Feature/fix cran notes

.Rbuildignore

@@ -2,6 +2,7 @@
 ^\..*/
 ^\.Rproj\.user$
 .*_cache/
+^\.github$
 ^data-raw/
 ^inst/snippets/
 ^revdep/
@@ -16,16 +17,10 @@
 ^CRAN-RELEASE$
 ^README\.Rmd$
 ^LICENSE\.md$
-^vignettes/_common.R$
-^vignettes/references.bib$
-
-# Docker
-^docker-compose\.yml$
-^R/utils-DockerCompose\.R$
 
 # pkgdown$
 ^docs$
 ^pkgdown$
 
-
-
+# cran
+^CRAN-SUBMISSION$

.Rprofile

@@ -1,71 +1,22 @@
 assign(".Rprofile", new.env(), envir = globalenv())
 
 # .First ------------------------------------------------------------------
-.First <- function(){
-    try(if(testthat::is_testing()) return())
-    try(readRenviron(".Renviron"), silent = TRUE)
+.First <- function() {
+    try(if (testthat::is_testing()) {
+        return()
+    }, silent = TRUE)
+    if (file.exists(".Renviron")) readRenviron(".Renviron")
 
-    # Package Management System
-    Date <- as.character(read.dcf("DESCRIPTION", "Date"));
-    URL <- if(is.na(Date)) "https://cran.rstudio.com/" else paste0("https://mran.microsoft.com/snapshot/", Date)
-    options(repos = URL)
-}
-
-# .Last -------------------------------------------------------------------
-.Last <- function(){
-    try(if(testthat::is_testing()) return())
-    try(system('docker-compose down'), silent = TRUE)
-}
-
-# Docker ------------------------------------------------------------------
-.Rprofile$docker$browse_url <- function(service){
-    path_script <- tempfile("system-", fileext = ".R")
-    job_name <- paste("Testing", as.character(read.dcf('DESCRIPTION', 'Package')), "in a Docker Container")
-    define_service <- paste0("service = c(", paste0(paste0("'",service,"'"), collapse = ", "),")")
-    define_service <- if(is.null(service)) "service = NULL" else define_service
-    writeLines(c(
-        "source('./R/utils-DockerCompose.R')",
-        define_service,
-        "DockerCompose$new()$browse_url(service)"), path_script)
-    .Rprofile$utils$run_script(path_script, job_name)
-}
-
-.Rprofile$docker$start <- function(service = NULL){
-    path_script <- tempfile("system-", fileext = ".R")
-    job_name <- paste("Testing", as.character(read.dcf('DESCRIPTION', 'Package')), "in a Docker Container")
-    define_service <- paste0("service <- c(", paste0(paste0("'",service,"'"), collapse = ", "),")")
-    define_service <- if(is.null(service)) "service = NULL" else define_service
-    writeLines(c(
-        "source('./R/utils-DockerCompose.R')",
-        define_service,
-        "DockerCompose$new()$start(service)"), path_script)
-    .Rprofile$utils$run_script(path_script, job_name)
-}
 
-.Rprofile$docker$stop <- function(){
-    path_script <- tempfile("system-", fileext = ".R")
-    job_name <- paste("Testing", as.character(read.dcf('DESCRIPTION', 'Package')), "in a Docker Container")
-    writeLines(c("source('./R/utils-DockerCompose.R'); DockerCompose$new()$stop()"), path_script)
-    .Rprofile$utils$run_script(path_script, job_name)
-}
-
-.Rprofile$docker$restart <- function(service = NULL){
-    path_script <- tempfile("system-", fileext = ".R")
-    job_name <- paste("Testing", as.character(read.dcf('DESCRIPTION', 'Package')), "in a Docker Container")
-    define_service <- paste0("service <- c(", paste0(paste0("'",service,"'"), collapse = ", "),")")
-    define_service <- if(is.null(service)) "service = NULL" else define_service
-    writeLines(c(
-        "source('./R/utils-DockerCompose.R')",
-        define_service,
-        "DockerCompose$new()$restart(service)"), path_script)
-    .Rprofile$utils$run_script(path_script, job_name)
-}
-
-.Rprofile$docker$reset <- function(){
-    path_script <- tempfile("system-", fileext = ".R")
-    job_name <- paste("Testing", as.character(read.dcf('DESCRIPTION', 'Package')), "in a Docker Container")
-    writeLines(c("source('./R/utils-DockerCompose.R'); DockerCompose$new()$reset()"), path_script)
-    .Rprofile$utils$run_script(path_script, job_name)
+    # Package Management System
+    r_version_date <- gsub(".*\\((\\d{4}-\\d{2}-\\d{2}).*", "\\1", R.Version()$version.string)
+    r_package_date <- as.character(read.dcf("DESCRIPTION", "Date"))
+    r_cran_date <- ifelse(is.na(r_package_date), r_version_date, r_package_date)
+    options(repos = c(CRAN = paste0("https://packagemanager.rstudio.com/cran/", r_cran_date)))
+
+    # Options
+    Sys.setenv(`_R_S3_METHOD_REGISTRATION_NOTE_OVERWRITES_` = "false")
+    Sys.setenv(`_R_CHECK_SYSTEM_CLOCK_` = 0)
 }
 
 # pkgdown -----------------------------------------------------------------
@@ -124,3 +75,9 @@ assign(".Rprofile", new.env(), envir = globalenv())
     invisible()
 }
 
+# .Last -------------------------------------------------------------------
+.Last <- function() {
+    try(if (testthat::is_testing()) {
+        return()
+    })
+}

.dev/CRAN/prepare-for-release.R

@@ -6,6 +6,14 @@ Sys.setenv(`_R_DEPENDS_ONLY` = "true")
 remotes::install_cran(c("devtools", "urlchecker", "rhub", "revdepcheck"))
 # remotes::install_github("r-lib/revdepcheck@master")
 
+# Printing Code -----------------------------------------------------------
+# Lint the package
+(report = lintr::lint_package(show_progress = TRUE))
+styler::style_pkg(
+    filetype = c("R", "Rprofile", "Rmd", "Rmarkdown", "Rnw", "qmd")[c(1,3)],
+    exclude_dirs = c("packrat", "renv", ".dev", ".git", ".github", ".Rproj.user", "docs", "inst"),
+    include_roxygen_examples = TRUE,
+)
 
 # Steps -------------------------------------------------------------------
 # devtools::build_readme()

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,41 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+  pull_request:
+
+name: R-CMD-check
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - name: Remove .Rprofile
+        # Delete .Rprofile if present.
+        run: rm -f ./.Rprofile
+
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck, any::roxygen2
+          needs: check
+
+      - name: Document the package
+        run: |
+         roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -0,0 +1,64 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: #[main, master]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - name: Remove .Rprofile
+        # Delete .Rprofile if present.
+        run: rm -f ./.Rprofile
+
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::pkgdown,
+            any::roxygen2,
+            any::covr,
+            any::usethis,
+            any::pkgload,
+            local::.,
+          needs: website
+
+      - name: Build site
+        run: |
+          roxygen2::roxygenise()
+          rmarkdown::render("README.Rmd", output_format = "md_document")
+          pkgload::load_all()
+          pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+          covr::codecov(type = "all")
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs