Merge pull request #84 from inbo/website-inbo

small fixes
inbo · Jan 11, 2022 · 45ed2fa · 45ed2fa
2 parents 1ec1bd4 + 4422a6f
commit 45ed2fa
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -5,6 +5,7 @@
 ^\.Rproj\.user$
 ^\.zenodo\.json$
 ^checklist.yml$
+^CITATION\.cff$
 ^codecov\.yml$
 ^data-raw$
 ^docs$
@@ -15,6 +16,6 @@
 CODE_OF_CONDUCT.md
 CONTRIBUTING.md
 create_docker.sh
-Dockerfile
 docker
+Dockerfile
 docs
diff --git a/.zenodo.json b/.zenodo.json
@@ -1,21 +1,27 @@
 {
- "creators": [
-      {
-        "name": "Thierry Onkelinx",
-        "affiliation": "Research Instute for Nature and Forest"
-      },
-      {
-        "name": "Floris Vanderhaeghe",
-        "affiliation": "Research Instute for Nature and Forest"
-      }
-    ],
-  "description": "INBOmd provides several templates to be used with RMarkdown",
-  "keywords": [
-    "R",
-    "LaTeX",
-    "reproducibility",
-    "Markdown"
+  "title": "INBOmd: Markdown Templates for INBO",
+  "version": "0.5.2",
+  "description": "Several templates to generate reports, presentations and posters.",
+  "creators": [
+    {
+      "name": "Onkelinx, Thierry",
+      "orcid": "https://orcid.org/0000-0001-8804-4216"
+    }
   ],
-  "license": "GPL-3",
-  "title": "INBOmd: RMarkdown Templates for INBO"
+  "upload_type": "software",
+  "access_rights": "open",
+  "license": "GPL-3.0",
+  "communities": {
+    "identifier": "inbo"
+  },
+  "contributors": [
+    {
+      "name": "Vanderhaeghe, Floris",
+      "orcid": "https://orcid.org/0000-0002-6378-6229"
+    },
+    {
+      "name": "Lommelen, Els",
+      "orcid": "https://orcid.org/0000-0002-3481-5684"
+    }
+  ]
 }
diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,20 @@
+cff-version: 1.2.0
+message: If you use this software, please cite it as below.
+authors:
+- family-names: Onkelinx
+  given-names: Thierry
+  orcid: https://orcid.org/0000-0001-8804-4216
+contact:
+- email: thierry.onkelinx@inbo.be
+  family-names: Onkelinx
+  given-names: Thierry
+- email: info@inbo.be
+  name: Research Institute for Nature and Forest
+title: 'INBOmd: Markdown Templates for INBO'
+version: 0.5.2
+abstract: Several templates to generate reports, presentations and posters.
+license: GPL-3.0
+type: software
+doi: 10.5281/zenodo.842223
+repository-code: https://github.com/inbo/inbomd
+identifiers: []
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: INBOmd
 Title: Markdown Templates for INBO
-Version: 0.5.1
+Version: 0.5.2
 Authors@R: c(
     person("Thierry", "Onkelinx", , "thierry.onkelinx@inbo.be", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8804-4216")),

diff --git a/Dockerfile b/Dockerfile
@@ -129,9 +129,12 @@ RUN  apt-get update \
     r-cran-R.utils \
   && Rscript -e 'remotes::install_cran("qrcode")'
 
-## Install qrcode
+## Install lipsum
 RUN  Rscript -e 'remotes::install_cran("lipsum")'
 
+## Install here
+RUN  Rscript -e 'remotes::install_cran("here")'
+
 ## Install webshot dependency
 RUN  Rscript -e 'webshot::install_phantomjs()'
 

diff --git a/NAMESPACE b/NAMESPACE
@@ -59,5 +59,7 @@ importFrom(rmarkdown,render)
 importFrom(rmarkdown,yaml_front_matter)
 importFrom(utils,compareVersion)
 importFrom(utils,file_test)
+importFrom(utils,head)
 importFrom(utils,install.packages)
 importFrom(utils,packageVersion)
+importFrom(utils,tail)
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,13 @@
+# INBOmd 0.5.2
+
+* Templates now mention url 'vlaanderen.be/inbo' instead of
+  'https://www.vlaanderen.be/inbo' or 'www.vlaanderen.be/inbo'.
+* Bug fix website 'inbomd_examples'.
+* `gitbook()` uses the same reference title for chapter bibliografies as the
+  main bibliography.
+* `references()` takes `lang` into account for HTML formats.
+* Bugfix in Dockerfile.
+
 # INBOmd 0.5.1
 
