomd.Rmd @@ -19,12 +19,12 @@ knitr::opts_chunk$set( # Goal The `INBOmd` package provides several styles for [`rmarkdown`](https://rmarkdown.rstudio.com/) files. -The styles are based on the corporate identity of the Research Institute for Nature and Forest +The styles are based on the corporate identity of the Research Institute for Nature and Forest (Instituut voor Natuur en Bosonderzoek, [INBO](vlaanderen.be/inbo/en/)). The styles itself are not intended for use by parties external to INBO. -We still provide them to other users as an inspiration and example on how to create their own corporate identity styles for `rmarkdown` files. +We still provide them to other users as an inspiration and example on how to create their own corporate identity styles for `rmarkdown` files. -All templates are based on [`bookdown`](https://yihui.org/bookdown/), which is an extension of `rmarkdown`. +All templates are based on [`bookdown`](https://pkg.yihui.org/bookdown/), which is an extension of `rmarkdown`. It is tailored towards writing books and technical documentation. ## Benefits of writing with `bookdown` @@ -35,14 +35,14 @@ It is tailored towards writing books and technical documentation. 1. No need to run `R` in a script and copy the output into another document. - `rmarkdown` will first execute the `R` code in the document and paste its output in a plain `markdown` file. This is then rendered into the requested output format. - This saves a lot of work and avoid copy/paste errors. -1. Storing the `R` code within the report makes it easy to rerun the report when the data is updated. +1. Storing the `R` code within the report makes it easy to rerun the report when the data is updated. 1. The plain text source code is lightweight. The source code of a report is seldom larger than a few hundred kilobyte. Yes, kilobyte. 1. Plain text files work great in combination with [version control systems](https://en.wikipedia.org/wiki/Version_control) like [Git](https://en.wikipedia.org/wiki/Git). 1. `bookdown` is a useful tool for conducting [open research](https://en.wikipedia.org/wiki/Open_research) and [open science](https://en.wikipedia.org/wiki/Open_science). 1. You can get multiple output formats from the same source. The report template can yield a pdf, an e-book and a website. -1. The author doesn't have to worry about the lay-out. The software takes care of that when rendering the documents. This frees up time which the author can invest in more important things. And it guarantees a consistent lay-out both with the document as across documents. +1. The author doesn't have to worry about the lay-out. The software takes care of that when rendering the documents. This frees up time which the author can invest in more important things. And it guarantees a consistent lay-out both with the document as across documents. # Available templates in `INBOmd` @@ -125,7 +125,7 @@ DOI, report number, depot number and other information to the meta data. `INBOmd` contains several templates which are available in RStudio. Go in the menu to `File > New File > R Markdown`. A new window will open were you select `From template`. This will show a list of all available templates. Select the template `INBOmd` you want, set the name of the new document and the base location. This will create a new directory with the specified name in the base location. Each report will reside in its own directory. -This new directory contains `_bookdown.yml` and an `.Rmd` file with the same base name as the directory. We highly recommend to rename the `.Rmd` file to `index.Rmd`, see usage section in the [bookdown](https://yihui.org/bookdown/usage) book for more details. Next you need to open `_bookdown.yml` in RStudio. Here you can configure the render settings of the report. `book_filename` defines the filename of the output. `output_dir` is the relative path for the output. +This new directory contains `_bookdown.yml` and an `.Rmd` file with the same base name as the directory. We highly recommend to rename the `.Rmd` file to `index.Rmd`, see usage section in the [bookdown](https://pkg.yihui.org/bookdown/usage) book for more details. Next you need to open `_bookdown.yml` in RStudio. Here you can configure the render settings of the report. `book_filename` defines the filename of the output. `output_dir` is the relative path for the output. Finally, you need to activate the `Build` pane in RStudio. By far the easiest way to do this, is the create a new project. Go in the menu to `File > New Project` and choose in the pop-up window `Existing directory`. Note that this only works if there is an `index.Rmd` file at the root of the project.