options for strict tests; few enhancements

.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

@@ -50,14 +50,16 @@ Suggests:
     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,
+    gogolewski/stringi, tidymodels/broom, cran/car, tidyverse/dplyr,
+    davidgohel/flextable, yihui/knitr, davidgohel/officer, Merck/r2rtf,
+    r-lib/testthat, tidyverse/tibble, tidyverse/tidyr, r-lib/withr,
+    r-lib/xml2
 Encoding: UTF-8
 Language: en-US
 LazyData: true

NEWS.md

@@ -13,29 +13,29 @@
 ## rtables 0.6.6
 ### New Features
  * Removed `ref_group` reordering in column splits so not to change the order.
- * Added `bold` argument to `as_html` to bold specified elements, and `header_sep_line` 
+ * Added `bold` argument to `as_html` to bold specified elements, and `header_sep_line`
    argument to print a horizontal line under the table header in rendered HTML output.
  * Duplicate referential footnotes are consolidated when tables are rendered.
  * Section divisors can be set for analysis rows.
  * Added setter and getter for section dividers (`section_div` and `section_div<-`). They also accept
    split section structure assignment.
- * Added `header_section_div` setters and getters for layout and table objects along with 
+ * Added `header_section_div` setters and getters for layout and table objects along with
    related `basic_table` parameter.
  * Added `na_str` argument to `analyze_colvars` to set custom string to print in place of missing values.
- * Added flat `data.frame` outputs for `as_result_df()` via flag parameters `as_viewer`, `as_strings`, and 
+ * Added flat `data.frame` outputs for `as_result_df()` via flag parameters `as_viewer`, `as_strings`, and
    `expand_colnames`.
- * Migrated `export_as_pdf` function to `formatters`. 
- 
+ * Migrated `export_as_pdf` function to `formatters`.
+
 ### Bug Fixes
  * Fixed a bug that was failing when wrapping and section dividers were used at the same time.
  * Fixed a bug in `as_result_df` causing misalignment of column names.
- * Fixed a bug that was not allowing path indexing as `row_paths()` was giving a different path due to it being made of 
+ * Fixed a bug that was not allowing path indexing as `row_paths()` was giving a different path due to it being made of
    named values.
  * Fixed a bug in `as_result_df` when called on tables with less than 3 rows.
 
 ### Miscellaneous
  * Applied `styler` and resolved package lint. Changed default indentation from 4 spaces to 2.
- * Added Developer Guide to pkgdown site with Debugging, Split Machinery, and Tabulation sections.
+ * Added Developer Guide with Debugging, Split Machinery, and Tabulation sections.
  * Whitespace is not trimmed when rendering tables with `as_html`.
  * Started deprecation cycle for `col_fnotes_here` to be replaced with `col_footnotes`.
  * Exported `section_div` methods now have a dedicated documentation page that is visible to users.
@@ -82,7 +82,7 @@
  * Removed superfluous warning which arose for custom split functions when reference group is is set (https://github.com/insightsengineering/rtables/issues/707#issuecomment-1678810598).
  * Fixed `qtable` labeling via `row_labels` ([#698](https://github.com/insightsengineering/rtables/issues/698)).
  * Error catching and test coverage for cases where `alt_counts_df` presents different splits from `df`.
- 
+
 ### Miscellaneous
  * Cleaned up spelling in documentation ([#685](https://github.com/insightsengineering/rtables/issues/685))
  * Custom appearance vignette updated with decimal alignment support.
@@ -99,16 +99,16 @@
 
