Add workflow for flint and fix some lints (#313)

.Rbuildignore

@@ -15,3 +15,7 @@
 ^.lintr$
 man-roxygen
 ^inst/NEWS\.Rd$
+
+
+# flint files
+^flint$

.github/workflows/flint.yaml

@@ -0,0 +1,37 @@
+# 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
+
+jobs:
+  flint:
+    runs-on: macOS-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: flint-${{ 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/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()
+        shell: Rscript {0}
+        env:
+          FLINT_ERROR_ON_LINT: true

R/import_man.R

@@ -237,6 +237,7 @@
             close(connection)
         },
         warning = function(w) {
+            # flint-ignore
             is_404 <<- grepl("404", w)
         }
     )

R/render_docs.R

@@ -83,7 +83,7 @@ render_docs <- function(
         # Delete everything in `_quarto/` besides `_freeze/`
         if (fs::dir_exists(docs_dir)) {
             docs_files <- fs::dir_ls(docs_dir)
-            if (freeze == TRUE) {
+            if (isTRUE(freeze)) {
                 docs_files <- Filter(
                     function(f) basename(f) != "_freeze",
                     docs_files

R/settings_docute.R

@@ -61,7 +61,7 @@
 
     if (length(fn_vignettes) > 0) {
         tmp <- sprintf("{title: '%s', link: '%s'}", titles, fn_vignettes)
-        tmp <- paste(tmp, collapse = ", ")
+        tmp <- toString(tmp)
         sidebar <- paste(sidebar, collapse = "\n")
         if (isTRUE(grepl("\\$ALTDOC_VIGNETTE_BLOCK", sidebar))) {
             sidebar <- gsub("\\$ALTDOC_VIGNETTE_BLOCK", "%s", sidebar)
@@ -86,7 +86,7 @@
         )
         titles <- fs::path_ext_remove(basename(fn_man))
         tmp <- sprintf("{title: '%s', link: '%s'}", titles, fn_man)
-        tmp <- paste(tmp, collapse = ", ")
+        tmp <- toString(tmp)
         sidebar <- paste(sidebar, collapse = "\n")
         if (isTRUE(grepl("\\$ALTDOC_MAN_BLOCK", sidebar))) {
             sidebar <- gsub("\\$ALTDOC_MAN_BLOCK", "%s", sidebar)

flint/config.yml

@@ -0,0 +1,53 @@
+keep:
+  - any_duplicated
+  - any_is_na
+  - class_equals
+  - condition_message
+  - double_assignment
+  - duplicate_argument
+  - empty_assignment
+  - equal_assignment
+  - equals_na
+  - expect_comparison
+  - expect_identical
+  - expect_length
+  - expect_named
+  - expect_not
+  - expect_null
+  - expect_true_false
+  - expect_type
+  - for_loop_index
+  - function_return
+  - implicit_assignment
+  - is_numeric
+  - length_levels
+  - length_test
+  - lengths
+  - library_call
+  - list_comparison
+  - literal_coercion
+  - matrix_apply
+  - missing_argument
+  - nested_ifelse
+  - numeric_leading_zero
+  - outer_negation
+  - package_hooks
+  - paste
+  - redundant_equals
+  - redundant_ifelse
+  - rep_len
+  - right_assignment
+  - sample_int
+  - semicolon
+  - seq
+  - sort
+  - stopifnot_all
+  - T_and_F_symbol
+  - undesirable_function
+  - undesirable_operator
+  - unnecessary_nesting
+  - which_grepl
+
+exclude:
+  - todo_comment
+  - unreachable_code

flint/rules/builtin/T_and_F_symbol.yml

@@ -0,0 +1,97 @@
+id: true_false_symbol
+language: r
+severity: warning
+rule:
+  pattern: T
+  kind: identifier
+  not:
+    any:
+      - precedes:
+          any:
+            - pattern: <-
+            - pattern: =
+            - regex: ^~$
+      - follows:
+          any:
+            - pattern: $
+            - regex: ^~$
+      - inside:
+          any:
+            - kind: parameter
+            - kind: call
+            - kind: binary_operator
+              follows:
+                regex: ^~$
+                stopBy: end
+          stopBy:
+            kind:
+              argument
+fix: TRUE
+message: Use TRUE instead of the symbol T.
+
+---
+
+id: true_false_symbol-2
+language: r
+severity: warning
+rule:
+  pattern: F
+  kind: identifier
+  not:
+    any:
+      - precedes:
+          any:
+            - pattern: <-
+            - pattern: =
+            - regex: ^~$
+      - follows:
+          any:
+            - pattern: $
+            - regex: ^~$
+      - inside:
+          any:
+            - kind: parameter
+            - kind: call
+            - kind: binary_operator
+              follows:
+                regex: ^~$
+                stopBy: end
+          stopBy:
+            kind:
+              argument
+fix: FALSE
+message: Use FALSE instead of the symbol F.
+
+---
+
+id: true_false_symbol-3
+language: r
+severity: warning
+rule:
+  pattern: T
+  kind: identifier
+  precedes:
+    any:
+      - pattern: <-
+      - pattern: =
+  not:
+    inside:
+      kind: argument
+message: Don't use T as a variable name, as it can break code relying on T being TRUE.
+
+---
+
+id: true_false_symbol-4
+language: r
+severity: warning
+rule:
+  pattern: F
+  kind: identifier
+  precedes:
+    any:
+      - pattern: <-
+      - pattern: =
+  not:
+    inside:
+      kind: argument
+message: Don't use F as a variable name, as it can break code relying on F being FALSE.

