Call the shared CTTIR workflows

.github/workflows/R-CMD-check.yaml

@@ -1,3 +1,5 @@
+# Calls the shared CTTIR workflow. Do not add steps here - change the
+# shared one at CTTIR/.github so every package moves together.
 on:
   push:
     branches: [main, master]
@@ -10,66 +12,8 @@ permissions: read-all
 
 jobs:
   R-CMD-check:
-    runs-on: ${{ matrix.config.os }}
-
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
-    strategy:
-      fail-fast: false
-      matrix:
-        config:
-          - {os: macOS-latest,   r: 'release'}
-          - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,  r: 'release'}
-          - {os: ubuntu-latest,  r: 'oldrel-1'}
-
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      R_KEEP_PKG_SOURCE: yes
-      _R_CHECK_FORCE_SUGGESTS_: false
-
-    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: ${{ matrix.config.http-user-agent }}
-          use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::rcmdcheck
-          needs: check
-
-      - name: Install Bioconductor Suggests (optional)
-        run: |
-          if (!requireNamespace("BiocManager", quietly = TRUE))
-            install.packages("BiocManager")
-          bioc_pkgs <- c("DESeq2", "edgeR", "limma", "ShortRead", "Biostrings",
-                         "Rsamtools", "GenomicAlignments", "GenomicFeatures",
-                         "GenomicRanges", "SummarizedExperiment", "Biobase",
-                         "ComplexHeatmap")
-          # Only install packages that are actually in Suggests
-          desc_suggests <- strsplit(read.dcf("DESCRIPTION")[, "Suggests"], ",\\s*")[[1]]
-          desc_suggests <- trimws(gsub("\\s*\\(.*\\)", "", desc_suggests))
-          to_install <- intersect(bioc_pkgs, desc_suggests)
-          if (length(to_install) > 0) {
-            message("Installing Bioconductor packages: ", paste(to_install, collapse = ", "))
-            tryCatch(
-              BiocManager::install(to_install, update = FALSE),
-              error = function(e) message("Bioconductor install skipped: ", e$message)
-            )
-          } else {
-            message("No Bioconductor Suggests found — skipping.")
-          }
-        shell: Rscript {0}
-        continue-on-error: true
-
-      - uses: r-lib/actions/check-r-package@v2
-        with:
-          upload-snapshots: true
-          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+    uses: CTTIR/.github/.github/workflows/R-CMD-check.yaml@main
+    with:
+      # Suggests Bioconductor packages that pak cannot solve without the
+      # Bioconductor repository declared.
+      bioc-repository: true

.github/workflows/lint.yaml

@@ -10,31 +10,7 @@ permissions: read-all
 
 jobs:
   lint:
-    runs-on: ubuntu-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::lintr, any::goodpractice
-          needs: lint
-
-      - name: Lint
-        run: lintr::lint_package()
-        shell: Rscript {0}
-        env:
-          LINTR_ERROR_ON_LINT: true
-
-      - name: Good practice (informational)
-        run: |
-          gp <- goodpractice::gp()
-          print(gp)
-        shell: Rscript {0}
-        continue-on-error: true
+    uses: CTTIR/.github/.github/workflows/lint.yaml@main
+    with:
+      # Report-only until this package house-linter count reaches zero.
+      blocking: false

.github/workflows/test-coverage.yaml

@@ -10,59 +10,10 @@ permissions: read-all
 
 jobs:
   test-coverage:
-    runs-on: ubuntu-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      _R_CHECK_FORCE_SUGGESTS_: false
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::covr, any::xml2
-          needs: coverage
-
-      - name: Install Bioconductor Suggests (optional)
-        run: |
-          if (!requireNamespace("BiocManager", quietly = TRUE))
-            install.packages("BiocManager")
-          bioc_pkgs <- c("DESeq2", "edgeR", "limma", "ShortRead", "Biostrings",
-                         "Rsamtools", "GenomicAlignments", "GenomicFeatures",
-                         "GenomicRanges", "SummarizedExperiment", "Biobase",
-                         "ComplexHeatmap")
-          desc_suggests <- strsplit(read.dcf("DESCRIPTION")[, "Suggests"], ",\\s*")[[1]]
-          desc_suggests <- trimws(gsub("\\s*\\(.*\\)", "", desc_suggests))
-          to_install <- intersect(bioc_pkgs, desc_suggests)
-          if (length(to_install) > 0) {
-            message("Installing Bioconductor packages: ", paste(to_install, collapse = ", "))
-            tryCatch(
-              BiocManager::install(to_install, update = FALSE),
-              error = function(e) message("Bioconductor install skipped: ", e$message)
-            )
-          } else {
-            message("No Bioconductor Suggests found — skipping.")
-          }
-        shell: Rscript {0}
-        continue-on-error: true
-
-      - name: Test 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}
-
-      - uses: codecov/codecov-action@v4
-        with:
-          fail_ci_if_error: ${{ github.event_name != 'pull_request' }}
-          file: ./cobertura.xml
-          plugin: noop
-          token: ${{ secrets.CODECOV_TOKEN }}
+    uses: CTTIR/.github/.github/workflows/test-coverage.yaml@main
+    with:
+      # Report-only for now. The shared workflow computes coverage with covr
+      # and an explicit exit rather than delegating the gate to Codecov;
+      # set a real floor once this package is re-baselined.
+      floor: 0
+    secrets: inherit