 ## rtables 0.6.1
  * Improved resilience of pagination machinery (`paginate_table`) by generalizing parameters' defaults (`cpp`, `lpp`, and `font_size`).
- * Moved `export_as_txt` to `formatters`. Added to reexports. 
+ * Moved `export_as_txt` to `formatters`. Added to reexports.
  * Migrated `export_as_rtf` to `formatters`. Not re-exported.
  * add `r2rtf` to Suggests
  * pagination logic has been migrated completely (excepting page_by splits) to `formatters` and is now invoked from there. paginate_table remains as a convenience function.
- * Removed warning in `str` method when called upon table objects. 
- * Provide `str` method for `VTableTree` objects with a default `max.level` of 3, as the infinite default from base is not 
+ * Removed warning in `str` method when called upon table objects.
+ * Provide `str` method for `VTableTree` objects with a default `max.level` of 3, as the infinite default from base is not
    useful or informative.
  * default `font_size` value is now `8` across pagination and export machinery
  * `margins` argument in pagination and export machinery now (correctly) interpreted as inches. This change is inherited from `formatters`
- * `lpp` and `cpp` now default to `NA_integer_`, which is interpreted as inferring their value from the physical page size specified. 
+ * `lpp` and `cpp` now default to `NA_integer_`, which is interpreted as inferring their value from the physical page size specified.
  * Horizontal pagination now occurs by default due to the above (because there is a default page type - `"letter"`. Pagination can still be turned off in either direction by setting `l/cpp` to `NULL` explicitly.
  * Referential footnotes now have both a `symbol` and an `index`. Messages associated with symbols will only appear once per page in the footer materials regardless of number of elements referenced in the page with that symbol. Matches and inherits from changes in `formatters`
  * Started deprecation cycle for `trim_zero_rows`.
@@ -143,7 +143,7 @@
  * `export_to_txt` now automatically paginates when any form of page dimension is provided
    (previously the default was unconditionally not paginating).
  * Versioned dependency on `formatters` increased to `>=0.4.0`
- 
+
 ## rtables 0.5.3
  * `[<-` now treats character `i` and `j` values as paths, the same as `[` always has.
  * `[<-` `CellValue` method now preserves `CellValue` attributes (e.g., format)
@@ -158,7 +158,7 @@
  * export functions now accepts `tf_wrap` and `max_width` and use them in both pagination (when turned on) *and* `toString` when used (pdf, txt exporters).
  * versioned dependency on `formatters` increased to `>0.3.3.10`
  * `export_as_pdf` now accepts standard page/font size parameters
- * original parameters (`width`, `height`, `fontsize` are soft deprecated (no warning) and 
+ * original parameters (`width`, `height`, `fontsize` are soft deprecated (no warning) and
    will be fully deprecated and then removed in the future.
  * `toString` method for `VTableTree` now accepts `tf_wrap` and `max_width`
  * `export_as_txt` and `export_as_pdf` now accept `cpp`, as well as `tf_wrap` and `max_width` and
@@ -187,7 +187,7 @@
  * Updated versioned dependency on `formatters` to `>=0.3.2.3`
  * Equivalent split functions with different enclosing environments (e.g., 2 identical calls to `add_combo_levels` [#340](https://github.com/insightsengineering/rtables/issues/304)) no longer block `rbind`ing
  * Fixed various documentation bugs where description section was being added to header.
- 
+
 ## rtables 0.5.1.4
  * empty level check for splitting variables reinstated.
 
@@ -201,7 +201,7 @@
  * `col_counts` getter and setter now accept `path` argument.
  * empty levels of a splitting variable now result in an informative error message (character and factor cases).
  * fixed bug in handling of column extra arguments that was preventing `cbind`ing tables from working correctly ([#324]](https://github.com/insightsengineering/rtables/issues/324))
- 
+
 ## rtables 0.5.1
  * empty factor levels are now *not* dropped for column splits when ref_group is set ([#323](https://github.com/insightsengineering/rtables/issues/323))
  * `linesep` argument to `toString` and related functions renamed to `hsep`
@@ -210,15 +210,15 @@
  * New `hsep` argument to `build_table` which sets the horizontal separator for the constructed table (and subtables thereof)
  * New `horizontal_sep` and `horizontal_sep<-` accessors for constructed tables, the latter of which is mandatorily recursive.
  * `split_rows_by(var, child_labels="hidden")` no longer removes the structural subtable corresponding to levels of `var` ([#314](https://github.com/insightsengineering/rtables/issues/314))
- 
+
 ## rtables 0.5.0
  * `formatable` dependency renamed to `formatters` for suitability of release to CRAN
- * Update versioned dependency of `formatters` (previously `formatable`) to `>=0.2.0` 
- 
+ * Update versioned dependency of `formatters` (previously `formatable`) to `>=0.2.0`
+
 ## rtables 0.4.1.0004
  * Fix bug when function format combined with NULL `cfun` caused error ([#307](https://github.com/insightsengineering/rtables/issues/307))
  * Fix bug in `path_enriched_df` (which powers `tsv` export), related to ([#308](https://github.com/insightsengineering/rtables/issues/308))
- 
+
 ## rtables 0.4.1.0002
  * added `table_shell` to display shell of table with formats
 
