Merge pull request #477 from UCD-SERG/update-lintr-config

update lintr config

Author: d-morrison

.Rbuildignore

@@ -36,3 +36,4 @@ allpopsamples_hlye.csv$
 ^vignettes/articles/\.quarto$
 ^vignettes/articles/*_files$
 ^man/check_strata\.Rd$
+^\.lintr\.R$

.lintr

@@ -0,0 +1,85 @@
+
+
+undesirable_functions <-
+  lintr::default_undesirable_functions |>
+  lintr::modify_defaults(
+
+    # following https://github.com/r-lib/devtools/blob/2aa51ef/.lintr.R:
+    # Base messaging
+    "message" = "use cli::cli_inform()",
+    "warning" = "use cli::cli_warn()",
+    "stop" = "use cli::cli_abort()",
+    # rlang messaging
+    "inform" = "use cli::cli_inform()",
+    "warn" = "use cli::cli_warn()",
+    "abort" = "use cli::cli_abort()",
+    # older cli
+    "cli_alert_danger" = "use cli::cli_inform()",
+    "cli_alert_info" = "use cli::cli_inform()",
+    "cli_alert_success" = "use cli::cli_inform()",
+    "cli_alert_warning" = "use cli::cli_inform()",
+
+    library = paste(
+      "\nuse `::`, `usethis::use_import_from()`, or `withr::local_package()`",
+      "instead of modifying the global search path.",
+      "\nSee:\n",
+      "<https://r-pkgs.org/code.html#sec-code-r-landscape> and\n",
+      "<https://r-pkgs.org/testing-design.html#sec-testing-design-self-contained>",
+      "\nfor more details."
+    ),
+
+    structure = NULL,
+    browser = NULL
+    # see https://github.com/r-lib/lintr/pull/2227 and
+    # rebuttal https://github.com/r-lib/lintr/pull/2227#issuecomment-1800302675
+
+  )
+
+# define snake_case with uppercase acronyms allowed;
+# see https://github.com/r-lib/lintr/issues/2844 for details:
+withr::local_package("rex")
+snake_case_ACROs1 <- rex::rex(
+  start,
+  maybe("."),
+  list(some_of(upper), maybe("s"), zero_or_more(digit)) %or% list(some_of(lower), zero_or_more(digit)),
+  zero_or_more(
+    "_",
+    list(some_of(upper), maybe("s"), zero_or_more(digit)) %or% list(some_of(lower), zero_or_more(digit))
+  ),
+  end
+)
+
+linters <- lintr::linters_with_defaults(
+  return_linter = NULL,
+  trailing_whitespace_linter = NULL,
+  lintr::redundant_equals_linter(),
+  lintr::pipe_consistency_linter(pipe = "|>"),
+  lintr::object_name_linter(
+    regexes = c(snake_case_ACROs1 = snake_case_ACROs1)
+  ),
+  lintr::undesirable_function_linter(
+    fun = undesirable_functions,
+    symbol_is_undesirable = TRUE
+  )
+)
+
+# prevent warnings from lintr::read_settings:
+rm(undesirable_functions)
+rm(snake_case_ACROs1)
+exclusions <- list(
+  `data-raw` = list(
+    pipe_consistency_linter = Inf,
+    undesirable_function_linter = Inf
+  ),
+  vignettes = list(
+    undesirable_function_linter = Inf,
+    object_name_linter = Inf
+  ),
+  "inst/examples" = list(
+    undesirable_function_linter = Inf
+  ),
+  "tests/testthat.R" = list(
+    undesirable_function_linter = Inf
+  )
+
+)

.lintr.R

@@ -1,7 +1,7 @@
 Type: Package
 Package: serocalculator
 Title: Estimating Infection Rates from Serological Data
-Version: 1.4.0.9000
+Version: 1.4.0.9001
 Authors@R: c(
     person("Kristina", "Lai", , "kwlai@ucdavis.edu", role = c("aut", "cre")),
     person("Chris", "Orwa", role = "aut"),
@@ -63,7 +63,8 @@ Suggests:
     qrcode,
     vdiffr,
     withr,
-    forcats
+    forcats,
+    rex
 LinkingTo: 
     Rcpp
 Config/testthat/edition: 3