Next version

.Rbuildignore

@@ -16,6 +16,7 @@
 ^data-raw$
 ^docs$
 ^man-roxygen$
+^organisation.yml$
 ^pkgdown$
 ^protocolhelper\.Rproj$
 ^publish$

.github/CODE_OF_CONDUCT.md

@@ -21,5 +21,5 @@ Instances of abusive, harassing, or otherwise unacceptable behaviour may be repo
 opening an issue or contacting one or more of the project maintainers.
 
 This Code of Conduct is adapted from the Contributor Covenant 
-(https://www.contributor-covenant.org), version 1.0.0, available at 
-https://contributor-covenant.org/version/1/0/0/.
+(http://contributor-covenant.org), version 1.0.0, available at 
+http://contributor-covenant.org/version/1/0/0/

.github/CONTRIBUTING.md

@@ -1,23 +1,14 @@
-# Contributing to protocolhelper
-
-This outlines how to propose a change to protocolhelper. For more detailed
-info about contributing to this package, please see the
-[**development contributing guide**](https://rstd.io/tidy-contrib).
+# CONTRIBUTING #
 
 ### Fixing typos
 
-Small typos or grammatical errors in documentation may be edited directly using
-the GitHub web interface, so long as the changes are made in the _source_ file.
-
-*  YES: you edit a roxygen comment in a `.R` file below `R/`.
-*  NO: you edit an `.Rd` file below `man/`.
+Small typos or grammatical errors in documentation may be edited directly using the GitHub web interface, so long as the changes are made in the _source_ file.
+E.g. edit a `roxygen2` comment in a `.R` file below `R/`, not in an `.Rd` file below `man/`.
 
 ### Prerequisites
 
-Before you make a substantial pull request, you should always file an issue and
-make sure someone from the team agrees that it’s a problem. If you’ve found a
-bug, create an associated issue and illustrate the bug with a minimal 
-[reprex](https://www.tidyverse.org/help/#reprex).
+Before you make a substantial pull request, you should always file an issue and make sure someone from the team agrees that it’s a problem. 
+If you’ve found a bug, create an associated issue and illustrate the bug with a minimal [reproducible example](https://www.tidyverse.org/help/#reprex).
 
