Merge branch 'main' into automated-renv-lock-propagation@devel

.Rbuildignore

@@ -33,3 +33,4 @@
 ^admiralvaccine.*\.tar\.gz$
 ^admiralvaccine.*\.tgz$
 ^\.devcontainer$
+^doc$

.github/ISSUE_TEMPLATE/05_onboard.yml

@@ -18,7 +18,7 @@ body:
         - label: Given a tour of Github from a Core member
         - label: Understand how to Create Issues and do a Pull Request
         - label: Understand the Programming Strategy
-        - label: Read and understand [Developer Guides Articles](https://pharmaverse.github.io/admiral/cran-release/index.html)
+        - label: Read and understand [Developer Guides Articles](https://pharmaverse.github.io/admiral/index.html)
         - label: Invited to all relevant meetings - Stand Ups, Retrospective, Sprint Planning, Question/Comments, Backlog, Community Meeting
         - label: Given access to Box and relevant documents
         - label: Given write access to Github Repository
@@ -33,7 +33,7 @@ body:
         - label: Given a tour of Github from a Core member
         - label: Understand how to Create Issues and do a Pull Request
         - label: Understand the Programming Strategy
-        - label: Read and understand [Developer Guides Articles](https://pharmaverse.github.io/admiral/cran-release/index.html)
+        - label: Read and understand [Developer Guides Articles](https://pharmaverse.github.io/admiral/index.html)
         - label: Invited to all relevant meetings - Question/Comments, Community Meeting
         - label: Given write access to Github Repository
         - label: Slack channel invites to admiral

.github/pull_request_template.md

@@ -1,16 +1,16 @@
-Thank you for your Pull Request! We have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiraldev/main/articles/development_process.html) to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the admiral codebase remains robust and consistent.
+Thank you for your Pull Request! We have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiral/CONTRIBUTING.html#detailed-development-process) to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the admiral codebase remains robust and consistent.
 
 Please check off each taskbox as an acknowledgment that you completed the task or check off that it is not relevant to your Pull Request. This checklist is part of the Github Action workflows and the Pull Request will not be merged into the `devel` branch until you have checked off each task.
 
 - [ ] Place Closes #<insert_issue_number> into the beginning of your Pull Request Title (Use Edit button in top-right if you need to update)
 - [ ] Code is formatted according to the [tidyverse style guide](https://style.tidyverse.org/). Run `styler::style_file()` to style R and Rmd files
-- [ ] Updated relevant unit tests or have written new unit tests - See [Unit Test Guide](https://pharmaverse.github.io/admiraldev/main/articles/unit_test_guidance.html#writing-unit-tests-in-admiral)
-- [ ] If you removed/replaced any function and/or function parameters, did you fully follow the [deprecation guidance](https://pharmaverse.github.io/admiraldev/main/articles/programming_strategy.html#deprecation)?
+- [ ] Updated relevant unit tests or have written new unit tests - See [Unit Test Guide](https://pharmaverse.github.io/admiraldev/articles/unit_test_guidance.html#writing-unit-tests-in-admiral)
+- [ ] If you removed/replaced any function and/or function parameters, did you fully follow the [deprecation guidance](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html#deprecation)?
 - [ ] Update to all relevant roxygen headers and examples.
 - [ ] Run `devtools::document()` so all `.Rd` files in the `man` folder and the `NAMESPACE` file in the project root are updated appropriately
 - [ ] Address any updates needed for vignettes and/or templates
 - [ ] Update `NEWS.md` if the changes pertain to a user-facing function (i.e. it has an `@export` tag) or documentation aimed at users (rather than developers)
-- [ ] Build admiral site `pkgdown::build_site()` and check that all affected examples are displayed correctly and that all new functions occur on the "[Reference](https://pharmaverse.github.io/admiral/cran-release/reference/index.html)" page.
+- [ ] Build admiral site `pkgdown::build_site()` and check that all affected examples are displayed correctly and that all new functions occur on the "[Reference](https://pharmaverse.github.io/admiral/reference/index.html)" page.
 - [ ] Address or fix all lintr warnings and errors - `lintr::lint_package()`
 - [ ] Run `R CMD check` locally and address all errors and warnings - `devtools::check()`
 - [ ] Link the issue so that it closes after successful merging.

