Faster testing with reduced number of levels

[Melkiades]

Ideally, we should be able to do tests with snapshot file sizes below 100Kbs. Before this I was getting stuck for tens of minutes on aet04 and I think we need this working faster and w/ lower memory footprint (it is impossible otherwise to review differences between versions). @zdz2101 can you help me track down if this is too much for the current test coverage?

The following reductions have been done in this PR:

Reducing levels of adae_pharmaverse for variable AEDECOD: keeping 15 levels out of 242 levels. Total kept (%): 46.8
Reducing levels of adlb_pharmaverse for variable PARAM: keeping 10 levels out of 49 levels. Total kept (%): 24.1

Fixes #127

[github-actions]

Unit Tests Summary

  1 files  111 suites   3m 4s ⏱️
245 tests 215 ✅  30 💤 0 ❌
480 runs  237 ✅ 243 💤 0 ❌

Results for commit b6adcce.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test suite performance difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
listing_lbl01	💚	$2.11$	$-1.60$	$0$	$0$	$0$	$0$
listing_lbl01_rls	💚	$2.11$	$-1.60$	$0$	$0$	$0$	$0$
listing_lbl02a_rls	💚	$3.24$	$-2.44$	$-1$	$0$	$0$	$0$
pagination_listing	💚	$9.37$	$-3.68$	$0$	$0$	$0$	$0$
pagination_table	💚	$25.85$	$-13.67$	$0$	$0$	$0$	$0$
table_aet01	💚	$3.51$	$-1.66$	$0$	$0$	$0$	$0$
table_aet01_aesi	💚	$5.22$	$-2.43$	$0$	$0$	$0$	$0$
table_aet02	💚	$128.76$	$-120.60$	$0$	$0$	$0$	$0$
table_aet03	💚	$37.53$	$-35.88$	$0$	$0$	$0$	$0$
table_aet04	💚	$372.37$	$-366.07$	$0$	$0$	$0$	$0$
table_aet04_pi	💚	$76.58$	$-69.56$	$0$	$0$	$0$	$0$
table_aet06	💚	$75.70$	$-71.97$	$0$	$0$	$0$	$0$
table_aet09	💚	$29.53$	$-27.56$	$0$	$0$	$0$	$0$
table_aet10	💚	$1.72$	$-1.59$	$0$	$0$	$0$	$0$
table_cmht01	💚	$3.29$	$-1.48$	$0$	$0$	$0$	$0$
table_cmt01	💚	$2.68$	$-1.17$	$0$	$0$	$0$	$0$
table_cmt01a	💚	$5.69$	$-2.60$	$0$	$0$	$0$	$0$
table_cmt01b	💚	$6.37$	$-2.93$	$0$	$0$	$0$	$0$
table_coxt01	💚	$3.22$	$-1.29$	$0$	$0$	$0$	$0$
table_disclosures	💚	$3.42$	$-1.73$	$0$	$0$	$0$	$0$
table_dmt01	💚	$4.97$	$-2.36$	$0$	$0$	$0$	$0$
table_dort01	💚	$2.77$	$-1.37$	$0$	$0$	$0$	$0$
table_dtht01	💚	$2.11$	$-1.06$	$0$	$0$	$0$	$0$
table_egt01	💚	$3.12$	$-1.58$	$0$	$0$	$0$	$0$
table_egt03	💚	$2.42$	$-1.20$	$0$	$0$	$0$	$0$
table_ent	💚	$28.52$	$-13.41$	$0$	$0$	$0$	$0$
table_ext01	💚	$3.10$	$-1.61$	$0$	$0$	$0$	$0$
table_lbt01	💚	$4.89$	$-2.91$	$0$	$0$	$0$	$0$
table_lbt02	💚	$2.73$	$-1.41$	$0$	$0$	$0$	$0$
table_lbt04	💚	$5.85$	$-4.60$	$0$	$0$	$0$	$0$
table_lbt05	💚	$37.07$	$-30.38$	$0$	$0$	$0$	$0$
table_lbt07	💚	$7.01$	$-4.61$	$0$	$0$	$0$	$0$
table_lbt10	💚	$2.53$	$-1.25$	$0$	$0$	$0$	$0$
table_lbt13	💚	$5.39$	$-2.98$	$0$	$0$	$0$	$0$
table_lbt14	💚	$175.11$	$-143.86$	$0$	$0$	$0$	$0$
table_lbt15	💚	$4.15$	$-2.68$	$0$	$0$	$0$	$0$
table_lgrt02	💚	$5.51$	$-2.30$	$0$	$0$	$0$	$0$
table_mht01	💚	$2.78$	$-1.36$	$0$	$0$	$0$	$0$
table_onct05	💚	$3.49$	$-1.76$	$0$	$0$	$0$	$0$
table_pkct01	💚	$2.36$	$-1.13$	$0$	$0$	$0$	$0$
table_pkpt03	💚	$2.24$	$-1.17$	$0$	$0$	$0$	$0$
table_pkpt05	💚	$2.02$	$-1.06$	$0$	$0$	$0$	$0$
table_rmpt06	💚	$2.85$	$-1.39$	$0$	$0$	$0$	$0$
table_rspt01	💚	$4.62$	$-2.37$	$0$	$0$	$0$	$0$
table_ttet01	💚	$6.48$	$-3.22$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
listing_lbl01	💚	$2.11$	$-1.60$	LBL01_listing_is_produced_correctly
listing_lbl01_rls	💚	$2.11$	$-1.60$	LBL01_RLS_listing_is_produced_correctly
listing_lbl02a_rls	💚	$3.24$	$-2.44$	LBL02A_RLS_listing_is_produced_correctly
pagination_listing	💚	$4.33$	$-1.31$	Direct_pagination_works_fine
pagination_listing	💚	$5.04$	$-2.37$	pagination_counts_the_right_number_of_lines_when_wrapping_on_keycols_is_present
pagination_table	💚	$3.23$	$-1.52$	AET04_variant_2_page_by_pagination_tests
pagination_table	💚	$3.95$	$-2.10$	Direct_pagination_with_standard_values
