Use ui_transform_data on tm_gtsummary

[llrs-roche]

Pull Request

tm_gtsummary() didn't use the exported helpers from teal to handle decorators.
This should fix it. I also updated the NEWS to mention it (and a chore commit about pkgdown)

[github-actions]

Unit Tests Summary

    1 files   38 suites   4m 14s ⏱️
  684 tests 565 ✅ 119 💤 0 ❌
1 033 runs  914 ✅ 119 💤 0 ❌

Results for commit 2bbd945.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test suite performance difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
examples	💚	$5.31$	$-4.68$	$0$	$+41$	$0$	$0$
shinytest2-tm_a_pca	💚	$226.26$	$-225.17$	$-38$	$+11$	$0$	$0$
shinytest2-tm_a_regression	💚	$90.29$	$-89.65$	$-24$	$+7$	$0$	$0$
shinytest2-tm_data_table	💚	$37.24$	$-36.86$	$-6$	$+4$	$0$	$0$
shinytest2-tm_file_viewer	💚	$44.81$	$-43.51$	$-9$	$+4$	$0$	$0$
shinytest2-tm_front_page	💚	$33.42$	$-32.89$	$-6$	$+3$	$0$	$0$
shinytest2-tm_g_association	💚	$47.59$	$-47.05$	$-9$	$+4$	$0$	$0$
shinytest2-tm_g_bivariate	💚	$102.88$	$-102.52$	$-40$	$+4$	$0$	$0$
shinytest2-tm_g_distribution	💚	$118.40$	$-118.15$	$-17$	$+3$	$0$	$0$
shinytest2-tm_g_response	💚	$50.12$	$-49.78$	$-13$	$+4$	$0$	$0$
shinytest2-tm_g_scatterplot	💚	$141.76$	$-141.29$	$-30$	$+5$	$0$	$0$
shinytest2-tm_g_scatterplotmatrix	💚	$47.40$	$-46.82$	$-5$	$+4$	$0$	$0$
shinytest2-tm_missing_data	💚	$69.20$	$-68.38$	$-18$	$+4$	$0$	$0$
shinytest2-tm_outliers	💚	$176.31$	$-175.30$	$-51$	$+10$	$0$	$0$
shinytest2-tm_t_crosstable	💚	$50.75$	$-50.00$	$-5$	$+4$	$0$	$0$
shinytest2-tm_variable_browser	💚	$98.14$	$-97.50$	$-17$	$+6$	$0$	$0$
tm_file_viewer	💔	$2.78$	$+1.10$	$0$	$0$	$0$	$0$
tm_g_distribution	💔	$20.18$	$+1.62$	$0$	$0$	$0$	$0$
tm_gtsummary	💔	$9.28$	$+2.97$	$+3$	$0$	$0$	$0$
tm_outliers	💔	$50.02$	$+2.71$	$0$	$0$	$0$	$0$
variable_browser	💔	$66.48$	$+1.20$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
examples	💚	$2.03$	$-2.00$	example_add_facet_labels.Rd
shinytest2-tm_a_pca	💚	$15.81$	$-15.72$	e2e_tm_a_pca_Changing_output_encodings_for_plot_type_does_not_generate_errors.
shinytest2-tm_a_pca	💚	$10.94$	$-10.85$	e2e_tm_a_pca_Changing_output_encodings_of_NA_action_does_not_generate_errors.
shinytest2-tm_a_pca	💚	$73.95$	$-73.87$	e2e_tm_a_pca_Changing_output_encodings_of_font_size_does_not_generate_errors.
shinytest2-tm_a_pca	💚	$34.35$	$-34.26$	e2e_tm_a_pca_Changing_output_encodings_of_plot_type_hides_and_shows_options.
shinytest2-tm_a_pca	💚	$15.41$	$-15.33$	e2e_tm_a_pca_Changing_output_encodings_of_standardization_does_not_generate_errors.
shinytest2-tm_a_pca	💚	$11.41$	$-11.33$	e2e_tm_a_pca_Changing_output_encodings_of_tables_display_does_not_generate_errors.
shinytest2-tm_a_pca	💚	$12.46$	$-12.37$	e2e_tm_a_pca_Changing_output_encodings_of_theme_does_not_generate_errors.
shinytest2-tm_a_pca	💚	$14.64$	$-14.56$	e2e_tm_a_pca_Color_by_columns_data_extract_must_be_from_non_selected_variable_set.
