Merge pull request #109 from inbo/0.3.4

0.3.4

.github/workflows/release.yml

@@ -20,7 +20,7 @@ jobs:
       - name: Get tag message
         run: |
           TAG=$(git tag --contains $(git rev-parse HEAD))
-          TAG_BODY=$(git tag --contains {{ github.sha }} -n100 | awk '(NR>1)')
+          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

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "checklist: A Thorough and Strict Set of Checks for R Packages and Source Code",
-  "version": "0.3.3",
+  "version": "0.3.4",
   "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: 0.3.3
+version: 0.3.4

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: checklist
 Title: A Thorough and Strict Set of Checks for R Packages and Source Code
-Version: 0.3.3
+Version: 0.3.4
 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)")),

Dockerfile

@@ -23,132 +23,90 @@ RUN apt-get update \
 
 COPY docker/.Rprofile $R_HOME/etc/Rprofile.site
 
-## install INLA
-RUN Rscript --no-save --no-restore -e 'remotes::install_cran("INLA", type = "source")'
-
 ## install assertthat
 RUN  apt update \
   && apt install -y --no-install-recommends r-cran-assertthat \
   && Rscript --no-save --no-restore -e 'remotes::install_cran("assertthat")'
 
-## install codemetar
-RUN  apt update \
-  && apt install -y --no-install-recommends r-cran-bookdown \
-  && Rscript --no-save --no-restore -e 'remotes::install_cran("bookdown")'
-
-## install codemetar
-RUN  Rscript --no-save --no-restore -e 'remotes::install_cran("codemetar")'
-
-## install covr
-RUN apt-get update \
-  && apt-get install  -y --no-install-recommends \
-    libharfbuzz-dev \
-    libfribidi-dev \
-    r-cran-covr \
-  && apt-get clean \
-  && Rscript --no-save --no-restore -e 'remotes::install_cran("covr")'
-
-## install curl
-RUN  apt update \
-  && apt install -y --no-install-recommends r-cran-curl \
-  && Rscript --no-save --no-restore -e 'remotes::install_cran("curl")'
-
 ## install desc
 RUN  apt update \
   && apt install -y --no-install-recommends r-cran-desc \
   && Rscript --no-save --no-restore -e 'remotes::install_cran("desc")'
 
-## install devtools
-RUN  apt update \
-  && apt install -y --no-install-recommends r-cran-devtools \
-  && Rscript --no-save --no-restore -e 'remotes::install_cran("devtools")'
-
 ## install fs
 RUN  apt update \
   && apt install -y --no-install-recommends r-cran-fs \
   && Rscript --no-save --no-restore -e 'remotes::install_cran("fs")'
 
-## install gert
+## install jsonlite
 RUN  apt update \
-  && apt install -y --no-install-recommends r-cran-gert \
-  && Rscript --no-save --no-restore -e 'remotes::install_cran("gert")'
+  && apt install -y --no-install-recommends r-cran-jsonlite \
+  && Rscript --no-save --no-restore -e 'remotes::install_cran("jsonlite")'
 
-## install hexSticker
-RUN apt-get update \
-  && apt-get install  -y --no-install-recommends \
-    libmagick++-dev \
-  && apt-get clean \
-  && Rscript --no-save --no-restore -e 'remotes::install_cran("hexSticker")'
+## install hunspell
+RUN  apt update \
+  && apt install -y --no-install-recommends r-cran-hunspell \
+  && Rscript --no-save --no-restore -e 'remotes::install_cran("hunspell")'
+
+## install R6
+RUN  apt update \
+  && apt install -y --no-install-recommends r-cran-r6 \
+  && Rscript --no-save --no-restore -e 'remotes::install_cran("R6")'
 
 ## install httr
 RUN  apt update \
   && apt install -y --no-install-recommends r-cran-httr \
   && Rscript --no-save --no-restore -e 'remotes::install_cran("httr")'
 
-## install hunspell
-RUN  apt update \
-  && apt install -y --no-install-recommends r-cran-hunspell \
-  && Rscript --no-save --no-restore -e 'remotes::install_cran("hunspell")'
-
-## install jsonlite
+## install gert
 RUN  apt update \
-  && apt install -y --no-install-recommends r-cran-jsonlite \
-  && Rscript --no-save --no-restore -e 'remotes::install_cran("jsonlite")'
+  && apt install -y --no-install-recommends r-cran-gert \
+  && Rscript --no-save --no-restore -e 'remotes::install_cran("gert")'
 
 ## install knitr
 RUN  apt update \
   && apt install -y --no-install-recommends r-cran-knitr \
   && Rscript --no-save --no-restore -e 'remotes::install_cran("knitr")'
 