.github/workflows/common.yml

@@ -13,77 +13,92 @@ on:
   push:
     branches:
       - main
-      - devel
       - pre-release
       - test
   # 'pull_request' events are triggered when PRs are
   # created against one of these target branches.
   pull_request:
     branches:
       - main
-      - devel
       - pre-release
       - test
   # 'release' events are triggered when...
   # you guessed it - when releases are made.
   release:
     types: [published]
 
-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: "4.1"
+
 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" >> $GITHUB_OUTPUT
+        shell: bash
   style:
     name: Code Style
     uses: pharmaverse/admiralci/.github/workflows/style.yml@main
     if: github.event_name == 'pull_request'
+    needs: get_r_version
     with:
-      r-version: "4.1"
+      r-version: "${{ 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: "4.1"
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   readme:
     name: Render README
     uses: pharmaverse/admiralci/.github/workflows/readme-render.yml@main
     if: github.event_name == 'push'
+    needs: get_r_version
     with:
-      r-version: "4.1"
+      r-version: "${{ 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: "4.1"
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   check:
     name: Check
     uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
     if: github.event_name == 'pull_request'
+    with:
+      error-on: warning # TODO: find a way to ignore specific notes
   docs:
     name: Documentation
     uses: pharmaverse/admiralci/.github/workflows/pkgdown.yml@main
     if: github.event_name == 'push'
+    needs: get_r_version
     with:
-      r-version: "4.1"
+      r-version: "${{ needs.get_r_version.outputs.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
+      skip-multiversion-docs: true
   linter:
     name: Lint
     uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main
     if: github.event_name == 'pull_request'
+    needs: get_r_version
     with:
-      r-version: "4.1"
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   links:
     name: Links
     uses: pharmaverse/admiralci/.github/workflows/links.yml@main
@@ -94,8 +109,9 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/code-coverage.yml@main
     if: >
       github.event_name == 'push' || github.event_name == 'pull_request'
+    needs: get_r_version
     with:
-      r-version: "4.1"
+      r-version: "${{ 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
@@ -105,11 +121,13 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/check-templates.yml@main
     if: >
       github.event_name == 'push' || github.event_name == 'pull_request'
+    needs: get_r_version
     with:
-      r-version: "4.1"
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   man-pages:
     name: Man Pages
     uses: pharmaverse/admiralci/.github/workflows/man-pages.yml@main
     if: github.event_name == 'pull_request'
+    needs: get_r_version
     with:
-      r-version: "4.1"
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"

.gitignore

@@ -1,56 +1,44 @@
 # History files
 .Rhistory
 .Rapp.history
-
 # Session Data files
 .RData
-
 # User-specific files
 .Ruserdata
-
 # 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/*.html
 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
-
 # Web Documentation files
 /docs/*
 !/docs/pkgdown.yml
-
 # R Environment Variables
 .Renviron
 admiralext.Rcheck/
 admiralext*.tar.gz
 admiralext*.tgz
-
 # MacOS
 .DS_Store
-
 inst/doc
 admiralvaccine.Rcheck/
 admiralvaccine*.tar.gz
 admiralvaccine*.tgz
-
 .Rproj.user
+/doc/
+/Meta/
+docs

DESCRIPTION

@@ -4,9 +4,9 @@ Title: Vaccine Extension Package for ADaM in 'R' Asset Library
 Version: 0.1.0
 Authors@R: c(
     person("Sukalpo", "Saha", email = "[email protected]", role = c("aut", "cre")),
-    person("Vikram", "S", email = "vikram.s@pfizer.com", role = "aut"),
+    person("Arjun", "Rubalingam", email = "arjun.rubalingam@pfizer.com", role = "aut"),
     person("Ben", "Straub", email = "[email protected]", role = "aut"),
-    person("Arjun", "Rubalingam", role = "aut"),
+    person("Vikram", "S", role = "aut"),
     person("Dhivya", "Kanagaraj", role = "aut"),
     person("Federico", "Baratin", role = "aut"),
     person("Yamini", "Purna Bollu", role = "aut"),
@@ -18,6 +18,7 @@ Authors@R: c(
     person("Ankur", "Jindal", role = "ctb"),
     person("Jayashree", "V", role = "ctb"),
     person("Jagadish", "Katam", role = "ctb"),
+    person("Lee", "Armishaw", role = "ctb"),
     person("Andrea", "Pammolli", role = "ctb"),
     person("Daniele", "Bottigliengo", role = "ctb"),
     person("Ranya", "Ben Hsain", role = "ctb"),
@@ -49,8 +50,8 @@ BugReports: https://github.com/pharmaverse/admiralvaccine/issues/
 Depends: 
     R (>= 3.5)
 Imports:
-    admiral (>= 0.10.2),
-    admiraldev (>= 0.4.0),
+    admiral (>= 1.0.0),
+    admiraldev (>= 1.0.0),
     assertthat (>= 0.2.1),
     dplyr (>= 0.8.4),
     hms (>= 0.5.3),
@@ -64,7 +65,6 @@ Imports:
     tidyr (>= 1.0.2),
     tidyselect (>= 1.0.0)
 Suggests:
-    admiral.test,
     covr,
     devtools,
     diffdf,
@@ -73,6 +73,7 @@ Suggests:
     lintr,
     methods,
     miniUI,
+    pharmaversesdtm,
     pkgdown,
     rmarkdown,
     roxygen2,