Benchmark / diffview against CRAN release v1.10.0

.Rbuildignore

@@ -7,6 +7,7 @@
 ^README-.*\.png$
 ^README\.Rmd$
 ^\.Rproj\.user$
+^\.dev$
 ^\.github$
 ^\.gitsum$
 ^\.lintr$
@@ -16,8 +17,11 @@
 ^doc$
 ^docs$
 ^gitsum$
+^hextools
 ^inst/WORDLIST$
+^inst/hextools$
 ^inst/hooks/.*$
+^pkgdown$
 ^revdep$
 ^tests/testmanual$
 ^tic\.R$

.github/workflows/check-full.yaml

@@ -12,33 +12,45 @@ jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
 
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }}) ${{ matrix.config.locale }}
 
     strategy:
       fail-fast: false
       matrix:
         config:
-          - {os: macos-latest,   r: 'release'}
+          - { os: macos-latest, r: "release" }
 
-          - {os: windows-latest, r: 'release'}
-          # Use 3.6 to trigger usage of RTools35
-          - {os: windows-latest, r: '3.6'}
+          - { os: windows-latest, r: "devel" }
+          - { os: windows-latest, r: "release" }
           # use 4.1 to check with rtools40's older compiler
-          - {os: windows-latest, r: '4.1'}
+          - { 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'}
+          - { os: ubuntu-latest, r: "devel", locale: "en_US", http-user-agent: "release" }
+          #- { os: ubuntu-latest, r: "release", locale: "zh_CN" }
+          - { 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:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - name: Set 'en_US' locale
+        if: matrix.config.locale == 'en_US'
+        run: |
+          sudo locale-gen en_US
+          echo "LC_ALL=en_US" >> $GITHUB_ENV
+
+      - name: Set 'zh_CN' locale
+        if: matrix.config.locale == 'zh_CN'
+        run: |
+          sudo locale-gen zh_CN
+          echo "LC_ALL=zh_CN" >> $GITHUB_ENV
+
+      - uses: actions/checkout@v5
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -50,12 +62,15 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
+          pak-version: devel
+          upgrade: "TRUE"
           extra-packages: any::rcmdcheck
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
-          error-on: 'ifelse(getRversion() > 3.6, "warning", "note")'
+          error-on: '"note"'
         env:
           _R_CHECK_FORCE_SUGGESTS_: false
+          _R_CHECK_STOP_ON_INVALID_NUMERIC_VERSION_INPUTS_: true

.github/workflows/check-no-warnings.yaml

@@ -0,0 +1,48 @@
+# execute all examples and tests with warnings turned into errors to look for new warnings
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: check-no-warnings
+
+jobs:
+   check-no-warnings:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          pak-version: devel
+          extra-packages: |
+            any::devtools
+            local::.
+
+      - name: Run examples
+        run: |
+          options(crayon.enabled = TRUE,  warn = 2L)
+          devtools::run_examples(fresh = TRUE, run_dontrun = TRUE, run_donttest = TRUE)
+        shell: Rscript {0}
+
+      - name: Run Tests
+        run: |
+            options(crayon.enabled = TRUE)
+            pkgload::load_all()
+            # this workaround needed to play nicely with parallel testing
+            # see: https://github.com/r-lib/testthat/issues/1912
+            test_script_paths <- testthat::find_test_scripts("tests/testthat")
+            test_with_warning_as_error <- function(path) {
+              withr::local_options(list(warn = 2L))
+              testthat::test_file(path, stop_on_failure = TRUE, stop_on_warning = TRUE)
+            }
+            purrr::walk(test_script_paths, test_with_warning_as_error)
+        shell: Rscript {0}

.github/workflows/pkgdown.yaml

@@ -20,7 +20,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v5
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -39,7 +39,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.2
+        uses: JamesIves/github-pages-deploy-action@v4.7.3
         with:
           clean: false
           branch: gh-pages

