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Create test snapshots & upgrade to testthat 3rd edition #801

Merged
merged 13 commits into from
Jan 19, 2023
Merged

Create test snapshots & upgrade to testthat 3rd edition #801

merged 13 commits into from
Jan 19, 2023

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edelarua
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Closes #784 and #656

@edelarua edelarua added documentation Improvements or additions to documentation enhancement sme labels Jan 19, 2023
@edelarua edelarua linked an issue Jan 19, 2023 that may be closed by this pull request
Upgrade testthat to use 3rd edition #656
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github-actions bot commented Jan 19, 2023 •
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Code Coverage Summary

Filename                                   Stmts    Miss  Cover    Missing
---------------------------------------  -------  ------  -------  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/abnormal_by_baseline.R                      63       0  100.00%
R/abnormal_by_marked.R                        52       5  90.38%   124-128
R/abnormal_by_worst_grade_worsen.R           113       3  97.35%   205-207
R/abnormal_by_worst_grade.R                   37       0  100.00%
R/abnormal.R                                  40       0  100.00%
R/analyze_vars_in_cols.R                      37       0  100.00%
R/combination_function.R                       9       0  100.00%
R/compare_variables.R                        138       3  97.83%   135, 247, 266
R/control_incidence_rate.R                    10       0  100.00%
R/control_logistic.R                           7       0  100.00%
R/control_step.R                              23       1  95.65%   58
R/control_survival.R                          15       0  100.00%
R/count_cumulative.R                          47       1  97.87%   52
R/count_missed_doses.R                        31       0  100.00%
R/count_occurrences_by_grade.R                84       3  96.43%   148, 163-164
R/count_occurrences.R                         61       1  98.36%   89
R/count_patients_events_in_cols.R             67       0  100.00%
R/count_patients_with_event.R                 72       0  100.00%
R/count_values.R                              24       0  100.00%
R/cox_regression_inter.R                     142       0  100.00%
R/cox_regression.R                           318       0  100.00%
R/coxph.R                                    168       7  95.83%   232-236, 281, 297, 306, 312-313
R/d_pkparam.R                                405       0  100.00%
R/decorate_grob.R                            167       6  96.41%   271-277, 384, 416, 426, 433
R/desctools_binom_diff.R                     668      68  89.82%   65, 100-101, 141-142, 145, 224, 250-261, 300, 302, 322, 326, 330, 334, 386, 389, 392, 395, 456, 464, 476-477, 483-486, 494, 497, 506, 509, 557-558, 560-561, 563-564, 566-567, 640, 652-665, 670, 717, 730, 734
R/df_explicit_na.R                            30       0  100.00%
R/estimate_multinomial_rsp.R                  47       1  97.87%   53
R/estimate_proportion.R                      198      10  94.95%   421-428, 432, 437, 545
R/fit_rsp_step.R                              36       0  100.00%
R/fit_survival_step.R                         36       0  100.00%
R/footnotes.R                                  5       0  100.00%
R/formats.R                                  115       3  97.39%   101, 138, 148
R/g_forest.R                                 441      26  94.10%   200, 252-253, 257-258, 326, 343-344, 349-350, 363, 379, 426, 457, 533, 542, 628-634, 637, 705, 708, 834
R/g_lineplot.R                               199      29  85.43%   177, 190, 218, 244-247, 324-331, 349-350, 356-366, 464, 472
R/g_step.R                                    68       1  98.53%   106
R/g_waterfall.R                               47       0  100.00%
R/h_adsl_adlb_merge_using_worst_flag.R        74       0  100.00%
R/h_biomarkers_subgroups.R                    38       0  100.00%
R/h_map_for_count_abnormal.R                  54       0  100.00%
R/h_pkparam_sort.R                            15       0  100.00%
R/h_response_biomarkers_subgroups.R           74       0  100.00%
R/h_response_subgroups.R                     171      12  92.98%   248-261
R/h_stack_by_baskets.R                        65       2  96.92%   96, 143
R/h_step.R                                   180       0  100.00%
R/h_survival_biomarkers_subgroups.R           78       0  100.00%
R/h_survival_duration_subgroups.R            200      12  94.00%   254-266
R/incidence_rate.R                            93       7  92.47%   69-76
R/individual_patient_plot.R                  133       0  100.00%
R/kaplan_meier_plot.R                        532      29  94.55%   256-260, 456, 627-629, 637-639, 665, 672-673, 845, 1030, 1272-1283
R/logistic_regression.R                      569       3  99.47%   279-280, 347
R/missing_data.R                              20       3  85.00%   29, 61, 71
R/odds_ratio.R                               106       0  100.00%
R/prop_diff_test.R                            87       0  100.00%
R/prop_diff.R                                255      11  95.69%   56-63, 190, 364, 508
R/prune_occurrences.R                         57       0  100.00%
R/response_biomarkers_subgroups.R             59       0  100.00%
R/response_subgroups.R                       164       0  100.00%
R/rtables_access.R                            36       0  100.00%
R/score_occurrences.R                         20       1  95.00%   119
R/split_cols_by_groups.R                      49       0  100.00%
R/stat.R                                      47       0  100.00%
R/summarize_ancova.R                          95       1  98.95%   198
R/summarize_change.R                          27       0  100.00%
R/summarize_colvars.R                          6       0  100.00%
R/summarize_glm_count.R                      164       4  97.56%   169, 174, 237, 306
R/summarize_num_patients.R                    65       5  92.31%   92-94, 185-186
R/summarize_patients_exposure_in_cols.R       46       0  100.00%
R/summarize_variables.R                      212       1  99.53%   477
R/survival_biomarkers_subgroups.R             59       0  100.00%
R/survival_coxph_pairwise.R                   73       9  87.67%   69-77
R/survival_duration_subgroups.R              171       0  100.00%
R/survival_time.R                             47       0  100.00%
R/survival_timepoint.R                       114       7  93.86%   147-153
R/utils_checkmate.R                           68       0  100.00%
R/utils_factor.R                              86       1  98.84%   93
R/utils_grid.R                               111       5  95.50%   150, 260-266
R/utils_rtables.R                             84       2  97.62%   344-345
R/utils.R                                    137      10  92.70%   100, 102, 106, 126, 129, 132, 136, 145-146, 334
R/wrap_text.R                                 66       5  92.42%   39, 60, 80, 87, 109
TOTAL                                       8827     298  96.62%

