Optimize package (#40)

.Rbuildignore

@@ -16,3 +16,11 @@ _pkgdown.yml
 tic.R
 ^_pkgdown\.yml$
 ^oddsratio\.Rproj$
+^\.ccache$
+^tic\.R$
+^\.travis\.yml$
+^\.lintr$
+^\.vscode$
+^\.github$
+^\.pre-commit-config\.yaml$
+^codemeta\.json$

.github/workflows/main.yml

@@ -0,0 +1,163 @@
+## tic GitHub Actions template: linux-macos-windows-deploy
+## revision date: 2020-05-21
+on:
+  push:
+  pull_request:
+  # 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: R CMD Check via {tic}
+
+jobs:
+  R-CMD-check:
+    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" }
+          - { os: macOS-latest, r: "devel" }
+          - { os: ubuntu-latest, r: "release" }
+
+    env:
+      # otherwise remotes::fun() errors cause the build to fail. Example: Unavailability of binaries
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      CRAN: ${{ matrix.config.cran }}
+      # we are not allowed to write to ~/.ccache on GH Actions
+      # setting some ccache options
+      CCACHE_BASEDIR: ${{ GITHUB.WORKSPACE }}
+      CCACHE_DIR: ${{ GITHUB.WORKSPACE }}/.ccache
+      CCACHE_NOHASHDIR: true
+      CCACHE_SLOPPINESS: include_file_ctime
+      # 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 }}
+      # macOS >= 10.15.4 linking
+      SDKROOT: /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
+      # use GITHUB_TOKEN from GItHub to workaround rate limits in {remotes}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/[email protected]
+
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+          Ncpus: 4
+
+      # LaTeX. Installation time:
+      # Linux: ~ 1 min
+      # macOS: ~ 1 min 30s
+      # Windows: never finishes
+      - uses: r-lib/actions/setup-tinytex@v1
+        if: runner.os != 'Windows'
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      # set date/week for use in cache creation
+      # https://github.community/t5/GitHub-Actions/How-to-set-and-access-a-Workflow-variable/m-p/42970
+      # - cache R packages daily
+      # - cache ccache weekly -> 'ccache' helps rebuilding the package cache faster
+      - name: "[Cache] Prepare daily timestamp for cache"
+        if: runner.os != 'Windows'
+        id: date
+        run: echo "::set-output name=date::$(date '+%d-%m')"
+
+      - name: "[Cache] Prepare weekly timestamp for cache"
+        if: runner.os != 'Windows'
+        id: datew
+        run: echo "::set-output name=datew::$(date '+%Y-%V')"
+
+      - name: "[Cache] Cache R packages"
+        if: runner.os != 'Windows'
+        uses: pat-s/[email protected]
+        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: "[Cache] Cache ccache"
+        if: runner.os != 'Windows'
+        uses: pat-s/[email protected]
+        with:
+          path: ${{ env.CCACHE_DIR}}
+          key: ${{ runner.os }}-r-${{ matrix.config.r }}-ccache-${{steps.datew.outputs.datew}}
+          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-ccache-${{steps.datew.outputs.datew}}
+
+      # install ccache and write config file
+      - name: "[Linux] ccache"
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt install ccache libcurl4-openssl-dev
