Merge pull request #69 from inbo/cran

avoid checks on CRAN

.Rbuildignore

@@ -1,16 +1,19 @@
 ^_pkgdown.yml$
 ^.*\.Rproj$
+^.*\.zenodo.json$
 ^.dockerignore$
 ^\.github$
 ^\.httr-oauth$
 ^\.Rproj\.user$
 ^\.zenodo\.json$
 ^checklist.yml$
+^CITATION\.cff$
 ^codecov\.yml$
+^codemeta\.json$
 ^data-raw$
+^docker-compose.test.yml$
 ^docker$
 ^Dockerfile$
-^docker-compose.test.yml$
 ^docs$
 ^LICENSE.md$
 ^man-roxygen$

.github/workflows/check_on_branch.yml

@@ -11,8 +11,9 @@ jobs:
   check-package:
     runs-on: ubuntu-latest
     name: "check package"
+    env:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: inbo/actions/check_pkg@master
-        with:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-          ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }}

.github/workflows/check_on_different_r_os.yml

@@ -97,3 +97,4 @@ jobs:
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check
+          retention-days: 5

.github/workflows/check_on_main.yml

@@ -12,9 +12,9 @@ jobs:
   check-package:
     runs-on: ubuntu-latest
     name: "check package"
+    env:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: inbo/actions/check_pkg@master
-        with:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-          ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }}
-          token: ${{ secrets.pat }}

.zenodo.json

@@ -1,22 +1,23 @@
 {
-    "title": "A Thorough and Strict Set of Checks for R Packages and Source Code",
-    "description": "An opinated set of rules for R packages and R source code projects an used at the Research Institute for Nature and Forest (INBO), Brussels, Belgium (<a href=\"https://www.inbo.be/en\">www.inbo.be</a>).",
-    "license": "GPL-3.0",
-    "upload_type": "other",
-    "access_right": "open",
-    "creators": [
-        {
-            "name": "Onkelinx, Thierry",
-            "affiliation": "Research Institute for Nature and Forest",
-            "orcid": "0000-0001-8804-4216"
-        }
-    ],
-    "keywords": [
-        "R",
-        "package",
-        "open science",
-        "continous integreation",
-        "unit test",
-        "code style"
-        ]
+  "title": ["checklist: A Thorough and Strict Set of Checks for R Packages and Source Code"],
+  "version": ["0.1.14"],
+  "description": ["An opinated set of rules for R packages and R source code projects."],
+  "creators": [
+    {
+      "name": ["Onkelinx, Thierry"],
+      "orcid": ["https://orcid.org/0000-0001-8804-4216"]
+    }
+  ],
+  "contributors": [
+    {
+      "name": ["Lommelen, Els"],
+      "orcid": ["https://orcid.org/0000-0002-3481-5684"]
+    }
+  ],
+  "upload_type": ["software"],
+  "access_rights": ["open"],
+  "license": ["GPL-3.0"],
+  "communities": {
+    "identifier": ["inbo"]
+  }
 }

CITATION.cff

@@ -0,0 +1,22 @@
+cff-version: 1.2.0
+message: If you use this software, please cite it as below.
+authors:
+- family-names: Onkelinx
+  given-names: Thierry
+  orcid: https://orcid.org/0000-0001-8804-4216
+contact:
+- email: [email protected]
+  family-names: Onkelinx
+  given-names: Thierry
+- email: [email protected]
+  name: Research Institute for Nature and Forest
+title: 'checklist: A Thorough and Strict Set of Checks for R Packages and Source Code'
+version: 0.1.14
+abstract: An opinated set of rules for R packages and R source code projects.
+license: GPL-3.0
+type: software
+doi: 10.5281/zenodo.4028303
+repository-code: https://github.com/inbo/checklist
+identifiers:
+- type: url
+  value: https://inbo.github.io/checklist/