shinytest2-tm_a_pca	💚	$11.26$	$-11.16$	e2e_tm_a_pca_Eigenvector_table_should_have_data_extract_selection_Murder_Assault_on_header.
shinytest2-tm_a_pca	💚	$14.29$	$-14.21$	e2e_tm_a_pca_Eigenvector_table_should_have_data_extract_selection_Murder_UrbanPop_on_header.
shinytest2-tm_a_pca	💚	$11.75$	$-11.53$	e2e_tm_a_pca_Module_is_initialised_with_the_specified_defaults_in_function_call.
shinytest2-tm_a_regression	💚	$9.69$	$-9.57$	e2e_tm_a_regression_Data_extract_spec_elements_are_initialized_with_the_default_values_specified_by_response_and_regressor_arg.
shinytest2-tm_a_regression	💚	$9.76$	$-9.66$	e2e_tm_a_regression_Data_parameter_and_module_label_is_passed_properly.
shinytest2-tm_a_regression	💚	$14.08$	$-14.00$	e2e_tm_a_regression_Outlier_definition_and_label_are_visible_by_default.
shinytest2-tm_a_regression	💚	$9.84$	$-9.75$	e2e_tm_a_regression_Outlier_definition_and_label_have_default_values_and_label_text.
shinytest2-tm_a_regression	💚	$20.05$	$-19.96$	e2e_tm_a_regression_Plot_type_has_7_specific_choices_changing_choices_does_not_throw_errors.
shinytest2-tm_a_regression	💚	$11.66$	$-11.57$	e2e_tm_a_regression_Plot_type_is_set_properly.
shinytest2-tm_a_regression	💚	$15.22$	$-15.14$	e2e_tm_a_regression_Unchecking_display_outlier_hides_outlier_label_and_definition.
shinytest2-tm_data_table	💚	$8.28$	$-8.18$	e2e_tm_data_table_Initializes_without_errors
shinytest2-tm_data_table	💚	$8.30$	$-8.20$	e2e_tm_data_table_Verify_checkbox_displayed_over_data_table
shinytest2-tm_data_table	💚	$9.29$	$-9.20$	e2e_tm_data_table_Verify_default_variable_selection_and_set_new_selection
shinytest2-tm_data_table	💚	$11.37$	$-11.27$	e2e_tm_data_table_Verify_module_displays_data_table
shinytest2-tm_file_viewer	💚	$9.70$	$-9.19$	e2e_tm_file_viewer_Initializes_without_errors_and_shows_files_tree_specified_in_input_path_argument
shinytest2-tm_file_viewer	💚	$11.67$	$-11.41$	e2e_tm_file_viewer_Shows_selected_image_file
shinytest2-tm_file_viewer	💚	$11.76$	$-11.50$	e2e_tm_file_viewer_Shows_selected_text_file
shinytest2-tm_file_viewer	💚	$11.68$	$-11.42$	e2e_tm_file_viewer_Shows_selected_url
shinytest2-tm_front_page	💚	$8.02$	$-7.87$	e2e_tm_front_page_Initializes_without_errors_and_check_html_elements
shinytest2-tm_front_page	💚	$13.09$	$-12.85$	e2e_tm_front_page_Verify_the_module_displays_metadata
shinytest2-tm_front_page	💚	$12.31$	$-12.17$	e2e_tm_front_page_Verify_the_module_displays_tables
shinytest2-tm_g_association	💚	$13.24$	$-13.12$	e2e_tm_g_association_Check_and_set_default_values_for_radio_buttons.
shinytest2-tm_g_association	💚	$12.56$	$-12.43$	e2e_tm_g_association_Data_extract_spec_elements_are_initialized_with_the_default_values_specified_by_ref_and_vars_arguments.
shinytest2-tm_g_association	💚	$9.83$	$-9.67$	e2e_tm_g_association_Data_parameter_and_module_label_is_passed_properly.
