updated actions and pkgdown config

ipeaGIT · Jan 21, 2025 · 1cdc8ba · 1cdc8ba
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commit 1cdc8ba
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -15,3 +15,5 @@
 ^cran-comments\.md$
 ^CRAN-RELEASE$
 ^CRAN-SUBMISSION$
+^_pkgdown\.yml$
+^pkgdown$
diff --git a/.github/workflows/R-CMD-check-CRAN.yaml b/.github/workflows/R-CMD-check-CRAN.yaml
@@ -9,7 +9,7 @@ on:
 name: R-CMD-check
 
 jobs:
-  R-CMD-check-CRAN:
+  check:
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
@@ -18,91 +18,27 @@ jobs:
       fail-fast: false
       matrix:
         config:
-        - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+        - {os: ubuntu-22.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
 
     env:
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+    - 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-r@v2
+      with:
+        r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-pandoc@v2
+    - 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}
+    - uses: r-lib/actions/setup-r-dependencies@v2
+      with:
+        extra-packages: any::rcmdcheck
+        needs: check
 
-      - name: Restore R package cache
-        uses: actions/cache@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}
-
-      - name: Install system dependencies (MacOS)
-        if: runner.os == 'macOS'
-        run: |
-          brew install pkg-config gdal proj geos
-          #  Install libgit2
-          brew install libgit2
-          
-      - name: "[Stage] [macOS] Install system libs for pkgdown"
-        if: runner.os == 'macOS' && matrix.config.pkgdown != ''
-        run: brew install harfbuzz fribidi
-
-      - name: Install dependencies
-        run: |
-          pak::local_install_dev_deps(upgrade = TRUE)
-          pak::pkg_install("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_: 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}
-
-      - 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
-
-      - name: Don't use tar from old Rtools to store the cache
-        if: ${{ runner.os == 'Windows' && startsWith(steps.install-r.outputs.installed-r-version, '3.6' ) }}
-        shell: bash
-        run: echo "C:/Program Files/Git/usr/bin" >> $GITHUB_PATH
+    - uses: r-lib/actions/check-r-package@v2
+      env:
+        _R_CHECK_CRAN_INCOMING_: false
+        NOT_CRAN: false
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -9,7 +9,7 @@ on:
 name: R-CMD-check
 
 jobs:
-  R-CMD-check:
+  check:
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
@@ -18,97 +18,28 @@ jobs:
       fail-fast: false
       matrix:
         config:
-        - {os: windows-, r: 'release'}
-        - {os: windows-, r: 'oldrel'}
+        - {os: windows-latest, r: 'release'}
         - {os: macOS-latest, r: 'release'}
-        - {os: macOS-latest, r: 'oldrel'}
-        - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/"}
-        - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/"}
-        - {os: ubuntu-20.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/"}
+        - {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:
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+    - 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
+    - uses: r-lib/actions/setup-r@v2
+      with:
+        r-version: ${{ matrix.config.r }}
 
-      - 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}
+    - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Restore R package cache
-        uses: actions/cache@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-
+    - uses: r-lib/actions/setup-r-dependencies@v2
+      with:
+        extra-packages: any::rcmdcheck
+        needs: check
 
-      - 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}
-
-      - name: Install system dependencies (MacOS)
-        if: runner.os == 'macOS'
-        run: |
-          brew install pkg-config gdal proj geos
-          #  Install libgit2
-          brew install libgit2
-          
-      - name: "[Stage] [macOS] Install system libs for pkgdown"
-        if: runner.os == 'macOS' && matrix.config.pkgdown != ''
-        run: brew install harfbuzz fribidi
-
-      - name: Install dependencies
-        run: |
-          pak::local_install_dev_deps(upgrade = TRUE)
-          pak::pkg_install("rcmdcheck")
-          pak::pkg_install("ipeaGIT/gtfs2gps")
-        shell: Rscript {0}
-
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - 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
-
-      - name: Don't use tar from old Rtools to store the cache
-        if: ${{ runner.os == 'Windows' && startsWith(steps.install-r.outputs.installed-r-version, '3.6' ) }}
-        shell: bash
-        run: echo "C:/Program Files/Git/usr/bin" >> $GITHUB_PATH
+    - uses: r-lib/actions/check-r-package@v2
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -2,18 +2,15 @@ on:
   push:
     branches:
       - master
-    tags:
-      -'*'
 
 name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     env:
-      RSPM: https://packagemanager.rstudio.com/cran/__linux__/bionic/latest
+      RSPM: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      HOMEBREW_NO_INSTALL_CLEANUP: TRUE
 
     steps:
       - uses: actions/checkout@v2
@@ -23,39 +20,13 @@ jobs:
 
       - 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}
-
-      - 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: ubuntu-20.04-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
-          restore-keys: ubuntu-20.04-${{ steps.install-r.outputs.installed-r-version }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          pak::local_system_requirements(execute = TRUE)
-          pak::pkg_system_requirements("pkgdown", execute = TRUE)
-        shell: Rscript {0}
-
-      - name: Install dependencies
-        run: |
-          pak::local_install_dev_deps(upgrade = TRUE)
-          pak::pkg_install("pkgdown")
-        shell: Rscript {0}
-
-      - name: Install package
-        run: R CMD INSTALL .
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
       - name: Build and deploy pkgdown site
         run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "[email protected].github.com"
+          git config --local user.name "GitHub Actions"
+          git config --local user.email "actions@github.com"
           Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -12,56 +12,50 @@ name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     env:
-      RSPM: https://packagemanager.rstudio.com/cran/__linux__/bionic/latest
+      RSPM: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-r@v2
-        id: install-r
 
-      - 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}
-
-      - 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: ubuntu-20.04-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
-          restore-keys: ubuntu-20.04-${{ steps.install-r.outputs.installed-r-version }}-1-
+          extra-packages: any::covr, any::xml2
+          needs: coverage
 
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
+      - name: Test coverage
         run: |
-          pak::local_system_requirements(execute = TRUE)
-          pak::pkg_system_requirements("covr", execute = TRUE)
+          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}
 
-      - name: Install system dependencies (MacOS)
-        if: runner.os == 'macOS'
-        run: |
-          brew install pkg-config gdal proj geos
-          #  Install libgit2
-          brew install libgit2
-          
-      - name: "[Stage] [macOS] Install system libs for pkgdown"
-        if: runner.os == 'macOS' && matrix.config.pkgdown != ''
-        run: brew install harfbuzz fribidi
-
-      - name: Install dependencies
+      - 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: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
         run: |
-          pak::local_install_dev_deps(upgrade = TRUE)
-          pak::pkg_install("covr")
-        shell: Rscript {0}
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
 
-      - name: Test coverage
-        run: covr::codecov(quiet = FALSE)
-        shell: Rscript {0}
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package