Add staged_dependencies for admiraldev (#26)

* Add staged_dependencies for admiraldev

* Add new line

* Fix admiraldev links.

* Fix admiraldev articles links.

* Remove R 4.1 a it causing dependencies issues. We want to use purrr >= 1.0.0

* Test latest lintr

* Test lintr with install package locally

* Add install pacakge variable for lintr

* Skip multi version pkgdown workflow.

* R build ignore staged_dependencies.yaml

.Rbuildignore

@@ -12,3 +12,4 @@
 ^LICENSE\.md$
 ^\.lintr$
 ^data-raw$
+^staged_dependencies.yaml$

.Rprofile

@@ -27,7 +27,7 @@ Sys.setenv("RENV_CONFIG_AUTO_SNAPSHOT" = FALSE)
 if (!Sys.getenv("RENV_AUTOLOADER_ENABLED") %in% c("false", "FALSE")) {
   .renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".")
   if (!file.exists("./renv/profile")) {
-    if (.renv_profile %in% c("4.1", "4.2", "4.3")) {
+    if (.renv_profile %in% c("4.2", "4.3")) {
       message("Set renv profile to `", .renv_profile, "`")
       Sys.setenv("RENV_PROFILE" = .renv_profile)
     } else {

.github/CONTRIBUTING.md

@@ -3,7 +3,7 @@
 This outlines how to propose a change to the aok package. For more detailed info
 about contributing to {oak}, and other [pharmaverse
 packages](https://pharmaverse.org/), please see the [development process
-guide](https://pharmaverse.github.io/admiraldev/main/articles/development_process.html)
+guide](https://pharmaverse.github.io/admiraldev/articles/development_process.html)
 as well as other Developer Guides in the Articles section of the [{admiral}
 website](https://pharmaverse.github.io/admiral/cran-release/index.html)
 
@@ -23,7 +23,7 @@ feedback. Since we are not a 100% fully resourced software development team it
 might be that some issues will take longer to respond to depending on the amount
 of overall issues.
 
- * Familiarize yourself with our [programming strategy](https://pharmaverse.github.io/admiraldev/main/articles/programming_strategy.html), guidance for [GitHub usage](https://pharmaverse.github.io/admiraldev/main/articles/git_usage.html) and [unit testing](https://pharmaverse.github.io/admiraldev/main/articles/unit_test_guidance.html).
+ * Familiarize yourself with our [programming strategy](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html), guidance for [GitHub usage](https://pharmaverse.github.io/admiraldev/articles/git_usage.html) and [unit testing](https://pharmaverse.github.io/admiraldev/articles/unit_test_guidance.html).
 
  * All newly [created issues](https://github.com/pharmaverse/oak/issues) will be
 reviewed within the next backlog meeting and the creator will receive an

.github/pull_request_template.md

@@ -1,6 +1,6 @@
 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)
+Guide](https://pharmaverse.github.io/admiraldev/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 oak codebase remains robust and consistent.
@@ -18,13 +18,13 @@ Request Title (Use Edit button in top-right if you need to update)
 - [ ] 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)
+[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/devel/articles/programming_strategy.html#deprecation)?
+[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/devel/articles/programming_strategy.html#categorization-of-functions) to tag appropriate keyword/family.
+[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

.github/workflows/common.yml

@@ -71,17 +71,15 @@ jobs:
       # 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]+)$
+      skip-multiversion-docs: true
   linter:
     name: Lint
-    uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main
+    uses: pharmaverse/admiralci/.github/workflows/lintr.yml@lintr-latest-cran
     if: github.event_name == 'pull_request'
     with:
       r-version: "4.3"
+      latest-lintr: "true"
+      install-package: "true"
   links:
     name: Links
     uses: pharmaverse/admiralci/.github/workflows/links.yml@main

.github/workflows/r-renv-lock.yml

@@ -22,7 +22,6 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: ubuntu-20.04, r: '4.1', repos: 'https://packagemanager.posit.co/cran/2022-03-10/'}
           - {os: ubuntu-20.04, r: '4.2', repos: 'https://packagemanager.posit.co/cran/2023-03-15/'}
           - {os: ubuntu-20.04, r: '4.3', repos: 'https://packagemanager.posit.co/cran/2023-04-20/'}
 

DESCRIPTION

@@ -19,11 +19,11 @@ Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
-Depends: R (>= 4.1)
+Depends: R (>= 4.2)
 Imports: 
     admiraldev,
-    dplyr,
-    purrr,
+    dplyr (>= 1.0.0),
+    purrr (>= 1.0.0),
     rlang (>= 1.0.0),
     stringr,
     tibble