DESCRIPTION

@@ -1,21 +1,14 @@
 Type: Package
 Package: checklist
 Title: A Thorough and Strict Set of Checks for R Packages and Source Code
-Version: 0.1.13
-Authors@R: 
-    c(person(given = "Thierry",
-             family = "Onkelinx",
-             role = c("aut", "cre"),
-             email = "[email protected]",
-             comment = c(ORCID = "0000-0001-8804-4216")),
-      person(given = "Els",
-             family = "Lommelen",
-             role = "ctb",
-             email = "[email protected]",
-             comment = c(ORCID = "0000-0002-3481-5684")),
-      person(given = "Research Institute for Nature and Forest",
-             role = c("cph", "fnd"),
-             email = "[email protected]"))
+Version: 0.1.14
+Authors@R: c(
+    person("Thierry", "Onkelinx", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0001-8804-4216")),
+    person("Els", "Lommelen", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0000-0002-3481-5684")),
+    person("Research Institute for Nature and Forest", , , "[email protected]", role = c("cph", "fnd"))
+  )
 Description: An opinated set of rules for R packages and R source code
     projects.
 License: GPL-3
@@ -30,6 +23,7 @@ Imports:
     devtools (> 2.4.0),
     git2r,
     httr,
+    jsonlite,
     lintr,
     pkgdown,
     rcmdcheck,
@@ -53,4 +47,4 @@ Additional_repositories: https://ropensci.r-universe.dev
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2

NAMESPACE

@@ -24,6 +24,8 @@ export(tidy_desc)
 export(update_citation)
 export(validate_email)
 export(write_checklist)
+export(write_citation_cff)
+export(write_zenodo_json)
 export(yesno)
 importFrom(R6,R6Class)
 importFrom(assertthat,"on_failure<-")
@@ -75,6 +77,7 @@ importFrom(grDevices,svg)
 importFrom(graphics,plot.new)
 importFrom(graphics,text)
 importFrom(httr,HEAD)
+importFrom(jsonlite,toJSON)
 importFrom(lintr,lint_dir)
 importFrom(lintr,lint_package)
 importFrom(pkgdown,build_site)

NEWS.md

@@ -1,3 +1,17 @@
+# checklist 0.1.14
+
+* Improve error message when changes in `CITATION` need to be commit. (#64)
+* `create_package()` can use maintainer information stored in the options.
+  See `usethis::use_description()` on how to set the option.
+* Add R universe badges to README.
+* Add `write_zenodo_json()` and `write_citation_cff()`.
+* Improve the checklist Github Actions.
+
+## Bugfix
+
+* `create_package()` replaces package name place holder with actual package name
+  in `_pkgdown.yml`.
+
 # checklist 0.1.13
 
 * A new function `update_citation()` creates or updates a default citation in

R/check_description.R

@@ -174,7 +174,7 @@ tidy_desc <- function(x = ".") {
 
 unchanged_repo <- function(repo, old_status) {
   current_status <- status(repo)
-  identical(
+  ok <- identical(
     current_status$staged,
     old_status$staged
   ) &&
@@ -186,6 +186,15 @@ unchanged_repo <- function(repo, old_status) {
       current_status$untracked,
       old_status$untracked
     )
+  new_files <- unlist(current_status)
+  old_files <- unlist(old_status)
+  changes <- c(
+    new_files[!new_files %in% old_files], old_files[!old_files %in% new_files]
+  )
+  attr(ok, "files") <- sprintf(
+    "changed files:\n%s", paste(changes, collapse = "\n")
+  )
+  return(ok)
 }
 
 #' Check the license of a package

R/check_documentation.R

@@ -66,20 +66,24 @@ check_documentation <- function(x = ".") {
   repo <- repository(x$get_path)
   status_before <- status(repo)
   document(x$get_path)
+  detect_changes <- unchanged_repo(repo, status_before)
+  si <- session_info(pkgs = "roxygen2")
   doc_error <- c(
     doc_error,
-    "Missing documentation. Run `devtools::document()`"[
-      !unchanged_repo(repo, status_before)
-    ]
+    sprintf(
+      "Running `devtools::document()` with roxygen2 %s %s",
+      si$packages$loadedversion[si$packages$package == "roxygen2"],
+      attr(detect_changes, "files")
+    )[!detect_changes]
   )
 
   if (file_test("-f", file.path(x$get_path, "README.Rmd"))) {
-    status_before <- status(repo)
     build_readme(x$get_path, encoding = "UTF-8")
+    current <- unlist(status(repo, ignored = TRUE))
     doc_error <- c(
       doc_error,
       "`README.Rmd` need to be rendered. Run `devtools::build_readme()`"[
-        !unchanged_repo(repo, status_before)
+        "README.md" %in% current
       ]
     )
   }

