Polish lint and styling actions

.Rbuildignore

@@ -23,4 +23,7 @@ create_dev_env.R
 ^\.pre-commit-config\.yaml$
 ^data-raw$
 .envrc
-.direnv
+.direnv
+
+# flint files
+^flint$

.github/workflows/flint-code-formatter.yaml

@@ -0,0 +1,55 @@
+# 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:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: flint-code-formatter
+
+jobs:
+  flint:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: rix-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - name: Install flint
+        run: install.packages("flint", repos = c("https://etiennebacher.r-universe.dev/", getOption("repos")))
+        shell: Rscript {0}
+
+      - name: Run flint
+        run: flint::lint_package(exclude_path = "inst")
+        shell: Rscript {0}
+
+      - name: config bot user and check for changes
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git diff-index --quiet HEAD || echo "has_changes=true" >> $GITHUB_ENV
+
+      - name: commit if changes
+        if: env.has_changes == 'true'
+        run: |
+          git add \*.R
+          git commit -m 'Check and format code with {flint}'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/run_rhub.yaml

@@ -2,8 +2,6 @@
 on:
   push:
     branches: [main, master]
-  pull_request:
-    branches: [main, master]
 
 name: run-rhub-checks
 
@@ -28,6 +26,8 @@ jobs:
           # signingKey: '${{ secrets.CACHIX_SIGNING_KEY }}'
           # If you chose API tokens for write access OR if you have a private cache
           authToken: '${{ secrets.CACHIX_AUTH }}'
-
+      
       - name: Run checks
-        run: nix-shell --run "Rscript -e \"rhub::rhub_check(platforms = c('linux','macos','macos-arm64','windows','ubuntu-next','ubuntu-release'), branch = 'main')\""
+        run: |
+          nix-shell --run "Rscript -e \"rhub::rhub_check(platforms = c('linux','macos','macos-arm64','windows','ubuntu-next','ubuntu-release'))\""
+

.github/workflows/styler.yaml → .github/workflows/style-and-lint.yaml

@@ -6,7 +6,7 @@ on:
   pull_request:
     branches: [main, master]
 
-name: styler
+name: style-and-lint
 
 permissions: write-all
 
@@ -20,6 +20,10 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
       - name: Install Nix
         uses: DeterminateSystems/nix-installer-action@main
 
@@ -33,31 +37,23 @@ jobs:
       - name: Run styler::style_pkg
         run: nix-shell --run "Rscript -e 'styler::style_pkg()'"
 
-      - name: Check if PR exists
-        id: check_pr
-        run: |
-          PR=$(gh pr list -S 'Style package' --json number --jq '.[0].number')
-          echo "PR_NUMBER=$PR" >> $GITHUB_ENV
+      - name: Run lintr
+        run: nix-shell --run "Rscript -e 'lintr::lint_package()'"
+        env:
+          LINTR_ERROR_ON_LINT: true
 
-      - name: Configure user and check for changes
+      - name: config bot user and check for changes
         run: |
-          git config --global user.email "[email protected]"
-          git config --global user.name "CI Robot"
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
           git diff-index --quiet HEAD || echo "has_changes=true" >> $GITHUB_ENV
-
-      - name: Commit and push changes
+          
+      - name: commit if changes
         if: env.has_changes == 'true'
         run: |
-          git add .
-          git commit -m "Styled package"
-          git push origin main:style_pkg --force
+          git add \*.R
+          git commit -m 'Style via {styler}'
 
-      - name: Create Pull Request
-        if: env.PR_NUMBER == ''
-        uses: peter-evans/create-pull-request@v6
+      - uses: r-lib/actions/pr-push@v2
         with:
-          branch: style_pkg
-          title: 'Style package'
-          body: 'Automated PR to style package using `styler:style_pkg()`'
-          base: main
-          branch-suffix: ''
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -7,6 +7,7 @@
 .httr-oauth
 inst/doc
 docs
+flint/cache_file_state.rds
 result
 /doc/
 /Meta/

.lintr

@@ -1,5 +1,11 @@
 linters: linters_with_defaults(
-    line_length_linter(100),
-    commented_code_linter = NULL
+    line_length_linter = line_length_linter(100),
+    commented_code_linter = NULL,
+    object_usage_linter = NULL,
+    cyclocomp_linter = NULL
+  )
+exclusions: list(
+    "tests/testthat/test-fetchers.R",
+    "vignettes/"
   )
 encoding: "UTF-8"

