Merge pull request #28 from inbo/0.1.7

0.1.7

.github/workflows/check_on_master.yml

@@ -3,7 +3,7 @@ on:
     branches:
       - master
   schedule:
-    - cron: '6 0 * * 1'
+    - cron: '6 0 15 * *'
 
 name: "check package on master"
 

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: checklist
 Title: A Thorough and Strict Set of Checks for R Packages and Source Code
-Version: 0.1.6
+Version: 0.1.7
 Authors@R: 
     c(person(given = "Thierry",
              family = "Onkelinx",
@@ -14,7 +14,8 @@ Authors@R:
 Description: An opinated set of rules for R packages and R source code
     projects.
 License: GPL-3
-URL: https://inbo.github.io/checklist, https://github.com/inbo/checklist
+URL: https://inbo.github.io/checklist, https://github.com/inbo/checklist,
+    https://doi.org/10.5281/zenodo.4028303
 BugReports: https://github.com/inbo/checklist/issues
 Imports:
     R6,
@@ -26,7 +27,6 @@ Imports:
     httr,
     lintr,
     rcmdcheck,
-    rmarkdown,
     rorcid,
     sessioninfo,
     utils,

NAMESPACE

@@ -30,6 +30,7 @@ importFrom(assertthat,noNA)
 importFrom(codemetar,give_opinions)
 importFrom(desc,desc)
 importFrom(desc,description)
+importFrom(devtools,build_readme)
 importFrom(devtools,document)
 importFrom(git2r,add)
 importFrom(git2r,branch_target)
@@ -56,8 +57,6 @@ importFrom(httr,add_headers)
 importFrom(lintr,lint_dir)
 importFrom(lintr,lint_package)
 importFrom(rcmdcheck,rcmdcheck)
-importFrom(rmarkdown,github_document)
-importFrom(rmarkdown,render)
 importFrom(rorcid,as.orcid)
 importFrom(sessioninfo,session_info)
 importFrom(stats,na.omit)

NEWS.md

@@ -1,3 +1,12 @@
+# checklist 0.1.7
+
+* Pushing to master should automatically create a release, using `set_tag()`.
+* Add a Zenodo DOI badge to the README and DOI URL to DESCRIPTION.
+* `check_description()` now checks authors (#7).
+    * INBO is set as copyright holder and funder.
+    * Every author has an ORCID.
+* `setup_package()` adds the required files for a `pkgdown` website (#21).
+
 # checklist 0.1.6
 
 * Drop the `codemeta.json` file.

R/check_description.R

@@ -65,9 +65,9 @@ check_description <- function(x = ".") {
     desc_error,
     "DESCRIPTION not tidy. Use `checklist::tidy_desc()`"[
       !unchanged_repo(repo, status_before)
-    ]
+    ],
+    check_authors(description)
   )
-
   x$add_error(desc_error, "DESCRIPTION")
 
   check_license(x = x)
@@ -197,3 +197,25 @@ Please send a pull request if you need support for this license.",
 
   return(x)
 }
+
+check_authors <- function(description) {
+  authors <- description$get_authors()
+  authors <- lapply(authors, unlist, recursive = FALSE)
+  inbo <- person(
+    given = "Research Institute for Nature and Forest",
+    role = c("cph", "fnd"), email = "[email protected]"
+  )
+  problems <- paste(
+    "Research Institute for Nature and Forest must be listed as copyright",
+    "holder and funder and use [email protected] as email."
+  )[!inbo %in% authors]
+  authors <- authors[!authors %in% inbo]
+  orcid <- sapply(authors, `[[`, "comment")
+  c(
+    problems,
+    "Every author and contributor must have an ORCID"[
+      any(names(orcid) != "ORCID")
+    ]
+  )
+
+}