 * Add language french for style Flanders

diff --git a/R/ebook.R b/R/ebook.R
@@ -54,10 +54,11 @@ ebook <- function() {
   )
   cover_image <- NULL
   if (has_name(fm, "cover")) {
-    if (!file.exists(file.path(getwd(), "cover.jpeg"))) {
+    cover_path <- file.path(getwd(), "cover.jpeg")
+    if (!file.exists(cover_path)) {
       pdf_convert(
         pdf = file.path(getwd(), fm$cover), format = "jpeg", pages = 1,
-        dpi = 770 * 25.4 / 210, filenames = file.path(getwd(), "cover.jpeg")
+        dpi = 770 * 25.4 / 210, filenames = cover_path
       )
     }
     cover_image <- "cover.jpeg"

diff --git a/R/gitbook.R b/R/gitbook.R
@@ -10,7 +10,7 @@
 #' @importFrom htmltools htmlDependency
 #' @importFrom pdftools pdf_convert
 #' @importFrom rmarkdown pandoc_variable_arg yaml_front_matter
-#' @importFrom utils packageVersion
+#' @importFrom utils head packageVersion tail
 #' @family output
 gitbook <- function() {
   fm <- yaml_front_matter(file.path(getwd(), "index.Rmd"))
@@ -58,15 +58,15 @@ gitbook <- function() {
     msg = "You need to render an INBOmd::gitbook() from it's working directory"
   )
   if (has_name(fm, "cover")) {
-    if (!file.exists(file.path(getwd(), "cover.jpeg"))) {
+    cover_path <- file.path(getwd(), "cover.jpeg")
+    if (!file.exists(cover_path)) {
       pdf_convert(
         pdf = file.path(getwd(), fm$cover), format = "jpeg", pages = 1,
-        dpi = 770 * 25.4 / 210, filenames = file.path(getwd(), "cover.jpeg")
+        dpi = 770 * 25.4 / 210, filenames = cover_path
       )
     }
     pandoc_args <- c(
-      pandoc_args,
-      pandoc_variable_arg("cover_image", file.path(getwd(), "cover.jpeg"))
+      pandoc_args, pandoc_variable_arg("cover_image", cover_path)
     )
   }
   resource_dir <- system.file("css_styles", package = "INBOmd")
@@ -80,7 +80,7 @@ gitbook <- function() {
   pandoc_args <- c(
     pandoc_args,
     pandoc_variable_arg(
-      "csspath", paste0("libs/INBOmd-", packageVersion("INBOmd"))
+      "csspath", file.path("libs", paste0("INBOmd-", packageVersion("INBOmd")))
     )
   )
   template <- system.file(
@@ -92,6 +92,16 @@ gitbook <- function() {
     split_bib = TRUE, table_css = TRUE, pandoc_args = pandoc_args,
     template = template, extra_dependencies = list(inbomd_dep)
   )
+  post <- config$post_processor  # in case a post processor have been defined
+  config$post_processor <- function(metadata, input, output, clean, verbose) {
+    x <- readLines(output, encoding = "UTF-8")
+    i <- head(grep('^<div id="refs" class="references[^"]*"[^>]*>$', x), 1)
+    if (length(i) > 0) {
+      x <- c(head(x, i - 1), "", tail(x, -i + 1))
+    }
+    writeLines(x, output)
+    post(metadata, input, output, clean, verbose)
+  }
   config$clean_supporting <- TRUE
   return(config)
 }
diff --git a/R/references.R b/R/references.R
@@ -5,15 +5,26 @@
 #' Only relevant for pdf output.
 #' @family utils
 #' @export
-#' @importFrom assertthat assert_that is.flag noNA
+#' @importFrom assertthat assert_that has_name is.flag noNA
 #' @importFrom knitr is_html_output
+#' @importFrom rmarkdown yaml_front_matter
 references <- function(appendix = FALSE, part = FALSE) {
   assert_that(is.flag(appendix), noNA(appendix))
   if (is_html_output()) {
-    output <- c(
-      "# Referenties {-}", "<div id='refs'></div>",
-      "# (APPENDIX) Bijlage {-}"[appendix]
+    fm <- yaml_front_matter(file.path(getwd(), "index.Rmd"))
+    style <- ifelse(has_name(fm, "style"), fm$style, "INBO")
+    lang <- ifelse(
+      has_name(fm, "lang"), fm$lang, ifelse(style == "Flanders", "en", "nl")
+    )
+    ref_title <- sprintf(
+      "# %s {-}",
+      c(nl = "Referenties", en = "Bibliography", fr = "Bibliographie")[lang]
+    )
+    app_title <- sprintf(
+      "# (APPENDIX) %s {-}",
+      c(nl = "Bijlage", en = "Appendix", fr = "Annexe")[lang]
     )
+    output <- c(ref_title, "<div id='refs'></div>", app_title[appendix])
   } else {
     assert_that(is.flag(part), noNA(part))
     output <- c(

