From 2f963650aef97329480587dbf70158eeede5eed0 Mon Sep 17 00:00:00 2001
From: Mike Lin <mlin@contractor.chanzuckerberg.com>
Date: Tue, 7 Nov 2023 16:40:02 -1000
Subject: [PATCH] [r] add r-dependency-check.yml nightly test of current
 release package (#769)

#751. Following #763, add an analogous nightly workflow for R to install the current release version of `cellxgene.census` then run the unit tests, to verify compatibility with the most up-to-date dependency versions (without any dependency caching).
---
 .github/workflows/r-dependency-check.yml | 38 ++++++++++++++++++++++++
 README.md                                |  1 +
 2 files changed, 39 insertions(+)
 create mode 100644 .github/workflows/r-dependency-check.yml

diff --git a/.github/workflows/r-dependency-check.yml b/.github/workflows/r-dependency-check.yml
new file mode 100644
index 000000000..9064d2849
--- /dev/null
+++ b/.github/workflows/r-dependency-check.yml
@@ -0,0 +1,38 @@
+name: R dependency checks
+
+# This workflow is intended to check that the latest release of the cellxgene.census R package
+# continues to function correctly using the latest upstream dependencies.
+
+on:
+  schedule:
+    - cron: "30 1 * * *"
+  workflow_dispatch: # used for debugging or manual validation
+
+jobs:
+  r-dependency-check:
+    name: r-dependency-check
+
+    strategy:
+      matrix:
+        os: [ubuntu-22.04, macos-latest]
+
+    runs-on: ${{matrix.os}}
+
+    steps:
+      - name: install OS dependencies
+        if: matrix.os == 'ubuntu-22.04'
+        run: sudo apt-get update && sudo apt-get install libcurl4-openssl-dev
+      - uses: r-lib/actions/setup-r@v2
+      - name: install cellxgene.census and dependencies
+        # This should follow our user-facing instructions to install cellxgene.census.
+        run: |
+            Rscript -e 'install.packages(c("cellxgene.census", "Seurat", "BiocManager", "testthat"), repos=c("https://chanzuckerberg.r-universe.dev", "https://cloud.r-project.org"), type="source")'
+            Rscript -e 'BiocManager::install("SingleCellExperiment")'
+      - name: run unit tests
+        # [re-]fetch the cellxgene.census source package which includes the unit test code to run
+        run: |
+            set -ex
+            Rscript -e 'download.packages("cellxgene.census", destdir=".", repos="https://chanzuckerberg.r-universe.dev", type="source")'
+            tar zxf cellxgene.census_*.tar.gz
+            cd cellxgene.census/tests
+            Rscript testthat.R
diff --git a/README.md b/README.md
index f4edd2a88..0a76f14c8 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,6 @@
 [![codecov](https://codecov.io/gh/chanzuckerberg/cellxgene-census/branch/main/graph/badge.svg?token=byX1pyDlc9)](https://codecov.io/gh/chanzuckerberg/cellxgene-census)
 [![Python dependency checks](https://github.com/chanzuckerberg/cellxgene-census/actions/workflows/py-dependency-check.yml/badge.svg)](https://github.com/chanzuckerberg/cellxgene-census/actions/workflows/py-dependency-check.yml)
+[![R dependency checks](https://github.com/chanzuckerberg/cellxgene-census/actions/workflows/r-dependency-check.yml/badge.svg)](https://github.com/chanzuckerberg/cellxgene-census/actions/workflows/r-dependency-check.yml)
 [![LTS compat checks](https://github.com/chanzuckerberg/cellxgene-census/actions/workflows/lts-compat-check.yml/badge.svg)](https://github.com/chanzuckerberg/cellxgene-census/actions/workflows/lts-compat-check.yml)
 
 # CZ CELLxGENE Discover Census