R/check_documentation.R

@@ -1,8 +1,7 @@
 #' Check the documentation
 #' @inheritParams read_checklist
 #' @export
-#' @importFrom devtools document
-#' @importFrom rmarkdown github_document render
+#' @importFrom devtools build_readme document
 #' @family package
 check_documentation <- function(x = ".") {
   if (!inherits(x, "Checklist") || !"checklist" %in% x$get_checked) {
@@ -38,11 +37,7 @@ check_documentation <- function(x = ".") {
 
   if (file_test("-f", file.path(x$get_path, "README.Rmd"))) {
     status_before <- status(repo)
-    render(
-      file.path(x$get_path, "README.Rmd"),
-      output_format = github_document(html_preview = FALSE),
-      encoding = "UTF-8"
-    )
+    build_readme(x$get_path, encoding = "UTF-8")
     doc_error <- c(
       doc_error,
       "`README.Rmd` need to be rendered. Run `devtools::build_readme()`"[

R/set_tag.R

@@ -4,10 +4,11 @@
 #' Otherwise it will only return a message.
 #' @export
 #' @inheritParams read_checklist
+#' @param token The GitHub access token
 #' @importFrom assertthat assert_that
 #' @importFrom git2r config is_detached repository tag tags
 #' @family package
-set_tag <- function(x = ".") {
+set_tag <- function(x = ".", token) {
   if (
     !as.logical(Sys.getenv("GITHUB_ACTIONS", "false")) ||
       Sys.getenv("GITHUB_REF") != "refs/heads/master" ||
@@ -57,48 +58,49 @@ set_tag <- function(x = ".") {
     user.name = "Checklist bot",
     user.email = "[email protected]"
   )
-  tag(
-    repo,
-    name = paste0("v", version),
-    message = paste(news[seq(start[current], end[current])], collapse = "\n")
+  tag_message <- paste(news[seq(start[current], end[current])], collapse = "\n")
+  tag(repo, name = paste0("v", version), message = tag_message)
+  cmd <- sprintf(
+    "cd %s; git push origin; git push origin v%s", repo$path, version
   )
-  cmd <- sprintf("cd %s; git push origin v%s", repo$path, version)
-  message(cmd)
   system(cmd)
 
-  create_release(repo = repo, version = version, message = message)
+  create_release(
+    repo = repo, version = version, tag_message = tag_message, token = token
+  )
   return(invisible(NULL))
 }
 
 #' @importFrom httr add_headers POST
 #' @importFrom git2r remote_url
-create_release <- function(repo, version, message) {
+create_release <- function(repo, version, tag_message, token) {
   url <- remote_url(repo, "origin")
   if (!grepl("github.com", url)) {
     warning("no `origin` or `origin` not on GitHub.")
     return(invisible(NULL))
   }
-  owner <- gsub(".*github.com:(.*?)/(.*?)\\.git", "\\1", url)
-  repo <- gsub(".*github.com:(.*?)/(.*?)\\.git", "\\1", url)
+  owner <- tolower(gsub(".*github.com:(.*?)/(.*?)\\.git", "\\1", url))
+  repo <- gsub(".*github.com:(.*?)/(.*?)\\.git", "\\2", url)
   url <- sprintf("https://api.github.com/repos/%s/%s/releases", owner, repo)
   body <- c(
-    tag_name = paste0("v", version),
-    name = paste("Version", version),
-    body = message,
+    tag_name = paste0("\"v", version, "\""),
+    name = paste("\"Version", version, "\""),
+    body = paste0("\"", tag_message, "\""),
     draft = "false",
-    release = "false"
+    prerelease = "false"
   )
   body <- sprintf(
     "{\n%s\n}",
     paste(
-      sprintf("  \"%s\" : \"%s\"", names(body), body),
-      collapse = "\n"
+      sprintf("  \"%s\" : %s", names(body), body),
+      collapse = ",\n"
     )
   )
   POST(
     url = url,
     config = add_headers(
-      "User-Agent" = "inbo/checklist package",
+      # "User-Agent" = "inbo/checklist package",
+      Authorization = paste("Bearer", token),
       accept = "application/vnd.github.v3+json"
     ),
     body = body,

