update github action with Sean's template

.github/workflows/basic_checks.yaml

@@ -1,14 +1,19 @@
-on: [push]
+on: [push, pull_request]
+
+env:
+  cache-version: v1
+  repo-name: jmacdon/bioc2021anno
+
 jobs:
   job1:
     runs-on: ubuntu-latest
     container: bioconductor/bioconductor_docker:devel
     steps:
       - uses: actions/checkout@v1
 
-      - name: Query dependencies
+      - name: Query dependencies and update old packages
         run: |
-          install.packages('remotes')
+          BiocManager::install(ask=FALSE)
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
         shell: Rscript {0}
 
@@ -17,8 +22,8 @@ jobs:
         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-
+          key: ${{ env.cache-version }}-${{ runner.os }}-r-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-r-
 
       # This lets us augment with additional dependencies
       - name: Install system dependencies
@@ -31,28 +36,19 @@ jobs:
           sudo -s eval "$sysreqs"
 
       - name: Install dependencies
-      # mother of god I hate this tidyverse crap
-        env:
-          R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
         run: |
+          options(repos = c(CRAN = "https://cran.r-project.org"))
+          BiocManager::repositories()
           remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories())
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
 
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "error", check_dir = "check")
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
-
-      - uses: docker/build-push-action@v1
-        with:
-          username: ${{ secrets.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
-          repository: jmacdon/bioc2021anno
-          tag_with_ref: true
-          tag_with_sha: true
-          tags: latest
+
 
       - name: Build pkgdown
         run: |
@@ -64,15 +60,27 @@ jobs:
           apt-get update
           apt-get -y install rsync
 
-      - name: Install SSH Client
-        uses: webfactory/ssh-agent@v0.4.1
-        with:
-          ssh-private-key: ${{ secrets.DEPLOY_KEY }}
-
       - name: Deploy 🚀
         uses: JamesIves/github-pages-deploy-action@releases/v3
         with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           BRANCH: gh-pages # The branch the action should deploy to.
           FOLDER: docs # The folder the action should deploy.
-          SSH: true
 
+      - uses: docker/build-push-action@v1
+        if: github.event_name == 'push' && github.ref == 'refs/heads/master'
+        with:
+          # The two entries below need to be entered as 
+          # github secrets. The "secret" names are "DOCKER_USERNAME"
+          # and "DOCKER_PASSWORD". See https://docs.github.com/en/actions/reference/encrypted-secrets#creating-encrypted-secrets-for-a-repository
+          # for detailed instructions. 
+          #
+          # DO NOT EDIT THESE ENTRIES HERE. Doing so will 
+          # expose your docker username and password on github.
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+          # Use the environment variable on first few lines to set repo name--just centralizes changes
+          repository: ${{ env.repo-name }}
+          tag_with_ref: true
+          tag_with_sha: true
+          tags: latest