Clean up (re-document, fix linters, update old magritr to native pipe)

[munoztd0]

As per we discussed runned a little clean up to be able to do the next PRs with ease of mind.

[Melkiades]

nice cleanup, pipe migration is thorough. one blocker though:

removing import(methods) (and the stats/utils importFroms) breaks the namespace load. R CMD check is 3 WARN 5 NOTE with could not find function "is" / "new". load_all hides it because it attaches the deps, only a real install/check shows it.

re-add @import methods + importFrom(stats, setNames, na.omit, quantile) + importFrom(utils, head, tail, head.matrix, tail.matrix) and it's good. prop.test/binom.test/relevel/tagList/%>% are actually unused now so dropping those is fine.

[shajoezhu]

omg! This finally happens! thanks so much man! @munoztd0

[Copilot]

Pull request overview

This PR modernizes the package’s examples/tests by migrating from magrittr piping to base R’s native pipe, and removes the magrittr dependency as part of a broader documentation / lint cleanup.

Changes:

• Replaced %>% with |> across vignettes, README(s), man pages, and tests.
• Removed magrittr from package dependencies and pre-commit setup, and updated generated NAMESPACE accordingly.
• Minor linter-style edits in a couple of R functions (e.g., avoiding explicit return() in tail position).

Reviewed changes

Copilot reviewed 118 out of 121 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
vignettes/title_footer.Rmd	Switch vignette examples from %>% to `
vignettes/tabulation_dplyr.Rmd	Switch vignette examples from %>% to `
vignettes/tabulation_concepts.Rmd	Switch vignette examples from %>% to `
vignettes/subsetting_tables.Rmd	Switch vignette examples from %>% to `
vignettes/split_functions.Rmd	Switch vignette examples from %>% to `
vignettes/sorting_pruning.Rmd	Switch vignette examples/prose from %>% to `
vignettes/rtables.Rmd	Switch vignette examples from %>% to `
vignettes/introspecting_tables.Rmd	Switch vignette examples from %>% to `
vignettes/guided_intermediate_translating_shells.Rmd	Switch vignette examples from %>% to `
vignettes/format_precedence.Rmd	Switch vignette examples from %>% to `
vignettes/example_analysis_coxreg.Rmd	Switch vignette examples from %>% to `
vignettes/dev-guide/dg_tabulation.Rmd	Switch dev-guide examples from %>% to `
vignettes/dev-guide/dg_table_hierarchy.Rmd	Switch dev-guide examples from %>% to `
vignettes/dev-guide/dg_split_machinery.Rmd	Switch dev-guide examples from %>% to `
vignettes/dev-guide/dg_printing.Rmd	Switch dev-guide examples from %>% to `
vignettes/dev-guide/dg_notes.Rmd	Switch dev-guide examples from %>% to `
vignettes/custom_appearance.Rmd	Switch vignette examples from %>% to `
vignettes/col_counts.Rmd	Switch vignette examples from %>% to `
vignettes/baseline.Rmd	Switch vignette examples from %>% to `
vignettes/ard_how_to.Rmd	Switch vignette examples from %>% to `
vignettes/advanced_usage.Rmd	Switch vignette examples from %>% to `
tests/testthat/test-sort-prune.R	Switch tests from %>% to `
tests/testthat/test-sanitize-struct.R	Switch tests from %>% to `
tests/testthat/test-result_data_frame.R	Switch tests from %>% to `
tests/testthat/test-pagination.R	Switch tests from %>% to `
tests/testthat/test-matrix_form.R	Switch tests from %>% to `
tests/testthat/test-make-afun.R	Switch tests from %>% to `
tests/testthat/test-indent-mod.R	Switch tests from %>% to `
tests/testthat/test-header-footer.R	Switch tests from %>% to `
tests/testthat/test-formatting.R	Switch tests from %>% to `
tests/testthat/test-exporters.R	Switch tests from %>% to `
tests/testthat/test-deprecated.R	Switch tests from %>% to `
tests/testthat/test-default_split_funs.R	Switch tests from %>% to `
tests/testthat/test-colby_constructors.R	Switch tests from %>% to `
tests/testthat/test-binding.R	Switch tests from %>% to `
tests/testthat/test-as_html.R	Switch tests from %>% to `
README.Rmd	Switch README examples from %>% to `
README.md	Switch README examples from %>% to `
R/Viewer.R	Update roxygen examples to use `
R/validate_table_struct.R	Small lint-style change (return(FALSE) → FALSE).
R/utils.R	Small lint-style change (avoid explicit return() in one branch).
R/tt_toString.R	Update roxygen examples to use `
R/tt_sort.R	Update roxygen examples to use `
R/tt_showmethods.R	Update roxygen examples to use `
R/tt_pos_and_access.R	Update roxygen examples to use `
R/tt_paginate.R	Update roxygen examples to use `
R/tt_export.R	Update roxygen examples to use `
