Upkeep

Author: llrs

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

@@ -4,9 +4,10 @@ on:
   push:
     branches: [devel, main, master]
   pull_request:
-    branches: [devel, main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -49,3 +50,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -4,12 +4,13 @@ on:
   push:
     branches: [devel, main, master]
   pull_request:
-    branches: [devel, main, master]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -19,6 +20,8 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
       - uses: actions/checkout@v4
         with:
@@ -41,7 +44,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/test-coverage.yaml

@@ -4,9 +4,10 @@ on:
   push:
     branches: [devel, main, master]
   pull_request:
-    branches: [devel, main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -25,23 +26,34 @@ jobs:
 
       - 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

DESCRIPTION

@@ -14,7 +14,7 @@ Description: Distributes samples in batches while making batches
     number of variables, both numeric and categorical. For quality control
     it provides functions to subset a representative sample.
 License: MIT + file LICENSE
-URL: https://experdesign.llrs.dev, https://github.com/llrs/experDesign/, https://github.com/llrs/experDesign
+URL: https://experdesign.llrs.dev, https://github.com/llrs/experDesign/
 BugReports: https://github.com/llrs/experDesign/issues
 Depends: 
     R (>= 3.5.0)

README.Rmd

@@ -18,12 +18,11 @@ knitr::opts_chunk$set(
 [![CRAN status](https://www.r-pkg.org/badges/version/experDesign)](https://CRAN.R-project.org/package=experDesign)
 [![CRAN checks](https://badges.cranchecks.info/worst/experDesign.svg)](https://cran.r-project.org/web/checks/check_results_experDesign.html)
 [![R-CMD-check](https://github.com/llrs/experDesign/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/llrs/experDesign/actions/workflows/R-CMD-check.yaml)
-[![Coverage status](https://codecov.io/gh/llrs/experDesign/branch/devel/graph/badge.svg)](https://app.codecov.io/github/llrs/experDesign)
+[![Codecov test coverage](https://codecov.io/gh/llrs/experDesign/graph/badge.svg)](https://app.codecov.io/gh/llrs/experDesign)
 [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![JOSS](https://joss.theoj.org/papers/10.21105/joss.03358/status.svg)](https://doi.org/10.21105/joss.03358) 
 [![DOI](https://zenodo.org/badge/142569201.svg)](https://zenodo.org/badge/latestdoi/142569201)
-
 <!-- badges: end -->
 
 The goal of experDesign is to help you distribute your samples before an experiment but after they are collected. 

README.md

@@ -10,16 +10,15 @@ status](https://www.r-pkg.org/badges/version/experDesign)](https://CRAN.R-projec
 [![CRAN
 checks](https://badges.cranchecks.info/worst/experDesign.svg)](https://cran.r-project.org/web/checks/check_results_experDesign.html)
 [![R-CMD-check](https://github.com/llrs/experDesign/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/llrs/experDesign/actions/workflows/R-CMD-check.yaml)
-[![Coverage
-status](https://codecov.io/gh/llrs/experDesign/branch/master/graph/badge.svg)](https://app.codecov.io/github/llrs/experDesign)
+[![Codecov test
+coverage](https://codecov.io/gh/llrs/experDesign/graph/badge.svg)](https://app.codecov.io/gh/llrs/experDesign)
 [![Lifecycle:
 stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![Project Status: Active - The project has reached a stable, usable
 state and is being actively
 developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![JOSS](https://joss.theoj.org/papers/10.21105/joss.03358/status.svg)](https://doi.org/10.21105/joss.03358)
 [![DOI](https://zenodo.org/badge/142569201.svg)](https://zenodo.org/badge/latestdoi/142569201)
-
 <!-- badges: end -->
 
 The goal of experDesign is to help you distribute your samples before an
@@ -120,9 +119,6 @@ combination with the original according to multiple statistics.
 omit <- c("Wr.Hnd", "NW.Hnd", "Fold", "Pulse", "Clap", "Exer", "Height", "M.I")
 (keep <- colnames(survey)[!colnames(survey) %in% omit])
 #> [1] "Sex"   "W.Hnd" "Smoke" "Age"
-```
-
-``` r
 head(survey[, keep])
 #>      Sex W.Hnd Smoke    Age
 #> 1 Female Right Never 18.250
@@ -131,18 +127,12 @@ head(survey[, keep])
 #> 4   Male Right Never 20.333
 #> 5   Male Right Never 23.667
 #> 6 Female Right Never 21.000
-```
-
-``` r
 
 # Set a seed for reproducibility
 set.seed(87732135)
 # Looking for groups at most of 70 samples.
 index <- design(pheno = survey, size_subset = 70, omit = omit, iterations = 100)
 #> Warning: There might be some problems with the data use check_data().
-```
-
-``` r
 index
 #> $SubSet1
 #>  [1]   3   9  10  14  16  21  23  24  25  30  44  46  56  57  59  62  63  68  69
@@ -175,9 +165,6 @@ a colleague with:
 ``` r
 head(batch_names(index))
 #> [1] "SubSet3" "SubSet3" "SubSet1" "SubSet4" "SubSet2" "SubSet2"
-```
-
-``` r
 # Or via inspect() to keep it in a matrix format:
 head(inspect(index, survey[, keep]))
 #>      Sex W.Hnd Smoke    Age   batch