.github/workflows/pre-commit.yaml

@@ -18,26 +18,26 @@ jobs:
       )
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.11.0
+        uses: styfle/cancel-workflow-action@0.12.1
         with:
           access_token: ${{ github.token }}
-      - uses: actions/checkout@v3
+
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          # your system installation code here
-          # sudo apt-get install -y libcurl4-openssl-dev
+
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v6.0.0
         with:
-          python-version: "3.9"
-          architecture: "x64"
+          python-version: "3.13"
+
+      - uses: r-lib/actions/setup-r@v2
+
       - name: Run pre-commit
-        uses: pre-commit/action@v3.0.0
-        env: 
+        uses: pre-commit/action@v3.0.1
+        env:
           SKIP: pkgdown
+
       - name: Commit files
         if: failure() && startsWith(github.ref, 'refs/heads')
         run: |
@@ -47,12 +47,14 @@ jobs:
             git checkout -- .github/workflows
             git commit -m "pre-commit" -a
           fi
+
       - name: Push changes
         if: failure() && startsWith(github.ref, 'refs/heads')
         uses: ad-m/github-push-action@master
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           branch: ${{ github.ref }}
+
     env:
       RENV_CONFIG_CACHE_ENABLED: FALSE
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/test-coverage.yaml

@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v5
 
       - uses: r-lib/actions/setup-r@v2
         with:

.github/workflows/touchstone-receive.yaml

@@ -24,7 +24,7 @@ jobs:
       config: ${{ steps.read_touchstone_config.outputs.config }}
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0
 

.gitignore

@@ -1,16 +1,20 @@
+.DS_Store
 .RData
 .Rhistory
 .Rproj.user
 .gitsum
+.vscode
 Meta
 R/scratch
+README.html
 doc
 docs
 gitsum
 inst/doc
 revdep/
 !revdep/*.md
 !revdep/problems.md
+tests/testthat/*/*-in_tree
 touchstone/*
 !touchstone/config.json
 !touchstone/script.R

.lintr

@@ -1,27 +1,28 @@
-linters: linters_with_defaults(
-   commented_code_linter = NULL,
-   cyclocomp_linter = cyclocomp_linter(40),
-   fixed_regex_linter = NULL,
-   function_argument_linter = NULL,
-   indentation_linter = NULL,
-   line_length_linter(120),
-   namespace_linter = NULL,
-   nested_ifelse_linter = NULL,
-   object_name_linter = NULL,
-   object_length_linter(70),
-   object_usage_linter = NULL,
-   todo_comment_linter = NULL,
-   extraction_operator_linter = NULL,
-   nonportable_path_linter = NULL,
-   string_boundary_linter = NULL,
-   undesirable_function_linter = NULL,
-   undesirable_operator_linter = NULL,
-   defaults = linters_with_tags(tags = NULL)
- )
+linters: all_linters(
+    commented_code_linter = NULL,
+    cyclocomp_linter = cyclocomp_linter(40),
+    fixed_regex_linter = NULL,
+    function_argument_linter = NULL,
+    indentation_linter = NULL,
+    line_length_linter(120L),
+    namespace_linter = NULL,
+    nzchar_linter = NULL,
+    object_name_linter = NULL,
+    object_length_linter(70L),
+    object_overwrite_linter = NULL,
+    object_usage_linter = NULL,
+    nonportable_path_linter = NULL,
+    pipe_consistency_linter = NULL,
+    string_boundary_linter = NULL,
+    strings_as_factors_linter = NULL, # since we use R >= 4.0
+    todo_comment_linter = NULL,
+    undesirable_function_linter = NULL,
+    undesirable_operator_linter = NULL
+  )
 exclusions: list(
-  "inst",
-  "man",
-  "tests",
-  "touchstone",
-  "vignettes"
- )
+    "inst",
+    "man",
+    "tests",
+    "touchstone",
+    "vignettes"
+  )