Merge pull request #241 from peterdavjohnson/master

bring PJ OPAG work to OPAG branch

.Rbuildignore

@@ -27,3 +27,4 @@ Spreadsheets
 ^tic\.R$
 rcppExports.cpp
 stanExports_*
+^data-raw$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,135 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+  schedule:
+    - cron: "0 0 * * *"
+
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      # prevent rgl issues because no X11 display is available
+      RGL_USE_NULL: true
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          # For the later part of v1, this serves to invalidate the cache whenever is needed.
+          # See https://stackoverflow.com/questions/63521430/clear-cache-in-github-actions
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}-v1
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-v1
+
+      # To install rgl in macOS it needs xquartz
+      - name: macOS dependencies
+        if: runner.os == 'macOS'
+        run: |
+          brew install xquartz
+
+      # Adds manual deps to rgl in first line
+      - name: Linux dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get install libglu1-mesa-dev libv8-dev
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      # To install rgl successfully in non-windows OS we need to export DISPLAY
+      - name: Install packages not windows
+        if: runner.os != 'Windows'
+        run: |
+          export DISPLAY=:99
+          Rscript -e 'remotes::install_deps(dependencies = TRUE); remotes::install_cran("rcmdcheck")'
+
+      - name: Install packages windows
+        if: runner.os == 'Windows'
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+          install.packages("rgl")
+        shell: Rscript {0}
+
+        # Why a separate check for macOS/Linux? Because rgl needs to export DISPLAY
+        # in the check as well (this is also present for installing)
+      - name: Check in macOS/Linux
+        if: runner.os != 'Windows'
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: |
+          export DISPLAY=:99
+          Rscript -e 'rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "warning", check_dir = "check")'
+
+      - name: Check in Windows
+        if: runner.os == 'Windows'
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+        # To make things simple we only run code coverage on linux
+        # because rstan generates problems installing
+      - name: Test coverage
+        if: runner.os == 'Linux'
+        run: covr::codecov()
+        shell: Rscript {0}
+
+        # To make things simpler, limit pkgdown deploy only to one OS
+        # Why export DISPLAY? Search for this term throughout this file
+        # for thorough explanation.
+      - name: Deploy package website to pkgdown
+        if: runner.os == 'Linux'
+        run: |
+          export DISPLAY=:99
+          R CMD INSTALL .
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Actions"
+          Rscript -e 'install.packages("pkgdown"); pkgdown::deploy_to_branch(new_process = FALSE)'
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.gitignore

@@ -20,3 +20,4 @@ Spreadsheets
 *.o
 *.so
 docs/
+.RData