Add force_install input to bypass caching

.github/workflows/rworkflows_force_install.yml

@@ -0,0 +1,57 @@
+name: rworkflows
+'on':
+  push:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+  pull_request:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+jobs:
+  rworkflows:
+    permissions: write-all
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    strategy:
+      fail-fast: ${{ false }}
+      matrix:
+        config:
+        - os: ubuntu-latest
+          r: auto
+          bioc: release
+          cont: ghcr.io/bioconductor/bioconductor_docker:RELEASE_3_19
+          python-version: 3.11
+        - os: macOS-latest
+          r: latest
+          bioc: release
+          python-version: 3.11
+        - os: windows-latest
+          r: latest
+          bioc: release
+          python-version: 3.11
+    steps:
+    - uses: neurogenomics/rworkflows@master
+      with:
+        run_bioccheck: ${{ false }}
+        run_rcmdcheck: ${{ true }}
+        as_cran: ${{ true }}
+        run_vignettes: ${{ true }}
+        has_testthat: ${{ true }}
+        run_covr: ${{ false }}
+        run_pkgdown: ${{ false }}
+        has_runit: ${{ false }}
+        # has_latex: ${{ true }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run_docker: ${{ false }}
+        DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
+        runner_os: ${{ runner.os }}
+        cache_version: cache-v1
+        force_install: ${{ true }}
+        # free_diskspace: ${{ true }}
+        # miniforge_variant: false

action.yml

@@ -169,6 +169,13 @@ inputs:
       Whether to run the workflow telemetry action: 
       https://github.com/catchpoint/workflow-telemetry-action
     default: true
+  force_install:
+    description: >
+      Whether to force install packages. If `true`, all packages will be
+      reinstalled, bypassing the cache.
+      Recommended to set to `true` when pushing changes without updating R
+      package version, such as during pre-release phase of developement.
+    default: false
 
 runs:
   using: 'composite'
@@ -342,7 +349,7 @@ runs:
          install.packages(c("rmarkdown","BiocManager"), dependencies = TRUE)
          message(paste('****', Sys.time(), 'pass number 1 at installing dependencies****'))
          repos <- BiocManager::repositories()
-         remotes::install_local(repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE, force=FALSE)
+         remotes::install_local(repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE, force=${{ inputs.force_install }})
       continue-on-error: true
       shell: Rscript {0}
 
@@ -354,7 +361,7 @@ runs:
         options(crayon.enabled = TRUE, timeout=Sys.getenv("timeout"))
         message(paste('****', Sys.time(), 'pass number 2 at installing dependencies****'))
         repos <- BiocManager::repositories()
-        remotes::install_local(repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE, force=FALSE)
+        remotes::install_local(repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE, force=${{ inputs.force_install }})
       shell: Rscript {0}
 
     - name: 🛠 Install RUnit (via BiocGenerics)