diff --git a/.github/workflows/basic_checks.yaml b/.github/workflows/basic_checks.yaml index ac3e545..902a13e 100644 --- a/.github/workflows/basic_checks.yaml +++ b/.github/workflows/basic_checks.yaml @@ -13,7 +13,7 @@ jobs: env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: TRUE GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - CRAN: https://packagemanager.posit.co/cran/__linux__/jammy/latest + CRAN: https://packagemanager.posit.co/cran/__linux__/noble/latest steps: - name: Checkout Repository @@ -21,7 +21,8 @@ jobs: - name: Query dependencies and update old packages run: | - BiocManager::install(ask=FALSE) + options(repos = c(CRAN = Sys.getenv("CRAN"))) + BiocManager::install(c("remotes", "rcmdcheck"), ask = FALSE) saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) shell: Rscript {0} @@ -35,9 +36,9 @@ jobs: - name: Install dependencies run: | - BiocManager::repositories() + options(repos = c(CRAN = Sys.getenv("CRAN"))) remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories()) - remotes::install_cran("rcmdcheck") + BiocManager::install(ask = FALSE, update = TRUE) shell: Rscript {0} - name: Check @@ -50,18 +51,10 @@ jobs: run: | PATH=$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 + - name: Upload pkgdown artifact + uses: actions/upload-pages-artifact@v3 with: - TOKEN: ${{ secrets.GITHUB_TOKEN }} - BRANCH: gh-pages # The branch the action should deploy to. - FOLDER: docs # The folder the action should deploy. + path: docs docker-build-and-push: #needs: r-build-and-check @@ -121,10 +114,22 @@ jobs: # https://github.com/docker/build-push-action - name: Build and push Docker image id: build-and-push - uses: docker/build-push-action@v5 + uses: docker/build-push-action@v6 with: context: . push: ${{ github.event_name != 'pull_request' }} tags: | ${{ env.IMAGE }}:latest ${{ env.IMAGE }}:${{ env.GIT_SHA }} + + deploy: + needs: r-build-and-check + permissions: + pages: write + id-token: write + runs-on: ubuntu-24.04 + steps: + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v4 +