Merge pull request #69 from pharmaverse/refactor_rversion

Refactor rversion

.github/workflows/common.yml

@@ -35,31 +35,48 @@ 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: "${{ needs.get_r_version.outputs.r-version }}"
   check:
     name: Check
     uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
@@ -68,8 +85,9 @@ jobs:
     name: Documentation
     uses: pharmaverse/admiralci/.github/workflows/pkgdown.yml@main
     if: github.event_name == 'push' || startsWith(github.ref, 'refs/tags/v')
+    needs: get_r_version
     with:
-      r-version: "4.1"
+      r-version: "${{ 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
@@ -82,8 +100,9 @@ jobs:
     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: "${{ needs.get_r_version.outputs.r-version }}"
   links:
     name: Links
     uses: pharmaverse/admiralci/.github/workflows/links.yml@main
@@ -93,8 +112,9 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/code-coverage.yml@main
     if: >
       github.event_name != 'release'
+    needs: get_r_version
     with:
-      r-version: "4.1"
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
       # Whether to skip code coverage badge creation
       # Setting to 'false' will require you to create
       # an orphan branch called 'badges' in your repository
@@ -103,5 +123,15 @@ jobs:
     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: "${{ needs.get_r_version.outputs.r-version }}"
+  templates:
+    name: Check Templates
+    uses: pharmaverse/admiralci/.github/workflows/check-templates.yml@main
+    secrets: inherit
+    if: github.event.review.state == 'approved'
+    needs: get_r_version
+    with:
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
+      push-templates-data: true

NAMESPACE

@@ -8,7 +8,6 @@ importFrom(admiraldev,assert_data_frame)
 importFrom(admiraldev,assert_filter_cond)
 importFrom(admiraldev,assert_logical_scalar)
 importFrom(admiraldev,assert_numeric_vector)
-importFrom(admiraldev,assert_order_vars)
 importFrom(admiraldev,assert_symbol)
 importFrom(admiraldev,assert_vars)
 importFrom(dplyr,arrange)

R/admiraltemplate-package.R

@@ -27,5 +27,5 @@
 #' @importFrom admiral derive_vars_dy
 #' @importFrom admiraldev assert_logical_scalar assert_character_vector assert_vars
 #'             assert_data_frame assert_character_scalar assert_numeric_vector assert_filter_cond
-#'             assert_symbol assert_order_vars
+#'             assert_symbol
 "_PACKAGE"

README.Rmd

@@ -16,7 +16,7 @@ dyn_link <- function(text,
                      base_url,
                      relative_url = "",
                      # Change to TRUE when admiral adopts multiversion docs
-                     is_multiversion = TRUE,
+                     is_multiversion = FALSE,
                      multiversion_default_ref = "main") {
   url <- paste(base_url, relative_url, sep = "/")
   if (is_multiversion) {

README.md

@@ -27,12 +27,12 @@ To be included as an `{admiral}` package extension we expect developers
 to adhere to the following standards:
 
 -   [Code of
-    Conduct](https://pharmaverse.github.io/admiral/main/CODE_OF_CONDUCT.html)
--   [Manifesto](https://pharmaverse.github.io/admiral/main/index.html?q=manifest#admiral-manifesto)
+    Conduct](https://pharmaverse.github.io/admiral/CODE_OF_CONDUCT.html)
+-   [Manifesto](https://pharmaverse.github.io/admiral/index.html?q=manifest#admiral-manifesto)
 -   [Programming
-    Strategy](https://pharmaverse.github.io/admiraldev/main/articles/programming_strategy.html)
+    Strategy](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html)
 -   [Development
-    Process](https://pharmaverse.github.io/admiraldev/main/articles/development_process.html)
+    Process](https://pharmaverse.github.io/admiraldev/articles/development_process.html)
 -   Follow consistent workflow checks
 -   A CRAN Release means 90% or greater test coverage
 
@@ -116,7 +116,7 @@ strictly be followed in this sequence.*
     they should join using this
     [link](https://join.slack.com/t/pharmaverse/shared_invite/zt-yv5atkr4-Np2ytJ6W_QKz_4Olo7Jo9A)).
     All should read up on the admiral
-    [site](https://pharmaverse.github.io/admiral/main/), especially the
+    [site](https://pharmaverse.github.io/admiral/), especially the
     developer guides which all need to be followed for package
     extensions.
 6.  Optionally it can be useful to host a kick-off meeting to decide how
@@ -183,10 +183,10 @@ strictly be followed in this sequence.*
     a common need for other TAs and if so consider instead raising an
     issue to `{admiral}` core. When designing new functions always try
     to stay aligned with the [programming
-    strategy.](https://pharmaverse.github.io/admiraldev/main/articles/programming_strategy.html).
+    strategy.](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html).
 17. Start development of your foundational first release 0.1.0. Follow a
     consistent [development
-    process](https://pharmaverse.github.io/admiraldev/main/articles/development_process.html)
+    process](https://pharmaverse.github.io/admiraldev/articles/development_process.html)
     to `{admiral}`.
 18. Line up testers from your companies and others and set expectations
     around when you believe a stable version would be available for user
@@ -197,7 +197,7 @@ strictly be followed in this sequence.*
     pharmaverse council rep.
 20. Raise an `{admiral}` repo issue to ensure your package extension
     site is linked from the core `{admiral}` site
-    [here.](https://pharmaverse.github.io/admiral/main/index.html#types-of-packages)
+    [here.](https://pharmaverse.github.io/admiral/index.html#types-of-packages)
 21. It is important that the `{admiral}` family of packages keep to a
     similar release schedule and cadence, in order to ease adoption by
     our users and to give clear expectations. The `{admiral}` core
@@ -215,7 +215,7 @@ strictly be followed in this sequence.*
 23. Plan any future further enhancements and make issues. When your team
     feels ready you can open up to development contributions for these
     from the wider community - see [this
-    page.](https://pharmaverse.github.io/admiral/main/CONTRIBUTING.html#type-1-contribution-with-code).
+    page.](https://pharmaverse.github.io/admiral/CONTRIBUTING.html#type-1-contribution-with-code).
     Please use the *“good first issue”* (ideal for new starters) &
     *“help wanted”* (ideal for more experienced contributors) issue
     labels.
@@ -239,7 +239,7 @@ contact us via slack if any issues arise.
         extension package is synced with other admiral packages
 6.  Update/Remove the following files to use your extension name:
     -   `DESCRIPTION` File - Name, Authors
-    -   `admiralext.Rproj`
+    -   `admiraltemplate.Rproj`
     -   `testthat.R`
     -   `News.md`
 7.  Run `devtools::load_all()` and resolve issues
@@ -248,11 +248,11 @@ contact us via slack if any issues arise.
     -   Reach out to slack for help with creating a hex sticker/logo to
         replace pharmaverse logo
 10. *Recommended*: Review the [documentation on the CI/CD
-    workflows](https://pharmaverse.github.io/admiralci/main/#what-these-workflows-do)
+    workflows](https://pharmaverse.github.io/admiralci/#what-these-workflows-do)
     for information about how to reuse the workflows from this template.
     Pay special attention to the section on creating the `badges` orphan
     branch in [this
-    section](https://pharmaverse.github.io/admiralci/main/#code-coverage).
+    section](https://pharmaverse.github.io/admiralci/#code-coverage).
 11. Test out a dummy branch and do a Pull Request to ensure CI/CD works.
 12. Any clearly dummy files like `R/my_first_fcn.R` or
     `inst/templates/ad_adxx.R` can be updated or removed.