+          mkdir -p ~/.R && echo -e 'CC=ccache gcc -std=gnu99\nCXX=ccache g++\nFC=ccache gfortran\nF77=ccache gfortran' > $HOME/.R/Makevars
+
+      # install ccache and write config file
+      # mirror the setup described in https://github.com/rmacoslib/r-macos-rtools
+      - name: "[macOS] ccache"
+        if: runner.os == 'macOS' && matrix.config.r == 'devel'
+        run: |
+          brew install ccache
+          # install SDK 10.13 (High Sierra, used by CRAN)
+          wget -nv https://github.com/phracker/MacOSX-SDKs/releases/download/10.15/MacOSX10.13.sdk.tar.xz
+          tar fxz MacOSX10.13.sdk.tar.xz
+          sudo mv MacOSX10.13.sdk /Library/Developer/CommandLineTools/SDKs/
+          rm -rf MacOSX10.13*
+          # install gfortran 8.2 (used by CRAN)
+          wget -nv https://github.com/fxcoudert/gfortran-for-macOS/releases/download/8.2/gfortran-8.2-Mojave.dmg
+          sudo hdiutil attach gfortran*.dmg
+          sudo installer -package /Volumes/gfortran*/gfortran*/gfortran*.pkg -target /
+          sudo hdiutil detach /Volumes/gfortran-8.2-Mojave
+          rm gfortran-8*
+          # set compiler flags
+          mkdir -p ~/.R && echo -e 'CC=ccache clang\nCPP=ccache clang\nCXX=ccache clang++\nCXX11=ccache clang++\nCXX14=ccache clang++\nCXX17=ccache clang++\nCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk\nCCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk\nCXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk\nCPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk -I/usr/local/include\nF77=ccache /usr/local/gfortran/bin/gfortran\nFC=ccache /usr/local/gfortran/bin/gfortran' > $HOME/.R/Makevars
+
+      # for some strange Windows reason this step and the next one need to be decoupled
+      - name: "[Stage] Prepare"
+        run: |
+          Rscript -e "if (!requireNamespace('remotes')) install.packages('remotes', type = 'source')"
+          Rscript -e "if (getRversion() < '3.2' && !requireNamespace('curl')) install.packages('curl', type = 'source')"
+
+      - name: "[Stage] Install"
+        if: matrix.config.os != 'macOS-latest' || matrix.config.r != 'devel'
+        run: Rscript -e "remotes::install_github('ropensci/tic')" -e "print(tic::dsl_load())" -e "tic::prepare_all_stages()" -e "tic::before_install()" -e "tic::install()"
+
+      # macOS devel needs its own stage because we need to work with an option to suppress the usage of binaries
+      - name: "[Stage] Prepare & Install (macOS-devel)"
+        if: matrix.config.os == 'macOS-latest' && matrix.config.r == 'devel'
+        run: |
+          echo -e 'options(Ncpus = 4, pkgType = "source", repos = structure(c(CRAN = "https://cloud.r-project.org/")))' > $HOME/.Rprofile
+          Rscript -e "remotes::install_github('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"
+        if: matrix.config.os == 'macOS-latest' && matrix.config.r == 'release'
+        run: Rscript -e "tic::after_success()"
+
+      - name: "[Stage] Upload R CMD check artifacts"
+        if: failure()
+        uses: actions/upload-artifact@master
+        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()"

