Package 'flint' reference manual

Title:	Find and Fix Lints in R Code
Description:	Lints are code patterns that are not optimal because they are inefficient, forget corner cases, or less readable. 'flint' provides a small set of functions to detect those lints and automatically fix them. It builds on 'astgrepr', which itself uses the Rust crate 'ast-grep' to parse and navigate R code.
Authors:	Etienne Bacher [aut, cre, cph]
Maintainer:	Etienne Bacher <[email protected]>
License:	MIT + file LICENSE
Version:	0.1.2
Built:	2024-12-08 13:45:21 UTC
Source:	https://github.com/etiennebacher/flint

Require usage of `anyDuplicated(x) > 0` over `any(duplicated(x))`

Description

See https://lintr.r-lib.org/reference/any_duplicated_linter.

Usage

any_duplicated_linter
any_duplicated_linter

Require usage of `anyNA(x)` over `any(is.na(x))`

Description

See https://lintr.r-lib.org/reference/any_is_na_linter.

Usage

any_is_na_linter
any_is_na_linter

Block comparison of class with `==`

Description

See https://lintr.r-lib.org/reference/class_equals_linter.

Usage

class_equals_linter
class_equals_linter

Block usage of `paste()` and `paste0()` with messaging functions using `...`

Description

See https://lintr.r-lib.org/reference/condition_message_linter.

Usage

condition_message_linter
condition_message_linter

double_assignment

Description

double_assignment

Usage

double_assignment_linter
double_assignment_linter

Duplicate argument linter

Description

See https://lintr.r-lib.org/reference/duplicate_argument_linter.

Usage

duplicate_argument_linter
duplicate_argument_linter

empty_assignment

Description

empty_assignment

Usage

empty_assignment_linter
empty_assignment_linter

equal_assignment

Description

equal_assignment

Usage

equal_assignment_linter
equal_assignment_linter

Equality check with NA linter

Description

See https://lintr.r-lib.org/reference/equals_na_linter.

Usage

equals_na_linter
equals_na_linter

Require usage of `expect_gt(x, y)` over `expect_true(x > y)` (and similar)

Description

See https://lintr.r-lib.org/reference/expect_comparison_linter.

Usage

expect_comparison_linter
expect_comparison_linter

Require usage of `expect_identical(x, y)` where appropriate

Description

See https://lintr.r-lib.org/reference/expect_identical_linter.

Usage

expect_identical_linter
expect_identical_linter

Require usage of `expect_length(x, n)` over `expect_equal(length(x), n)`

Description

See https://lintr.r-lib.org/reference/expect_length_linter.

Usage

expect_length_linter
expect_length_linter

Require usage of `expect_named(x, n)` over `expect_equal(names(x), n)`

Description

See https://lintr.r-lib.org/reference/expect_named_linter.

Usage

expect_named_linter
expect_named_linter

Require usage of `expect_false(x)` over `expect_true(!x)`

Description

See https://lintr.r-lib.org/reference/expect_not_linter.

Usage

expect_not_linter
expect_not_linter

Require usage of `expect_null` for checking `NULL`

Description

See https://lintr.r-lib.org/reference/expect_null_linter.

Usage

expect_null_linter
expect_null_linter

Require usage of `expect_true(x)` over `expect_equal(x, TRUE)`

Description

See https://lintr.r-lib.org/reference/expect_true_false_linter.

Usage

expect_true_false_linter
expect_true_false_linter

Require usage of `expect_type(x, type)` over `expect_equal(typeof(x), type)`

Description

See https://lintr.r-lib.org/reference/expect_type_linter.

Usage

expect_type_linter
expect_type_linter

Automatically replace lints

Description

fix(), fix_package(), and fix_dir() all replace lints in files. The only difference is in the input they take:

fix() takes path to files or directories
fix_dir() takes a path to one directory
fix_package() takes a path to the root of a package and looks at the following list of folders: R, tests, inst, vignettes, data-raw, demo, exec.

fix_text() takes some text input. Its main interest is to be able to quickly experiment with some lints and fixes.

