add CI actions; clean namespace

.github/workflows/tic.yml

@@ -0,0 +1,103 @@
+## tic GitHub Actions template: linux-macos-windows-deploy
+## revision date: 2022-11-23
+on:
+  workflow_dispatch:
+  push:
+    branches:
+    - main
+    - master
+    - cran-*
+  pull_request:
+    branches:
+    - main
+    - master
+  # for now, CRON jobs only run on the default branch of the repo (i.e. usually on master)
+  schedule:
+    # * is a special character in YAML so you have to quote this string
+    - cron: "0 4 * * *"
+
+name: tic
+
+jobs:
+  all:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          # use a different tic template type if you do not want to build on all listed platforms
+          - { os: windows-latest, r: "release" }
+          - { os: macOS-latest, r: "release", pkgdown: "true", latex: "true" }
+          - { os: ubuntu-latest, r: "devel" }
+          - { os: ubuntu-latest, r: "release" }
+
+    env:
+      # make sure to run `tic::use_ghactions_deploy()` to set up deployment
+      TIC_DEPLOY_KEY: ${{ secrets.TIC_DEPLOY_KEY }}
+      # prevent rgl issues because no X11 display is available
+      RGL_USE_NULL: true
+      # if you use bookdown or blogdown, replace "PKGDOWN" by the respective
+      # capitalized term. This also might need to be done in tic.R
+      BUILD_PKGDOWN: ${{ matrix.config.pkgdown }}
+      # use GITHUB_TOKEN from GitHub to workaround rate limits in {remotes}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          Ncpus: 4
+
+      - uses: r-lib/actions/setup-tinytex@v2
+        if: matrix.config.latex == 'true'
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      # set date/week for use in cache creation
+      # https://github.community/t5/GitHub-Actions/How-to-set-and-access-a-Workflow-variable/m-p/42970
+      # - cache R packages daily
+      - name: "[Cache] Prepare daily timestamp for cache"
+        if: runner.os != 'Windows'
+        id: date
+        run: echo "date=$(date '+%d-%m')" >> $GITHUB_OUTPUT
+
+      - name: "[Cache] Cache R packages"
+        if: runner.os != 'Windows'
+        uses: pat-s/always-upload-cache@v3
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{steps.date.outputs.date}}
+          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-${{steps.date.outputs.date}}
+
+      - name: "[Stage] Install pak"
+        run: Rscript -e "install.packages('pak', repos = 'https://r-lib.github.io/p/pak/stable')"
+
+      - name: "[Stage] Install"
+        run: Rscript -e "if (grepl('Ubuntu', Sys.info()[['version']]) && !grepl('Under development', R.version[['status']])) {options(repos = c(CRAN = sprintf('https://packagemanager.rstudio.com/all/__linux__/%s/latest', system('lsb_release -cs', intern = TRUE))))}else{options(repos = c(CRAN = 'cloud.r-project.org'))}; pak::pkg_install('ropensci/tic')" -e "print(tic::dsl_load())" -e "tic::prepare_all_stages()" -e "tic::before_install()" -e "tic::install()"
+
+      - name: "[Stage] Script"
+        run: Rscript -e 'tic::script()'
+
+      - name: "[Stage] After Success"
+        run: Rscript -e "tic::after_success()"
+
+      - name: "[Stage] Upload R CMD check artifacts"
+        if: failure()
+        uses: actions/upload-artifact@v2
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
+      - name: "[Stage] Before Deploy"
+        run: |
+          Rscript -e "tic::before_deploy()"
+
+      - name: "[Stage] Deploy"
+        run: Rscript -e "tic::deploy()"
+
+      - name: "[Stage] After Deploy"
+        run: Rscript -e "tic::after_deploy()"

NAMESPACE

@@ -1,10 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
-export(hello_world)
 export(sg_apply)
 export(sg_make_plan)
 import(data.table)
 importFrom(future.apply,future_Map)
 importFrom(future.apply,future_lapply)
 importFrom(prospectr,savitzkyGolay)
-useDynLib(specprepper, .registration = TRUE)

tic.R

@@ -0,0 +1,8 @@
+# installs dependencies, runs R CMD check, runs covr::codecov()
+do_package_checks()
+
+if (ci_on_ghactions() && ci_has_env("BUILD_PKGDOWN")) {
+  # creates pkgdown site and pushes to gh-pages branch
+  # only for the runner with the "BUILD_PKGDOWN" env var set
+  do_pkgdown()
+}