diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index 05bdfad..cc3ab4b 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -17,43 +17,32 @@ jobs: env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - - name: Checkout bedstat@${{ github.event.inputs.branch }} - uses: actions/checkout@v2 + - uses: actions/checkout@v23 with: # The branch, tag or SHA to checkout. When checking out the repository that # triggered a workflow, this defaults to the reference or SHA for that event. # Otherwise, uses the default branch. ref: ${{ github.event.inputs.branch }} - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-pandoc@v2 - - uses: r-lib/actions/setup-pandoc@v1 - - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true - - name: Restore R package cache - uses: actions/cache@v2 + - uses: r-lib/actions/setup-r-dependencies@v2 with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- + extra-packages: any::pkgdown, local::. + needs: website - - name: Install dependencies - run: | - remotes::install_deps(dependencies = TRUE) - install.packages("pkgdown", type = "binary") + - name: Build site + run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) shell: Rscript {0} - - name: Install package - run: R CMD INSTALL . - - - name: Deploy package documentation - run: | - git config --local user.email "actions@github.com" - git config --local user.name "GitHub Actions" - Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE, commit_message="deploy docs with a github action")' + - name: Deploy to GitHub pages + if: github.event_name != 'pull_request' + uses: JamesIves/github-pages-deploy-action@v4.4.1 + with: + clean: false + branch: gh-pages + folder: docs \ No newline at end of file diff --git a/NEWS.md b/NEWS.md index 7fac20d..b62e384 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,8 +1,9 @@ -# pepr 0.5.0 - unreleased +# pepr 0.5.0 - 2023-11-16 ## Fixed * result class of appended attributes; it's no longer wrapped in a `list` +* various other fixes and improvements ## Changed @@ -12,6 +13,7 @@ * possibility to configure the sample and subsample table index attributes in the `Project` object constructor * possibility to initialize `Project` with no configuration file +* ability to initialize a project from URL * auto initialization file detection: CSV (sample table) or YAML (project config) * duplicated sample auto-merging