Merge pull request #14 from hsvab/dro/add_ci_workflows

Add CI workflows to improve code quality
hsvab · Oct 11, 2023 · b948229 · b948229
2 parents 129c08c + 4e4c342
commit b948229
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Showing 14 changed files with 387 additions and 19 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,6 +1,17 @@
-^odbr\.Rproj$
-^\.Rproj\.user$
-^data-raw$
+.lintr
+.RData
+.Rhistory
+.parquet
+^.*\.Rproj$
+^CRAN-SUBMISSION$
 ^LICENSE\.md$
-^\.github$
 ^README\.Rmd$
+^\.Rproj\.user$
+^\.github$
+^_pkgdown\.yml$
+^codecov\.yml$
+^cran-comments\.md$
+^data-raw$
+^data_prep
+^docs$
+^pkgdown$
diff --git a/.github/workflows/R-CMD-check-CRAN.yaml b/.github/workflows/R-CMD-check-CRAN.yaml
@@ -0,0 +1,106 @@
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+name: R-CMD-check-CRAN
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  R-CMD-check-CRAN:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+        - {os: ubuntu-latest, r: 'release', rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest"}
+
+    env:
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - 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}
+
+      - 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
+
+      - 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, '4.2' ) }}
+        shell: bash
+        run: echo "C:/Program Files/Git/usr/bin" >> $GITHUB_PATH
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,113 @@
+on:
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches:
+      - main
+      - dev
+
+name: R-CMD-check
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+        - {os: windows-latest, r: 'release'}
+        - {os: windows-latest, r: 'oldrel'}
+        - {os: macOS-latest, r: 'release'}
+        # - {os: macOS-latest, r: 'oldrel'}
+        - {os: ubuntu-latest, r: 'devel', rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest"}
+        - {os: ubuntu-latest, r: 'release', rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest"}
+        - {os: ubuntu-latest, r: 'oldrel', rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest"}
+
+    env:
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - 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}
+
+      - 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
+
+      - 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: R-CMD-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 = "R-CMD-check")
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: find R-CMD-check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload R-CMD-check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
+          path: R-CMD-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, '4.2' ) }}
+        shell: bash
+        run: echo "C:/Program Files/Git/usr/bin" >> $GITHUB_PATH
diff --git a/.github/workflows/coverage.yaml b/.github/workflows/coverage.yaml
@@ -0,0 +1,55 @@
+---
+# Workflow derived from https https://github.com/r-lib/actions/blob/v2/examples/test-coverage.yaml
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, dev]
+  pull_request:
+    branches: [main, dev]
+
+name: test-coverage
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/.github/workflows/lint-project.yaml b/.github/workflows/lint-project.yaml
@@ -0,0 +1,32 @@
+---
+# 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]
+  pull_request:
+    branches: [main, master]
+
+name: lint-project
+
+jobs:
+  lint-project:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install lintr
+        run: install.packages("lintr")
+        shell: Rscript {0}
+
+      - name: Lint root directory
+        run: lintr::lint_dir()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -0,0 +1,33 @@
+---
+# 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]
+  pull_request:
+    branches: [main, master]
+
+name: lint
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -2,15 +2,19 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, dev]
   pull_request:
-    branches: [main, master]
+    branches: [main, dev]
   release:
     types: [published]
   workflow_dispatch:
 
 name: pkgdown
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   pkgdown:
     runs-on: ubuntu-latest

diff --git a/.lintr b/.lintr
@@ -0,0 +1,4 @@
+linters: linters_with_defaults(
+    line_length_linter(120),
+    object_usage_linter = NULL
+  )