shinytest2-tm_g_association	💚	$11.96$	$-11.84$	e2e_tm_g_association_Module_plot_is_visible.
shinytest2-tm_g_bivariate	💚	$24.48$	$-24.39$	e2e_tm_g_bivariate_Coloring_options_are_hidden_when_coloring_is_toggled_off.
shinytest2-tm_g_bivariate	💚	$28.63$	$-28.54$	e2e_tm_g_bivariate_Facetting_options_are_hidden_when_facet_is_toggled_off.
shinytest2-tm_g_bivariate	💚	$10.98$	$-10.88$	e2e_tm_g_bivariate_Module_is_initialised_with_the_specified_defaults.
shinytest2-tm_g_bivariate	💚	$38.78$	$-38.70$	e2e_tm_g_bivariate_Setting_encoding_inputs_produces_outputs_without_validation_errors.
shinytest2-tm_g_distribution	💚	$24.09$	$-24.00$	e2e_tm_g_distribution_Histogram_encoding_inputs_produce_output_without_validation_errors.
shinytest2-tm_g_distribution	💚	$77.99$	$-77.91$	e2e_tm_g_distribution_Module_is_initialised_with_the_specified_defaults.
shinytest2-tm_g_distribution	💚	$16.32$	$-16.24$	e2e_tm_g_distribution_QQ_plot_encoding_inputs_produce_output_without_validation_errors.
shinytest2-tm_g_response	💚	$10.32$	$-10.24$	e2e_tm_g_response_deselecting_response_produces_validation_error.
shinytest2-tm_g_response	💚	$10.51$	$-10.43$	e2e_tm_g_response_deselecting_x_produces_validation_error.
shinytest2-tm_g_response	💚	$19.29$	$-19.19$	e2e_tm_g_response_encoding_inputs_produce_output_without_validation_errors.
shinytest2-tm_g_response	💚	$10.00$	$-9.92$	e2e_tm_g_response_module_is_initialised_with_the_specified_defaults.
shinytest2-tm_g_scatterplot	💚	$14.08$	$-13.98$	e2e_tm_g_scatterplot_Base_for_the_log_transformation_can_be_applied.
shinytest2-tm_g_scatterplot	💚	$12.12$	$-12.04$	e2e_tm_g_scatterplot_Get_validation_error_when_facetting_with_the_same_row_col_variable.
shinytest2-tm_g_scatterplot	💚	$10.52$	$-10.43$	e2e_tm_g_scatterplot_Module_is_initialised_with_the_specified_defaults.
shinytest2-tm_g_scatterplot	💚	$90.42$	$-90.33$	e2e_tm_g_scatterplot_The_encoding_inputs_are_set_without_validation_errors.
shinytest2-tm_g_scatterplot	💚	$14.61$	$-14.52$	e2e_tm_g_scatterplot_The_log_transform_is_only_possible_for_positive_numeric_vars.
shinytest2-tm_g_scatterplotmatrix	💚	$14.03$	$-13.89$	e2e_tm_g_scatterplotmatrix_Change_plot_settings
shinytest2-tm_g_scatterplotmatrix	💚	$9.90$	$-9.74$	e2e_tm_g_scatterplotmatrix_Initializes_without_errors
shinytest2-tm_g_scatterplotmatrix	💚	$11.37$	$-11.23$	e2e_tm_g_scatterplotmatrix_Verify_default_values_and_settings_data_extracts_for_data_selection
shinytest2-tm_g_scatterplotmatrix	💚	$12.11$	$-11.96$	e2e_tm_g_scatterplotmatrix_Verify_module_displays_data_table
shinytest2-tm_missing_data	💚	$19.76$	$-19.56$	e2e_tm_missing_data_Check_default_settings_and_visibility_of_the_combinations_graph_and_encodings
shinytest2-tm_missing_data	💚	$19.73$	$-19.52$	e2e_tm_missing_data_Default_settings_and_visibility_of_the_summary_graph
shinytest2-tm_missing_data	💚	$10.60$	$-10.39$	e2e_tm_missing_data_Initializes_without_errors
