Documentation (#175)

* add vignettes * add doc * Apply suggestions from code review Co-authored-by: Stefan Bundfuss <[email protected]> * Update vignettes/common_structure.Rmd * Update vignettes/common_structure.Rmd * Update vignettes/common_structure.Rmd * Update vignettes/common_structure.Rmd * Update vignettes/common_structure.Rmd * Update vignettes/common_structure.Rmd * Update vignettes/cran-status.Rmd * Update vignettes/get_started.Rmd * Update vignettes/get_started.Rmd * Update vignettes/get_started.Rmd Co-authored-by: Stefan Bundfuss <[email protected]> * Update vignettes/get_started.Rmd * Update vignettes/get_started.Rmd * Update vignettes/get_started.Rmd * Update vignettes/pkgdown.Rmd * update doc * updates * update doc and common.yml template * update navbar and readme * updates * fix r cmd check notes * add cheetsheat and fix pkgdown non multi version doc * update buildignore * add logo * fix clean param * Doc updates (#187) * Update pkgdown.yml * [actions skip] Add/Update README.md for main * update cheatsheet * update cheatsheet * fix * fix pdf rendering * fix * fix hex * [actions skip] Add/Update README.md for main * fix rendering --------- Co-authored-by: GitHub Actions <[email protected]> * updates * update buildignore * fix url * fix notes * typo fix * fix * fix * fix * reduce pdf size --------- Co-authored-by: pharmaverse-bot <[email protected]> Co-authored-by: Stefan Bundfuss <[email protected]> Co-authored-by: GitHub Actions <[email protected]>
pharmaverse · Feb 12, 2024 · e48e3cf · e48e3cf
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diff --git a/.github/workflows/common.yml.inactive b/.github/workflows/common.yml.inactive
@@ -4,139 +4,140 @@
 # but can be easily used by any other R package
 name: Admiral Workflows
 
+---
+# Source: https://github.com/pharmaverse/admiralci
+# Common workflows designed for Admiral
+# but can be easily used by any other R package
+name: admiral CI/CD Workflows
+
 on:
   # 'workflow_dispatch' gives you the ability
   # to run this workflow on demand, anytime
   workflow_dispatch:
   # 'push' events are triggered when commits
   # are pushed to one of these branches
   push:
+    tags:
+      - "v*"
     branches:
       - main
-      - devel
-      - pre-release
-      - test
+      - patch
   # 'pull_request' events are triggered when PRs are
   # created against one of these target branches.
   pull_request:
     branches:
       - main
-      - devel
-      - pre-release
-      - test
+      - patch
   # 'release' events are triggered when...
   # you guessed it - when releases are made.
   release:
     types: [published]
-  schedule:
-    - cron: '21 13 * * 1,3,5'
-
-env:
-  # R version to use for the workflows
-  R_VERSION: "3.6"
 
