Merge pull request #114 from inbo/hotfix

Hotfix

.github/workflows/check_on_different_r_os.yml

@@ -64,6 +64,9 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         if: runner.os != 'linux'
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
 
       - uses: r-lib/actions/check-r-package@v2
         with:

.github/workflows/release.yml

@@ -5,27 +5,33 @@ on:
     tags:
       - v*
   workflow_run:
-    workflows: ["check package on main"]
+    workflows: ["check package on main with checklist"]
     types:
       - completed
 
 jobs:
-
-  build:
+  prepare:
     runs-on: ubuntu-latest
-    permissions:
-      contents: write
+    outputs:
+      tag: ${{ steps.gettag.outputs.tag }}
+      body: ${{ steps.gettag.outputs.body }}
     steps:
       - uses: actions/checkout@v3
-      - name: Get tag message
+      - name: Get tag
         run: |
+          git fetch --tags --force
           TAG=$(git tag --contains $(git rev-parse HEAD))
-          TAG_BODY=$(git tag --contains $(git rev-parse HEAD) -n100 | awk '(NR>2)')
-          echo "TAG=$TAG" >> $GITHUB_OUTPUT
-          echo "TAG_BODY=$TAG_BODY" >> $GITHUB_OUTPUT
-        id: tag-body
+          echo "tag=$TAG" >> "$GITHUB_OUTPUT"
+          echo "body=$TAG_BODY" >> "$GITHUB_OUTPUT"
+        id: gettag
+  publish:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    needs: prepare
+    steps:
       - uses: ncipollo/release-action@v1
         with:
-          name: Release ${{ steps.tag-body.outputs.TAG }}
-          tag: ${{ steps.tag-body.outputs.TAG }}
-          body: ${{ steps.tag-body.outputs.TAG_BODY }}
+          name: Release ${{needs.prepare.outputs.tag}}
+          tag: ${{needs.prepare.outputs.tag}}
+          body: ${{needs.prepare.outputs.body}}

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "checklist: A Thorough and Strict Set of Checks for R Packages and Source Code",
-  "version": "0.3.4",
+  "version": "0.3.5",
   "license": "GPL-3.0",
   "upload_type": "software",
   "description": "<p>An opinionated set of rules for R packages and R source code\nprojects.<\/p>",

CITATION.cff

@@ -25,4 +25,4 @@ identifiers:
   value: 10.5281/zenodo.4028303
 - type: url
   value: https://inbo.github.io/checklist/
-version: 0.3.4
+version: 0.3.5

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: checklist
 Title: A Thorough and Strict Set of Checks for R Packages and Source Code
-Version: 0.3.4
+Version: 0.3.5
 Authors@R: c(
     person("Thierry", "Onkelinx", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8804-4216", affiliation = "Research Institute for Nature and Forest (INBO)")),

NEWS.md

@@ -1,3 +1,10 @@
+# checklist 0.3.5
+
+* Fix release GitHub Action.
+* Bugfix in `update_citation()` on a `DESCRIPTION`.
+* `check_spelling()` handles Roxygen2 tags `@aliases`, `@importMethodsFrom`,
+  `@include`, `@keywords`, `@method`, `@name`, `@slot`
+
 # checklist 0.3.4
 
 * `check_spelling()` ignores numbers.

R/citation_description.R

@@ -73,7 +73,7 @@ description_author_format <- function(i, x) {
     )[x[[i]]$role]
   )
   formatted$organisation <- ifelse(
-    is.null(x[[i]]), "", gsub(".*@", "", x[[i]]$email)
+    is.null(x[[i]]$email), "", gsub(".*@", "", x[[i]]$email)
   )
   if (is.null(x[[i]]$comment)) {
     formatted$orcid <- ""

R/citation_meta_class.R

@@ -468,7 +468,10 @@ citation_r <- function(meta) {
       "\"%s (%s) %s. Version %s. %s\"",
       paste(authors_plain, collapse = "; "), format(Sys.Date(), "%Y"),
       cit_meta$title, cit_meta$version,
-      paste0(paste(c(cit_meta$source, cit_meta$url), collapse = "; "), "")
+      ifelse(
+        length(cit_meta$url), paste(cit_meta$url, collapse = "; "),
+        cit_meta$source
+      )
     ),
     keywords = paste0("\"", paste(cit_meta$keywords, collapse = "; "), "\"")
   )

R/spelling_parse.R

@@ -9,7 +9,7 @@ spelling_parse_r <- function(r_file, wordlist) {
   text <- ifelse(keep, raw_text, "")
 
   # remove multiline tags
-  c("examples", "importFrom", "aliases") |>
+  c("aliases", "examples", "importFrom", "importMethodsFrom") |>
     paste(collapse = "|") |>
     sprintf(fmt = "^#'\\s*@(%s)") |>
     grep(text) -> multiline
@@ -35,16 +35,16 @@ spelling_parse_r <- function(r_file, wordlist) {
     gsub("", text) -> text
 
   # remove the tag and the first word
-  c("param", "reference") |>
+  c("param", "reference", "slot") |>
     paste(collapse = "|") |>
     sprintf(fmt = "^#'\\s*@(%s)\\s+(\\w|\\.)+") |>
     gsub("", text, perl = TRUE) -> text
 
