Parallelisation with Future

.Rbuildignore

@@ -1,19 +1,31 @@
-^\.Rhistory
-^\.Rproj\.user
-^\.git
-^\.github
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.Rhistory$
+^\.git$
+^\.github$
 ^\.gitignore
+^[.]?air[.]toml$
+^[.]?jarl[.]toml$
+^AGENTS\.md$
 ^_pkgdown\.yml
-^SIMplyBee\.Rproj
+^cran-comments\.html$
+^cran-comments\.md$
+^cran-comments_files$
+^covr$
 ^docs
+^notes_pkg_dev\.Rmd$
+^vignettes/*_files$
+^vignettes/\.quarto$
 ^vignettes/*R
 ^vignettes/*RData
 ^vignettes/*pdf
 ^vignettes/F2\_Variance\_calculations*
 ^vignettes/SIMplyBee\_logo\_hex\.R
 ^vignettes/SIMplyBee\_logo\_hex\.png
 ^vignettes/SIMplyBee\_logo\_small\.png
-^.*\.Rproj$
-^\.Rproj\.user$
-^doc$
 ^Meta$
+^SIMplyBee\.Rproj
+
+^literature$
+^dev$
+^TestingVarianceComponents\.R$

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

@@ -2,23 +2,42 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [devel, master]
+    branches: [main, devel]
   pull_request:
-    branches: [devel, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: macos-latest, r: "release" }
+          - { os: windows-latest, r: "release" }
+          - { os: ubuntu-latest, r: "devel", http-user-agent: "release" }
+          - { os: ubuntu-latest, r: "release" }
+          - { os: ubuntu-latest, r: "oldrel-1" }
+
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
@@ -27,3 +46,6 @@ jobs:
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/document.yaml

@@ -0,0 +1,46 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    paths: ["R/**"]
+
+name: document.yaml
+
+permissions: read-all
+
+jobs:
+  document:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: roxygen2
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: Commit and push changes
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add man/\* NAMESPACE DESCRIPTION
+          git commit -m "Update documentation" || echo "No changes to commit"
+          git pull --ff-only
+          git push origin

.github/workflows/test-coverage.yaml

@@ -0,0 +1,75 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, devel]
+  pull_request:
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: ubuntu-latest, r: "release" }
+          # - { os: macos-latest, r: "release" }
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            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 }}
+          fail_ci_if_error: false
+          files: cobertura.xml # generated during the process
+          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
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -7,29 +7,56 @@
 
 # User-specific files
 .Ruserdata
+Rplots.pdf
 
 # Example code in package build process
 *-Ex.R
 
 # Output files from R CMD build
 /*.tar.gz
+src/*.o
+src/*.so
 
 # Output files from R CMD check
 /*.Rcheck/
 
-# RStudio files
+# Local IDE state
 .Rproj.user/
+.idea/
+.vscode/
+
+# Compiled code and coverage output
+/src/**/*.o
+/src/**/*.so
+/src/**/*.dll
+/src/**/*.dylib
+/src/**/*.gcda
+/src/**/*.gcno
+/covr/
+
+# Binary package builds
+/SIMplyBee_*.tgz
+/SIMplyBee_*.zip
+
+# Installed documentation and rendered development documents
+/inst/doc/
+/README.html
+/README_files/
+/cran-comments.html
+/cran-comments_files/
 
 # produced vignettes
 vignettes/*.html
 vignettes/*.pdf
+vignettes/*_files/
 
 # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
 .httr-oauth
 
 # knitr and R markdown default cache directories
 *_cache/
 /cache/
+.quarto/
 
 # Temporary files created by R markdown
 *.utf8.md
@@ -40,5 +67,7 @@ vignettes/*.pdf
 
 # Other
 .DS_Store
-src/*.o
-src/*.so
+/doc/
+/Meta/
+
+literature/*.pdf