-## install lintr
-RUN Rscript --no-save --no-restore -e 'remotes::install_cran("lintr")'
-
-## install microbenchmark
-RUN  Rscript --no-save --no-restore -e 'remotes::install_cran("microbenchmark")'
-
-## install mockery
+## install sessioninfo
 RUN  apt update \
-  && apt install -y --no-install-recommends r-cran-mockery \
-  && Rscript --no-save --no-restore -e 'remotes::install_cran("mockery")'
-
-## install pdftools
-RUN  apt-get update \
-  && apt-get install -y --no-install-recommends \
-       libpoppler-cpp-dev \
-       r-cran-pdftools \
-  && Rscript --no-save --no-restore -e 'remotes::install_cran("pdftools")'
+  && apt install -y --no-install-recommends r-cran-sessioninfo \
+  && Rscript --no-save --no-restore -e 'remotes::install_cran("sessioninfo")'
 
-## install pkgdown
-RUN  apt-get update \
-  && apt-get install -y --no-install-recommends \
-       libfontconfig1-dev \
-       libfreetype6-dev \
-       libjpeg-dev \
-       libpng-dev \
-       libtiff5-dev \
-  && Rscript --no-save --no-restore -e 'remotes::install_cran("pkgdown")'
+## install withr
+RUN  apt update \
+  && apt install -y --no-install-recommends r-cran-withr \
+  && Rscript --no-save --no-restore -e 'remotes::install_cran("withr")'
 
-## install R6
+## install yaml
 RUN  apt update \
-  && apt install -y --no-install-recommends r-cran-r6 \
-  && Rscript --no-save --no-restore -e 'remotes::install_cran("R6")'
+  && apt install -y --no-install-recommends r-cran-yaml \
+  && Rscript --no-save --no-restore -e 'remotes::install_cran("yaml")'
 
-## install rcmdcheck
+## install curl
 RUN  apt update \
-  && apt install -y --no-install-recommends r-cran-rcmdcheck \
-  && Rscript --no-save --no-restore -e 'remotes::install_cran("rcmdcheck")'
+  && apt install -y --no-install-recommends r-cran-curl \
+  && Rscript --no-save --no-restore -e 'remotes::install_cran("curl")'
 
 ## install renv
 RUN Rscript --no-save --no-restore -e 'remotes::install_cran("renv")'
 
-## install rgdal
+## install covr
 RUN apt-get update \
   && apt-get install  -y --no-install-recommends \
-    libgdal-dev \
-    libproj-dev \
-    r-cran-rgdal \
+    libharfbuzz-dev \
+    libfribidi-dev \
+    r-cran-covr \
   && apt-get clean \
-  && Rscript --no-save --no-restore -e 'remotes::install_cran("rgdal")'
+  && Rscript --no-save --no-restore -e 'remotes::install_cran("covr")'
+
+## install lintr
+RUN Rscript --no-save --no-restore -e 'remotes::install_cran("lintr")'
+
+## install rcmdcheck
+RUN  apt update \
+  && apt install -y --no-install-recommends r-cran-rcmdcheck \
+  && Rscript --no-save --no-restore -e 'remotes::install_cran("rcmdcheck")'
 
 ## install rmarkdown
 RUN  apt update \
@@ -160,42 +118,75 @@ RUN  apt update \
   && apt install -y --no-install-recommends r-cran-roxygen2 \
   && Rscript --no-save --no-restore -e 'remotes::install_cran("roxygen2")'
 
+## install INLA
+RUN Rscript --no-save --no-restore -e 'remotes::install_cran("INLA", type = "source")'
+
+## install bookdown
+RUN  apt update \
+  && apt install -y --no-install-recommends r-cran-bookdown \
+  && Rscript --no-save --no-restore -e 'remotes::install_cran("bookdown")'
+
+## install mockery
+RUN  apt update \
+  && apt install -y --no-install-recommends r-cran-mockery \
+  && Rscript --no-save --no-restore -e 'remotes::install_cran("mockery")'
+
+## install pdftools
+RUN  apt-get update \
+  && apt-get install -y --no-install-recommends \
+       libpoppler-cpp-dev \
+       r-cran-pdftools \
+  && Rscript --no-save --no-restore -e 'remotes::install_cran("pdftools")'
+
 ## install rstudioapi
 RUN  apt update \
   && apt install -y --no-install-recommends r-cran-rstudioapi \
   && Rscript --no-save --no-restore -e 'remotes::install_cran("rstudioapi")'
 
-## install sessioninfo
+## install codemetar
+RUN  Rscript --no-save --no-restore -e 'remotes::install_cran("codemetar")'
+
+## install testthat
 RUN  apt update \
-  && apt install -y --no-install-recommends r-cran-sessioninfo \
-  && Rscript --no-save --no-restore -e 'remotes::install_cran("sessioninfo")'
+  && apt install -y --no-install-recommends r-cran-testthat \
+  && Rscript --no-save --no-restore -e 'remotes::install_cran("testthat")'
 
-## install showtext
-RUN Rscript --no-save --no-restore -e 'remotes::install_cran("showtext")'
+## install pkgdown
+RUN  apt-get update \
+  && apt-get install -y --no-install-recommends \
+       libfontconfig1-dev \
+       libfreetype6-dev \
+       libjpeg-dev \
+       libpng-dev \
+       libtiff5-dev \
+  && Rscript --no-save --no-restore -e 'remotes::install_cran("pkgdown")'
 
