Updating gha

.github/workflows/check-standard.yaml

@@ -0,0 +1,47 @@
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      R_FORCE_TEST: true
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::rcmdcheck
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          args: '"--no-manual"'
+

.github/workflows/pkgdown.yaml

@@ -32,7 +32,10 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::.
+          extra-packages: |
+            any::pkgdown
+            any::corrplot
+            local::.
           needs: website
 
       - name: Build site

.github/workflows/test-coverage.yaml

@@ -12,7 +12,8 @@ jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
-      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}  # Corrected token name
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_FORCE_TEST: true
 
     steps:
       - uses: actions/checkout@v4
@@ -25,11 +26,39 @@ jobs:
         with:
           extra-packages: |
             any::covr
-            any::glmnet
-            any::pROC
-            any::survival
+            any::xml2
           needs: coverage
 
       - name: Test coverage
-        run: covr::codecov(quiet=FALSE)
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          print(cov)
+          covr::to_cobertura(cov)
         shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

tests/test.R

@@ -0,0 +1,5 @@
+if (requireNamespace("tinytest", quietly=TRUE)) {
+  if (identical(tolower(Sys.getenv("R_FORCE_TEST")), "true")) {
+    tinytest::test_package("plmmr", pattern="^[^_].*\\.[rR]$")
+  }
+}