From 2e9ce49113cf7f3142387de175c2da7a8b1ace04 Mon Sep 17 00:00:00 2001
From: rh <raban@hellebo.de>
Date: Sat, 22 Aug 2026 10:34:52 +0200
Subject: [PATCH 1/2] Call the shared CTTIR workflows

Replaces copied R-CMD-check and test-coverage YAML with caller stubs and
adds the house lint workflow. Behaviour that comes with the shared
versions: an oldrel-3 job so the R version DESCRIPTION claims is actually
built, --as-cran, a coverage gate computed with covr and an explicit exit
rather than delegated to Codecov, and fail_ci_if_error on upload.

Coverage floor is 0 for now - this fixes the measurement, not the gate.
Lint is report-only.
---
 .github/workflows/R-CMD-check.yaml   | 49 +++++-----------------------
 .github/workflows/lint.yaml          | 16 +++++++++
 .github/workflows/test-coverage.yaml | 43 +++++-------------------
 3 files changed, 34 insertions(+), 74 deletions(-)
 create mode 100644 .github/workflows/lint.yaml

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index e3d0f1a..d586089 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -1,8 +1,10 @@
+# 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]
+    branches: [main, master]
   pull_request:
-    branches: [main]
+    branches: [main, master]
 
 name: R-CMD-check
 
@@ -10,41 +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
-
-    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
-
-      - 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
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
new file mode 100644
index 0000000..c1ccbce
--- /dev/null
+++ b/.github/workflows/lint.yaml
@@ -0,0 +1,16 @@
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: lint
+
+permissions: read-all
+
+jobs:
+  lint:
+    uses: CTTIR/.github/.github/workflows/lint.yaml@main
+    with:
+      # Report-only until this package house-linter count reaches zero.
+      blocking: false
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index a91336d..bb19507 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -1,8 +1,8 @@
 on:
   push:
-    branches: [main]
+    branches: [main, master]
   pull_request:
-    branches: [main]
+    branches: [main, master]
 
 name: test-coverage
 
@@ -10,35 +10,10 @@ permissions: read-all
 
 jobs:
   test-coverage:
-    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::covr, any::xml2
-          needs: coverage
-
-      - 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' && true || false }}
-          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

From 13c9b401ec48c58d290bbb01579f5e1f63892d37 Mon Sep 17 00:00:00 2001
From: rh <raban@hellebo.de>
Date: Sat, 22 Aug 2026 10:59:08 +0200
Subject: [PATCH 2/2] Re-run against the fixed shared workflows

CTTIR/.github now gives lint the CTTIR r-universe (several packages
Suggest sibling CTTIR packages, and pak could not solve them) and marks
oldrel-3 informational (it was failing on a 404 Bioconductor mirror for
old R, not on package code).