R/tt_dotabulation.R	Update roxygen examples to use `
R/tt_compatibility.R	Update roxygen examples to use `
R/tt_compare_tables.R	Update roxygen examples to use `
R/tt_as_df.R	Update roxygen examples to use `
R/tt_afun_utils.R	Update roxygen examples to use `
R/tree_accessors.R	Update roxygen examples to use `
R/summary.R	Update roxygen examples to use `
R/package.R	Remove package-level roxygen import directives (now just \"_PACKAGE\").
R/make_split_fun.R	Update roxygen examples to use `
R/indent.R	Update roxygen examples to use `
R/default_split_funs.R	Update roxygen examples to use `
R/custom_split_funs.R	Update roxygen examples to use `
NAMESPACE	Remove magrittr/stats/utils importFrom lines and other import cleanup.
man/vil.Rd	Switch Rd examples from \\%>\\% to `
man/Viewer.Rd	Switch Rd examples from \\%>\\% to `
man/varcuts.Rd	Switch Rd examples from \\%>\\% to `
man/value_formats.Rd	Switch Rd examples from \\%>\\% to `
man/ttap.Rd	Switch Rd examples from \\%>\\% to `
man/trim_rows.Rd	Switch Rd examples from \\%>\\% to `
man/trim_prune_funs.Rd	Switch Rd examples from \\%>\\% to `
man/trim_levels_to_map.Rd	Switch Rd examples from \\%>\\% to `
man/tostring.Rd	Switch Rd examples from \\%>\\% to `
man/table_structure.Rd	Switch Rd examples from \\%>\\% to `
man/table_shell.Rd	Switch Rd examples from \\%>\\% to `
man/summarize_row_groups.Rd	Switch Rd examples from \\%>\\% to `
man/subset_cols.Rd	Switch Rd examples from \\%>\\% to `
man/split_rows_by.Rd	Switch Rd examples from \\%>\\% to `
man/split_rows_by_multivar.Rd	Switch Rd examples from \\%>\\% to `
man/split_funcs.Rd	Switch Rd examples from \\%>\\% to `
man/split_cols_by.Rd	Switch Rd examples from \\%>\\% to `
man/split_cols_by_multivar.Rd	Switch Rd examples from \\%>\\% to `
man/sort_at_path.Rd	Switch Rd examples from \\%>\\% to `
man/section_div.Rd	Switch Rd examples from \\%>\\% to `
man/sanitize_table_struct.Rd	Switch Rd examples from \\%>\\% to `
man/row_paths_summary.Rd	Switch Rd examples from \\%>\\% to `
man/rm_all_colcounts.Rd	Switch Rd examples from \\%>\\% to `
man/ref_fnotes.Rd	Switch Rd examples from \\%>\\% to `
man/reexports.Rd	Switch Rd examples from \\%>\\% to `
man/prune_table.Rd	Switch Rd examples from \\%>\\% to `
man/paginate.Rd	Switch Rd examples from \\%>\\% to `
man/matrix_form-VTableTree-method.Rd	Switch Rd examples from \\%>\\% to `
man/make_split_fun.Rd	Switch Rd examples from \\%>\\% to `
man/make_col_row_df.Rd	Switch Rd examples from \\%>\\% to `
man/label_at_path.Rd	Switch Rd examples from \\%>\\% to `
man/int_methods.Rd	Switch Rd examples from \\%>\\% to `
man/insert_rrow.Rd	Switch Rd examples from \\%>\\% to `
man/insert_row_at_path.Rd	Switch Rd examples from \\%>\\% to `
man/in_rows.Rd	Switch Rd examples from \\%>\\% to `
man/gfc.Rd	Switch Rd examples from \\%>\\% to `
man/facet_colcount.Rd	Switch Rd examples from \\%>\\% to `
man/do_base_split.Rd	Switch Rd examples from \\%>\\% to `
man/dimensions.Rd	Switch Rd examples from \\%>\\% to `
man/data.frame_export.Rd	Switch Rd examples from \\%>\\% to `
man/custom_split_funs.Rd	Switch Rd examples from \\%>\\% to `
man/coltree_structure.Rd	Switch Rd examples from \\%>\\% to `
man/clear_imods.Rd	Switch Rd examples from \\%>\\% to `
man/cell_values.Rd	Switch Rd examples from \\%>\\% to `
man/build_table.Rd	Switch Rd examples from \\%>\\% to `
man/brackets.Rd	Switch Rd examples from \\%>\\% to `
man/basic_table.Rd	Switch Rd examples from \\%>\\% to `
man/append_topleft.Rd	Switch Rd examples from \\%>\\% to `
man/analyze.Rd	Switch Rd examples from \\%>\\% to `
man/analyze_colvars.Rd	Switch Rd examples from \\%>\\% to `
man/add_overall_level.Rd	Switch Rd examples from \\%>\\% to `
man/add_overall_col.Rd	Switch Rd examples from \\%>\\% to `
man/add_existing_table.Rd	Switch Rd examples from \\%>\\% to `
man/add_combo_facet.Rd	Switch Rd examples from \\%>\\% to `
man/add_colcounts.Rd	Switch Rd examples from \\%>\\% to `
DESCRIPTION	Remove magrittr dependency + add contributor entry + adjust Config/Needs/verdepcheck.
.pre-commit-config.yaml	Remove magrittr from roxygenize hook dependencies.

Files not reviewed (3)

• man/Viewer.Rd: Generated file
• man/add_colcounts.Rd: Generated file
• man/add_combo_facet.Rd: Generated file

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[munoztd0]

omg! This finally happens! thanks so much man! @munoztd0

Anytime! Please let me know if you need this kinda of help enywhere else in the NEST ecosytem, I am always here to help/support it.

[Melkiades]

Good to go!! Thanks @munoztd0