Usage

fix(
  path = ".",
  linters = NULL,
  exclude_path = NULL,
  exclude_linters = NULL,
  force = FALSE,
  verbose = TRUE
)

fix_dir(
  path = ".",
  linters = NULL,
  exclude_path = NULL,
  exclude_linters = NULL,
  force = FALSE,
  verbose = TRUE
)

fix_package(
  path = ".",
  linters = NULL,
  exclude_path = NULL,
  exclude_linters = NULL,
  force = FALSE,
  verbose = TRUE
)

fix_text(text, linters = NULL, exclude_linters = NULL)
fix(
  path = ".",
  linters = NULL,
  exclude_path = NULL,
  exclude_linters = NULL,
  force = FALSE,
  verbose = TRUE
)

fix_dir(
  path = ".",
  linters = NULL,
  exclude_path = NULL,
  exclude_linters = NULL,
  force = FALSE,
  verbose = TRUE
)

fix_package(
  path = ".",
  linters = NULL,
  exclude_path = NULL,
  exclude_linters = NULL,
  force = FALSE,
  verbose = TRUE
)

fix_text(text, linters = NULL, exclude_linters = NULL)

Arguments

`path`	A valid path to a file or a directory. Relative paths are accepted.
`linters`	A character vector with the names of the rules to apply. See the entire list of rules with `list_linters()`.
`exclude_path`	One or several paths that will be ignored from the `path` selection.
`exclude_linters`	One or several linters that will not be checked. Values can be the names of linters (such as `"any_is_na"`) or its associated function, such as `any_is_na_linter()` (this is mostly for compatibility with `lintr`).
`force`	Force the application of fixes on the files. This is used only in the case where Git is not detected, several files will be modified, and the code is run in a non-interactive setting.
`verbose`	Show messages.
`text`	Text to analyze (and to fix if necessary).

Ignoring lines

flint supports ignoring single lines of code with ⁠# flint-ignore⁠. For example, this will not warn:

# flint-ignore
any(duplicated(x))

However, this will warn for the second any(duplicated()):

# flint-ignore
any(duplicated(x))
any(duplicated(y))

To ignore more than one line of code, use ⁠# flint-ignore-start⁠ and ⁠# flint-ignore-end⁠:

# flint-ignore-start
any(duplicated(x))
any(duplicated(y))
# flint-ignore-end

Examples

# `fix_text()` is convenient to explore with a small example
fix_text("any(duplicated(rnorm(5)))")

fix_text("any(duplicated(rnorm(5)))
any(is.na(x))
")

# Setup for the example with `fix()`
destfile <- tempfile()
cat("
x = c(1, 2, 3)
any(duplicated(x), na.rm = TRUE)

any(duplicated(x))

if (any(is.na(x))) {
  TRUE
}

any(
  duplicated(x)
)", file = destfile)

fix(destfile)
cat(paste(readLines(destfile), collapse = "\n"))
# `fix_text()` is convenient to explore with a small example
fix_text("any(duplicated(rnorm(5)))")

fix_text("any(duplicated(rnorm(5)))
any(is.na(x))
")

# Setup for the example with `fix()`
destfile <- tempfile()
cat("
x = c(1, 2, 3)
any(duplicated(x), na.rm = TRUE)

any(duplicated(x))

if (any(is.na(x))) {
  TRUE
}

any(
  duplicated(x)
)", file = destfile)

fix(destfile)
cat(paste(readLines(destfile), collapse = "\n"))

Block usage of for loops directly overwriting the indexing variable

Description

See https://lintr.r-lib.org/reference/for_loop_index_linter.

Usage

for_loop_index_linter
for_loop_index_linter

Lint common mistakes/style issues cropping up from return statements

Description

See https://lintr.r-lib.org/reference/function_return_linter.

Usage

function_return_linter
function_return_linter

implicit_assignment

Description

implicit_assignment

Usage

implicit_assignment_linter
implicit_assignment_linter

Redirect `is.numeric(x) || is.integer(x)` to just use `is.numeric(x)`

Description

See https://lintr.r-lib.org/reference/is_numeric_linter.

