docs, tests, formats

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

@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -29,7 +30,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -47,3 +48,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/lint.yaml

@@ -4,17 +4,18 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: lint
+name: lint.yaml
+
+permissions: read-all
 
 jobs:
   lint:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

.github/workflows/pkgdown.yaml

@@ -4,12 +4,13 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -19,8 +20,10 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -39,7 +42,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/test-coverage.yaml

@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,36 +16,47 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - 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::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          print(cov)
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v5
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: scribe
 Title: Command Argument Parsing
-Version: 0.3.0.9002
+Version: 0.3.0.9003
 Authors@R: 
     person(
       given   = "Jordan Mark",
@@ -16,7 +16,7 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 Language: en-US
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.3
 Depends:
     R (>= 3.6)
 Imports:

R/arg.R

@@ -1,4 +1,3 @@
-
 #' New command argument
 #'
 #' Make a new [scribeArg] object
@@ -13,25 +12,25 @@
 #' @family scribe
 #' @export
 new_arg <- function(
-    aliases = "",
-    action  = arg_actions(),
-    default = NULL,
-    convert = scribe_convert(),
-    n       = NA_integer_,
-    info    = NULL,
-    options = list(),
-    stop    = c("none", "hard", "soft"),
-    execute = invisible
+  aliases = "",
+  action = arg_actions(),
+  default = NULL,
+  convert = scribe_convert(),
+  n = NA_integer_,
+  info = NULL,
+  options = list(),
+  stop = c("none", "hard", "soft"),
+  execute = invisible
 ) {
   scribeArg$new(
     aliases = aliases,
-    action  = action,
+    action = action,
     default = default,
     convert = convert,
-    n       = n,
-    info    = info,
+    n = n,
+    info = info,
     options = options,
-    stop    = stop,
+    stop = stop,
     execute = execute
   )
 }
@@ -48,7 +47,7 @@
     execute = function(self, ca) {
       if (isTRUE(self$get_value())) {
         ca$help()
         return(exit())
       }
     }
   )
@@ -68,7 +67,7 @@
       if (isTRUE(self$get_value())) {
         .Deprecated("For {scribe} package version, use ---version instead")
         ca$version()
         return(exit())
       }
     }
   )
@@ -78,19 +77,19 @@
 
 # nolint next: cyclocomp_linter.
 arg_initialize <- function(
-    self,
-    aliases = "",
-    action  = arg_actions(),
-    default = NULL,
-    convert = scribe_convert(),
-    n       = NA_integer_,
-    info    = NA_character_,
-    options = list(),
-    stop    = c("none", "hard", "soft"),
-    execute = invisible
+  self,
+  aliases = "",
+  action = arg_actions(),
+  default = NULL,
+  convert = scribe_convert(),
+  n = NA_integer_,
+  info = NA_character_,
+  options = list(),
+  stop = c("none", "hard", "soft"),
+  execute = invisible
 ) {
-  action  <- match.arg(action, arg_actions())
-  info    <- info    %||% NA_character_
+  action <- match.arg(action, arg_actions())
+  info <- info %||% NA_character_
   options <- options %||% list()
 
   if (action == "default") {
@@ -314,7 +313,7 @@
     list = {
       left <- paste(
         to_string(self$get_aliases(), sep = ", "),
-        sprintf("[%s]", if (self$n == 1) "ARG" else  sprintf("..%i", self$n))
+        sprintf("[%s]", if (self$n == 1) "ARG" else sprintf("..%i", self$n))
       )
 
       right <- self$info
@@ -374,7 +373,7 @@
   nm
 }
 
-arg_get_action  <- function(self) {
+arg_get_action <- function(self) {
   self$action %||% character()
 }
 
@@ -508,7 +507,7 @@
   methods::is(x, "scribeArg")
 }
 
-ARG_PAT <- "^-[a-z]$|^---?[a-z]+$|^--?[a-z](+[-]?[a-z]+)+$"  # nolint: object_name_linter, line_length_linter.
+ARG_PAT <- "^-[a-z]$|^---?[a-z]+$|^--?[a-z](+[-]?[a-z]+)+$" # nolint: object_name_linter, line_length_linter.
 
 arg_actions <- function() {
   c("default", "list", "flag", "dots")

R/class-args.R

@@ -1,4 +1,3 @@
-
 #' {scribe} argument
 #'
 #' ReferenceClass object for managing arguments
@@ -75,32 +74,32 @@
 # nolint next: object_name_linter.
 scribeArg <- methods::setRefClass(
   "scribeArg",
-  fields       = list(
-    aliases    = "character",
-    action     = "character",
-    default    = "ANY",
-    convert    = "ANY",
-    n          = "integer",
-    info       = "character",
-    options    = "list",
+  fields = list(
+    aliases = "character",
+    action = "character",
+    default = "ANY",
+    convert = "ANY",
+    n = "integer",
+    info = "character",
+    options = "list",
     positional = "logical",
-    resolved   = "logical",
-    value      = "ANY",
-    stop       = "character",
-    execute    = "function"
+    resolved = "logical",
+    value = "ANY",
+    stop = "character",
+    execute = "function"
   )
 )
 
 scribeArg$methods(
   initialize = function(
     aliases = "",
-    action  = arg_actions(),
+    action = arg_actions(),
     default = NULL,
     convert = scribe_convert(),
-    n       = NA_integer_,
-    info    = NA_character_,
+    n = NA_integer_,
+    info = NA_character_,
     options = list(),
-    stop    = c("none", "hard", "soft"),
+    stop = c("none", "hard", "soft"),
     execute = invisible
   ) {
     "
@@ -109,15 +108,15 @@ scribeArg$methods(
     See \\strong{fields} for parameter information.
     "
     arg_initialize(
-      self    = .self,
+      self = .self,
       aliases = aliases,
-      action  = action,
+      action = action,
       default = default,
       convert = convert,
-      n       = n,
-      info    = info,
+      n = n,
+      info = info,
       options = options,
-      stop    = stop,
+      stop = stop,
       execute = execute
     )
   },
@@ -186,7 +185,7 @@ scribeSuperArg$methods(
     }
 
     arg_initialize(
-      self    = .self,
+      self = .self,
       aliases = aliases,
       ...
     )

R/class-command-args.R

@@ -1,4 +1,3 @@
-
 #' {scribe} command arguments
 #'
 #' Reference class object for managing command line arguments.
@@ -205,13 +204,13 @@ scribeCommandArgs$methods(
 
   add_argument = function(
     ...,
-    action  = arg_actions(),
+    action = arg_actions(),
     default = NULL,
     convert = scribe_convert(),
-    n       = NA_integer_,
-    info    = NULL,
+    n = NA_integer_,
+    info = NULL,
     options = list(),
-    stop    = c("none", "hard", "soft"),
+    stop = c("none", "hard", "soft"),
     execute = invisible
   ) {
     "Add a \\link{scribeArg} to \\code{args}