 ### Pull request process
 
@@ -97,13 +88,18 @@ To do this, you can use the following code:
     version_number = version_number, theme = "water", language = "nl"
   )
 ```
+### Code of Conduct
 
+Please note that this project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). 
+By contributing to this project you agree to abide by its terms.
 
+### Prefer to Email? 
 
+Email the person listed as maintainer in the `DESCRIPTION` file of this repo.
 
-### Code of Conduct
+Though note that private discussions over email don't help others - of course
+email is totally warranted if it's a sensitive problem of any kind.
 
-Please note that the protocolhelper project is released with a
-[Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this
-project you agree to abide by its terms.
+### Thanks for contributing!
 
+This contributing guide is adapted from the `tidyverse` contributing guide available at https://raw.githubusercontent.com/r-lib/usethis/master/inst/templates/tidy-contributing.md 

.github/workflows/check_on_branch.yml

@@ -10,16 +10,12 @@ 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 }}
-      ZENODO_SANDBOX: ${{ secrets.ZENODO_SANDBOX }}
-    permissions:
-      contents: read
     steps:
-      - uses: r-lib/actions/setup-pandoc@v2
-        with:
-          pandoc-version: '3.1.11'
-
       - uses: inbo/actions/check_pkg@main
+        with:
+          path: "."
+          # aptget: "" (optional)
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          ZENODO_SANDBOX: ${{ secrets.ZENODO_SANDBOX }}

.github/workflows/check_on_different_r_os.yml

@@ -22,8 +22,8 @@ jobs:
         config:
           - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-22.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
-          - {os: ubuntu-22.04,   r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
+          - {os: ubuntu-24.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/noble/latest"}
+          - {os: ubuntu-24.04,   r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/noble/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

.github/workflows/release.yml

@@ -10,28 +10,21 @@ on:
       - completed
 
 jobs:
-  prepare:
+  publish:
     runs-on: ubuntu-latest
-    outputs:
-      tag: ${{ steps.gettag.outputs.tag }}
-      body: ${{ steps.gettag.outputs.body }}
+    permissions:
+      contents: write
     steps:
       - uses: actions/checkout@v3
       - name: Get tag
         run: |
           git fetch --tags --force
           TAG=$(git tag --contains $(git rev-parse HEAD))
-          echo "tag=$TAG" >> "$GITHUB_OUTPUT"
-          echo "body=$TAG_BODY" >> "$GITHUB_OUTPUT"
-        id: gettag
-  publish:
-    runs-on: ubuntu-latest
-    permissions:
-      contents: write
-    needs: prepare
-    steps:
+          TAG_BODY=$(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 ${{needs.prepare.outputs.tag}}
-          tag: ${{needs.prepare.outputs.tag}}
-          body: ${{needs.prepare.outputs.body}}
+          name: Release ${{ env.tag }}
+          tag: ${{ env.tag }}
+          bodyFile: body.md

.gitignore

@@ -1,4 +1,5 @@
 
+!source/**/_extensions/**
 # Example code in package build process
 # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
 # Output files from R CMD build
@@ -11,20 +12,29 @@
 # knitr and R markdown default cache directories
 # produced vignettes
 *-Ex.R
+*.[rR][dD]ata
+*.[rR]ds
 *.dbf
 *.doc*
+*.eps
 *.gddoc
 *.gdsheet
 *.gpkg
 *.html
 *.knit.md
 *.mdb
+*.pdf
 *.shp*
 *.shx
+*.sty
+*.tex
 *.utf8.md
 *.xls*
+*_cache
 *_cache/
 *_files
+*_freeze
+*_libs
 .DS_Store
 .RData
 .Rapp.history
@@ -34,6 +44,7 @@
 .Rproj.user/
 .Ruserdata
 .httr-oauth
+.quarto
 /*.Rcheck/
 /*.tar.gz
 /cache/

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "protocolhelper: Helper Functions to Manage Protocols",
-  "version": "0.8.1",
+  "version": "0.8.2",
   "license": "GPL-3.0",
   "upload_type": "software",
   "description": "<p>Helper functions to manage INBO protocols.<\/p>",

CITATION.cff

@@ -32,4 +32,4 @@ abstract: "Helper functions to manage INBO protocols."
 identifiers:
 - type: url
   value: https://inbo.github.io/protocolhelper/
-version: 0.8.1
+version: 0.8.2

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: protocolhelper
 Title: Helper Functions to Manage Protocols
-Version: 0.8.1
+Version: 0.8.2
 Authors@R: c(
     person("Hans", "Van Calster", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8595-8426", affiliation = "Research Institute for Nature and Forest (INBO)")),
@@ -10,19 +10,20 @@ Authors@R: c(
            comment = c(ORCID = "0000-0002-6378-6229", affiliation = "Research Institute for Nature and Forest (INBO)")),
     person("Els", "Lommelen", , "[email protected]", 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)", , , "[email protected]", role = c("cph", "fnd"))
+    person("Research Institute for Nature and Forest (INBO)", , , "[email protected]", role = c("cph", "fnd"),
+           comment = c(ROR = "https://ror.org/00j54wy13"))
   )
 Description: Helper functions to manage INBO protocols.