   # remove the entire line for certain tags
   c(
     "author", "docType", "export", "exportClass", "exportMethod", "family",
-    "importClassesFrom", "importFrom", "inherit\\w*Params", "keywords", "name",
-    "rdname", "seealso", "title", "template"
+    "importClassesFrom", "importFrom", "include", "inherit\\w*Params",
+    "keywords", "name", "method", "rdname", "seealso", "title", "template"
   ) |>
     paste(collapse = "|") |>
     sprintf(fmt = "^#'\\s*@(%s) .*") |>

R/use_author.R

@@ -279,7 +279,9 @@ ask_orcid <- function(prompt = "orcid: ") {
     return(orcid)
   }
   while (!validate_orcid(orcid)) {
-    cat("\nPlease provide a valid ORCiD in the format `0000-0000-0000-0000`\n")
+    message(
+      "\nPlease provide a valid ORCiD in the format `0000-0000-0000-0000`\n"
+    )
     orcid <- readline(prompt = prompt)
   }
   return(orcid)

inst/CITATION

@@ -2,12 +2,12 @@ citHeader("To cite `checklist` in publications please use:")
 # begin checklist entry
 bibentry(
   bibtype = "Manual",
-  title = "checklist: A Thorough and Strict Set of Checks for R Packages and Source Code. Version 0.3.4",
+  title = "checklist: A Thorough and Strict Set of Checks for R Packages and Source Code. Version 0.3.5",
   author = c( author = c(person(given = "Thierry", family = "Onkelinx"))),
   year = 2023,
   url = "https://inbo.github.io/checklist/",
   abstract = "An opinionated set of rules for R packages and R source code projects.",
-  textVersion = "Onkelinx, Thierry (2023) checklist: A Thorough and Strict Set of Checks for R Packages and Source Code. Version 0.3.4. https://github.com/inbo/checklist/; https://inbo.github.io/checklist/",
+  textVersion = "Onkelinx, Thierry (2023) checklist: A Thorough and Strict Set of Checks for R Packages and Source Code. Version 0.3.5. https://inbo.github.io/checklist/",
   keywords = "quality control; documentation; publication",
   doi = "10.5281/zenodo.4028303",
 )

inst/package_template/check_on_different_r_os.yml

@@ -42,6 +42,9 @@ jobs:
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
 
       - uses: r-lib/actions/check-r-package@v2
         with:

inst/package_template/release.yml

@@ -5,27 +5,33 @@ on:
     tags:
       - v*
   workflow_run:
-    workflows: ["check package on main"]
+    workflows: ["check package on main with checklist"]
     types:
       - completed
 
 jobs:
-
-  build:
+  prepare:
     runs-on: ubuntu-latest
-    permissions:
-      contents: write
+    outputs:
+      tag: ${{ steps.gettag.outputs.tag }}
+      body: ${{ steps.gettag.outputs.body }}
     steps:
       - uses: actions/checkout@v3
-      - name: Get tag message
+      - name: Get tag
         run: |
+          git fetch --tags --force
           TAG=$(git tag --contains $(git rev-parse HEAD))
-          TAG_BODY=$(git tag --contains $(git rev-parse HEAD) -n100 | awk '(NR>2)')
-          echo "TAG=$TAG" >> $GITHUB_OUTPUT
-          echo "TAG_BODY=$TAG_BODY" >> $GITHUB_OUTPUT
-        id: tag-body
+          echo "tag=$TAG" >> "$GITHUB_OUTPUT"
+          echo "body=$TAG_BODY" >> "$GITHUB_OUTPUT"
+        id: gettag
+  publish:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    needs: prepare
+    steps:
       - uses: ncipollo/release-action@v1
         with:
-          name: Release ${{ steps.tag-body.outputs.TAG }}
-          tag: ${{ steps.tag-body.outputs.TAG }}
-          body: ${{ steps.tag-body.outputs.TAG_BODY }}
+          name: Release ${{needs.prepare.outputs.tag}}
+          tag: ${{needs.prepare.outputs.tag}}
+          body: ${{needs.prepare.outputs.body}}

tests/testthat/test_a_author.R

@@ -3,7 +3,7 @@ test_that("author tools", {
   stub(ask_orcid, "readline", mock(""))
   expect_equal(ask_orcid(), "")
   stub(ask_orcid, "readline", mock("junk", "0000-0002-1825-0097"))
-  expect_equal(ask_orcid(), "0000-0002-1825-0097")
+  expect_equal(suppressMessages(ask_orcid()), "0000-0002-1825-0097")
 
   root <- tempfile("author")
   expect_false(is_dir(root))

tests/testthat/test_e_bookdown_zenodo.R

@@ -1,6 +1,7 @@
 test_that("bookdown_zenodo() works", {
   skip_if_not_installed("zen4R")
   skip_if_not_installed("bookdown")
+  skip_if(Sys.getenv("MY_UNIVERSE") != "") # skip test on r-universe.dev
   expect_match(Sys.getenv("ZENODO_SANDBOX"), "^\\w{60}$")
   sandbox_token <- Sys.getenv("ZENODO_SANDBOX")