.github/workflows/update-tic.yml

@@ -0,0 +1,52 @@
+on:
+  schedule:
+    # * is a special character in YAML so you have to quote this string
+    - cron: "0 4 * * *"
+
+name: Update tic
+
+jobs:
+  update-tic:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: macOS-latest, r: "release" }
+
+    env:
+      # use GITHUB_TOKEN from GitHub to workaround rate limits in {remotes}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          persist-credentials: false
+
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+          Ncpus: 4
+
+      - name: "[Stage] Dependencies"
+        run: |
+            brew install curl libsodium
+            Rscript -e "if (!requireNamespace('remotes')) install.packages('remotes', type = 'source')"
+            Rscript -e "remotes::install_github('ropensci/tic', dependencies = TRUE)"
+
+      - name: "[Stage] Update YAMLs"
+        run: |
+            Rscript -e "tic::update_yml()"
+
+      - name: "[Stage] Create Pull Request"
+        uses: peter-evans/create-pull-request@v2
+        with:
+          token: ${{ secrets.TIC_UPDATE }}
+          title: "Update tic templates [ci-skip]"
+          commit-message: "update tic templates"
+          body: "{tic} templates can be updated :rocket: :robot:"
+          branch: update-tic
+          base: master

.gitignore

@@ -8,3 +8,97 @@ inst/doc
 _gh-pages
 vignettes/*.html
 vignettes/*.R
+.vscode
+
+# Created by https://www.gitignore.io/api/r
+# Edit at https://www.gitignore.io/?templates=r
+### R ###
+# History files
+.Rapp.history
+# Session Data files
+.RDataTmp
+# User-specific files
+# Example code in package build process
+*-Ex.R
+# Output files from R CMD build
+/*.tar.gz
+# Output files from R CMD check
+/*.Rcheck/
+# RStudio files
+.Rproj.user/
+# produced vignettes
+vignettes/*.pdf
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+### R.Bookdown Stack ###
+# R package: bookdown caching files
+/*_files/
+# End of https://www.gitignore.io/api/r
+# Created by https://www.gitignore.io/api/visualstudiocode
+# Edit at https://www.gitignore.io/?templates=visualstudiocode
+### VisualStudioCode ###
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+### VisualStudioCode Patch ###
+# Ignore all local history of files
+.history
+# End of https://www.gitignore.io/api/visualstudiocode
+# Created by https://www.gitignore.io/api/macos
+# Edit at https://www.gitignore.io/?templates=macos
+### macOS ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+# Icon must end with two \r
+Icon
+# Thumbnails
+._*
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+# End of https://www.gitignore.io/api/macos
+# Created by https://www.gitignore.io/api/windows
+# Edit at https://www.gitignore.io/?templates=windows
+### Windows ###
+# Windows thumbnail cache files
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+# Dump file
+*.stackdump
+# Folder config file
+[Dd]esktop.ini
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+# Windows shortcuts
+*.lnk
+# End of https://www.gitignore.io/api/windows
+docs/

.lintr

@@ -0,0 +1,9 @@
+linters: with_defaults(
+    # lintr defaults: https://github.com/jimhester/lintr#available-linters
+    # the following setup changes/removes certain linters
+    assignment_linter = NULL, # do not force using <- for assignments
+    object_name_linter = object_name_linter(c("snake_case", "CamelCase")), # only allow snake case and camel case object names
+    cyclocomp_linter = NULL, # do not check function complexity
+    commented_code_linter = NULL, # allow code in comments
+    line_length_linter = line_length_linter(100)
+    )

.pre-commit-config.yaml

@@ -0,0 +1,54 @@
+# All available hooks: https://pre-commit.com/hooks.html
+# R specific hooks: https://github.com/lorenzwalthert/precommit
+repos:
+-   repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.0.0.9048
+    hooks: 
+    -   id: style-files
+        args: [--style_pkg=styler, --style_fun=tidyverse_style]    
+    -   id: roxygenize
+    # codemeta must be above use-tidy-description when both are used
+    # -   id: codemeta-description-updated
+    -   id: use-tidy-description
+    -   id: spell-check
+        exclude: >
+          (?x)^(
+          data/.*| 
+          (.*/|)\.Rprofile|
+          (.*/|)\.Renviron|
+          (.*/|)\.gitignore|
+          (.*/|)NAMESPACE|
+          (.*/|)WORDLIST|
+          (.*/|)\.travis.yml|
+          (.*/|)appveyor.yml|
+          (.*/|)\.Rbuildignore|
+          (.*/|)\.pre-commit-.*|
+          .*\.[rR]|
+          .*\.Rproj|
+          .*\.py|
+          .*\.feather|
+          .*\.rds|
+          .*\.Rds|
+          .*\.sh|
+          .*\.RData
+          )$
+    -   id: lintr
+    -   id: readme-rmd-rendered
+    -   id: parsable-R
+    -   id: no-browser-statement
+    -   id: deps-in-desc
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.1.0
+    hooks: 
+    -   id: check-added-large-files
+        args: ['--maxkb=200']
+    -   id: end-of-file-fixer
+        exclude: '\.Rd'
+-   repo: local
+    hooks:
+    -   id: forbid-to-commit
+        name: Don't commit common R artifacts
+        entry: Cannot commit .Rhistory, .RData, .Rds or .rds.
+        language: fail
+        files: '\.Rhistory|\.RData|\.Rds|\.rds$'
+        # `exclude: <regex>` to allow committing specific files.