shinytest2-tm_missing_data	💚	$19.11$	$-18.91$	e2e_tm_missing_data_Validate_functionality_and_UI_response_for_By_Variable_Levels_
shinytest2-tm_outliers	💚	$16.55$	$-16.44$	e2e_tm_outliers_Data_extract_spec_elements_are_initialized_with_the_default_values_specified_by_outlier_var_and_categorical_var_argument.
shinytest2-tm_outliers	💚	$11.88$	$-11.78$	e2e_tm_outliers_Data_parameter_and_module_label_is_passed_properly.
shinytest2-tm_outliers	💚	$16.51$	$-16.41$	e2e_tm_outliers_Default_radio_buttons_are_set_properly.
shinytest2-tm_outliers	💚	$12.18$	$-12.08$	e2e_tm_outliers_Method_parameters_are_set_properly.
shinytest2-tm_outliers	💚	$12.25$	$-12.15$	e2e_tm_outliers_Module_is_divided_into_3_tabs.
shinytest2-tm_outliers	💚	$34.13$	$-34.03$	e2e_tm_outliers_Outlier_definition_text_and_range_are_displayed_properly_depending_on_method.
shinytest2-tm_outliers	💚	$16.03$	$-15.92$	e2e_tm_outliers_Outlier_table_is_displayed_with_proper_content.
shinytest2-tm_outliers	💚	$18.87$	$-18.77$	e2e_tm_outliers_Outliers_summary_table_is_displayed_with_proper_content.
shinytest2-tm_outliers	💚	$14.34$	$-14.25$	e2e_tm_outliers_Plot_type_is_correctly_set_by_default_and_has_appropriate_possible_options.
shinytest2-tm_outliers	💚	$23.58$	$-23.48$	e2e_tm_outliers_Plot_type_is_hidden_when_Boxplot_tab_is_not_selected.
shinytest2-tm_t_crosstable	💚	$15.29$	$-15.17$	e2e_tm_t_crosstable_Change_plot_settings
shinytest2-tm_t_crosstable	💚	$10.09$	$-9.71$	e2e_tm_t_crosstable_Initializes_without_errors
shinytest2-tm_t_crosstable	💚	$12.86$	$-12.74$	e2e_tm_t_crosstable_Verify_default_values_and_settings_data_extracts_for_data_selection
shinytest2-tm_t_crosstable	💚	$12.51$	$-12.39$	e2e_tm_t_crosstable_Verify_module_displays_data_table
shinytest2-tm_variable_browser	💚	$14.47$	$-14.36$	e2e_tm_variable_browser_Selecting_treat_variable_as_factor_changes_the_table_headers.
shinytest2-tm_variable_browser	💚	$16.51$	$-16.40$	e2e_tm_variable_browser_changing_display_density_encoding_doesn_t_show_errors.
shinytest2-tm_variable_browser	💚	$19.39$	$-19.28$	e2e_tm_variable_browser_changing_outlier_definition_encoding_doesn_t_show_errors.
shinytest2-tm_variable_browser	💚	$22.07$	$-21.97$	e2e_tm_variable_browser_changing_plot_setting_encodings_doesn_t_show_errors.
shinytest2-tm_variable_browser	💚	$13.05$	$-12.94$	e2e_tm_variable_browser_content_is_displayed_correctly.
shinytest2-tm_variable_browser	💚	$12.64$	$-12.54$	e2e_tm_variable_browser_selection_of_categorical_variable_has_a_table_with_level_header.
tm_gtsummary	💔	$2.07$	$+2.03$	tm_gtsummary_module_server_behavior_with_decorators_one_decorator_executes_successfully
variable_browser	💔	$11.06$	$+1.34$	UI_switches_and_controls_server_handles_different_outlier_definition_thresholds
variable_browser	💚	$5.00$	$-1.08$	testServer_for_data_exceptions_server_function_handles_different_ggplot_themes

