From 08ceb6352cf173d7b5cec0411c7f756d684e3fda Mon Sep 17 00:00:00 2001
From: Fred Feng <fredfeng@umich.edu>
Date: Tue, 14 Nov 2023 10:47:02 -0500
Subject: [PATCH] Update GitHub action for building website.

---
 .github/workflows/website.yml | 74 +++++++++++++++++------------------
 1 file changed, 37 insertions(+), 37 deletions(-)

diff --git a/.github/workflows/website.yml b/.github/workflows/website.yml
index e351785..f411853 100644
--- a/.github/workflows/website.yml
+++ b/.github/workflows/website.yml
@@ -31,9 +31,9 @@ jobs:
         run: |
           gem install github-pages bundler kramdown kramdown-parser-gfm
 
-      - name: Install Python modules
-        run: |
-          python3 -m pip install --upgrade pip setuptools wheel pyyaml==5.3.1 requests
+      # - name: Install Python modules
+      #   run: |
+      #     python3 -m pip install --upgrade pip setuptools wheel pyyaml==5.3.1 requests
 
       - name: Checkout the lesson
         uses: actions/checkout@master
@@ -41,10 +41,10 @@ jobs:
           fetch-depth: 0
           ref: ${{ github.event.pull_request.head.sha }}
 
-      - name: Look for R-markdown files
-        id: check-rmd
-        run: |
-          echo "::set-output name=count::$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})"
+      # - name: Look for R-markdown files
+      #   id: check-rmd
+      #   run: |
+      #     echo "::set-output name=count::$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})"
 
       # - name: Set up R
       #   if: steps.check-rmd.outputs.count != 0
@@ -52,40 +52,40 @@ jobs:
       #   with:
       #     r-version: 'release'
 
-      - name: Restore R Cache
-        if: steps.check-rmd.outputs.count != 0
-        uses: actions/cache@v2
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+      # - name: Restore R Cache
+      #   if: steps.check-rmd.outputs.count != 0
+      #   uses: actions/cache@v2
+      #   with:
+      #     path: ${{ env.R_LIBS_USER }}
+      #     key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+      #     restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
 
-      - name: Install needed packages
-        if: steps.check-rmd.outputs.count != 0
-        run: |
-          source('bin/dependencies.R')
-          install_required_packages()
-        shell: Rscript {0}
+      # - name: Install needed packages
+      #   if: steps.check-rmd.outputs.count != 0
+      #   run: |
+      #     source('bin/dependencies.R')
+      #     install_required_packages()
+      #   shell: Rscript {0}
 
-      - name: Query dependencies
-        if: steps.check-rmd.outputs.count != 0
-        run: |
-          source('bin/dependencies.R')
-          deps <- identify_dependencies()
-          create_description(deps)
-          use_bioc_repos()
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+      # - name: Query dependencies
+      #   if: steps.check-rmd.outputs.count != 0
+      #   run: |
+      #     source('bin/dependencies.R')
+      #     deps <- identify_dependencies()
+      #     create_description(deps)
+      #     use_bioc_repos()
+      #     saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+      #     writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+      #   shell: Rscript {0}
 
 
-      - name: Install system dependencies for R packages
-        if: steps.check-rmd.outputs.count != 0
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd || echo "Nothing to update"
-          done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
+      # - name: Install system dependencies for R packages
+      #   if: steps.check-rmd.outputs.count != 0
+      #   run: |
+      #     while read -r cmd
+      #     do
+      #       eval sudo $cmd || echo "Nothing to update"
+      #     done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
 
       - name: Render the markdown and confirm that the site can be built
         run: make site