Usage

is_numeric_linter
is_numeric_linter

Require usage of nlevels over length(levels(.))

Description

See https://lintr.r-lib.org/reference/length_levels_linter.

Usage

length_levels_linter
length_levels_linter

Check for a common mistake where length is applied in the wrong place

Description

See https://lintr.r-lib.org/reference/length_test_linter.

Usage

length_test_linter
length_test_linter

Require usage of `lengths()` where possible

Description

See https://lintr.r-lib.org/reference/lengths_linter.

Usage

lengths_linter
lengths_linter

Library call linter

Description

See https://lintr.r-lib.org/reference/library_call_linter.

Usage

library_call_linter
library_call_linter

List all lints in a file or a directory

Description

lint(), lint_text(), lint_package(), and lint_dir() all produce a data.frame containing the lints, their location, and potential fixes. The only difference is in the input they take:

lint() takes path to files or directories
lint_text() takes some text input
lint_dir() takes a path to one directory
lint_package() takes a path to the root of a package and looks at the following list of folders: R, tests, inst, vignettes, data-raw, demo, exec.

Usage

lint(
  path = ".",
  linters = NULL,
  exclude_path = NULL,
  exclude_linters = NULL,
  open = TRUE,
  use_cache = TRUE,
  verbose = TRUE
)

lint_dir(
  path = ".",
  linters = NULL,
  open = TRUE,
  exclude_path = NULL,
  exclude_linters = NULL,
  use_cache = TRUE,
  verbose = TRUE
)

lint_package(
  path = ".",
  linters = NULL,
  open = TRUE,
  exclude_path = NULL,
  exclude_linters = NULL,
  use_cache = TRUE,
  verbose = TRUE
)

lint_text(text, linters = NULL, exclude_linters = NULL)
lint(
  path = ".",
  linters = NULL,
  exclude_path = NULL,
  exclude_linters = NULL,
  open = TRUE,
  use_cache = TRUE,
  verbose = TRUE
)

lint_dir(
  path = ".",
  linters = NULL,
  open = TRUE,
  exclude_path = NULL,
  exclude_linters = NULL,
  use_cache = TRUE,
  verbose = TRUE
)

lint_package(
  path = ".",
  linters = NULL,
  open = TRUE,
  exclude_path = NULL,
  exclude_linters = NULL,
  use_cache = TRUE,
  verbose = TRUE
)

lint_text(text, linters = NULL, exclude_linters = NULL)

Arguments

`path`	A valid path to a file or a directory. Relative paths are accepted.
`linters`	A character vector with the names of the rules to apply. See the entire list of rules with `list_linters()`.
`exclude_path`	One or several paths that will be ignored from the `path` selection.
`exclude_linters`	One or several linters that will not be checked. Values can be the names of linters (such as `"any_is_na"`) or its associated function, such as `any_is_na_linter()` (this is mostly for compatibility with `lintr`).
`open`	If `TRUE` (default) and if this is used in the RStudio IDE, lints will be shown with markers.
`use_cache`	Do not re-parse files that haven't changed since the last time this function ran.
`verbose`	Show messages.
`text`	Text to analyze.

Value

A dataframe where each row is a lint. The columns show the text, its location (both the position in the text and the file in which it was found) and the severity.

Ignoring lines

flint supports ignoring single lines of code with ⁠# flint-ignore⁠. For example, this will not warn:

# flint-ignore
any(duplicated(x))

However, this will warn for the second any(duplicated()):

# flint-ignore
any(duplicated(x))
any(duplicated(y))

To ignore more than one line of code, use ⁠# flint-ignore-start⁠ and ⁠# flint-ignore-end⁠:

# flint-ignore-start
any(duplicated(x))
any(duplicated(y))
# flint-ignore-end

Examples

# `lint_text()` is convenient to explore with a small example
lint_text("any(duplicated(rnorm(5)))")

lint_text("any(duplicated(rnorm(5)))
any(is.na(x))
")

