From bac8bd83042fa38bd86db39690efc15c4760c2bb Mon Sep 17 00:00:00 2001
From: Levi Waldron <lwaldron.research@gmail.com>
Date: Mon, 27 Jul 2026 12:05:12 +0200
Subject: [PATCH 1/4] ci: add GitHub Actions workflow and update .Rbuildignore

---
 .Rbuildignore            |  1 +
 .github/workflows/ci.yml | 21 +++++++++++++++++++++
 2 files changed, 22 insertions(+)
 create mode 100644 .Rbuildignore
 create mode 100644 .github/workflows/ci.yml

diff --git a/.Rbuildignore b/.Rbuildignore
new file mode 100644
index 0000000..bb0224d
--- /dev/null
+++ b/.Rbuildignore
@@ -0,0 +1 @@
+.github/
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 0000000..69ab52c
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,21 @@
+name: CI
+
+on:
+  push:
+    branches: [ devel, main, master, RELEASE_* ]
+  pull_request:
+    branches: [ devel, main, master, RELEASE_* ]
+
+jobs:
+  bioccheck:
+    # Required only if you set enable_pkgdown: true
+    # permissions:
+    #   pages: write
+    #   id-token: write
+    uses: bioconductor/workflows/.github/workflows/bioccheck.yml@main
+    with:
+      error_on: 'warning'
+      enable_pkgdown: false
+    # Required only if you want test coverage via Codecov
+    # secrets:
+    #   CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
\ No newline at end of file

From c38090d09e9a1ee2dd2b5813bdf3f3f0483bb444 Mon Sep 17 00:00:00 2001
From: Levi Waldron <lwaldron.research@gmail.com>
Date: Mon, 27 Jul 2026 06:12:09 -0400
Subject: [PATCH 2/4] escape the `.` in .github in .Rbuildignore

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
---
 .Rbuildignore | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index bb0224d..c503c4f 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1 +1 @@
-.github/
+^\.github$

From 451c69d45ead39244f8dd081c5c3687b587bb153 Mon Sep 17 00:00:00 2001
From: Levi Waldron <lwaldron.research@gmail.com>
Date: Mon, 27 Jul 2026 06:25:19 -0400
Subject: [PATCH 3/4] Rename CI workflow to Bioconductor CI

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 69ab52c..736dcc9 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,4 +1,4 @@
-name: CI
+name: Bioconductor CI
 
 on:
   push:
@@ -18,4 +18,4 @@ jobs:
       enable_pkgdown: false
     # Required only if you want test coverage via Codecov
     # secrets:
-    #   CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
\ No newline at end of file
+    #   CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

From cbd20bfa5ebcd761352b2f091fe024e2582c099f Mon Sep 17 00:00:00 2001
From: Levi Waldron <lwaldron.research@gmail.com>
Date: Mon, 27 Jul 2026 06:40:11 -0400
Subject: [PATCH 4/4] Change error_on from 'warning' to 'error' in CI

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 736dcc9..778d014 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -14,7 +14,7 @@ jobs:
     #   id-token: write
     uses: bioconductor/workflows/.github/workflows/bioccheck.yml@main
     with:
-      error_on: 'warning'
+      error_on: 'error'
       enable_pkgdown: false
     # Required only if you want test coverage via Codecov
     # secrets: