diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 99b9f370..a3ac6182 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -1,14 +1,10 @@ -# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. -# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: push: - branches: - - main - - master + branches: [main, master] pull_request: - branches: - - main - - master + branches: [main, master] name: R-CMD-check @@ -22,87 +18,32 @@ jobs: fail-fast: false matrix: config: + - {os: macos-latest, r: 'release'} - {os: windows-latest, r: 'release'} - - {os: macOS-latest, r: 'release'} - - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} env: - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - RSPM: ${{ matrix.config.rspm }} GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - HDF5_VERSION: 1.12.0 - HDF5_DIR: ${{ github.workspace }}/cache/hdf5 + R_KEEP_PKG_SOURCE: yes steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - - name: Cache HDF5 - uses: actions/cache@v2 - with: - path: ${{ env.HDF5_DIR }} - key: ${{ runner.os }}-hdf5-${{ env.HDF5_VERSION }} - - - name: Build HDF5 - if: runner.os != 'Windows' && steps.cache-hdf5.outputs.cache-hit != 'true' - run: | - chmod a+x ./inst/hdf5_installer.sh - ./inst/hdf5_installer.sh - ls ${{ env.HDF5_DIR }} - - uses: r-lib/actions/setup-pandoc@v2 - + - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} - - - name: Install remotes - run: | - install.packages('remotes') - shell: Rscript {0} - - - name: Install system dependencies - if: runner.os == 'Linux' - run: | - while read -r cmd - do - eval sudo $cmd - done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') + http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true - - name: Query dependencies - run: | - install.packages('ravemanager', repos = c(beauchamplab = "https://beauchamplab.r-universe.dev", dipterix = "https://dipterix.r-universe.dev", CRAN = "https://cloud.r-project.org")) - Sys.setenv("RAVE_LIB_PATH" = .libPaths()[[1]]) - ravemanager::install(finalize = FALSE) - rave::download_sample_data('YAB', replace_if_exists = TRUE) - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Cache R packages - if: runner.os != 'Windows' - 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- - - - name: Install dependencies - run: | - remotes::install_deps(dependencies = TRUE) - remotes::install_cran("rcmdcheck") - shell: Rscript {0} - - - name: Check - env: - _R_CHECK_CRAN_INCOMING_REMOTE_: false - run: | - options(crayon.enabled = TRUE) - rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") - shell: Rscript {0} + extra-packages: any::rcmdcheck + needs: check - - name: Upload check results - if: failure() - uses: actions/upload-artifact@main + - uses: r-lib/actions/check-r-package@v2 with: - name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: check + upload-snapshots: true diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index c33f40fd..ed7650c7 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -1,65 +1,48 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: push: - branches: - - main - - master + branches: [main, master] + pull_request: + branches: [main, master] + release: + types: [published] + workflow_dispatch: name: pkgdown jobs: pkgdown: - runs-on: macOS-latest + runs-on: ubuntu-latest + # Only restrict concurrency for non-PR jobs + concurrency: + group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - HDF5_VERSION: 1.12.0 - HDF5_DIR: ${{ github.workspace }}/cache/hdf5 + permissions: + contents: write steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - - name: Cache HDF5 - uses: actions/cache@v2 - with: - path: ${{ env.HDF5_DIR }} - key: ${{ runner.os }}-hdf5-${{ env.HDF5_VERSION }} - - - name: Build HDF5 - if: steps.cache-hdf5.outputs.cache-hit != 'true' - run: | - chmod a+x ./inst/hdf5_installer.sh - ./inst/hdf5_installer.sh - ls ${{ env.HDF5_DIR }} - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-pandoc@v2 - - uses: r-lib/actions/setup-pandoc@v1 - - - name: Query dependencies - run: | - h5cc=file.path(Sys.getenv("HDF5_DIR"), "bin/h5cc") - h5cc=normalizePath(h5cc) - install.packages("hdf5r", configure.args=sprintf("--with-hdf5=%s", h5cc)) - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true - - name: Cache R packages - 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 - 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)' + - 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 diff --git a/DESCRIPTION b/DESCRIPTION index 750aede7..77f1b0ac 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -19,11 +19,10 @@ Description: R Analysis and Visualization of 'ECOG/iEEG' Data License: GPL-3 Encoding: UTF-8 Language: en-US -URL: https://rave.wiki +URL: https://rave.wiki, + https://beauchamplab.github.io/rave/ BugReports: https://github.com/beauchamplab/rave/issues -RoxygenNote: 7.2.1 -Depends: - R (>= 3.6.0) +RoxygenNote: 7.2.3 Imports: utils, stats, diff --git a/README.md b/README.md index a41a0585..472a69af 100644 --- a/README.md +++ b/README.md @@ -6,6 +6,6 @@ For all RAVE info, including installation instructions, visit https://rave.wiki -[![R-CMD-check](https://github.com/beauchamplab/rave/workflows/R-CMD-check/badge.svg)](https://github.com/beauchamplab/rave/actions) +[![R-CMD-check](https://github.com/beauchamplab/rave/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/beauchamplab/rave/actions/workflows/R-CMD-check.yaml) diff --git a/_pkgdown.yml b/_pkgdown.yml index 68c9b958..ac4c8b5d 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1 +1,4 @@ -url: https://beauchamplab.github.io/rave +url: https://beauchamplab.github.io/rave/ +template: + bootstrap: 5 +