# Setup for the example with `lint()`
destfile <- tempfile()
cat("
x = c(1, 2, 3)
any(duplicated(x), na.rm = TRUE)

any(duplicated(x))

if (any(is.na(x))) {
  TRUE
}

any(
  duplicated(x)
)", file = destfile)

lint(destfile)
# `lint_text()` is convenient to explore with a small example
lint_text("any(duplicated(rnorm(5)))")

lint_text("any(duplicated(rnorm(5)))
any(is.na(x))
")

# Setup for the example with `lint()`
destfile <- tempfile()
cat("
x = c(1, 2, 3)
any(duplicated(x), na.rm = TRUE)

any(duplicated(x))

if (any(is.na(x))) {
  TRUE
}

any(
  duplicated(x)
)", file = destfile)

lint(destfile)

Get the list of linters in `flint`

Description

Get the list of linters in flint

Usage

list_linters()
list_linters()

Value

A character vector

Examples

list_linters()
list_linters()

Require usage of correctly-typed literals over literal coercions

Description

See https://lintr.r-lib.org/reference/literal_coercion_linter.

Usage

literal_coercion_linter
literal_coercion_linter

Require usage of `colSums(x)` or `rowSums(x)` over `apply(x, ., sum)`

Description

See https://lintr.r-lib.org/reference/matrix_apply_linter.

Usage

matrix_apply_linter
matrix_apply_linter

Missing argument linter

Description

See https://lintr.r-lib.org/reference/missing_argument_linter.

Usage

missing_argument_linter
missing_argument_linter

Block usage of nested `ifelse()` calls

Description

See https://lintr.r-lib.org/reference/nested_ifelse_linter.

Usage

nested_ifelse_linter
nested_ifelse_linter

Require usage of a leading zero in all fractional numerics

Description

See https://lintr.r-lib.org/reference/numeric_leading_zero_linter.

Usage

numeric_leading_zero_linter
numeric_leading_zero_linter

Require usage of `!any(x)` over `all(!x)`, `!all(x)` over `any(!x)`

Description

See https://lintr.r-lib.org/reference/outer_negation_linter.

Usage

outer_negation_linter
outer_negation_linter

Package hooks linter

Description

See https://lintr.r-lib.org/reference/package_hooks_linter.

Usage

package_hooks_linter
package_hooks_linter

Raise lints for several common poor usages of `paste()`

Description

See https://lintr.r-lib.org/reference/paste_linter.

Usage

paste_linter
paste_linter

Block usage of `==`, `!=` on logical vectors

Description

See https://lintr.r-lib.org/reference/redundant_equals_linter.

Usage

redundant_equals_linter
redundant_equals_linter

Prevent `ifelse()` from being used to produce `TRUE`/`FALSE` or `1`/`0`

Description

See https://lintr.r-lib.org/reference/redundant_ifelse_linter.

Usage

redundant_ifelse_linter
redundant_ifelse_linter

Require usage of rep_len(x, n) over rep(x, length.out = n)

Description

See https://lintr.r-lib.org/reference/rep_len_linter.

Usage

rep_len_linter
rep_len_linter

right_assignment

Description

right_assignment

Usage

right_assignment_linter
right_assignment_linter

Require usage of sample.int(n, m, ...) over sample(1:n, m, ...)

Description

See https://lintr.r-lib.org/reference/sample_int_linter.

Usage

sample_int_linter
sample_int_linter

Semicolon linter

Description

See https://lintr.r-lib.org/reference/semicolon_linter.

Usage

semicolon_linter
semicolon_linter

Sequence linter

Description

See https://lintr.r-lib.org/reference/seq_linter.

Usage

seq_linter
seq_linter

Setup flint

Description

This stores the default rules and internal files in inst/flint. It also imports sgconfig.yml that is used by ast-grep. This file must live at the root of the project and cannot be renamed.

Usage

setup_flint(path = ".")
setup_flint(path = ".")

Arguments

path

Path to package or project root.

Value

Imports files necessary for flint to work but doesn't return any value in R.

