Update eccb_workflow.Rmd #70
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name: Check, build, and push image | |
on: [push, pull_request] | |
env: | |
cache-version: v1 | |
jobs: | |
r-build-and-check: | |
runs-on: ubuntu-latest | |
container: bioconductor/bioconductor_docker:devel | |
env: | |
R_REMOTES_NO_ERRORS_FROM_WARNINGS: TRUE | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
CRAN: https://packagemanager.posit.co/cran/__linux__/jammy/latest | |
steps: | |
- name: Checkout Repository | |
uses: actions/checkout@v4 | |
- name: Query dependencies and update old packages | |
run: | | |
BiocManager::install(ask=FALSE) | |
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@v4 | |
with: | |
path: /usr/local/lib/R/site-library | |
key: ${{ env.cache-version }}-${{ runner.os }}-r-${{ hashFiles('.github/depends.Rds') }} | |
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-r- | |
- name: Install dependencies | |
run: | | |
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 = "--no-manual", error_on = "warning", check_dir = "check") | |
shell: Rscript {0} | |
- name: Build pkgdown | |
run: | | |
PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site(".")' | |
# deploy needs rsync? Seems so. | |
- name: Install deploy dependencies | |
run: | | |
apt-get update | |
apt-get -y install rsync | |
- name: Deploy 🚀 | |
uses: JamesIves/github-pages-deploy-action@v4 | |
with: | |
TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
BRANCH: gh-pages # The branch the action should deploy to. | |
FOLDER: docs # The folder the action should deploy. | |
docker-build-and-push: | |
#needs: r-build-and-check | |
runs-on: ubuntu-latest | |
permissions: | |
contents: read | |
packages: write | |
# This is used to complete the identity challenge | |
# with sigstore/fulcio when running outside of PRs. | |
id-token: write | |
steps: | |
- name: Checkout Repository | |
uses: actions/checkout@v4 | |
- name: Set Environment Variables | |
run: | | |
REPO_LOWER="$(echo "${{ github.repository }}" | tr '[:upper:]' '[:lower:]')" | |
REGISTRY=ghcr.io | |
echo "BUILD_DATE=$(date +'%Y-%m-%d %H:%M:%S')" >> $GITHUB_ENV | |
echo "GIT_SHA=$(echo ${{ github.sha }} | cut -c1-7)" >> $GITHUB_ENV | |
echo "REGISTRY=${REGISTRY}" >> $GITHUB_ENV | |
echo "IMAGE=${REGISTRY}/${REPO_LOWER}" >> $GITHUB_ENV | |
- name: Show environment | |
run: | | |
env | |
# Install the cosign tool except on PR | |
# https://github.com/sigstore/cosign-installer | |
- name: Install cosign | |
if: github.event_name != 'pull_request' | |
uses: sigstore/cosign-installer@v3 | |
- name: Setup Docker buildx | |
uses: docker/setup-buildx-action@v3 | |
# Login against a Docker registry except on PR | |
# https://github.com/docker/login-action | |
- name: Log into registry ${{ env.REGISTRY }} | |
if: github.event_name != 'pull_request' | |
uses: docker/login-action@v3 | |
with: | |
registry: ${{ env.REGISTRY }} | |
username: ${{ github.actor }} | |
password: ${{ secrets.GITHUB_TOKEN }} | |
# Extract metadata (tags, labels) for Docker | |
# https://github.com/docker/metadata-action | |
- name: Extract Docker metadata | |
id: meta | |
uses: docker/metadata-action@v5 | |
with: | |
images: ${{ env.IMAGE }} | |
# Build and push Docker image with Buildx (don't push on PR) | |
# https://github.com/docker/build-push-action | |
- name: Build and push Docker image | |
id: build-and-push | |
uses: docker/build-push-action@v5 | |
with: | |
context: . | |
push: ${{ github.event_name != 'pull_request' }} | |
tags: | | |
${{ env.IMAGE }}:latest | |
${{ env.IMAGE }}:${{ env.GIT_SHA }} |