version

.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:
@@ -15,38 +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-renv@v2
-
       - 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@v4
+        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 }}
+          file: ./cobertura.xml
+          plugin: 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: REDCapCAST
 Title: REDCap Metadata Casting and Castellated Data Handling
-Version: 25.1.1
+Version: 25.2.1
 Authors@R: c(
     person("Andreas Gammelgaard", "Damsbo", email = "agdamsbo@clin.au.dk", 
     role = c("aut", "cre"),comment = c(ORCID = "0000-0002-7559-1154")), 

NEWS.md

@@ -1,3 +1,7 @@
+# REDCapCAST 25.2.1
+
+* FIX: `as_factor()` now interprets empty variables with empty levels attribute as logicals to avoid returning factors with empty levels.
+
 # REDCapCAST 25.1.1
 
 The newly introduced extension of `forcats::fct_drop()` has been corrected to work as intended as a method.

R/as_factor.R

@@ -7,6 +7,8 @@
 #' Please refer to parent functions for extended documentation.
 #' To avoid redundancy calls and errors, functions are copy-pasted here
 #'
+#' Empty variables with empty levels attribute are interpreted as logicals
+#'
 #' @param x Object to coerce to a factor.
 #' @param ... Other arguments passed down to method.
 #' @param only_labelled Only apply to labelled columns?
@@ -24,7 +26,14 @@
 #'   labels = c(Unknown = 9, Refused = 10),
 #'   class = "haven_labelled"
 #' ) |>
-#'   as_factor()
+#'   as_factor() |> class()
+#' structure(rep(NA,10),
+#'   class = c("labelled")
+#' ) |>
+#'   as_factor() |> summary()
+#'
+#' rep(NA,10) |> as_factor()
+#'
 #' @importFrom forcats as_factor
 #' @export
 #' @name as_factor
@@ -46,8 +55,6 @@ as_factor.logical <- function(x, ...) {
   set_attr(x, labels, overwrite = FALSE)
 }
 
-
-
 #' @rdname as_factor
 #' @export
 as_factor.numeric <- function(x, ...) {
@@ -121,7 +128,13 @@ as_factor.haven_labelled <- function(x, levels = c("default", "labels", "values"
 
   x <- structure(x, label = label)
 
-  set_attr(x, labels_all, overwrite = FALSE)
+  out <- set_attr(x, labels_all, overwrite = FALSE)
+
+  if (all_na(out) & length(levels(out))==0){
+    as_factor.logical(out)
+  } else {
+    out
+  }
 }
 
 #' @export

README.md

@@ -1,7 +1,6 @@
 <!-- badges: start -->
 
-[![GitHub R package version](https://img.shields.io/github/r-package/v/agdamsbo/REDCapCAST)](https://github.com/agdamsbo/REDCapCAST) [![CRAN/METACRAN](https://img.shields.io/cran/v/REDCapCAST)](https://CRAN.R-project.org/package=REDCapCAST) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8013984.svg)](https://doi.org/10.5281/zenodo.8013984) [![R-hub](https://github.com/agdamsbo/REDCapCAST/actions/workflows/rhub.yaml/badge.svg)](https://github.com/agdamsbo/REDCapCAST/actions/workflows/rhub.yaml) [![R-CMD-check](https://github.com/agdamsbo/REDCapCAST/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/agdamsbo/REDCapCAST/actions/workflows/R-CMD-check.yaml) [![Page deployed](https://github.com/agdamsbo/REDCapCAST/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/agdamsbo/REDCapCAST/actions/workflows/pages/pages-build-deployment) [![Codecov test coverage](https://codecov.io/gh/agdamsbo/REDCapCAST/branch/master/graph/badge.svg)](https://app.codecov.io/gh/agdamsbo/REDCapCAST?branch=master) [![CRAN downloads](https://cranlogs.r-pkg.org/badges/grand-total/REDCapCAST)](https://cran.r-project.org/package=REDCapCAST) [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html)
-
+[![GitHub R package version](https://img.shields.io/github/r-package/v/agdamsbo/REDCapCAST)](https://github.com/agdamsbo/REDCapCAST) [![CRAN/METACRAN](https://img.shields.io/cran/v/REDCapCAST)](https://CRAN.R-project.org/package=REDCapCAST) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8013984.svg)](https://doi.org/10.5281/zenodo.8013984) [![R-hub](https://github.com/agdamsbo/REDCapCAST/actions/workflows/rhub.yaml/badge.svg)](https://github.com/agdamsbo/REDCapCAST/actions/workflows/rhub.yaml) [![R-CMD-check](https://github.com/agdamsbo/REDCapCAST/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/agdamsbo/REDCapCAST/actions/workflows/R-CMD-check.yaml) [![Page deployed](https://github.com/agdamsbo/REDCapCAST/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/agdamsbo/REDCapCAST/actions/workflows/pages/pages-build-deployment) [![CRAN downloads](https://cranlogs.r-pkg.org/badges/grand-total/REDCapCAST)](https://cran.r-project.org/package=REDCapCAST) [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html) [![Codecov test coverage](https://codecov.io/gh/agdamsbo/REDCapCAST/graph/badge.svg)](https://app.codecov.io/gh/agdamsbo/REDCapCAST)
 <!-- badges: end -->
 
 # REDCapCAST package <img src="man/figures/logo.png" align="right"/>

man/as_factor.Rd

@@ -63,6 +63,8 @@ ta loss in case of rich formatted and labelled data.
 \details{
 Please refer to parent functions for extended documentation.
 To avoid redundancy calls and errors, functions are copy-pasted here
+
+Empty variables with empty levels attribute are interpreted as logicals
 }
 \examples{
 # will preserve all attributes
@@ -77,5 +79,12 @@ structure(c(1, 2, 3, 2, 10, 9),
   labels = c(Unknown = 9, Refused = 10),
   class = "haven_labelled"
 ) |>
-  as_factor()
+  as_factor() |> class()
+structure(rep(NA,10),
+  class = c("labelled")
+) |>
+  as_factor() |> summary()
+
+rep(NA,10) |> as_factor()
+
 }