.pre-commit-config.yaml

@@ -0,0 +1,27 @@
+# All available hooks: https://pre-commit.com/hooks.html
+# R specific hooks: https://github.com/lorenzwalthert/precommit
+repos:
+-   repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.4.3.9001
+    hooks: 
+    -   id: style-files
+        args: [--style_pkg=styler, --style_fun=tidyverse_style, --cache-root=styler-perm]
+        require_serial: true
+    -   id: lintr
+        exclude: >
+          (?x)^(
+          tests/testthat/test-fetchers\.R|
+          vignettes/.*
+          )$
+    -   id: parsable-R
+        exclude: > 
+          (?x)^(
+          tests/testthat/in/.*|
+          )$
+    -   id: no-browser-statement
+
+default_stages: ["commit"]
+
+ci:
+    # skip: [consistent-release-tag, spell-check-ordered-exclude, pkgdown]
+    autoupdate_schedule: monthly

R/detect_os.R

@@ -21,7 +21,10 @@ detect_os <- function() {
 #' @noRd
 generate_locale_archive <- function(os) {
   if (os == "Linux" || os == "Darwin") {
-    'LOCALE_ARCHIVE = if pkgs.system == \"x86_64-linux\" then  \"${pkgs.glibcLocales}/lib/locale/locale-archive\" else \"\";'
+    paste0(
+      'LOCALE_ARCHIVE = if pkgs.system == \"x86_64-linux\" then ',
+      '\"${pkgs.glibcLocales}/lib/locale/locale-archive\" else \"\";'
+    )
   } else {
     stop("Operating System unsupported")
   }

R/fetchers.R

@@ -96,7 +96,11 @@ fetchzip <- function(archive_pkg, sri_hash = NULL) {
 #' @noRd
 remove_base <- function(list_imports) {
   imports_nobase <- gsub(
-    "(^base$)|(^compiler$)|(^datasets$)|(^grDevices$)|(^graphics$)|(^grid$)|(^methods$)|(^parallel$)|(^profile$)|(^splines$)|(^stats$)|(^stats4$)|(^tcltk$)|(^tools$)|(^translations$)|(^utils$)",
+    paste0(
+      "(^base$)|(^compiler$)|(^datasets$)|(^grDevices$)|(^graphics$)|(^grid$)|",
+      "(^methods$)|(^parallel$)|(^profile$)|(^splines$)|(^stats$)|",
+      "(^stats4$)|(^tcltk$)|(^tools$)|(^translations$)|(^utils$)"
+    ),
     NA_character_,
     list_imports
   )
@@ -233,7 +237,14 @@ fetchgits <- function(git_pkgs) {
 
     paste(lapply(git_pkgs, fetchgit), collapse = "\n")
   } else {
-    stop("There is something wrong with the input. Make sure it is either a list of three elements 'package_name', 'repo_url' and 'commit' or a list of lists with these three elements")
+    stop(
+      paste0(
+        "There is something wrong with the input. ",
+        "Make sure it is either a list of three elements ",
+        "'package_name', 'repo_url' and 'commit', or ",
+        "a list of lists with these three elements"
+      )
+    )
   }
 }
 

R/get_latest.R

@@ -1,5 +1,6 @@
 #' Get the latest R version and packages
-#' @param r_version Character. R version to look for, for example, "4.2.0". If a nixpkgs revision is provided instead, this gets returned.
+#' @param r_version Character. R version to look for, for example, "4.2.0". If a
+#' nixpkgs revision is provided instead, this gets returned.
 #' @return A character. The commit hash of the latest nixpkgs-unstable revision
 #' @importFrom curl new_handle curl_fetch_memory handle_reset
 #' @importFrom jsonlite fromJSON
@@ -18,7 +19,13 @@ get_latest <- function(r_version) {
   } else if (
     !(r_version %in% c("bleeding_edge", "frozen_edge", available_r()))
   ) {
-    stop("The provided R version is likely wrong.\nPlease check that you provided a correct R version.\nYou can list available versions using `available_r()`.\nYou can also directly provide a commit, but you need to make sure it points to the right repo used by `rix()`.\nYou can also use 'bleeding_edge' and 'frozen_edge'.")
+    stop(
+      "The provided R version is likely wrong.\nPlease check that you ",
+      "provided a correct R version.\nYou can list available versions using ",
+      "`available_r()`.\nYou can also directly provide a commit, but you need ",
+      "to make sure it points to the right repo used by `rix()`.\nYou can ",
+      "also use 'bleeding_edge' and 'frozen_edge'."
+    )
   } else if (!is_online) {
     stop("ERROR! You don't seem to be connected to the internet.")
   } else if (r_version == "bleeding_edge") {
@@ -33,11 +40,14 @@ get_latest <- function(r_version) {
 #' @noRd
 get_right_commit <- function(r_version) {
   if (r_version == "frozen_edge") {
+    # nolint next: line_length_linter
     api_url <- "https://api.github.com/repos/rstats-on-nix/nixpkgs/commits?sha=r-daily"
-  } else if (r_version %in% Filter(function(x) `!=`(x, "latest"), available_r())) { # all but latest
-
+  } else if (
+    r_version %in% Filter(function(x) `!=`(x, "latest"), available_r())
+  ) { # all but latest
     return(sysdata$revision[sysdata$version == r_version])
   } else {
+    # nolint next: line_length_linter
     api_url <- "https://api.github.com/repos/NixOS/nixpkgs/commits?sha=nixpkgs-unstable"
   }
 

