updated actions and pkgdown config

ipeaGIT · Jan 17, 2025 · 3fa6639 · 3fa6639
1 parent 24df767
commit 3fa6639
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diff --git a/.github/workflows/R-CMD-check-CRAN.yaml b/.github/workflows/R-CMD-check-CRAN.yaml
@@ -1,19 +1,23 @@
+# 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
 on:
   push:
     paths:
       - r-package/**
     branches:
       - master
+      - dev
   pull_request:
     paths:
       - r-package/**
     branches:
       - master
+      - dev
 
-name: check_as_cran
+name: R-CMD-check-CRAN
 
 jobs:
-  check_as_cran:
+  R-CMD-check:
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
@@ -32,70 +36,20 @@ jobs:
       - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-r@v2
-        id: install-r
         with:
           r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Install pak and query dependencies
-        run: |
-          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
-          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
-        shell: Rscript {0}
-        working-directory: r-package
-
-      - name: Restore R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: |
-            ${{ env.R_LIBS_USER }}/*
-            !${{ env.R_LIBS_USER }}/pak
-          key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
-          restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
-
-      - name: Install system dependencies (Linux)
-        if: runner.os == 'Linux'
-        run: |
-          pak::local_system_requirements(execute = TRUE)
-          pak::pkg_system_requirements("rcmdcheck", execute = TRUE)
-        shell: Rscript {0}
-        working-directory: r-package
-
-      - name: Install dependencies
-        run: |
-          pak::local_install_dev_deps(upgrade = TRUE)
-          pak::pkg_install("rcmdcheck")
-        shell: Rscript {0}
-        working-directory: r-package
-
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
-        working-directory: r-package
+          extra-packages: any::rcmdcheck
+          needs: check
+          working-directory: r-package
 
-      - name: Check
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          working-directory: r-package
         env:
-          _R_CHECK_CRAN_INCOMING_: false
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
           NOT_CRAN: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-        working-directory: r-package
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
-          path: check
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,5 +1,3 @@
-# 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
 on:
   push:
     paths:
@@ -27,69 +25,36 @@ jobs:
       matrix:
         config:
         - {os: windows-latest, r: 'release'}
-        - {os: windows-latest, r: 'oldrel'}
         - {os: macOS-latest, r: 'release'}
-        - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-        - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-        - {os: ubuntu-20.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+        - {os: ubuntu-22.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
+        - {os: ubuntu-22.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
+        - {os: ubuntu-22.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v4
-
-      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
-          use-public-rspm: true
 
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Java setup
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v1
         with:
-          distribution: 'temurin'
           java-version: '21'
-
-      - 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}
-        working-directory: r-package
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@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 system dependencies (Linux)
-        if: runner.os == 'Linux'
-        run: brew install gdal proj
-        working-directory: r-package
-
-      - name: Install macOS system dependencies
-        if: runner.os == 'macos'
-        run: brew install gdal proj
-        working-directory: r-package
-
+          java-package: jdk
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck
           needs: check
-        working-directory: r-package
+          working-directory: r-package
 
       - uses: r-lib/actions/check-r-package@v2
         with:
-          upload-snapshots: true
-
+          working-directory: r-package
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -3,73 +3,37 @@ on:
     paths:
       - r-package/**
       - README.md
-      - .github/workflows/pkgdown.yaml
     branches:
       - master
 
 name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: ubuntu-20.04
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    runs-on: ubuntu-22.04
+
     steps:
       - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-r@v2
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Java setup
-        uses: actions/setup-java@v1
-        with:
-          java-version: '21'
-          java-package: jdk
-
-      - 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}
-        working-directory: r-package
-
-      - name: Cache R packages
-        uses: actions/cache@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 system dependencies
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-          sudo apt install libharfbuzz-dev libfribidi-dev
-        working-directory: r-package
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown")
-        shell: Rscript {0}
-        working-directory: r-package
-
       - name: Copy README.md to r-package/index.md
         run: cp README.md r-package/index.md
 
       - name: Update r-package/index.md figures source
         run: sed -i 's/\"r-package\//\"/g' r-package/index.md
 
-      - name: Install package
-        run: R CMD INSTALL .
-        working-directory: r-package
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+          working-directory: r-package
 
-      - name: Deploy package
+      - name: Build and deploy pkgdown site
         run: |
-          git config --local user.email "[email protected]"
           git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(pkg = "./r-package", new_process = FALSE)'
+          git config --local user.email "[email protected]"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+        working-directory: r-package
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -4,68 +4,54 @@ on:
       - r-package/**
     branches:
       - dev
-      - main
       - master
   pull_request:
     paths:
       - r-package/**
     branches:
       - dev
-      - main
       - master
 
 name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: ubuntu-20.04
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    runs-on: ubuntu-22.04
+
     steps:
       - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-r@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
       - name: Java setup
         uses: actions/setup-java@v1
         with:
           java-version: '21'
           java-package: jdk
 
-      - 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}
-        working-directory: r-package
-
-      - 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-
-
-      - name: Install system dependencies
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-        working-directory: r-package
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+          working-directory: r-package
 
-      - name: Install dependencies
+      - name: Test coverage
         run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
         working-directory: r-package
 
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
-        working-directory: r-package
+      - uses: codecov/codecov-action@v4
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+          working-directory: r-package
diff --git a/r-package/pkgdown/_pkgdown.yml b/r-package/pkgdown/_pkgdown.yml
@@ -1,4 +1,8 @@
-destination: ../docs
+url: https://ipeagit.github.io/r5r/
+
+template:
+  bootstrap: 5
+  light-switch: true
 
 development:
   mode: auto
@@ -40,4 +44,3 @@ reference:
     - r5r_cache
     - download_r5
     - stop_r5
-