diff --git a/README.md b/README.md
@@ -9,7 +9,8 @@
 ![GitHub repo size](https://img.shields.io/github/repo-size/inbo/inbomd.svg)
 [![DOI](https://zenodo.org/badge/66824259.svg)](https://zenodo.org/badge/latestdoi/66824259)
 
-INBOmd contains templates to generate several types of documents with the corporate identity of INBO or the Flemish government. The current package has following Rmarkdown templates:
+INBOmd contains templates to generate several types of documents with the corporate identity of INBO or the Flemish government.
+The current package has following Rmarkdown templates:
 
 - INBO report: reports rendered to pdf, html (gitbook style) and epub
 - INBO slides: presentations rendered to pdf
@@ -18,21 +19,27 @@ INBOmd contains templates to generate several types of documents with the corpor
 
 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://inbomd.netlify.app/articles/introduction.html).
+More details, including instructions for installation and usage are available at the [INBOmd website](https://inbo.github.io/INBOmd/articles/introduction.html).
 
 ## In the wild
 
 Below are some documents created with INBOmd
 
-1. https://inbomd-examples.netlify.com
+1. https://inbo.github.io/inbomd_examples
 1. https://doi.org/10.21436/inbor.14030462
 1. https://doi.org/10.21436/inbop.14901626
 1. https://pureportal.inbo.be/portal/files/12819590/rbelgium_20170307.pdf
 1. https://doi.org/10.21436/inbor.12304086
 
 ## Installation
 
-INBOmd requires a working installation of XeLaTeX. We highly recommend to use the TinyTeX. Close all open R sessions and start a fresh R session. Execute the commands below. This will install TinyTeX on your machine. No admin rights are required. Although TinyTeX is a lightweight installation, it still is several 100 MB large.
+INBOmd requires a working installation of XeLaTeX.
+We highly recommend to use the TinyTeX.
+Close all open R sessions and start a fresh R session.
+Execute the commands below.
+This will install TinyTeX on your machine.
+No admin rights are required.
+Although TinyTeX is a lightweight installation, it still is several 100 MB large.
 
 ```
 update.packages(ask = FALSE, checkBuilt = TRUE)
@@ -44,7 +51,8 @@ if (!tinytex:::is_tinytex()) {
 }
 ```
 
-Once TinyTeX is installed, you need to restart RStudio. Then you can proceed with the installation of `INBOmd`.
+Once TinyTeX is installed, you need to restart RStudio.
+Then you can proceed with the installation of `INBOmd`.
 
 ```
 if (!"remotes" %in% rownames(installed.packages())) {
@@ -59,12 +67,3 @@ tinytex::tlmgr_conf(
 )
 tinytex::tlmgr_install(c("hyphen-dutch", "hyphen-french"))
 ```
-
-Make your system fonts available in R
-
-```
-if (!"extrafont" %in% rownames(installed.packages())) {
-  install.packages("extrafont")
-}
-extrafont::font_import()
-```
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -41,5 +41,5 @@ authors:
   Thierry Onkelinx:
     href: "https://www.muscardinus.be"
   Research Institute for Nature and Forest:
-    href: "https://www.vlaanderen.be/inbo/en-gb"
-    html: "<img src='reference/figures/logo-en.png' height=24>"
+    href: "vlaanderen.be/inbo/en"
+    html: "<img src='https://inbo.github.io/INBOmd/reference/figures/logo-en.png' height=24>"
diff --git a/docker/entrypoint.sh b/docker/entrypoint.sh
@@ -1,10 +1,5 @@
 #!/bin/sh -l
 