R/check_filename.R

@@ -104,7 +104,7 @@ Failing folder: `%s`",
     paste(
       c(
         "\\.[a-zA-Z]+ignore", "\\.Rprofile", "\\.[a-zA-Z]+\\.(json|yml)",
-        "CITATION", "DESCRIPTION", "NAMESPACE",
+        "CITATION", "DESCRIPTION", "NAMESPACE", "CITATION.cff",
         "README\\.R?md", "NEWS\\.md", # nolint
         "CODE_OF_CONDUCT.md", "CONTRIBUTING.md", "LICENSE.md", "SUPPORT.md",
         "SECURITY.md", "FUNDING.yml",

R/create_package.R

@@ -13,6 +13,8 @@
 #' @param maintainer The output of [utils::person()] or [`orcid2person()`].
 #'   If you use [utils::person()], then you must provide `given`, `family`,
 #'   `role`, `email` and  `comment` with valid `ORCID`.
+#'   When missing, the functions looks for `usethis.description` in the options.
+#'   See [usethis::use_description()] for more information.
 #' @export
 #' @importFrom assertthat assert_that is.string
 #' @importFrom git2r add  init
@@ -48,6 +50,17 @@ create_package <- function(
     msg =
       "Please install the `roxygen2` package. `install.packages(\"roxygen2\")`"
   )
+  if (missing(maintainer)) {
+    utd <- getOption("usethis.description")
+    assert_that(
+      has_name(utd, "Authors@R"),
+      msg = paste(
+        "maintainer not provided and no usethis::use_description defaults",
+        "available."
+      )
+    )
+    maintainer <- head(eval(parse(text = utd$"Authors@R")), 1)
+  }
   assert_that(inherits(maintainer, "person"))
   assert_that(dir.exists(path), msg = sprintf("`%s` is not a directory", path))
   assert_that(is.string(package))
@@ -241,25 +254,15 @@ allowed:
   add(
     repo = repo, file.path(".github", "workflows", "release.yml"), force = TRUE
   )
-  file.copy(
-    system.file(
-      file.path("package_template", "remove_old_artifacts.yml"),
-      package = "checklist"
-    ),
-    file.path(path, ".github", "workflows", "remove_old_artifacts.yml"),
-    overwrite = TRUE
-  )
-  add(
-    repo = repo, file.path(".github", "workflows", "release.yml"), force = TRUE
-  )
 
   # prepare pkgdown
-  file.copy(
+  pkgd <- readLines(
     system.file(
       file.path("package_template", "_pkgdown.yml"), package = "checklist"
-    ),
-    file.path(path, "_pkgdown.yml")
+    )
   )
+  pkgd <- gsub("\\{\\{\\{ Package \\}\\}\\}", package, pkgd)
+  writeLines(pkgd, file.path(path, "_pkgdown.yml"))
   add(repo = repo, "_pkgdown.yml")
 
   dir.create(file.path(path, "pkgdown"), showWarnings = FALSE)

R/setup_package.R

@@ -194,25 +194,15 @@ allowed:
   add(
     repo = repo, file.path(".github", "workflows", "release.yml"), force = TRUE
   )
-  file.copy(
-    system.file(
-      file.path("package_template", "remove_old_artifacts.yml"),
-      package = "checklist"
-    ),
-    file.path(path, ".github", "workflows", "remove_old_artifacts.yml"),
-    overwrite = TRUE
-  )
-  add(
-    repo = repo, file.path(".github", "workflows", "release.yml"), force = TRUE
-  )
 
   # Add pkgdown website
-  file.copy(
+  pkgd <- readLines(
     system.file(
       file.path("package_template", "_pkgdown.yml"), package = "checklist"
-    ),
-    file.path(path, "_pkgdown.yml")
+    )
   )
+  pkgd <- gsub("\\{\\{\\{ Package \\}\\}\\}", package, pkgd)
+  writeLines(pkgd, file.path(path, "_pkgdown.yml"))
   add(repo = repo, "_pkgdown.yml", force = TRUE)
   dir.create(file.path(path, "pkgdown"), showWarnings = FALSE)
   file.copy(