 # Docs on concurrency:
 # https://docs.github.com/en/actions/using-jobs/using-concurrency
 concurrency:
   group: admiral-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
+env:
+  R_VERSION: "release"
+
 jobs:
+  get_r_version:
+    name: Get R version
+    runs-on: ubuntu-latest
+    outputs:
+      r-version: ${{ steps.get_r_version.outputs.R_VERSION }}
+    steps:
+      - name: Get R Version for Downstream Container Jobs
+        id: get_r_version
+        run: echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT
+        shell: bash
   style:
     name: Code Style
     uses: pharmaverse/admiralci/.github/workflows/style.yml@main
     if: github.event_name == 'pull_request'
+    needs: get_r_version
     with:
-      r-version: $R_VERSION
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   spellcheck:
     name: Spelling
     uses: pharmaverse/admiralci/.github/workflows/spellcheck.yml@main
     if: github.event_name == 'pull_request'
+    needs: get_r_version
     with:
-      r-version: $R_VERSION
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   readme:
     name: Render README
     uses: pharmaverse/admiralci/.github/workflows/readme-render.yml@main
     if: github.event_name == 'push'
+    needs: get_r_version
     with:
-      r-version: $R_VERSION
-      # This workflow autoformats the README.md file after
-      # it has been rendered. If you want to skip that,
-      # set the following value to 'true'
-      skip-md-formatting: false
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   validation:
     name: Validation
     uses: pharmaverse/admiralci/.github/workflows/r-pkg-validation.yml@main
     if: github.event_name == 'release'
+    needs: get_r_version
     with:
-      r-version: $R_VERSION
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   check:
     name: Check
     uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
-    if: github.event_name == 'pull_request'
     with:
-      # Control how you want the errors to manifest
-      # by supplying the 'error_on' parameter to
-      # rcmdcheck::rcmdcheck() here.
-      error-on: note
+      error-on: warning # TODO: find a way to ignore specific notes
+    if: github.event_name == 'pull_request'
   docs:
     name: Documentation
     uses: pharmaverse/admiralci/.github/workflows/pkgdown.yml@main
-    if: github.event_name == 'push'
+    if: github.event_name == 'push' || startsWith(github.ref, 'refs/tags/v')
+    needs: get_r_version
     with:
-      r-version: $R_VERSION
-      # Whether to skip multiversion docs
-      # Note that if you have multiple versions of docs,
-      # your URL links are likely to break due to path changes
-      skip-multiversion-docs: false
-      # Ref to use for the multiversion docs landing page
-      multiversion-docs-landing-page: main
+      r-version: "release"
+      skip-multiversion-docs: true
+    secrets:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
   linter:
     name: Lint
     uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main
+    needs: get_r_version
     if: github.event_name == 'pull_request'
     with:
-      r-version: $R_VERSION
-      # Set to true to lint all files each time
-      # the job is run on pull request
-      lint-all-files: false
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   links:
     name: Links
     uses: pharmaverse/admiralci/.github/workflows/links.yml@main
-    if: >
-      github.event_name == 'push' || github.event_name == 'pull_request'
+    if: github.event_name == 'pull_request'
   coverage:
     name: Code Coverage
     uses: pharmaverse/admiralci/.github/workflows/code-coverage.yml@main
     if: >
-      github.event_name == 'push' || github.event_name == 'pull_request'
+      github.event_name != 'release'
+    needs: get_r_version
     with:
-      r-version: $R_VERSION
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
       # Whether to skip code coverage badge creation
       # Setting to 'false' will require you to create
       # an orphan branch called 'badges' in your repository
       skip-coverage-badges: false
-  templates:
-    name: Check Templates
-    uses: pharmaverse/admiralci/.github/workflows/check-templates.yml@main
-    if: >
-      github.event_name == 'push' || github.event_name == 'pull_request'
-    with:
-      r-version: $R_VERSION
   man-pages:
     name: Man Pages
     uses: pharmaverse/admiralci/.github/workflows/man-pages.yml@main
     if: github.event_name == 'pull_request'
+    needs: get_r_version
     with:
-      r-version: $R_VERSION
-  cran-status:
-    name: CRAN Status
-    uses: pharmaverse/admiralci/.github/workflows/cran-status.yml@main
-    if: github.event_name == 'schedule'
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
+  templates:
+    name: Check Templates
+    uses: pharmaverse/admiralci/.github/workflows/check-templates.yml@main
+    secrets: inherit
+    if: github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch'
+    needs: get_r_version
     with:
-      # Whom should the issue be assigned to if errors are encountered
-      # in the CRAN status checks?
-      issue-assignees: ""
-      # Create an issue if one or more of the following
-      # statuses are reported on the check report.
-      status-types: "NOTE,WARNING,ERROR"
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
+  vbump:
+    name: Version Bump 🤜🤛
+    if: github.event_name == 'push'
+    uses: insightsengineering/r.pkg.template/.github/workflows/version-bump.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.PHARMAVERSE_BOT }}
diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml
@@ -242,10 +242,14 @@ jobs:
           rlang::env_binding_lock(env = pkgdown_env)
           rlang::env_lock(pkgdown_env)
           require(desc::desc_get("Package"), character.only = TRUE)
+          clean = FALSE
+          if ("${{ inputs.skip-multiversion-docs }}" == "true"){
+            clean = TRUE
+          }
           pkgdown::deploy_to_branch(
             new_process = FALSE,
             ${SUBDIR_OPTION}
-            clean = FALSE
+            clean = clean
           )
           EOF
         env:

diff --git a/.github/workflows/spellcheck.yml b/.github/workflows/spellcheck.yml
@@ -35,7 +35,7 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  roxygen:
+  spellcheck:
     name: Spellcheck
     runs-on: ubuntu-latest
     container:

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,9 +1,12 @@
 Package: admiralci
 Type: Package
-Title: ADaM in R Asset Library - CI/CD Workflows
+Title: CI/CD Workflows for Admiral
 Version: 0.0.1
 Authors@R: c(
-    person("Open", "Source", email = "[email protected]", role = c("aut", "cre")))
+    person("Dinakar", "Kulkarni", role = c("aut")),
+    person("Daphne", "Grasselly", role = c("aut", "cre"), email="[email protected]"),
+    person("Adam", "Forys", role = c("aut")),
+    person("Franciszek", "Walkowiak", role = c("aut")))
 Description: A set of common CI/CD workflows originally designed and developed for
     Admiral R package hosted in the Pharmaverse GitHub organization.
 License: Apache License (>= 2)