Merge pull request #1 from pharmaverse/remove_renv

Remove renv and other sundry items

.github/pull_request_template.md

@@ -1,18 +1,18 @@
-Thank you for your Pull Request! We have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiraldev/devel/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.
+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 `main` 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, which should consider realistic data scenarios and edge cases, e.g. empty datasets, errors, boundary cases etc. - See [Unit Test Guide](https://pharmaverse.github.io/admiraldev/devel/articles/unit_test_guidance.html#tests-should-be-robust-to-cover-realistic-data-scenarios)
-- [ ] If you removed/replaced any function and/or function parameters, did you fully follow the [deprecation guidance](https://pharmaverse.github.io/admiraldev/devel/articles/programming_strategy.html#deprecation)?
-- [ ] Update to all relevant roxygen headers and examples, including keywords and families. Refer to the [categorization of functions](https://pharmaverse.github.io/admiraldev/devel/articles/programming_strategy.html#categorization-of-functions) to tag appropriate keyword/family.
+- [ ] Updated relevant unit tests or have written new unit tests, which should consider realistic data scenarios and edge cases, e.g. empty datasets, errors, boundary cases etc. - See [Unit Test Guide](https://pharmaverse.github.io/admiraldev/articles/unit_test_guidance.html#tests-should-be-robust-to-cover-realistic-data-scenarios)
+- [ ] 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, including keywords and families. Refer to the [categorization of functions](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html#categorization-of-functions) to tag appropriate keyword/family.
 - [ ] 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. 
+- [ ] Update `NEWS.md` under the header `# admiralpeds (development version)` 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 admiralpeds site `pkgdown::build_site()` and check that all affected examples are displayed correctly and that all new functions occur on the Reference 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 in the Development Section on the right hand side.
-- [ ] Address all merge conflicts and resolve appropriately 
+- [ ] Address all merge conflicts and resolve appropriately
 - [ ] Pat yourself on the back for a job well done! Much love to your accomplishment!

.github/workflows/common.yml

@@ -15,14 +15,12 @@ on:
       - "v*"
     branches:
       - main
-      - devel
       - patch
   # 'pull_request' events are triggered when PRs are
   # created against one of these target branches.
   pull_request:
     branches:
       - main
-      - devel
       - patch
   # 'release' events are triggered when...
   # you guessed it - when releases are made.
@@ -36,8 +34,8 @@ concurrency:
   cancel-in-progress: true
 
 env:
-  R_VERSION: "4.1"
-  
+  R_VERSION: "release"
+
 jobs:
   get_r_version:
     name: Get R version
@@ -80,27 +78,24 @@ jobs:
   check:
     name: Check
     uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
+    with:
+      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' || startsWith(github.ref, 'refs/tags/v')
     needs: get_r_version
     with:
-      r-version: "${{ needs.get_r_version.outputs.r-version }}"
-      # Whether to skip multiversion docs
-      # Note that if you have multiple versions of docs,
-      # your URL links are likely to break due to path changes
-      skip-multiversion-docs: false
-      latest-tag-alt-name: cran-release
-      multiversion-docs-landing-page: cran-release
-      branches-or-tags-to-list: >-
-        ^cran-release$|^main$|^v([0-9]+\\.)?([0-9]+\\.)?([0-9]+)$
+      r-version: "release"
+      skip-multiversion-docs: true
+    secrets:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
   linter:
     name: Lint
     uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main
-    if: github.event_name == 'pull_request'
     needs: get_r_version
+    if: github.event_name == 'pull_request'
     with:
       r-version: "${{ needs.get_r_version.outputs.r-version }}"
   links:
@@ -130,8 +125,13 @@ jobs:
     name: Check Templates
     uses: pharmaverse/admiralci/.github/workflows/check-templates.yml@main
     secrets: inherit
-    if: github.event.review.state == 'approved'
+    if: github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch'
     needs: get_r_version
     with:
       r-version: "${{ needs.get_r_version.outputs.r-version }}"
-      push-templates-data: true
+  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 }}

DESCRIPTION

@@ -1,7 +1,7 @@
-Package: admiraltemplate
+Package: admiralpeds
 Type: Package
 Title: ADaM in R Asset Library - Extension
-Version: 0.0.3
+Version: 0.0.1
 Authors@R: c(
     person("Open", "Source", email = "admiraltemplate@pharmaverse.com", role = c("aut", "cre")))
 Description: A toolbox for programming Clinical Data Standards Interchange Consortium
@@ -16,12 +16,12 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
-Depends: R (>= 3.5)
+RoxygenNote: 7.3.1
+Depends: R (>= 4.0)
 Imports:
-    admiral (>= 0.10.0),
-    admiraldev (>= 0.5.0),
-    dplyr (>= 0.8.4),
+    admiral (>= 1.0.0),
+    admiraldev (>= 1.0.0),
+    dplyr (>= 1.0.5),
     hms (>= 0.5.3),
     lifecycle (>= 0.1.0),
     lubridate (>= 1.7.4),
@@ -32,21 +32,16 @@ Imports:
     tidyr (>= 1.0.2),
     tidyselect (>= 1.1.0)
 Suggests:
-    pharmaversesdtm,
-    covr,
-    devtools,
     diffdf,
     DT,
+    htmltools,
     knitr,
-    lintr,
     methods,
-    miniUI,
-    pkgdown,
+    pharmaversesdtm (>= 0.2.0),
+    reactable,
+    readxl,
     rmarkdown,
-    roxygen2,
-    spelling,
     testthat (>= 3.0.0),
-    tibble,
-    usethis,
+    tibble
 VignetteBuilder: knitr
 Config/testthat/edition: 3

_pkgdown.yml

@@ -1,4 +1,4 @@
-url: https://pharmaverse.github.io/admiraltemplate
+url: https://pharmaverse.github.io/admiralpeds
 
 template:
   bootstrap: 5
@@ -14,6 +14,9 @@ news:
   cran_dates: true
 reference:
 
+development:
+  mode: auto
+
 - title: Derivations for Adding Variables
 - subtitle: ADXX-specific
   desc: Derivation Functions helpful for building the ADXX dataset