R/setup_package.R

@@ -100,27 +100,43 @@ allowed:
   dir.create(file.path(path, ".github", "workflows"), showWarnings = FALSE)
   file.copy(
     system.file("package_template/check_on_branch.yml", package = "checklist"),
-    file.path(path, ".github", "workflows", "check_on_branch.yml")
+    file.path(path, ".github", "workflows", "check_on_branch.yml"),
+    overwrite = TRUE
   )
   add(repo = repo, ".github/workflows/check_on_branch.yml", force = TRUE)
   file.copy(
     system.file("package_template/check_on_master.yml", package = "checklist"),
-    file.path(path, ".github", "workflows", "check_on_master.yml")
+    file.path(path, ".github", "workflows", "check_on_master.yml"),
+    overwrite = TRUE
   )
   add(repo = repo, ".github/workflows/check_on_master.yml", force = TRUE)
   file.copy(
     system.file(
       "package_template/check_on_different_r_os.yml",
       package = "checklist"
     ),
-    file.path(path, ".github", "workflows", "check_on_different_r_os.yml")
+    file.path(path, ".github", "workflows", "check_on_different_r_os.yml"),
+    overwrite = TRUE
   )
   add(
     repo = repo,
     ".github/workflows/check_on_different_r_os.yml",
     force = TRUE
   )
 
+  # Add pkgdown website
+  file.copy(
+    system.file("package_template/_pkgdown.yml", package = "checklist"),
+    file.path(path, "_pkgdown.yml")
+  )
+  add(repo = repo, "_pkgdown.yml", force = TRUE)
+  dir.create(file.path(path, "pkgdown"), showWarnings = FALSE)
+  file.copy(
+    system.file("package_template/pkgdown.css", package = "checklist"),
+    file.path(path, "pkgdown", "extra.css"), overwrite = TRUE
+  )
+  add(repo = repo, "pkgdown/extra.css", force = TRUE)
+
   message("package prepared for checklist::check_package()")
   return(invisible(NULL))
 }

README.Rmd

@@ -12,6 +12,7 @@ output: github_document
 [![Codecov test coverage](https://codecov.io/gh/inbo/checklist/branch/master/graph/badge.svg)](https://codecov.io/gh/inbo/checklist?branch=master)
 ![GitHub code size in bytes](https://img.shields.io/github/languages/code-size/inbo/checklist.svg)
 ![GitHub repo size](https://img.shields.io/github/repo-size/inbo/checklist.svg)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4028303.svg)](https://doi.org/10.5281/zenodo.4028303)
 
 ```{r setup, include = FALSE}
 knitr::opts_chunk$set(

README.md

@@ -17,6 +17,7 @@ coverage](https://codecov.io/gh/inbo/checklist/branch/master/graph/badge.svg)](h
 bytes](https://img.shields.io/github/languages/code-size/inbo/checklist.svg)
 ![GitHub repo
 size](https://img.shields.io/github/repo-size/inbo/checklist.svg)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4028303.svg)](https://doi.org/10.5281/zenodo.4028303)
 
 The goal of `checklist` is to provide an elaborate and strict set of
 checks for R packages and R code.

entrypoint_package.sh

@@ -54,7 +54,7 @@ elif [ "$GITHUB_REF" != "refs/heads/master" ]; then
 else
   git checkout master
   echo '\nUpdating tag...\n';
-  Rscript --no-save --no-restore -e 'checklist::set_tag()';
+  Rscript --no-save --no-restore -e 'checklist::set_tag(token = "$2")';
 
   echo '\nPush pkgdown website...\n'
   cp -R docs ../docs

inst/package_template/check_on_master.yml

@@ -3,7 +3,7 @@ on:
     branches:
       - master
   schedule:
-    - cron: '6 0 * * 1'
+    - cron: '6 0 15 * *'
 
 name: "check package on master"