Merge pull request #560 from olivroy/ci

Update CI + apply some linting

.Rbuildignore

@@ -49,3 +49,4 @@ tests/testthat/test-utils_profiling.R
 tests/testthat/test-write_testthat_file.R
 tests/testthat/test-yaml.R
 tests/testthat/test-yaml_exec.R
+^.lintr$

.github/workflows/R-CMD-check.yaml

@@ -1,17 +1,23 @@
+# 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
+#
+# NOTE: This workflow is overkill for most R packages and
+# check-standard.yaml is likely a better choice.
+# usethis::use_github_action("check-standard") will install it.
 on:
   push:
-    branches:
-      - main
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
+    branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
-    
+
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
 
     strategy:
@@ -21,21 +27,18 @@ jobs:
           - {os: macos-latest,   r: 'release'}
 
           - {os: windows-latest, r: 'release'}
-          # # use 4.2 to check with rtools42's older compiler
-          - {os: windows-latest, r: '4.2'}
-          # # use 4.1 to check with rtools40's older compiler
-          - {os: windows-latest, r: '4.1'}
-
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
-          - {os: ubuntu-latest,   r: 'oldrel-2'}
-          - {os: ubuntu-latest,   r: 'oldrel-3'}
-          - {os: ubuntu-latest,   r: 'oldrel-4'}
+          # use 4.0 or 4.1 to check with rtools40's older compiler
+          - {os: windows-latest, r: 'oldrel-4'}
+
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
+          - {os: ubuntu-latest,  r: 'oldrel-2'}
+          - {os: ubuntu-latest,  r: 'oldrel-3'}
+          - {os: ubuntu-latest,  r: 'oldrel-4'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      GITHUB_PAT: ${{ secrets.GHA_PAT }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
@@ -57,3 +60,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/lint.yaml

@@ -1,56 +1,34 @@
-on: [push, pull_request]
+# 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
+name: lint.yaml
+
+permissions: read-all
 
 jobs:
   lint:
     runs-on: ubuntu-latest
-
     env:
-      GITHUB_PAT: ${{ secrets.GHA_PAT }}
-
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v2
-
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::.
-          needs: website
-
-      - name: Install package
-        run: R CMD INSTALL .
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("lintr")
-        shell: Rscript {0}
+          extra-packages: any::lintr, local::.
+          needs: lint
 
       - name: Lint
-        run: |
-          out <- 
-            lintr::lint_package(
-              linters = lintr::linters_with_defaults(
-                object_usage_linter = NULL,
-                trailing_whitespace_linter = NULL,
-                cyclocomp_linter = NULL,
-                indentation_linter = NULL
-              ),
-            exclusions = c(
-              list.files("tests", recursive = TRUE, full.names = TRUE),
-              list.files("man", recursive = TRUE, full.names = TRUE),
-              list.files("vignettes", recursive = TRUE, full.names = TRUE),
-              list.files("data-raw", recursive = TRUE, full.names = TRUE),
-              list.files("inst", recursive = TRUE, full.names = TRUE)
-            )
-          )
-          print(out)
-          if (length(out)) stop("lints found")
+        run: lintr::lint_package()
         shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.github/workflows/pkgdown.yaml

@@ -1,37 +1,50 @@
+# 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
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
     # Only restrict concurrency for non-PR jobs
     concurrency:
-       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
-      GITHUB_PAT: ${{ secrets.GHA_PAT }}
-
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-
-      - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::pkgdown, local::.
           needs: website
-
-      - name: Install package
-        run: R CMD INSTALL .
-
-      - name: Build and deploy pkgdown site
-        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: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -1,43 +1,61 @@
+# 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
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
+    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
-      GITHUB_PAT: ${{ secrets.GHA_PAT }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - 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
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
-
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.lintr

@@ -0,0 +1,14 @@
+linters: linters_with_defaults(
+  object_usage_linter = NULL,
+  trailing_whitespace_linter = NULL,
+  # cyclocomp_linter is no longer a default linter in lintr 3.2.0
+  cyclocomp_linter = NULL,
+  indentation_linter = NULL
+  )
+exclusions: list(
+  "tests",
+  "man",
+  "vignettes",
+  "data-raw",
+  "inst"
+  )

R/column_roles.R

@@ -805,7 +805,7 @@ get_column_role_character <- function(data_column) {
 
   }
 
-  return("string")
+  "string"
 }
 
 get_column_role_numeric <- function(data_column) {
@@ -864,7 +864,7 @@ get_column_role_numeric <- function(data_column) {
     return(paste0(role, "numeric.continuous"))
   }
 
-  return(paste0(role, "numeric"))
+  paste0(role, "numeric")
 }
 
 strptime_8601_formats <-

R/get_multiagent_report.R

@@ -1510,6 +1510,6 @@ generate_cell_content <- function(
 
     return(cell_content)
   }
-
+  NULL
   # nocov end
 }

R/has_columns.R

@@ -215,10 +215,10 @@ has_columns <- function(
       } 
       # Return length-0 vector if "column not found" or "0 columns" error
       return(character(0L))
-    } else {
-    ## If columns succesfully resolved to character, return only existing ones
-      return(intersect(columns, colnames(x)))
     }
+
+    ## If columns succesfully resolved to character, return only existing ones
+    intersect(columns, colnames(x))
   }
 
   # A list of columns (character vector) selected by elements of `columns`

R/interrogate.R

@@ -3161,7 +3161,7 @@ perform_action <- function(
     }
   }
 
-  return(NULL)
+  NULL
 }
 
 perform_end_action <- function(agent) {
@@ -3258,7 +3258,7 @@ perform_end_action <- function(agent) {
     y %>% rlang::f_rhs() %>% rlang::eval_tidy()
   })
 
-  return(NULL)
+  NULL
 }
 
 add_table_extract <- function(

R/utils.R

@@ -1633,16 +1633,14 @@ print_time <- function(time_diff_s) {
 
   if (time_diff_s < 1) {
     return("")
-  } else {
-    return(
-      paste0(
-        " {.time_taken (",
-        round(time_diff_s, 1) %>%
-          formatC(format = "f", drop0trailing = FALSE, digits = 1),
-        " s)}"
-      )
-    )
   }
+
+  paste0(
+    " {.time_taken (",
+    round(time_diff_s, 1) %>%
+      formatC(format = "f", drop0trailing = FALSE, digits = 1),
+    " s)}"
+  )
 }
 
 gt_missing <- 

R/validate_rmd.R

@@ -674,8 +674,7 @@ stop_if_not <- function(...) {
 
     return(TRUE)
 
-  } else {
-
-    return()
   }
+
+  NULL
 }