Merge branch 'main' into 785_colsubsetexpr_refactor

.github/workflows/check.yaml

@@ -3,9 +3,17 @@ name: Check 🛠
 
 on:
   pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
+    branches:
+      - main
   push:
     branches:
       - main
+  workflow_dispatch:
 
 jobs:
   audit:
@@ -33,34 +41,52 @@ jobs:
       unit-test-report-brand: >-
         https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/thumbs/rtables.png
   coverage:
-    if: github.event_name == 'pull_request'
     name: Coverage 📔
     uses: insightsengineering/r.pkg.template/.github/workflows/test-coverage.yaml@main
     secrets:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
-    with:
-      sd-direction: upstream
+  linter:
+    if: github.event_name != 'push'
+    name: SuperLinter 🦸‍♀️
+    uses: insightsengineering/r.pkg.template/.github/workflows/linter.yaml@main
   roxygen:
     name: Roxygen 🅾
     uses: insightsengineering/r.pkg.template/.github/workflows/roxygen.yaml@main
     secrets:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
     with:
-      sd-direction: upstream
+      auto-update: true
   gitleaks:
     name: gitleaks 💧
     uses: insightsengineering/r.pkg.template/.github/workflows/gitleaks.yaml@main
+  spelling:
+    name: Spell Check 🆎
+    uses: insightsengineering/r.pkg.template/.github/workflows/spelling.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
   links:
-    if: github.event_name == 'pull_request'
+    if: github.event_name != 'push'
     name: Check URLs 🌐
     uses: insightsengineering/r.pkg.template/.github/workflows/links.yaml@main
-  version:
-    name: Version Check 🏁
-    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
-    uses: insightsengineering/r.pkg.template/.github/workflows/version.yaml@main
   vbump:
     name: Version Bump 🤜🤛
     if: github.event_name == 'push'
     uses: insightsengineering/r.pkg.template/.github/workflows/version-bump.yaml@main
     secrets:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
+  version:
+    name: Version Check 🏁
+    uses: insightsengineering/r.pkg.template/.github/workflows/version.yaml@main
+  licenses:
+    name: License Check 🃏
+    uses: insightsengineering/r.pkg.template/.github/workflows/licenses.yaml@main
+  style:
+    if: github.event_name != 'push'
+    name: Style Check 👗
+    uses: insightsengineering/r.pkg.template/.github/workflows/style.yaml@main
+    with:
+      auto-update: true
+  grammar:
+    if: github.event_name != 'push'
+    name: Grammar Check 🔤
+    uses: insightsengineering/r.pkg.template/.github/workflows/grammar.yaml@main

