Reduce dependencies on lozen etc

.github/workflows/build-pkgdown.yml

@@ -3,16 +3,6 @@
 on:
   workflow_call:
     inputs:
-      build_testdown:
-        description: 'Generate testdown report?'
-        required: false
-        type: boolean
-        default: false
-      build_code_coverage:
-        description: 'Generate code coverage report?'
-        required: false
-        type: boolean
-        default: false
       is_main_push:
         type: boolean
         default: false
@@ -28,7 +18,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
@@ -40,44 +30,21 @@ jobs:
         with:
           extra-packages: any::pkgdown, local::.
           needs: website
+
       - name: Build pkgdown site
-        env:
-          INPUT_TESTDOWN: ${{ inputs.build_testdown }}
-          INPUT_CODE_COVERAGE: ${{ inputs.build_code_coverage }}
-          R_KEEP_PKG_SOURCE: "yes"
-          TESTTHAT_PROGRESS: "plain"
-          R_BACKTRACE_ON_ERROR: "full"
         run: |
-          reports_to_build <- c()
-          if (Sys.getenv("INPUT_TESTDOWN") == 'true') {
-            reports_to_build <- c(reports_to_build, "testdown")
-          }
-          if (Sys.getenv("INPUT_CODE_COVERAGE") == 'true') {
-            reports_to_build <- c(reports_to_build, "coverage")
-          }
-          if (length(reports_to_build) > 0) {
-            lozen::build_pkgdown_with_reports(
-              pkg = ".",
-              pkgdown_path = "docs",
-              assets_path = "pkgdown/assets",
-              reports = reports_to_build
-            )
-          } else {
-            pkgdown::build_site(
-              override = list(destination = "docs")
-            )
-          }
+          pkgdown::build_site(override = list(destination = "docs"))
         shell: Rscript {0}
 
       - name: Save pkgdown output
         uses: actions/upload-artifact@v7
         with:
-          name: pkgdown-site-with-reports
+          name: pkgdown-site
           path: docs/
 
       - name: Deploy package
         if: github.event_name == 'push' && github.ref == 'refs/heads/main'
         uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./docs
+          publish_dir: ./docs

.github/workflows/call-calc_coverage.yml

@@ -1,6 +1,5 @@
-# Runs covr::codecov() to calculate code coverage.
+# Runs covr::package_coverage() to calculate code coverage and uploads to Codecov.
 name: call-calc_coverage
-
 on:
   pull_request:
     branches:
@@ -15,22 +14,44 @@ on:
       - 'LICENSE'
       - 'man'
       - 'README.md'
-  push:
-    branches:
-      - dev
-    paths-ignore:
-      - .devcontainer
-      - .github
-      - '.gitignore'
-      - '.Rbuildignore'
-      - 'CONTRIBUTING.md'
-      - 'LICENSE'
-      - 'man'
-      - 'README.md'
   workflow_dispatch:
-
+# Cancel active CI runs for a PR before starting another run
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
-  call-workflow:
-    uses: nmfs-ost/ghactions4r/.github/workflows/calc-coverage.yml@main
-    secrets:
-      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+  calc-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v5
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Calculate coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(
+              normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"),
+              "package"
+            )
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          fail_ci_if_error: true

.github/workflows/call-update-pkgdown.yml

@@ -17,6 +17,4 @@ jobs:
   call-workflow:
     uses: ./.github/workflows/build-pkgdown.yml
     with:
-      build_testdown: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
-      build_code_coverage: false
-      is_main_push: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+      is_main_push: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}

DESCRIPTION

@@ -34,17 +34,12 @@ Imports:
     tidyr
 Suggests:
     knitr,
-    lozen,
     purrr,
     rmarkdown,
-    testdown,
     testthat (>= 3.0.0),
     utils
 VignetteBuilder:
     knitr
-Remotes:
-    github::ThinkR-open/lozen,
-    github::ThinkR-open/testdown
 Config/roxygen2/version: 8.0.0
 Config/testthat/edition: 3
 Config/testthat/parallel: false

vignettes/a2_meta.Rmd

@@ -66,6 +66,8 @@ filtered_traits <- dplyr::filter(
   Number > 0,
   trait %in% c("LengthMax")
 )
+
+filtered_traits$study_id <- seq_len(nrow(filtered_traits))
 ```
 
 ### Variance weighting