From 20a6f8aff72b6a5a41e5821bef096347cec14572 Mon Sep 17 00:00:00 2001
From: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: Tue, 3 Dec 2024 12:57:18 -0800
Subject: [PATCH] Added actions for check and doc building.

---
 .github/workflows/build-pkgdown.yaml | 55 ++++++++++++++++++++++++++++
 .github/workflows/r-cmd-check.yaml   | 42 +++++++++++++++++++++
 2 files changed, 97 insertions(+)
 create mode 100644 .github/workflows/build-pkgdown.yaml
 create mode 100644 .github/workflows/r-cmd-check.yaml

diff --git a/.github/workflows/build-pkgdown.yaml b/.github/workflows/build-pkgdown.yaml
new file mode 100644
index 0000000..1fba915
--- /dev/null
+++ b/.github/workflows/build-pkgdown.yaml
@@ -0,0 +1,55 @@
+on:
+  push:
+    branches:
+      - master
+  workflow_dispatch:
+
+name: Build pkgdown
+
+jobs:
+  build:
+    name: Build pkgdown
+    runs-on: ubuntu-latest
+    container: bioconductor/bioconductor_docker:devel
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - run: |
+          sudo apt-get update
+          sudo apt-get install -y rsync
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Set directories
+        run: |
+          echo "R_PKG_DIR=${R_HOME}/site-library" >> $GITHUB_ENV
+
+      - name: Restore the package directory
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.R_PKG_DIR }}
+          key: pkgdown-packages
+
+      - name: Install dependencies
+        shell: Rscript {0}
+        run: |
+          stuff <- read.dcf("DESCRIPTION")
+          stuff <- stuff[,intersect(colnames(stuff), c("Imports", "LinkingTo", "Suggests", "Depends"))]
+          deps <- sub(" .*", "", unlist(strsplit(stuff, ",\\s*"), use.names=FALSE))
+          BiocManager::install(c("pkgdown", deps))
+
+      - name: Install self
+        run: R CMD INSTALL .
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
+
diff --git a/.github/workflows/r-cmd-check.yaml b/.github/workflows/r-cmd-check.yaml
new file mode 100644
index 0000000..a98116c
--- /dev/null
+++ b/.github/workflows/r-cmd-check.yaml
@@ -0,0 +1,42 @@
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+
+name: R CMD check
+
+jobs:
+  check:
+    name: R CMD check
+    runs-on: ubuntu-latest
+    container: bioconductor/bioconductor_docker:devel
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set directories
+        run: |
+          echo "R_PKG_DIR=${R_HOME}/site-library" >> $GITHUB_ENV
+
+      - name: Restore the package directory
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.R_PKG_DIR }}
+          key: check-packages
+
+      - name: Install dependencies
+        shell: Rscript {0}
+        run: |
+          stuff <- read.dcf("DESCRIPTION")
+          stuff <- stuff[,intersect(colnames(stuff), c("Imports", "LinkingTo", "Suggests", "Depends"))]
+          deps <- sub(" .*", "", unlist(strsplit(stuff, ",\\s*"), use.names=FALSE))
+          BiocManager::install(deps)
+
+      - name: Build the package
+        run: R CMD build .
+  
+      - name: Check the package
+        run: |
+          tarball=$(ls *.tar.gz)
+          R CMD check --no-manual $tarball