Update CI + add example

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

@@ -4,9 +4,8 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
 
 permissions: read-all
 
@@ -43,9 +42,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: |
-            any::sf
-            any::rcmdcheck
+          extra-packages: any::rcmdcheck
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2

.github/workflows/pkgdown.yaml

@@ -4,12 +4,11 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
 
 permissions: read-all
 

.github/workflows/style.yaml

@@ -4,7 +4,7 @@ on:
   push:
     paths: ["**.[rR]", "**.[qrR]md", "**.[rR]markdown", "**.[rR]nw", "**.[rR]profile"]
 
-name: Style
+name: style.yaml
 
 permissions: read-all
 

.github/workflows/test-coverage.yaml

@@ -4,9 +4,8 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
 
 permissions: read-all
 
@@ -25,10 +24,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: |
-            any::sf
-            any::covr
-            any::xml2
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
@@ -43,7 +39,8 @@ jobs:
 
       - uses: codecov/codecov-action@v4
         with:
-          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          # 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 }}
           file: ./cobertura.xml
           plugin: noop
           disable_search: true

DESCRIPTION

@@ -44,12 +44,14 @@ Suggests:
     rmarkdown,
     RSQLite,
     sf,
-    testthat (>= 3.0.0),
+    testthat (>= 3.2.0),
     tibble,
     tidygraph
 VignetteBuilder: 
     knitr
 Config/testthat/edition: 3
+Config/Needs/check: sf
+Config/Needs/coverage: sf
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)

R/clean_names.R

@@ -33,7 +33,7 @@
 #'   support using `clean_names()` on `sf` and `tbl_graph` (from
 #'   `tidygraph`) objects as well as on database connections through
 #'   `dbplyr`. For cleaning other named objects like named lists
-#'   and vectors, use `make_clean_names()`. When `set_labels` is set to `TRUE`, the old names, 
+#'   and vectors, use `make_clean_names()`. When `set_labels` is set to `TRUE`, the old names,
 #'   stored as column labels, can be restored using `sjlabelled::label_to_colnames()`.
 #'
 #' @export
@@ -83,14 +83,13 @@ clean_names.default <- function(dat, ..., set_labels = FALSE) {
   if (is.null(names(dat))) {
     dimnames(dat) <- lapply(dimnames(dat), make_clean_names, ...)
   } else {
-    if (set_labels){
+    if (set_labels) {
       old_names <- names(dat)
-      for (i in seq_along(old_names)){
+      for (i in seq_along(old_names)) {
         attr(dat[[i]], "label") <- old_names[[i]]
       }
     }
     names(dat) <- make_clean_names(names(dat), ...)
-
   }
   dat
 }
@@ -112,9 +111,9 @@ clean_names.sf <- function(dat, ..., set_labels = FALSE) {
   sf_cleaned <- make_clean_names(sf_names[cols_to_rename], ...)
   # rename original df
   names(dat)[cols_to_rename] <- sf_cleaned
-  
-  if(set_labels){
-    for (i in seq_along(sf_names[cols_to_rename])){
+
+  if (set_labels) {
+    for (i in seq_along(sf_names[cols_to_rename])) {
       attr(dat[[i]], "label") <- sf_names[[i]]
     }
   }
@@ -131,7 +130,7 @@ clean_names.tbl_graph <- function(dat, ...) {
       call. = FALSE
     )
   } # nocov end
-  
+
   dplyr::rename_all(dat, .funs = make_clean_names, ...)
 }
 

README.Rmd

@@ -26,7 +26,7 @@ options(width = 110)
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/sfirke/janitor/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/sfirke/janitor/actions/workflows/R-CMD-check.yaml)
-[![Coverage Status](https://img.shields.io/codecov/c/github/sfirke/janitor/main.svg)](https://app.codecov.io/github/sfirke/janitor?branch=main)
+[![Codecov test coverage](https://codecov.io/gh/sfirke/janitor/graph/badge.svg)](https://app.codecov.io/gh/sfirke/janitor)
 [![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version-ago/janitor)](https://cran.r-project.org/package=janitor)
 ![!Monthly Downloads](https://cranlogs.r-pkg.org/badges/janitor)