@@ -236,14 +236,14 @@
  * new `tt_to_flextable` coercion function
  * new `export_as_pdf` exporter function
  * `value_at` and `cell_values` functions now have methods for `TableRow` objects making them usable in sorting/pruning functions
- 
+
 ## rtables 0.3.8.9001
  * new `trim_levels_to_map` split function based on `[@wwojciech](https://github.com/wwojciech)`'s work in [#203](https://github.com/insightsengineering/rtables/issues/203)
  * support for column referential footnotes
  * support for adding footnotes to existing table via `fnotes_at_path<-` function
  * `trim_levels_in_group` now trims empty levels of outer (split) variable by default
  * `value_at` and `cell_values` now work for `tablerow` objects
- * Fixed `as_html` bug in `multivar` split columns case 
+ * Fixed `as_html` bug in `multivar` split columns case
  * Fixed pagination off-by-one error
 
 
@@ -319,8 +319,8 @@ tables in the context of clinical trials.
 
 ## rtables 0.3.2.17.9041
 
-* Allow single variable to be used within `split_cols_by_multivar` 
-* Various removal of defunct 
+* Allow single variable to be used within `split_cols_by_multivar`
+* Various removal of defunct
 
 ## rtables 0.3.2.17.9040
 
@@ -366,7 +366,7 @@ tables in the context of clinical trials.
 
 ## rtables 0.3.2.17.9027
 
-* issues with no news: 
+* issues with no news:
 
 ## rtables 0.1.7
 
@@ -389,7 +389,7 @@ tables in the context of clinical trials.
 * `col_by` in `rtabulate` now accepts matrices:
   - `col_by_to_matrix`, `col_by_to_factor`, `by_factor_to_matrix`.
   - `by_add_total`, `by_all`, `by_combine`, `by_quartile`, `by_compare_subset`,  `by_hierarchical`, `by_drop_empty_cols`.
-  
+
 * New utility functions to deal with variable labels:
   - `label`, `var_labels<-`, `var_labels`, `var_labels_remove`, `var_relabel`, `with_label`.
 

R/Viewer.R

@@ -12,7 +12,6 @@ NULL
 #' @return not meaningful. Called for the side effect of opening a browser or viewer pane.
 #'
 #' @examples
-#'
 #' if (interactive()) {
 #'   sl5 <- factor(iris$Sepal.Length > 5,
 #'     levels = c(TRUE, FALSE),

R/argument_conventions.R

@@ -53,7 +53,7 @@ NULL
 #' @param hsep character(1). Set of character(s) to be repeated as the separator
 #'   between the header and body of the table when rendered as text. Defaults to
 #'   a connected horizontal line (unicode 2014) in locals that use a UTF
-#'   charset, and to `-` elsewhere (with a once per session warning). See 
+#'   charset, and to `-` elsewhere (with a once per session warning). See
 #'   [formatters::set_default_hsep()] for further information.
 #' @param indent_size numeric(1). Number of spaces to use per indent level.
 #'   Defaults to 2
@@ -228,7 +228,7 @@ lyt_args <- function(lyt, var, vars, label, labels_var, varlabels, varnames, spl
 #'   represents a single facet.
 #' @param header_section_div character(1). String which will be used to divide the header
 #'   from the table. See [header_section_div()] for getter and setter of these.
-#'   Please consider changing last element of [section_div()] when concatenating 
+#'   Please consider changing last element of [section_div()] when concatenating
 #'   tables that need a divider between them.
 #' @param page_title character. Page specific title(s).
 #' @rdname constr_args