Diff against main

Filename        Stmts    Miss  Cover
------------  -------  ------  -------
R/g_forest.R        0     -16  +3.63%
TOTAL               0     -16  +0.18%

Results for commit: ac0b98d

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

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github-actions bot commented Jan 19, 2023 •
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Unit Tests Summary

       1 files     134 suites   2m 39s ⏱️
   879 tests    879 ✔️     0 💤 0 ❌
1 495 runs  1 335 ✔️ 160 💤 0 ❌

Results for commit 24fd6d5.

♻️ This comment has been updated with latest results.

Melkiades
Melkiades requested changes Jan 19, 2023
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@Melkiades Melkiades left a comment •
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Really amazing job Emily! With this, I think we can split scda in a couple of days during next week. Also, well done including testthat 3! I think you need to specify it also in the DESCRIPTION (Set the Config/testthat/edition field to 3).

Fix the error in the new test:

  ── Error ('test-g_forest.R:4'): (code run outside of `test_that()`) ────────────
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `dplyr::mutate(., ARM = fct_relevel(ARM, "B: Placebo"), rsp = AVALC == 
      "CR")`: Problem while computing `ARM = fct_relevel(ARM, "B: Placebo")`.
  Caused by error in `fct_relevel()`:
  ! could not find function "fct_relevel"

The other comments are not super necessary but take a look at them, they are fast fixes.

I read (beside the guide from testthat itself), this summary guide, and I think we should add a note to the future tern tests that highlights the need of proper test naming. I think it is already almost there. We need just to make sure of this (I think with test-g_forest.R you moved already towards this).

PS: I did not check if you changed everything already but it looks like it and I trust you ;)

Melkiades
Melkiades approved these changes Jan 19, 2023
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Lgtm!! Great, great job @edelarua ^^

fyi @shajoezhu

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AMAZING! Thanks so much @edelarua

@edelarua edelarua merged commit 872f99e into main Jan 19, 2023
@edelarua edelarua deleted the 784_table_snapshots@main branch January 19, 2023 18:01
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Update table (and all) tests to check also correct indentation Upgrade testthat to use 3rd edition
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@edelarua @shajoezhu @Melkiades