Create a Github Actions workflow for `flint`

Description

Create a Github Actions workflow for flint

Usage

setup_flint_gha(path = ".", overwrite = FALSE)
setup_flint_gha(path = ".", overwrite = FALSE)

Arguments

`path`	Root path to the package.
`overwrite`	Whether to overwrite `.github/workflows/flint.yaml` if it already exists.

Usage

unreachable_code_linter
unreachable_code_linter

When flint is updated, it can ship new built-in rules or update existing ones. update_flint() will automatically add those new rules to the flint/rules/builtin folder. Custom rules stored in flint/rules/custom are not affected.

Usage

update_flint(path = ".")
update_flint(path = ".")

Arguments

path

Path to package or project root.

Value

Can add new files in the flint/rules folder, doesn't return anything.

Examples

## Not run: 
  update_flint()

## End(Not run)
## Not run: 
  update_flint()

## End(Not run)

Require usage of grep over which(grepl(.))

Description

See https://lintr.r-lib.org/reference/which_grepl_linter.

Usage

which_grepl_linter
which_grepl_linter

Package 'flint'

Help Index

Require usage of anyDuplicated(x) > 0 over any(duplicated(x))

Description

Usage

Require usage of anyNA(x) over any(is.na(x))

Description

Usage

Block comparison of class with ==

Description

Usage

Block usage of paste() and paste0() with messaging functions using ...

Description

Usage

double_assignment

Description

Usage

Duplicate argument linter

Description

Usage

empty_assignment

Description

Usage

equal_assignment

Description

Usage

Equality check with NA linter

Description

Usage

Require usage of expect_gt(x, y) over expect_true(x > y) (and similar)

Description

Usage

Require usage of expect_identical(x, y) where appropriate

Description

Usage

Require usage of expect_length(x, n) over expect_equal(length(x), n)

Description

Usage

Require usage of expect_named(x, n) over expect_equal(names(x), n)

Description

Usage

Require usage of expect_false(x) over expect_true(!x)

Description

Usage

Require usage of expect_null for checking NULL

Description

Usage

Require usage of expect_true(x) over expect_equal(x, TRUE)

Description

Usage

Require usage of expect_type(x, type) over expect_equal(typeof(x), type)

Description

Usage

Automatically replace lints

Description

Usage

Arguments

Ignoring lines

Examples

Block usage of for loops directly overwriting the indexing variable

Description

Usage

Lint common mistakes/style issues cropping up from return statements

Description

Usage

implicit_assignment

Description

Usage

Redirect is.numeric(x) || is.integer(x) to just use is.numeric(x)

Description

Usage

Require usage of nlevels over length(levels(.))

Description

Usage

Check for a common mistake where length is applied in the wrong place

Description

Usage

Require usage of lengths() where possible

Description

Usage

Require usage of `anyDuplicated(x) > 0` over `any(duplicated(x))`

Require usage of `anyNA(x)` over `any(is.na(x))`

Block comparison of class with `==`

Block usage of `paste()` and `paste0()` with messaging functions using `...`

Require usage of `expect_gt(x, y)` over `expect_true(x > y)` (and similar)

Require usage of `expect_identical(x, y)` where appropriate

Require usage of `expect_length(x, n)` over `expect_equal(length(x), n)`

Require usage of `expect_named(x, n)` over `expect_equal(names(x), n)`

Require usage of `expect_false(x)` over `expect_true(!x)`

Require usage of `expect_null` for checking `NULL`

Require usage of `expect_true(x)` over `expect_equal(x, TRUE)`

Require usage of `expect_type(x, type)` over `expect_equal(typeof(x), type)`

Redirect `is.numeric(x) || is.integer(x)` to just use `is.numeric(x)`

Require usage of `lengths()` where possible

Get the list of linters in `flint`

Require usage of `colSums(x)` or `rowSums(x)` over `apply(x, ., sum)`

Block usage of nested `ifelse()` calls

Require usage of `!any(x)` over `all(!x)`, `!all(x)` over `any(!x)`

Raise lints for several common poor usages of `paste()`

Block usage of `==`, `!=` on logical vectors

Prevent `ifelse()` from being used to produce `TRUE`/`FALSE` or `1`/`0`

Create a Github Actions workflow for `flint`