README.md

@@ -17,8 +17,8 @@
 <!-- badges: start -->
 
 [![R-CMD-check](https://github.com/sfirke/janitor/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/sfirke/janitor/actions/workflows/R-CMD-check.yaml)
-[![Coverage
-Status](https://img.shields.io/codecov/c/github/sfirke/janitor/main.svg)](https://app.codecov.io/github/sfirke/janitor?branch=main)
+[![Codecov test
+coverage](https://codecov.io/gh/sfirke/janitor/graph/badge.svg)](https://app.codecov.io/gh/sfirke/janitor)
 [![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version-ago/janitor)](https://cran.r-project.org/package=janitor)
 ![!Monthly Downloads](https://cranlogs.r-pkg.org/badges/janitor)

janitor.Rproj

@@ -12,6 +12,9 @@ Encoding: UTF-8
 RnwWeave: Sweave
 LaTeX: pdfLaTeX
 
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source

tests/testthat/test-clean-names.R

@@ -190,14 +190,14 @@ test_that("labels are created in default method (feature request #563)", {
   dat_df <- dplyr::tibble(`a a` = c(11, 22), `b b` = c(2, 3))
   dat_df_clean_labels <- clean_names(dat_df, set_labels = TRUE)
   dat_df_clean <- clean_names(dat_df)
-  
-  for (i in seq_along(names(dat_df))){
+
+  for (i in seq_along(names(dat_df))) {
     # check that old names are saved as labels when set_labels is TRUE
     expect_equal(attr(dat_df_clean_labels[[i]], "label"), names(dat_df)[[i]])
     # check that old names are not stored if set_labels is not TRUE
     expect_null(attr(dat_df_clean[[i]], "label"))
-    }
-  
+  }
+
   # expect names are always cleaned
   expect_equal(names(dat_df_clean), c("a_a", "b_b"))
   expect_equal(names(dat_df_clean_labels), c("a_a", "b_b"))
@@ -482,9 +482,8 @@ test_that("Names are cleaned appropriately without attaching sf", {
   # last column name
   issue_578_sf <- readRDS("testdata/issue-578-sf.rds")
   issue_578_sf_clean <- clean_names(issue_578_sf)
-  expect_error(
-    print(issue_578_sf_clean),
-    NA
+  expect_no_error(
+    print(issue_578_sf_clean)
   )
 })
 
@@ -605,19 +604,19 @@ test_that("Tests for cases beyond default snake for sf objects", {
 
 test_that("labels are created in sf method (feature request #563)", {
   skip_if_not_installed("sf")
-  
+
   dat_df <- dplyr::tibble(`a a` = c(11, 22), `b b` = c(2, 3))
   dat_sf <- dat_df
-  dat_sf$x <- c(1,2)
-  dat_sf$y <- c(1,2) 
+  dat_sf$x <- c(1, 2)
+  dat_sf$y <- c(1, 2)
   dat_sf <- sf::st_as_sf(dat_sf, coords = c("x", "y"))
   dat_sf_clean_labels <- clean_names(dat_sf, set_labels = TRUE)
   dat_sf_clean <- clean_names(dat_sf)
-  
-  for (i in seq_along(names(dat_df))){
+
+  for (i in seq_along(names(dat_df))) {
     # check that old names are saved as labels when set_labels is TRUE
     expect_equal(attr(dat_sf_clean_labels[[i]], "label"), names(dat_sf)[[i]])
-    
+
     # check that old names are not stored if set_labels is not TRUE
     expect_null(attr(dat_sf_clean[[i]], "label"))
   }
@@ -724,5 +723,5 @@ test_that("groupings are preserved, #260", {
   df_grouped <- iris %>% dplyr::group_by(Sepal.Length, Sepal.Width) # nonsense for analysis but doesn't matter
   df_grouped_renamed <- df_grouped %>% clean_names(case = "lower_camel")
   expect_equal(dplyr::group_vars(df_grouped_renamed), c("sepalLength", "sepalWidth")) # group got renamed
-  expect_equal(names(df_grouped_renamed), c("sepalLength", "sepalWidth", "petalLength", "petalWidth", "species"))
+  expect_named(df_grouped_renamed, c("sepalLength", "sepalWidth", "petalLength", "petalWidth", "species"))
 })

vignettes/janitor.Rmd

@@ -6,7 +6,7 @@ output:
     toc: true
     toc_depth: 3
 vignette: >
-  %\VignetteIndexEntry{janitor}
+  %\VignetteIndexEntry{Overview of janitor functions}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -15,7 +15,7 @@ vignette: >
 knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
 library(janitor)
 ```
-The janitor functions expedite the initial data exploration and cleaning that comes with any new data set.  This catalog describes the usage for each function.
+The janitor functions expedite the initial data exploration and cleaning that comes with any new data set. This catalog describes the usage for each function.
 
 # Major functions
 Functions for everyday use.
@@ -212,6 +212,17 @@ For instance, here a vector with a date and an Excel datetime sees both values s
 convert_to_date(c("2020-02-29", "40000.1"))
 ```
 
+### Coerce different strings together.
+
+`paste_skip_na()` can be used to skip `NA` values when coercing multiple columns together.
+This is useful since `paste()` just pastes `"NA"` instead of ignoring it.
+
+```{r}
+paste("x", NA, "y")
+
+paste_skip_na("x", NA, "y")
+```
+
 ### Elevate column names stored in a data.frame row
 
 If a data.frame has the intended variable names stored in one of its rows, `row_to_names()` will elevate the specified row to become the names of the data.frame and optionally (by default) remove the row in which names were stored and/or the rows above it.