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anthonyokc · Oct 1, 2023 · 14a3714 · 14a3714
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -0,0 +1,19 @@
+^renv$
+^renv\.lock$
+CODE_OF_CONDUCT.md
+SECURITY.md
+^.*\.Rproj$
+^\.Rproj\.user$
+^_pkgdown\.yml$
+^vignettes/hello\.Rmd$
+^docs$
+^\.github$
+README.*
+^\.lintr$
+^staged_dependencies\.yaml$
+coverage.*
+^\.pre-commit-config\.yaml$
+^codemeta\.json$
+init.sh
+workflows.md
+images
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1,2 @@
+# Auto detect text files and perform LF normalization
+* text=auto
diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
@@ -0,0 +1,79 @@
+---
+name: Check 🛠
+
+on:
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
+    branches:
+      - main
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  audit:
+    name: Audit Dependencies 🕵️‍♂️
+    uses: insightsengineering/r.pkg.template/.github/workflows/audit.yaml@main
+  r-cmd:
+    name: R CMD Check 🧬
+    uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    with:
+      additional-env-vars: |
+        _R_CHECK_CRAN_INCOMING_REMOTE_=false
+      additional-r-cmd-check-params: --as-cran
+  coverage:
+    name: Coverage 📔
+    uses: insightsengineering/r.pkg.template/.github/workflows/test-coverage.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  linter:
+    if: github.event_name == 'pull_request'
+    name: SuperLinter 🦸‍♀️
+    uses: insightsengineering/r.pkg.template/.github/workflows/linter.yaml@main
+  roxygen:
+    name: Roxygen 🅾
+    uses: insightsengineering/r.pkg.template/.github/workflows/roxygen.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    with:
+      auto-update: true
+  gitleaks:
+    name: gitleaks 💧
+    uses: insightsengineering/r.pkg.template/.github/workflows/gitleaks.yaml@main
+  spelling:
+    if: github.event_name == 'pull_request'
+    name: Spell Check 🆎
+    uses: insightsengineering/r.pkg.template/.github/workflows/spelling.yaml@main
+  links:
+    if: github.event_name == 'pull_request'
+    name: Check URLs 🌐
+    uses: insightsengineering/r.pkg.template/.github/workflows/links.yaml@main
+  vbump:
+    name: Version Bump 🤜🤛
+    if: github.event_name == 'push'
+    uses: insightsengineering/r.pkg.template/.github/workflows/version-bump.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  version:
+    name: Version Check 🏁
+    uses: insightsengineering/r.pkg.template/.github/workflows/version.yaml@main
+  licenses:
+    name: License Check 🃏
+    uses: insightsengineering/r.pkg.template/.github/workflows/licenses.yaml@main
+  style:
+    if: github.event_name == 'pull_request'
+    name: Style Check 👗
+    uses: insightsengineering/r.pkg.template/.github/workflows/style.yaml@main
+    with:
+      auto-update: true
+  grammar:
+    if: github.event_name == 'pull_request'
+    name: Grammar Check 🔤
+    uses: insightsengineering/r.pkg.template/.github/workflows/grammar.yaml@main
diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
@@ -0,0 +1,41 @@
+---
+name: Docs 📚
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - "inst/templates/**"
+      - "_pkgdown.y[a]ml"
+      - DESCRIPTION
+      - "**.md"
+      - "**.Rmd"
+      - "man/**"
+      - "LICENSE.*"
+      - NAMESPACE
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
+    branches:
+      - main
+    paths:
+      - "inst/templates/**"
+      - "_pkgdown.y[a]ml"
+      - DESCRIPTION
+      - "**.md"
+      - "**.Rmd"
+      - "man/**"
+      - "LICENSE.*"
+      - NAMESPACE
+  workflow_dispatch:
+
+jobs:
+  docs:
+    name: Pkgdown Docs 📚
+    uses: insightsengineering/r.pkg.template/.github/workflows/pkgdown.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/post-release.yaml.shared b/.github/workflows/post-release.yaml.shared
@@ -0,0 +1,15 @@
+---
+name: Post release ✨
+
+on:
+  release:
+    types: ["released"]
+
+jobs:
+  vbump:
+    name: Version Bump 🤜🤛
+    uses: insightsengineering/r.pkg.template/.github/workflows/version-bump.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    with:
+      vbump-after-release: true
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
@@ -0,0 +1,54 @@
+---
+name: Release 🎈
+
+on:
+  push:
+    tags:
+      - "v*"
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Build package 🎁
+    needs: release
+    uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    with:
+      skip-r-cmd-check: true
+      skip-r-cmd-install: true
+  docs:
+    name: Pkgdown Docs 📚
+    needs: release
+    uses: insightsengineering/r.pkg.template/.github/workflows/pkgdown.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    with:
+      default-landing-page: latest-tag
+  validation:
+    name: R Package Validation report 📃
+    needs: release
+    uses: insightsengineering/r.pkg.template/.github/workflows/validation.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  release:
+    name: Create release 🎉