 ## install sysfonts
 RUN Rscript --no-save --no-restore -e 'remotes::install_cran("sysfonts")'
 
-## install testthat
-RUN  apt update \
-  && apt install -y --no-install-recommends r-cran-testthat \
-  && Rscript --no-save --no-restore -e 'remotes::install_cran("testthat")'
+## install showtext
+RUN Rscript --no-save --no-restore -e 'remotes::install_cran("showtext")'
 
-## install withr
-RUN  apt update \
-  && apt install -y --no-install-recommends r-cran-withr \
-  && Rscript --no-save --no-restore -e 'remotes::install_cran("withr")'
+## install hexSticker
+RUN apt-get update \
+  && apt-get install  -y --no-install-recommends \
+    libmagick++-dev \
+  && apt-get clean \
+  && Rscript --no-save --no-restore -e 'remotes::install_cran("hexSticker")'
 
-## install yaml
+## install devtools
 RUN  apt update \
-  && apt install -y --no-install-recommends r-cran-yaml \
-  && Rscript --no-save --no-restore -e 'remotes::install_cran("yaml")'
+  && apt install -y --no-install-recommends r-cran-devtools \
+  && Rscript --no-save --no-restore -e 'remotes::install_cran("devtools")'
 
 ## install zen4R
 RUN  apt update \
   && apt install -y --no-install-recommends libsecret-1-dev \
   && Rscript --no-save --no-restore -e 'remotes::install_cran("zen4R")'
 
+## install microbenchmark
+RUN  Rscript --no-save --no-restore -e 'remotes::install_cran("microbenchmark")'
+
 ## install checklist
 COPY . /checklist/
 RUN Rscript --no-save --no-restore -e 'remotes::install_local("checklist", upgrade = "always")'

NEWS.md

@@ -1,3 +1,14 @@
+# checklist 0.3.4
+
+* `check_spelling()` ignores numbers.
+* Ask which GitHub organisation to use when create a new project.
+  Default equals the organisation's default.
+* GitHub Action for project allow to install package prior to checking the
+  project.
+  Use this in case `check_lintr()` returns an error about global variables in a
+  function and you did `require()` the package.
+* Fix release GitHub Action.
+
 # checklist 0.3.3
 
 * New `organisation()` class to hold the requirements of the organisation.

R/check_project.R

@@ -8,11 +8,6 @@
 #' @importFrom fs is_file
 #' @family project
 check_project <- function(x = ".", fail = !interactive(), quiet = FALSE) {
-  assert_that(
-    inherits(x, "checklist") || is_file(path(x, "checklist.yml")),
-    msg = "Please initialise the project first with `setup_project()`"
-  )
-
   x <- read_checklist(x = x)
   if (x$package) {
     return(check_package(x = x, fail = fail, quiet = quiet))

R/read_checklist.R

@@ -43,14 +43,14 @@ read_checklist <- function(x = ".") {
   }
   if (allowed$package) {
     x <- checklist$new(
-      x = x, package = TRUE,
+      x = current, package = TRUE,
       language = ifelse(
         has_name(allowed$spelling, "default"), allowed$spelling$default, "en-GB"
       )
     )
   } else {
     x <- checklist$new(
-      x = x, package = FALSE,
+      x = current, package = FALSE,
       language = ifelse(
         has_name(allowed$spelling, "default"), allowed$spelling$default, "en-GB"
       )

R/set_tag.R

@@ -76,7 +76,9 @@ set_tag <- function(x = ".") {
     repo = repo
   )
 
-  tag_message <- paste(news[seq(start[current], end[current])], collapse = "\n")
+  tag_message <- paste(
+    news[seq(start[current] + 2, end[current])], collapse = "\n"
+  )
   git_tag_create(
     name = paste0("v", version), message = tag_message, repo = repo
   )

R/setup_project.R

@@ -258,25 +258,18 @@ preferred_protocol <- function() {
     config <- read_yaml(config_file)
   }
   if (
-    !has_name(config, "git") || !has_name(config$git, "protocol") ||
-    !has_name(config$git, "organisation")
+    !has_name(config, "git") || !has_name(config$git, "protocol")
   ) {
-    org <- organisation$new()
-    sprintf(
-      "What is your default GitHub organisation. Leave empty for `%s`.",
-      org$get_github
-    ) |>
-      readline() -> config[["git"]][["organisation"]]
-    if (config[["git"]][["organisation"]] == "") {
-      config[["git"]][["organisation"]] <- org$get_github
-    }
     c("https (easy)", "ssh (more secure)") |>
       menu_first(title = "Which protocol do you prefer?") -> protocol
     config[["git"]][["protocol"]] <- c("https", "ssh")[protocol]
     dirname(config_file) |>
       dir_create()
     write_yaml(x = config, file = config_file, fileEncoding = "UTF-8")
   }
+  org <- organisation$new()
+  sprintf("Which GitHub organisation. Leave empty for `%s`.", org$get_github) |>
+    readline() -> config[["git"]][["organisation"]]
   ifelse(
     config$git$protocol == "https", "https://github.com/%s/%%s.git",
     "[email protected]:%s/%%s.git"