Results for commit 03a5d42

♻️ This comment has been updated with latest results.

[averissimo]

💯

Missed something

[llrs-roche]

Thanks for the review. I updated the server part too. Good catch.

I also took the PR to add some validation on the module output.
maybe on that call we could provide a class: validate(errorClass = "teal-error")?

Sorry for not providing an app to test this, here is one now:

tm_gtsummary(
  by = teal.transform::data_extract_spec(
    dataname = "test_data",
    select = teal.transform::select_spec(
      choices = "am",
      selected = "am",
      multiple = FALSE
    )
  ),
  include = teal.transform::data_extract_spec(
    dataname = "test_data",
    select = teal.transform::select_spec(
      choices = c("carb", "cyl"),
      selected = c("carb", "cyl"),
      multiple = TRUE,
      fixed = FALSE
    )
  ),
  decorators = list(table = list(teal_transform_module(), teal_transform_module()))
) |> 
  init(data = teal_data(test_data = mtcars), modules = _) |> runApp()

[github-actions]

Code Coverage Summary

Filename                      Stmts    Miss  Cover    Missing
--------------------------  -------  ------  -------  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/geom_mosaic.R                  73       0  100.00%
R/tm_a_pca.R                    852       0  100.00%
R/tm_a_regression.R             751     391  47.94%   497-524, 531-534, 541-542, 546-556, 560, 564-576, 581-596, 601-623, 626-634, 638-666, 671-681, 684-710, 717-741, 744-769, 776-783, 786-812, 819-847, 850-875, 882-901, 904-930, 937-951, 954-980, 1005, 1009
R/tm_data_table.R               204      11  94.61%   110, 115-120, 225, 325, 330, 349
R/tm_file_viewer.R              172      50  70.93%   141-152, 156-163, 165-167, 172-182, 184, 204, 229-235, 237-238, 240, 244-250
R/tm_front_page.R               143       0  100.00%
R/tm_g_association.R            320      72  77.50%   226-294, 319, 325, 474, 488
R/tm_g_bivariate.R              672     196  70.83%   332-471, 505, 511-514, 585, 590, 595, 616-618, 655-658, 668-682, 684-685, 712-721, 763, 829, 940, 987, 989, 991, 998-1008
R/tm_g_distribution.R          1106      60  94.58%   412-420, 426-429, 468-469, 471, 473, 482, 484, 488-491, 495-498, 501, 513-514, 569, 580, 594, 889, 1073-1077, 1146-1150, 1152-1158, 1289-1292, 1310-1312, 1398-1399
R/tm_g_response.R               345      87  74.78%   184-185, 192, 198, 259-325, 348-352, 425, 430, 447-453, 531, 537, 550
R/tm_g_scatterplot.R            709     259  63.47%   359-501, 534-537, 575, 624, 636, 650, 667, 672, 698-711, 787-798, 837, 845-882, 894-896, 906-912, 919-921, 932-940, 942-943, 945, 949, 983-996, 1040, 1060
R/tm_g_scatterplotmatrix.R      272     110  59.56%   246-293, 357, 371-379, 396-437, 486-494, 562, 576
R/tm_gtsummary.R                152       1  99.34%   258
R/tm_missing_data.R            1180     167  85.85%   129, 488, 494, 507, 512, 532-538, 547-553, 620-635, 676, 680, 721, 739-746, 771, 787-790, 848-927, 931-933, 964-971, 1104, 1241, 1280, 1332-1334, 1344-1364, 1472, 1474, 1477-1478
R/tm_outliers.R                1029     186  81.92%   400, 428, 438-439, 441-442, 517-531, 533, 613, 616, 654-706, 709-747, 759, 790, 809, 812-827, 888-891, 965-993, 1117, 1220-1223, 1227, 1230-1233, 1239-1248, 1250, 1254-1263, 1266-1267, 1269
R/tm_rmarkdown.R                159       0  100.00%
R/tm_t_crosstable.R             263      56  78.71%   227-269, 292-293, 309, 318, 425, 438-447
R/tm_variable_browser.R         887      27  96.96%   395, 597, 812-826, 956, 984, 986, 1058-1059, 1067, 1165, 1246, 1278, 1310
R/utils.R                       142      15  89.44%   146, 177, 227, 288-291, 300-306, 314, 350, 353
R/zzz.R                           2       2  0.00%    2-3
TOTAL                          9433    1690  82.08%

Diff against main

Filename               Stmts    Miss  Cover
-------------------  -------  ------  -------
R/tm_gtsummary.R        +152      +1  +99.34%
R/tm_missing_data.R       +8       0  +0.10%
R/utils.R                -47      -6  +0.55%
TOTAL                   +113      -5  +0.27%

Results for commit: 2bbd945

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[averissimo]

💯