-echo 'repository:     ' $GITHUB_REPOSITORY
-echo 'ref:            ' $GITHUB_REF
-echo 'head_ref:       ' $GITHUB_HEAD_REF
-echo 'Event:          ' $GITHUB_EVENT_NAME
-
 export HOME=/root
 
 cd $GITHUB_WORKSPACE
@@ -27,3 +22,16 @@ echo '\nAll Rmarkdown files rendered successfully\n'
 if [ $GITHUB_REPOSITORY = "inbo/inbomd" ] ; then
   cp -R /examples/docs/. $GITHUB_WORKSPACE/docs/.
 fi
+
+if [ $GITHUB_EVENT_NAME = "push" ] ; then
+  cd /
+  git clone --depth 1 -b gh-pages https://$INPUT_TOKEN@github.com/inbo/inbomd_examples
+  cd /inbomd_examples
+  git rm -rf --quiet .
+  cp -R $GITHUB_WORKSPACE/docs/. /inbomd_examples/.
+  git add --all
+  git config --global user.email "bwk@inbo.be"
+  git config --global user.name "INBO BMK"
+  git commit --amend -m "Automated update of gh-pages with inbomd_examples"
+  git push --force --set-upstream origin gh-pages
+fi
diff --git a/inst/CITATION b/inst/CITATION
@@ -2,12 +2,12 @@ citHeader("To cite `INBOmd` in publications please use:")
 # begin checklist entry
 citEntry(
   entry = "Manual",
-  title = "INBOmd: Markdown Templates for INBO. Version 0.5.1",
+  title = "INBOmd: Markdown Templates for INBO. Version 0.5.2",
   author = c(person(given = "Thierry", family = "Onkelinx")),
-  year = 2021,
+  year = 2022,
   url = "https://github.com/inbo/inbomd",
   abstract = "Several templates to generate reports, presentations and posters.",
-  textVersion = "Onkelinx, Thierry (2021) INBOmd: Markdown Templates for INBO. Version 0.5.1. https://github.com/inbo/inbomd, https://doi.org/10.5281/zenodo.842223",
+  textVersion = "Onkelinx, Thierry (2022) INBOmd: Markdown Templates for INBO. Version 0.5.2. https://github.com/inbo/inbomd, https://doi.org/10.5281/zenodo.842223",
   doi = "10.5281/zenodo.842223",
 )
 # end checklist entry
diff --git a/inst/local_tex/tex/latex/beamer/themes/inboposter2015/beamerthemeinboposter2015.sty b/inst/local_tex/tex/latex/beamer/themes/inboposter2015/beamerthemeinboposter2015.sty
@@ -281,7 +281,7 @@
     \begin{minipage}[b][30mm][b]{250mm}
       \begin{flushright}
         \usebeamerfont{email}\usebeamercolor[fg]{footline}\@email\\
-        \usebeamerfont{footline}\usebeamercolor[fg]{footline}www.vlaanderen.be/inbo
+        \usebeamerfont{footline}\usebeamercolor[fg]{footline}vlaanderen.be/inbo
       \end{flushright}
     \end{minipage}
     }

diff --git a/inst/local_tex/tex/latex/beamer/themes/vlaanderen/beamerthemeinbo.sty b/inst/local_tex/tex/latex/beamer/themes/vlaanderen/beamerthemeinbo.sty
@@ -18,7 +18,7 @@
 \coverhorizontal{TRUE}
 \coveroffset{0mm}
 \coverhoffset{0mm}
-\website{www.vlaanderen.be/inbo}
+\website{vlaanderen.be/inbo}
 
 \RequirePackage{inboimage_2015}
 

diff --git a/inst/local_tex/tex/latex/beamer/themes/vlaanderen/beamerthemeinboenglish.sty b/inst/local_tex/tex/latex/beamer/themes/vlaanderen/beamerthemeinboenglish.sty
@@ -18,7 +18,7 @@
 \coverhorizontal{TRUE}
 \coveroffset{0mm}
 \coverhoffset{0mm}
-\website{www.vlaanderen.be/inbo}
+\website{vlaanderen.be/inbo}
 \slidelogo{}
 
 \RequirePackage{inboimage_2015}