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Update eccb_workflow.Rmd #70

Update eccb_workflow.Rmd

Update eccb_workflow.Rmd #70

Workflow file for this run

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 }}