+    uses: insightsengineering/r.pkg.template/.github/workflows/release.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  r-cmd:
+    name: R CMD Check 🧬
+    needs: [release, docs]
+    uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    with:
+      additional-env-vars: |
+        _R_CHECK_CRAN_INCOMING_REMOTE_=false
+      additional-r-cmd-check-params: --as-cran
+  coverage:
+    name: Coverage 📔
+    needs: [release, docs]
+    uses: insightsengineering/r.pkg.template/.github/workflows/test-coverage.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/scheduled.yaml.shared b/.github/workflows/scheduled.yaml.shared
@@ -0,0 +1,28 @@
+---
+name: Scheduled 🕰️
+
+on:
+  schedule:
+    - cron: '45 3 * * 0'
+  workflow_dispatch:
+
+jobs:
+  dependency-test:
+    strategy:
+      fail-fast: false
+      matrix:
+        test-strategy: ["min", "release", "max"]
+    uses: insightsengineering/r.pkg.template/.github/workflows/verdepcheck.yaml@main
+    name: Dependency Test - ${{ matrix.test-strategy }} 🔢
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      GCHAT_WEBHOOK: ${{ secrets.GCHAT_WEBHOOK }}
+    with:
+      strategy: ${{ matrix.test-strategy }}
+      additional-env-vars: |
+        PKG_SYSREQS_DRY_RUN=true
+  branch-cleanup:
+    name: Branch Cleanup 🧹
+    uses: insightsengineering/r.pkg.template/.github/workflows/branch-cleanup.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,33 @@
+.DS_Store
+.httr-oauth
+.project
+.RData
+.Rhistory
+.Rproj.user
+.Ruserdata
+.settings/**
+*.html
+*.Rcheck
+*.rprof
+*.sas.txt
+*~
+/.project
+devel/*
+doc
+docs
+inst/outputs/*
+logs
+Meta
+packrat/lib*/
+temp
+temp_w
+templates/
+tmp.*
+vignettes/*.html
+vignettes/*.md
+vignettes/*.R
+coverage.*
+.vscode/
+node_modules/
+package-lock.json
+package.json
diff --git a/.lintr b/.lintr
@@ -0,0 +1,5 @@
+linters: linters_with_defaults(
+  line_length_linter = line_length_linter(120),
+  cyclocomp_linter = NULL,
+  object_usage_linter = NULL
+  )
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,82 @@
+---
+# All available hooks: https://pre-commit.com/hooks.html
+# R specific hooks: https://github.com/lorenzwalthert/precommit
+repos:
+  - repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.3.2.9013
+    hooks:
+      - id: style-files
+        args: [--style_pkg=styler, --style_fun=tidyverse_style]
+      - id: roxygenize
+        additional_dependencies:
+          - plumber
+          - shiny
+      # codemeta must be above use-tidy-description when both are used
+      # -   id: codemeta-description-updated
+      - id: use-tidy-description
+      - id: spell-check
+        exclude: >
+          (?x)^(
+          data/.*|
+          (.*/|)\.Rprofile|
+          (.*/|)\.Renviron|
+          (.*/|)\.gitignore|
+          (.*/|)NAMESPACE|
+          (.*/|)DESCRIPTION|
+          (.*/|)WORDLIST|
+          (.*/|)LICENSE|
+          (.*/|)\.Rbuildignore|
+          (.*/|)\.lintr|
+          (.*/|)_pkgdown.yaml|
+          (.*/|)staged_dependencies.yaml|
+          (.*/|)\.pre-commit-.*|
+          \.github/.*|
+          .*\.[rR]|
+          .*\.Rproj|
+          .*\.py|
+          .*\.png|
+          .*\.feather|
+          .*\.rds|
+          .*\.Rds|
+          .*\.sh|
+          .*\.RData
+          )$
+      - id: lintr
+      - id: readme-rmd-rendered
+      - id: parsable-R
+      - id: no-browser-statement
+      - id: deps-in-desc
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v3.0.0-alpha.9-for-vscode
+    hooks:
+      - id: prettier
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-added-large-files
+        args: ["--maxkb=200"]
+      - id: end-of-file-fixer
+        exclude: '\.Rd'
+      - id: trailing-whitespace
+        exclude: '\.Rd'
+      - id: check-yaml
+      - id: no-commit-to-branch
+      - id: mixed-line-ending
+        args: ["--fix=lf"]
+      - id: detect-aws-credentials
+        args: ["--allow-missing-credentials"]
+      - id: detect-private-key
+      - id: forbid-new-submodules
+      - id: check-symlinks
+  - 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.
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.35.0
+    hooks:
+      - id: markdownlint
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -0,0 +1,31 @@
+Type: Package
+Package: anthonyverse
+Title: R Package Template
+Version: 0.1.0
+Date: 2023-07-05
+Authors@R:
+    person("anthonyokc", , , "anthonyokc@example.com", role = c("aut", "cre"))
+Description: R package template with GitHub Actions workflows included.
+License: Apache License 2.0 | file LICENSE
+URL: https://github.com/anthonyokc/anthonyverse/
+BugReports: https://github.com/anthonyokc/anthonyverse/issues
+Depends:
+    R (>= 3.6)
+Imports:
+    plumber,
+    shiny,
+    stringr
+Suggests:
+    future,
+    httr,
+    knitr,
+    shinytest,
+    testthat (>= 2.0)
+VignetteBuilder:
+    knitr
+biocViews:
+Encoding: UTF-8
+Language: en-US
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3