flint/rules/builtin/absolute_path.yml

@@ -0,0 +1,13 @@
+# id: absolute_path-1
+# language: r
+# severity: warning
+# rule:
+#   kind: string_content
+#   any:
+#     - regex: '^~[[:alpha:]]'
+#     - regex: '^~/[[:alpha:]]'
+#     - regex: '^[[:alpha:]]:'
+#     - regex: '^(/|~)$'
+#     - regex: '^/[[:alpha:]]'
+#     - regex: '^\\'
+# message: Do not use absolute paths.

flint/rules/builtin/any_duplicated.yml

@@ -0,0 +1,91 @@
+id: any_duplicated-1
+language: r
+severity: warning
+rule:
+  pattern: any($$$ duplicated($MYVAR) $$$)
+fix: anyDuplicated(~~MYVAR~~) > 0
+message: anyDuplicated(x, ...) > 0 is better than any(duplicated(x), ...).
+
+---
+
+id: any_duplicated-2
+language: r
+severity: warning
+rule:
+  any:
+    - pattern: length(unique($MYVAR)) == length($MYVAR)
+    - pattern: length($MYVAR) == length(unique($MYVAR))
+fix: anyDuplicated(~~MYVAR~~) == 0L
+message: anyDuplicated(x) == 0L is better than length(unique(x)) == length(x).
+
+---
+
+id: any_duplicated-3
+language: r
+severity: warning
+rule:
+  pattern: length(unique($MYVAR)) != length($MYVAR)
+fix: anyDuplicated(~~MYVAR~~) != 0L
+message: |
+  Use anyDuplicated(x) != 0L (or > or <)  instead of length(unique(x)) != length(x)
+  (or > or <).
+
+---
+
+id: any_duplicated-4
+language: r
+severity: warning
+rule:
+  any:
+    - pattern: nrow($DATA) != length(unique($DATA$µCOL))
+    - pattern: length(unique($DATA$µCOL)) != nrow($DATA)
+fix: anyDuplicated(~~DATA~~$~~COL~~) != 0L
+message: |
+  anyDuplicated(DF$col) != 0L is better than length(unique(DF$col)) != nrow(DF)
+
+---
+
+# id: any_duplicated-5
+# language: r
+# severity: warning
+# rule:
+#   any:
+#     - pattern:
+#         context: nrow($DATA) != length(unique($DATA[["µCOL"]]))
+#         strictness: ast
+#     - pattern:
+#         context: length(unique($DATA[["µCOL"]])) != nrow($DATA)
+#         strictness: ast
+# fix: anyDuplicated(~~DATA~~[["~~COL~~"]]) != 0L
+# message: |
+#   anyDuplicated(DF[["col"]]) != 0L is better than length(unique(DF[["col"]])) != nrow(DF)
+#
+# ---
+
+id: any_duplicated-6
+language: r
+severity: warning
+rule:
+  any:
+    - pattern: nrow($DATA) == length(unique($DATA$µCOL))
+    - pattern: length(unique($DATA$µCOL)) == nrow($DATA)
+fix: anyDuplicated(~~DATA~~$~~COL~~) == 0L
+message: |
+  anyDuplicated(DF$col) == 0L is better than length(unique(DF$col)) == nrow(DF)
+
+# ---
+#
+# id: any_duplicated-7
+# language: r
+# severity: warning
+# rule:
+#   any:
+#     - pattern:
+#         context: nrow($DATA) == length(unique($DATA[["µCOL"]]))
+#         strictness: ast
+#     - pattern:
+#         context: length(unique($DATA[["µCOL"]])) == nrow($DATA)
+#         strictness: ast
+# fix: anyDuplicated(~~DATA~~[["~~COL~~"]]) == 0L
+# message: |
+#   anyDuplicated(DF[["col"]]) == 0L is better than length(unique(DF[["col"]])) == nrow(DF)

flint/rules/builtin/any_is_na.yml

@@ -0,0 +1,25 @@
+id: any_na-1
+language: r
+severity: warning
+rule:
+  any:
+    - pattern: any(is.na($MYVAR))
+    - pattern: any(na.rm = $NARM, is.na($MYVAR))
+    - pattern: any(is.na($MYVAR), na.rm = $NARM)
+fix: anyNA(~~MYVAR~~)
+message: anyNA(x) is better than any(is.na(x)).
+
+---
+
+id: any_na-2
+language: r
+severity: warning
+rule:
+  any:
+    - pattern: NA %in% $ELEM
+    - pattern: NA_real_ %in% $ELEM
+    - pattern: NA_logical_ %in% $ELEM
+    - pattern: NA_character_ %in% $ELEM
+    - pattern: NA_complex_ %in% $ELEM
+fix: anyNA(~~ELEM~~)
+message: anyNA(x) is better than NA %in% x.