Upkeep

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

@@ -8,6 +8,8 @@ on:
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -29,13 +31,16 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Install JAGS macOS
         if: runner.os == 'macOS'
-        run: brew install jags
+        run: |
+          curl -o wjags.pkg -L0 -k --url https://downloads.sourceforge.net/project/mcmc-jags/JAGS/4.x/Mac%20OS%20X/JAGS-4.3.2.pkg
+          sudo installer -pkg wjags.pkg -target /
+          rm wjags.pkg
 
       - name: Download JAGS Windows
         if: runner.os == 'Windows'
@@ -61,3 +66,4 @@ 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

@@ -11,6 +11,8 @@ on:
 
 name: pkgdown
 
+permissions: read-all
+
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
@@ -19,8 +21,10 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -39,7 +43,7 @@ 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

@@ -6,7 +6,9 @@ on:
   pull_request:
     branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,36 +17,45 @@ 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")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          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

R/pars.R

@@ -1,3 +1,4 @@
+#' @exportS3Method NULL
 pars.character <- function(x, ...) {
   check_dots_empty()
   if (is.null(x)) {

README.Rmd

@@ -15,8 +15,8 @@ knitr::opts_chunk$set(
 <!-- badges: start -->
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![R-CMD-check](https://github.com/poissonconsulting/embr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/poissonconsulting/embr/actions/workflows/R-CMD-check.yaml)
-[![codecov](https://codecov.io/github/poissonconsulting/embr/branch/main/graph/badge.svg?token=RSs3t4kgR0)](https://codecov.io/github/poissonconsulting/mbr)
-[![License: MIT](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/license/mit/)
+[![Codecov test coverage](https://codecov.io/gh/poissonconsulting/embr/graph/badge.svg)](https://app.codecov.io/gh/poissonconsulting/embr)
+[![License: MIT](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT)
 <!-- badges: end -->
 
 # embr

README.md

@@ -5,7 +5,8 @@
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![R-CMD-check](https://github.com/poissonconsulting/embr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/poissonconsulting/embr/actions/workflows/R-CMD-check.yaml)
-[![codecov](https://codecov.io/github/poissonconsulting/embr/branch/main/graph/badge.svg?token=RSs3t4kgR0)](https://codecov.io/github/poissonconsulting/mbr)
+[![Codecov test
+coverage](https://codecov.io/gh/poissonconsulting/embr/graph/badge.svg)](https://app.codecov.io/gh/poissonconsulting/embr)
 [![License:
 MIT](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT)
 <!-- badges: end -->

embr.Rproj

@@ -1,5 +1,5 @@
 Version: 1.0
-ProjectId: 135c8bd8-5114-4457-922f-3110af1e31d0
+ProjectId: 2d8840dd-7990-4d4a-ae0f-b9292df991df
 
 RestoreWorkspace: No
 SaveWorkspace: No