.pre-commit-config.yaml

@@ -1,23 +1,24 @@
+---
 # All available hooks: https://pre-commit.com/hooks.html
 # R specific hooks: https://github.com/lorenzwalthert/precommit
+default_stages: [commit]
+default_language_version:
+  python: python3
 repos:
--   repo: https://github.com/lorenzwalthert/precommit
+  - repo: https://github.com/lorenzwalthert/precommit
     rev: v0.4.0
     hooks:
-    -   id: roxygenize
-        # roxygen requires loading pkg -> add dependencies from DESCRIPTION
+      - id: roxygenize
         additional_dependencies:
-        - formatters
-        - magrittr
-        - methods
-        - checkmate
-        - htmltools
-        - stats
-        - stringi
-    # codemeta must be above use-tidy-description when both are used
-    # -   id: codemeta-description-updated
-    -   id: use-tidy-description
-    -   id: spell-check
+          - formatters
+          - magrittr
+          - methods
+          - checkmate
+          - htmltools
+          - stats
+          - stringi
+      - id: use-tidy-description
+      - id: spell-check
         exclude: >
           (?x)^(
           .*\.[rR]|
@@ -40,40 +41,44 @@ repos:
           (.*/|)\.Rprofile|
           (.*/|)\.travis\.y[a]?ml|
           (.*/|)appveyor\.y[a]?ml|
+          (.*/|)CODEOWNERS|
+          (.*/|)DESCRIPTION|
+          (.*/|)LICENSE|
           (.*/|)NAMESPACE|
+          (.*/|)staged_dependencies\.y[a]?ml|
           (.*/|)renv/settings\.dcf|
           (.*/|)renv\.lock|
           (.*/|)WORDLIST|
           \.github/workflows/.*|
           data/.*|
           )$
-    -   id: readme-rmd-rendered
-    -   id: parsable-R
-    -   id: no-browser-statement
-    -   id: no-debug-statement
-    -   id: deps-in-desc
--   repo: https://github.com/pre-commit/pre-commit-hooks
+      - id: readme-rmd-rendered
+      - id: parsable-R
+      - id: no-browser-statement
+      - id: no-debug-statement
+      - id: deps-in-desc
+  - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
     hooks:
-    -   id: check-added-large-files
+      - id: check-added-large-files
         args: ['--maxkb=200']
-    -   id: file-contents-sorter
+      - id: file-contents-sorter
         files: '^\.Rbuildignore$'
-    -   id: end-of-file-fixer
+      - id: end-of-file-fixer
         exclude: '\.Rd'
--   repo: https://github.com/pre-commit-ci/pre-commit-ci-config
+  - repo: https://github.com/pre-commit-ci/pre-commit-ci-config
     rev: v1.6.1
     hooks:
     # Only reuiqred when https://pre-commit.ci is used for config validation
-    -   id: check-pre-commit-ci-config
--   repo: local
+      - id: check-pre-commit-ci-config
+  - repo: local
     hooks:
-    -   id: forbid-to-commit
+      - id: forbid-to-commit
         name: Don't commit common R artifacts
         entry: Cannot commit .Rhistory, .RData, .Rds or .rds.
         language: fail
         files: '\.(Rhistory|RData|Rds|rds)$'
         # `exclude: <regex>` to allow committing specific files
 
 ci:
-    autoupdate_schedule: monthly
+  autoupdate_schedule: monthly

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rtables
 Title: Reporting Tables
-Version: 0.6.6.9010
+Version: 0.6.6.9011
 Date: 2024-02-23
 Authors@R: c(
     person("Gabriel", "Becker", , "[email protected]", role = "aut",
@@ -29,7 +29,7 @@ URL: https://github.com/insightsengineering/rtables,
     https://insightsengineering.github.io/rtables/
 BugReports: https://github.com/insightsengineering/rtables/issues
 Depends:
-    formatters (>= 0.5.5),
+    formatters (>= 0.5.5.9005),
     magrittr (>= 1.5),
     methods,
     R (>= 2.10)
@@ -46,18 +46,21 @@ Suggests:
     knitr (>= 1.42),
     officer (>= 0.5.0),
     r2rtf (>= 0.3.2),
+    rmarkdown (>= 2.19),
     survival (>= 3.3-1),
     testthat (>= 3.0.4),
     tibble (>= 3.2.1),
     tidyr (>= 1.1.3),
+    withr (>= 2.0.0),
     xml2 (>= 1.1.0)
 VignetteBuilder:
     knitr
 Config/Needs/verdepcheck: insightsengineering/formatters,
-    tidyverse/magrittr, rstudio/htmltools, tidymodels/broom, cran/car,
-    mllg/checkmate, tidyverse/dplyr, davidgohel/flextable, yihui/knitr,
-    davidgohel/officer, Merck/r2rtf, r-lib/testthat, tidyverse/tibble,
-    tidyverse/tidyr, r-lib/xml2
+    tidyverse/magrittr, mllg/checkmate, rstudio/htmltools,
+    gagolews/stringi, tidymodels/broom, cran/car, tidyverse/dplyr,
+    davidgohel/flextable, yihui/knitr, davidgohel/officer, Merck/r2rtf,
+    rstudio/rmarkdown, r-lib/testthat, tidyverse/tibble, tidyverse/tidyr, r-lib/withr,
+    r-lib/xml2
 Encoding: UTF-8
 Language: en-US
 LazyData: true