R/make_nixpkgs_url.R

@@ -1,5 +1,6 @@
 #' make_nixpkgs_url Find the right Nix revision
-#' @param r_version Character. R version to look for, for example, "4.2.0". If a nixpkgs revision is provided instead, this gets returned.
+#' @param r_version Character. R version to look for, for example, "4.2.0". If a
+#' nixpkgs revision is provided instead, this gets returned.
 #' @return A character. The url to use
 #'
 #' @examples
@@ -15,7 +16,9 @@ make_nixpkgs_url <- function(r_ver) {
   latest_commit <- get_latest(r_ver)
 
   list(
-    "url" = paste0("https://github.com/", github_repo, "archive/", latest_commit, ".tar.gz"),
+    "url" = paste0(
+      "https://github.com/", github_repo, "archive/", latest_commit, ".tar.gz"
+    ),
     "latest_commit" = latest_commit,
     "r_ver" = r_ver
   )

R/nix_build.R

@@ -28,18 +28,19 @@ nix_build <- function(project_path = ".",
     choices = c("simple", "quiet", "verbose")
   )
   # if nix store is not PATH variable; e.g. on macOS (system's) RStudio
-  PATH <- set_nix_path()
+  PATH <- set_nix_path() # nolint: object_name_linter
   if (isTRUE(nzchar(Sys.getenv("NIX_STORE")))) {
     # for Nix R sessions, guarantee that the system's user library
     # (R_LIBS_USER) is not in the search path for packages => run-time purity
     current_libpaths <- .libPaths()
     # don't do this in covr test environment, because this sets R_LIBS_USER
     # to multiple paths
-    R_LIBS_USER <- Sys.getenv("R_LIBS_USER")
+    R_LIBS_USER <- Sys.getenv("R_LIBS_USER") # nolint: object_name_linter
     if (isFALSE(nzchar(Sys.getenv("R_COVR")))) {
       remove_r_libs_user()
     }
   } else {
+    # nolint next: object_name_linter
     LD_LIBRARY_PATH_default <- Sys.getenv("LD_LIBRARY_PATH")
     if (nzchar(LD_LIBRARY_PATH_default)) {
       # On some systems, like Ubuntu 22.04, we found that a preset
@@ -56,7 +57,7 @@ nix_build <- function(project_path = ".",
       fix_ld_library_path()
       cat(
         "* Current LD_LIBRARY_PATH in system R session is:",
-        LD_LIBRARY_PATH_default
+        LD_LIBRARY_PATH_default # nolint: object_name_linter
       )
       cat("\n", "Setting `LD_LIBRARY_PATH` to `''` during `nix_build()`")
     }
@@ -65,6 +66,7 @@ nix_build <- function(project_path = ".",
   nix_dir <- normalizePath(project_path)
   nix_file <- file.path(nix_dir, "default.nix")
 
+  # nolint start: line_length_linter
   stopifnot(
     "`project_path` must be character of length 1." =
       is.character(project_path) && length(project_path) == 1L,
@@ -73,6 +75,7 @@ nix_build <- function(project_path = ".",
     "`nix-build` not available. To install, we suggest you follow https://zero-to-nix.com/start/install ." =
       isTRUE(has_nix_build)
   )
+  # nolint end
 
   max_jobs <- getOption("rix.nix_build_max_jobs", default = 1L)
   stopifnot(