Merge pull request #86 from mayer79/update-code-cov

Update code coverage version

Author: mayer79

.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:
@@ -15,36 +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-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@v5
+        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 }}
+          files: ./cobertura.xml
+          plugins: 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: missRanger
 Title: Fast Imputation of Missing Values
-Version: 2.6.1
+Version: 2.6.2
 Authors@R: 
     person("Michael", "Mayer", , "mayermichael79@gmail.com", role = c("aut", "cre"))
 Description: Alternative implementation of the beautiful 'MissForest'

NEWS.md

@@ -1,3 +1,9 @@
+# missRanger 2.6.2
+
+### Maintenance
+
+- Update code coverage version [#86](https://github.com/mayer79/missRanger/pull/86).
+
 # missRanger 2.6.1
 
 ### Improvement

README.md

@@ -3,7 +3,7 @@
 <!-- badges: start -->
 
 [![R-CMD-check](https://github.com/mayer79/missRanger/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/mayer79/missRanger/actions/workflows/R-CMD-check.yaml)
-[![Codecov test coverage](https://codecov.io/gh/mayer79/missRanger/branch/main/graph/badge.svg)](https://app.codecov.io/gh/mayer79/missRanger?branch=main)
+[![Codecov test coverage](https://codecov.io/gh/mayer79/missRanger/graph/badge.svg)](https://app.codecov.io/gh/mayer79/missRanger)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/missRanger)](https://cran.r-project.org/package=missRanger)
 
 [![](https://cranlogs.r-pkg.org/badges/missRanger)](https://cran.r-project.org/package=missRanger) 

missRanger.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: dee62308-91e7-4f63-a78c-171191f0f386
 
 RestoreWorkspace: Default
 SaveWorkspace: Default

packaging.R

@@ -1,6 +1,6 @@
-#=============================================================================
+# =============================================================================
 # Put together the package
-#=============================================================================
+# =============================================================================
 
 # WORKFLOW: UPDATE EXISTING PACKAGE
 # 1) Modify package content and documentation.
@@ -15,15 +15,15 @@ library(usethis)
 use_description(
   fields = list(
     Title = "Fast Imputation of Missing Values",
-    Version = "2.6.1",
-    Description = "Alternative implementation of the beautiful 'MissForest' algorithm used to impute 
-    mixed-type data sets by chaining random forests, introduced by Stekhoven, D.J. and 
-    Buehlmann, P. (2012) <doi:10.1093/bioinformatics/btr597>. Under the hood, it uses the 
-    lightning fast random forest package 'ranger'. Between the iterative model fitting, 
-    we offer the option of using predictive mean matching. This firstly avoids imputation 
-    with values not already present in the original data (like a value 0.3334 in 0-1 coded variable). 
-    Secondly, predictive mean matching tries to raise the variance in the resulting conditional 
-    distributions to a realistic level. This would allow, e.g., to do multiple imputation when 
+    Version = "2.6.2",
+    Description = "Alternative implementation of the beautiful 'MissForest' algorithm used to impute
+    mixed-type data sets by chaining random forests, introduced by Stekhoven, D.J. and
+    Buehlmann, P. (2012) <doi:10.1093/bioinformatics/btr597>. Under the hood, it uses the
+    lightning fast random forest package 'ranger'. Between the iterative model fitting,
+    we offer the option of using predictive mean matching. This firstly avoids imputation
+    with values not already present in the original data (like a value 0.3334 in 0-1 coded variable).
+    Secondly, predictive mean matching tries to raise the variance in the resulting conditional
+    distributions to a realistic level. This would allow, e.g., to do multiple imputation when
     repeating the call to missRanger(). Out-of-sample application is supported as well.",
     `Authors@R` = "person('Michael', 'Mayer', email = 'mayermichael79@gmail.com', role = c('aut', 'cre'))",
     Depends = "R (>= 3.5.0)",
@@ -42,8 +42,10 @@ use_gpl_license(2)
 use_github_links() # use this if this project is on github
 
 # Your files that do not belong to the package itself (others are added by "use_* function")
-use_build_ignore(c("^packaging.R$", "[.]Rproj$", "^backlog$",
-                   "^cran-comments.md$", "^logo.png$"), escape = FALSE)
+use_build_ignore(c(
+  "^packaging.R$", "[.]Rproj$", "^backlog$",
+  "^cran-comments.md$", "^logo.png$"
+), escape = FALSE)
 
 # If your code uses the pipe operator %>%
 # use_pipe()
@@ -81,9 +83,9 @@ use_github_action("pkgdown")
 
 use_revdep()
 
-#=============================================================================
+# =============================================================================
 # Finish package building (can use fresh session)
-#=============================================================================
+# =============================================================================
 
 library(devtools)
 
@@ -98,7 +100,7 @@ install()
 if (FALSE) {
   check_win_devel()
   check_rhub()
-  
+
   # Takes long # devtools::install_github("r-lib/revdepcheck")
   revdepcheck::revdep_check(num_workers = 4L, bioc = FALSE)