Merge pull request #97 from inbo/v0.4.8

V0.4.8

.github/workflows/check_on_different_r_os.yml

@@ -33,14 +33,17 @@ jobs:
       ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
       - uses: r-lib/actions/setup-pandoc@v2
 
+      - uses: r-lib/actions/setup-tinytex@v2
+      - run: tlmgr --version
+
       - name: Query dependencies
         run: |
           install.packages('remotes')

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "protocolhelper: Helper Functions to Manage Protocols",
-  "version": "0.4.7",
+  "version": "0.4.8",
   "description": "Helper functions to manage INBO protocols.",
   "creators": [
     {

CITATION.cff

@@ -17,7 +17,7 @@ contact:
 - email: [email protected]
   name: Research Institute for Nature and Forest
 title: 'protocolhelper: Helper Functions to Manage Protocols'
-version: 0.4.7
+version: 0.4.8
 abstract: Helper functions to manage INBO protocols.
 license: GPL-3.0
 type: software

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: protocolhelper
 Title: Helper Functions to Manage Protocols
-Version: 0.4.7
+Version: 0.4.8
 Authors@R: c(
     person("Hans", "Van Calster", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8595-8426")),
@@ -30,8 +30,10 @@ Imports:
     knitr,
     purrr,
     R6,
+    reactable,
     rmarkdown,
     rprojroot,
+    slickR,
     stringr,
     xfun,
     xml2,
@@ -48,5 +50,5 @@ Encoding: UTF-8
 Language: en-GB
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.3
 SystemRequirements: Pandoc (>= 2.0.0)

NAMESPACE

@@ -16,11 +16,12 @@ export(create_sip)
 export(create_sop)
 export(create_spp)
 export(get_path_to_protocol)
+export(get_protocol_type)
 export(get_protocolnumbers)
 export(get_short_titles)
 export(get_version_number)
+export(increment_version_number)
 export(insert_protocolsection)
-export(protocol_css)
 export(protocolcheck)
 export(render_protocol)
 export(update_protocol)
@@ -36,6 +37,7 @@ importFrom(assertthat,noNA)
 importFrom(assertthat,validate_that)
 importFrom(bookdown,gitbook)
 importFrom(bookdown,markdown_document2)
+importFrom(bookdown,pdf_book)
 importFrom(bookdown,render_book)
 importFrom(checklist,clean_git)
 importFrom(checklist,new_branch)
@@ -99,6 +101,7 @@ importFrom(stringr,str_subset)
 importFrom(utils,file_test)
 importFrom(utils,head)
 importFrom(utils,tail)
+importFrom(utils,write.csv)
 importFrom(xfun,read_utf8)
 importFrom(xfun,write_utf8)
 importFrom(xml2,read_xml)
@@ -110,11 +113,13 @@ importFrom(yaml,as.yaml)
 importFrom(yaml,read_yaml)
 importFrom(ymlthis,as_yml)
 importFrom(ymlthis,use_index_rmd)
+importFrom(ymlthis,use_output_yml)
 importFrom(ymlthis,use_yml_file)
 importFrom(ymlthis,yml_author)
 importFrom(ymlthis,yml_bookdown_opts)
 importFrom(ymlthis,yml_date)
 importFrom(ymlthis,yml_discard)
 importFrom(ymlthis,yml_empty)
+importFrom(ymlthis,yml_output)
 importFrom(ymlthis,yml_replace)
 importFrom(ymlthis,yml_toplevel)

NEWS.md

@@ -1,3 +1,13 @@
+# protocolhelper 0.4.8
+
+## Minor changes
+
+* various improvements to website homepage, including Dutch and English version
+
+## Bug fixes
+
+* fixed bug in passing metadata to `pandoc`
+
 # protocolhelper 0.4.7
 
 ## Minor changes

R/add_captions.R

@@ -40,6 +40,7 @@
 #' @importFrom assertthat is.string
 #'
 #' @export
+#' @family convert
 #'
 add_captions <- function(
   from,

R/add_dependencies.R

@@ -19,6 +19,7 @@
 #' @importFrom purrr transpose
 #'
 #' @export
+#' @family creation
 #'
 #' @examples
 #' \dontrun{

R/add_subprotocols.R

@@ -28,6 +28,7 @@
 #'
 #'
 #' @export
+#' @family creation
 #'
 #' @examples
 #' \dontrun{
@@ -130,7 +131,7 @@ add_one_subprotocol <-
                     pandoc_args = c(
                       "--markdown-headings=atx",
                       "--shift-heading-level-by=1",
-                      "--metadata=suppress-bibliography[:TRUE]"
+                      "--metadata=suppress-bibliography=TRUE"
                     )
                   ),
                   output_file = mdfile,
@@ -146,7 +147,7 @@ add_one_subprotocol <-
                     pandoc_args = c(
                       "--markdown-headings=atx",
                       "--shift-heading-level-by=1",
-                      "--metadata=suppress-bibliography[:TRUE]"
+                      "--metadata=suppress-bibliography=TRUE"
                     )
                   ),
                   output_file = mdfile,
@@ -288,6 +289,7 @@ add_one_subprotocol <-
 #' @importFrom purrr map map_lgl
 #'
 #' @export
+#' @family creation
 add_subprotocols <-
   function(code_mainprotocol,
            fetch_remote = TRUE) {

R/check_all.R

@@ -6,6 +6,7 @@
 #'
 #' @return A report of all failed checks.
 #' @export
+#' @family check
 #'
 check_all <- function(protocol_code, fail = !interactive()) {
   cat("Checking protocol YAML block with metadata (frontmatter) ...")

R/check_frontmatter.R

@@ -20,7 +20,7 @@
 #' @importFrom purrr map_lgl map_chr
 #'
 #' @export
-#'
+#' @family check
 #'
 check_frontmatter <- function(
     protocol_code,

R/check_helpers.R

@@ -61,6 +61,7 @@ check_protocolcode <- function(protocolcode) {
 #'
 #' @return Logical. TRUE if check digit is correct.
 #' @export
+#' @family check
 #'
 #' @examples
 #' validate_orcid("0000-0002-6378-6229")
@@ -93,6 +94,7 @@ validate_orcid <- function(orcid) {
 #' @return a character vector of previously encountered problems and problems
 #' identified for author names and `orcid` ids.
 #' @export
+#' @family check
 check_all_author_info <- function(
     author_list,
     problems_vect

R/check_structure.R

@@ -20,6 +20,7 @@
 #' @importFrom fs dir_ls path_rel
 #'
 #' @export
+#' @family check
 #'
 check_structure <- function(protocol_code, fail = !interactive()) {
   check_protocolcode(protocol_code)

R/convert_docx.R

@@ -37,6 +37,7 @@
 #' @importFrom assertthat assert_that
 #' @importFrom fs path_rel
 #' @export
+#' @family convert
 convert_docx_to_rmd <- function(
   from,
   to = sub("docx$", "Rmd", from),