From a04ec1b9c24555d96d0ff9094b64d00c618a2cd8 Mon Sep 17 00:00:00 2001
From: bschilder <brian_schilder@alumni.brown.edu>
Date: Thu, 31 Aug 2023 13:42:42 +0100
Subject: [PATCH 1/2] Add rworkflows

---
 .github/workflows/rworkflows.yml | 57 ++++++++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 .github/workflows/rworkflows.yml

diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml
new file mode 100644
index 000000000..5815f4dd8
--- /dev/null
+++ b/.github/workflows/rworkflows.yml
@@ -0,0 +1,57 @@
+name: rworkflows
+'on':
+  push:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+  pull_request:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+jobs:
+  rworkflows:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    strategy:
+      fail-fast: ${{ false }}
+      matrix:
+        config:
+        - os: ubuntu-latest
+          bioc: devel
+          r: auto
+          cont: bioconductor/bioconductor_docker:devel
+          rspm: https://packagemanager.rstudio.com/cran/__linux__/focal/release
+        - os: macOS-latest
+          bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+        - os: windows-latest
+          bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+    steps:
+    - uses: neurogenomics/rworkflows@master
+      with:
+        run_bioccheck: ${{ false }}
+        run_rcmdcheck: ${{ true }}
+        as_cran: ${{ true }}
+        run_vignettes: ${{ true }}
+        has_testthat: ${{ true }}
+        run_covr: ${{ true }}
+        run_pkgdown: ${{ true }}
+        has_runit: ${{ false }}
+        has_latex: ${{ false }}
+        GITHUB_TOKEN: ${{ secrets.PAT_GITHUB }}
+        run_docker: ${{ true }}
+        docker_user: mydockeruser
+        docker_org: mydockerorg
+        DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
+        runner_os: ${{ runner.os }}
+        cache_version: cache-v1

From dabc39d9ac30f8b32fb39b96611dabc46e70cb8c Mon Sep 17 00:00:00 2001
From: bschilder <brian_schilder@alumni.brown.edu>
Date: Fri, 1 Sep 2023 20:18:15 +0100
Subject: [PATCH 2/2] fix rworkflows token

---
 .github/workflows/rworkflows.yml | 8 +++++---
 README.md                        | 1 +
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml
index 5815f4dd8..d80ce0cd6 100644
--- a/.github/workflows/rworkflows.yml
+++ b/.github/workflows/rworkflows.yml
@@ -14,6 +14,8 @@ name: rworkflows
     - RELEASE_**
 jobs:
   rworkflows:
+    permissions:
+      contents: write
     runs-on: ${{ matrix.config.os }}
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
     container: ${{ matrix.config.cont }}
@@ -48,10 +50,10 @@ jobs:
         run_pkgdown: ${{ true }}
         has_runit: ${{ false }}
         has_latex: ${{ false }}
-        GITHUB_TOKEN: ${{ secrets.PAT_GITHUB }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run_docker: ${{ true }}
-        docker_user: mydockeruser
-        docker_org: mydockerorg
+        docker_user: satijalab
+        docker_org: satijalab
         DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
         runner_os: ${{ runner.os }}
         cache_version: cache-v1
diff --git a/README.md b/README.md
index 427ab3a20..af25d54ac 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,6 @@
 [![Build Status](https://travis-ci.com/satijalab/seurat.svg?branch=master)](https://app.travis-ci.com:443/github/satijalab/seurat)
 [![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/satijalab/seurat?branch=master&svg=true)](https://ci.appveyor.com/project/satijalab/seurat)
+[![rworkflows](https://github.com/satijalab/seurat/workflows/rworkflows/badge.svg)](https://github.com/satijalab/seurat/actions)
 [![CRAN Version](https://www.r-pkg.org/badges/version/Seurat)](https://cran.r-project.org/package=Seurat)
 [![CRAN Downloads](https://cranlogs.r-pkg.org/badges/Seurat)](https://cran.r-project.org/package=Seurat)