From b2b43b555d08e8605693ac77ce9f770167f5e46f Mon Sep 17 00:00:00 2001
From: LiNk-NY <marcel.ramos@roswellpark.org>
Date: Thu, 26 Oct 2023 14:54:00 -0400
Subject: [PATCH] add build_site.yml to RELEASE_3_18 branch

---
 .github/workflows/build_site.yml | 70 ++++++++++++++++++++++++++++++++
 .github/workflows/pr_check.yml   | 50 -----------------------
 2 files changed, 70 insertions(+), 50 deletions(-)
 create mode 100644 .github/workflows/build_site.yml
 delete mode 100644 .github/workflows/pr_check.yml

diff --git a/.github/workflows/build_site.yml b/.github/workflows/build_site.yml
new file mode 100644
index 0000000..112cdc9
--- /dev/null
+++ b/.github/workflows/build_site.yml
@@ -0,0 +1,70 @@
+name: Release R CMD check and build site
+
+on:
+  push:
+    branches:
+      - RELEASE_3_18
+
+jobs:
+  checkRelease:
+    runs-on: ubuntu-22.04
+    container: bioconductor/bioconductor_docker:RELEASE_3_18
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CRAN: https://packagemanager.posit.co/cran/__linux__/jammy/latest
+      version-name: RELEASE_3_18
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+        with:
+          ref: RELEASE_3_18
+
+      - name: Query dependencies
+        run: |
+          BiocManager::install("remotes")
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v3
+        with:
+          path: /usr/local/lib/R/site-library
+          key: ${{ runner.os }}-r-${{ env.version-name }}-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-r-${{ env.version-name }}-
+
+      - name: Install Dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories())
+          BiocManager::install(c("rcmdcheck", "pkgdown"), ask = FALSE, update = TRUE)
+        shell: Rscript {0}
+
+      - name: System dependencies
+        run: |
+          pip install ghp-import
+
+      - name: Check Package
+        id: rcmdcheck
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "error", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Build pkgdown
+        run: |
+           PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site()'
+
+      - name: Install deploy dependencies
+        run: |
+          apt-get update
+          apt-get -y install rsync
+
+      - name: Deploy 🚀
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          BRANCH: gh-pages # The branch the action should deploy to.
+          FOLDER: docs # The folder the action should deploy.
diff --git a/.github/workflows/pr_check.yml b/.github/workflows/pr_check.yml
deleted file mode 100644
index 08245f8..0000000
--- a/.github/workflows/pr_check.yml
+++ /dev/null
@@ -1,50 +0,0 @@
-name: Devel PR CMD check
-
-on:
-  push:
-    branches-ignore:
-      - devel
-      - RELEASE_3_*
-  pull_request:
-    branches:
-      - devel
-
-jobs:
-  checkDevel:
-    runs-on: ubuntu-22.04
-    container: bioconductor/bioconductor_docker:devel
-
-    env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
-    steps:
-      - name: Checkout Repository
-        uses: actions/checkout@v3
-
-      - name: Query dependencies
-        run: |
-          BiocManager::install(c("remotes", "Bioconductor/BiocManager"))
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v1
-        with:
-          path: /usr/local/lib/R/site-library
-          key: ${{ runner.os }}-r-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-r-1-
-
-      - name: Install Dependencies
-        run: |
-          options(repos = c(CRAN = "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"))
-          remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories())
-          BiocManager::install(c("rcmdcheck", "BiocCheck"), ask = FALSE, update = TRUE)
-        shell: Rscript {0}
-
-      - name: Check Package
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "error", check_dir = "check")
-        shell: Rscript {0}