 License: GPL-3
 URL: https://inbo.github.io/protocolhelper/,
     https://github.com/inbo/protocolhelper
 BugReports: https://github.com/inbo/protocolhelper/issues
 Depends: 
-    R (>= 3.6)
+    R (>= 4.1.0)
 Imports: 
     assertthat,
     bookdown,
-    checklist (>= 0.4.1),
+    checklist (>= 0.5.1),
     cli,
     commonmark,
     fs,
@@ -47,7 +48,6 @@ Suggests:
     png,
     reactable,
     rlang,
-    slickR,
     testthat (>= 2.1.0),
     tinytex,
     zen4R
@@ -59,5 +59,5 @@ Encoding: UTF-8
 Language: en-GB
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 SystemRequirements: Pandoc (>= 2.0.0)

NAMESPACE

@@ -124,6 +124,7 @@ importFrom(xml2,xml_find_all)
 importFrom(xml2,xml_text)
 importFrom(yaml,as.yaml)
 importFrom(yaml,read_yaml)
+importFrom(yaml,write_yaml)
 importFrom(ymlthis,as_yml)
 importFrom(ymlthis,use_index_rmd)
 importFrom(ymlthis,use_yml_file)

NEWS.md

@@ -1,3 +1,14 @@
+# protocolhelper 0.8.2
+
+## Enhancement
+
+* Fixed a layout issue in the html version (DOI appearing in wrong place)
+* Handle multiple reviewers in metadata table (#134)
+
+## Bug fix
+
+* Fix `render_release` failure in case of multiple reviewers (#137)
+
 # protocolhelper 0.8.1
 
 ## Bug fix

R/add_subprotocols.R

@@ -346,7 +346,7 @@ add_subprotocols <-
     prm_na <- map_lgl(prm, is.na)
     assert_that(all(prm_list | prm_na))
 
-    for (i in seq_len(length(yml$params$dependencies$value))) {
+    for (i in seq_along(yml$params$dependencies$value)) {
       if (yml$params$dependencies$value[[i]]$appendix) {
         add_one_subprotocol(
           code_subprotocol = yml$params$dependencies$value[[i]]$protocol_code,

R/check_frontmatter.R

@@ -183,13 +183,14 @@ check_frontmatter <- function(
     ]
   )
 
+  vn <- get_version_number()
   problems <- c(
     problems,
     paste0(
       "version number in the YAML of index.Rmd needs to be updated.\n",
       "Please use protocolhelper::update_version_number()."
     )[
-      !identical(get_version_number(), yml_protocol$version_number)
+      !identical(vn, yml_protocol$version_number)
     ]
   )
 

R/convert_docx.R

@@ -1,7 +1,7 @@
 #' @title Convert a docx-file (a protocol) to an (R)markdown file
 #'
 #' @description This function is derived from the
-#' [`redoc::dedoc()`](https://noamross.github.io/redoc/reference/dedoc.html)
+#' `redoc::dedoc()`
 #' function and uses `pandoc` to convert between docx and markdown.
 #' Several options are preset to end-up with a markdown document that is in
 #' syntax as close as possible to Rmarkdown files in RStudio.

R/create_protocol.R

@@ -264,6 +264,10 @@ create_protocol <- function(
   yaml <- c(
     yaml,
     paste("language:", language),
+    paste(
+      "lang:",
+      paste0(language, "-BE"[language == "nl"], "-GB"[language == "en"])
+    ),
     paste("date:", "\"`r Sys.Date()`\""),
     paste("protocol_code:", protocol_code),
     paste0("version_number: \"", version_number, "\""),
@@ -272,10 +276,21 @@ create_protocol <- function(
     paste("project_name:", project_name)[!is.null(project_name)],
     "community: \"inbo\"", # required by citation_meta
     paste0("publisher: ", inbo_affiliation[[language]]),
+    "rightsholder:",
+    "  - name:",
+    paste0("      given: ", inbo_affiliation[[language]]),
+    "    email: [email protected]",
+    "    ror: https://ror.org/00j54wy13",
+    "funder:",
+    "  - name:",
+    paste0("      given: ", inbo_affiliation[[language]]),
+    "    email: [email protected]",
+    "    ror: https://ror.org/00j54wy13",
     "site: bookdown::bookdown_site",
     "bibliography: references.yaml"[language == "en"],
     "bibliography: referenties.yaml"[language == "nl"],
     "link-citations: TRUE",
+    "license: CC-BY 4.0", # required by citation_meta
     "csl: https://raw.githubusercontent.com/citation-style-language/styles/master/research-institute-for-nature-and-forest.csl" # nolint
   )
 

R/create_protocol_helpers.R

@@ -688,9 +688,11 @@ yaml_interactive <- function() {
     strsplit(";") |>
     unlist() |>
     gsub(pattern = "^\\s+", replacement = "") |>
-    gsub(pattern = "\\s+$", replacement = "") |>
-    paste(collapse = "; ") |>
-    sprintf(fmt = "keywords: \"%s\"") -> keywords
+    gsub(pattern = "\\s+$", replacement = "") -> keywords
+
+  paste0("'", keywords, "'") |>
+    paste(collapse = ",") |>
+    sprintf(fmt = "keywords: [%s]") -> keywords
 
   c(
     yaml,

R/get_version_number.R

@@ -48,8 +48,9 @@ get_version_number <- function(path = ".") {
 
   # list all index.Rmd files
   indexpaths <- dir_ls(
-    path = path, recurse = TRUE,
-    regexp = "source\\/s[fpioa]p\\/.+\\/index\\.Rmd"
+    path = path,
+    recurse = TRUE,
+    regexp = "index\\.Rmd$"
   )
 
   # read YAML front matter
@@ -107,6 +108,7 @@ increment_version_number <- function(versions) {
       paste0(lastyear, ".", increment),
       paste0(currentyear, ".01")
     )
+    new_version <- unname(new_version)
     return(new_version)
   } else {
     new_version <- paste0(format(Sys.Date(), "%Y"), ".01")