pagination_table	💚	$3.04$	$-1.63$	Pagination_with_specific_column_widths_and_minimum_lines_per_page
pagination_table	💚	$10.95$	$-6.06$	Pagination_works_also_if_table_is_decorated
pagination_table	💚	$3.19$	$-1.61$	Pagination_works_for_page_types
table_aet02	💚	$5.53$	$-5.03$	AET02_variant_10_is_produced_correctly
table_aet02	💚	$6.75$	$-6.21$	AET02_variant_11_is_produced_correctly
table_aet02	💚	$5.23$	$-4.73$	AET02_variant_12_is_produced_correctly
table_aet02	💚	$8.11$	$-7.32$	AET02_variant_1_is_produced_correctly
table_aet02	💚	$9.16$	$-8.27$	AET02_variant_2_is_produced_correctly
table_aet02	💚	$38.35$	$-36.82$	AET02_variant_3_is_produced_correctly
table_aet02	💚	$3.56$	$-3.36$	AET02_variant_4_is_produced_correctly
table_aet02	💚	$5.78$	$-5.17$	AET02_variant_5_is_produced_correctly
table_aet02	💚	$5.32$	$-4.82$	AET02_variant_6_is_produced_correctly
table_aet02	💚	$29.93$	$-28.82$	AET02_variant_7_is_produced_correctly
table_aet02	💚	$5.37$	$-4.88$	AET02_variant_8_is_produced_correctly
table_aet02	💚	$5.67$	$-5.15$	AET02_variant_9_is_produced_correctly
table_aet03	💚	$37.53$	$-35.88$	AET03_variant_1_is_produced_correctly
table_aet04	💚	$12.08$	$-11.74$	AET04_variant_11_is_produced_correctly_with_Incidence_Rate_of_at_Least_X_all_SOCs_w_o_preferred_terms_removed_
table_aet04	💚	$70.26$	$-69.17$	AET04_variant_1_is_produced_correctly
table_aet04	💚	$41.17$	$-40.20$	AET04_variant_2_is_produced_correctly_Fill_in_of_Treatment_Groups_
table_aet04	💚	$81.92$	$-80.86$	AET04_variant_3_is_produced_correctly_Fill_in_of_Grades_
table_aet04	💚	$68.68$	$-67.62$	AET04_variant_4_is_produced_correctly_Collapsing_of_Grades_grades_1_2_grades_3_4_5_
table_aet04	💚	$73.01$	$-71.89$	AET04_variant_6_is_produced_correctly_with_an_Incidence_Rate_of_at_Least_5_totals_restricted_
table_aet04	💚	$13.36$	$-13.03$	AET04_variant_8_is_produced_correctly_with_an_Incidence_Rate_of_at_Least_X_Patients_
table_aet04	💚	$11.90$	$-11.57$	AET04_variant_9_is_produced_correctly_with_a_Difference_in_Incidence_Rate_of_at_Least_X_
table_aet04_pi	💚	$9.96$	$-9.13$	AET04_PI_full_table_is_produced_correctly
table_aet04_pi	💚	$8.23$	$-7.42$	AET04_PI_variant_1_is_produced_correctly
table_aet04_pi	💚	$11.77$	$-10.90$	AET04_PI_variant_2_is_produced_correctly
table_aet04_pi	💚	$8.49$	$-7.71$	AET04_PI_variant_3_is_produced_correctly
table_aet04_pi	💚	$7.76$	$-7.03$	AET04_PI_variant_4_is_produced_correctly
table_aet04_pi	💚	$8.07$	$-7.27$	AET04_PI_variant_5_is_produced_correctly
table_aet04_pi	💚	$9.84$	$-8.70$	AET04_PI_variant_6_is_produced_correctly
table_aet04_pi	💚	$9.68$	$-8.84$	AET04_PI_variant_7_is_produced_correctly
table_aet04_pi	💚	$2.79$	$-2.55$	AET04_PI_variant_8_is_produced_correctly
table_aet06	💚	$9.25$	$-8.46$	AET06_variant_1_is_produced_correctly
table_aet06	💚	$15.19$	$-13.92$	AET06_variant_3_is_produced_correctly
table_aet06	💚	$51.26$	$-49.59$	AET06_variant_5_is_produced_correctly
table_aet09	💚	$5.74$	$-5.02$	AET09_variant_1_is_produced_correctly_AE_related_to_study_drug
table_aet09	💚	$23.80$	$-22.54$	AET09_variant_2_is_produced_correctly_AE_related_to_study_drug_including_high_level_terms_
table_aet10	💚	$1.72$	$-1.59$	AET10_default_variant_is_produced_correctly
table_cmht01	💚	$2.41$	$-1.08$	CMHT01_variant_2_is_produced_correctly
table_cmt01b	💚	$2.46$	$-1.27$	CMT01B_variant_4_is_produced_correctly
table_egt01	💚	$3.12$	$-1.58$	EGT01_default_variant_is_produced_correctly
table_ent	💚	$8.93$	$-4.53$	ENT01_IT_is_produced_correctly
table_ent	💚	$5.54$	$-2.40$	ENT01a_IT_is_produced_correctly
table_ent	💚	$8.25$	$-3.83$	ENT02_IT_is_produced_correctly
table_ent	💚	$5.80$	$-2.65$	ENT02a_IT_is_produced_correctly
table_lbt01	💚	$4.89$	$-2.91$	LBT01_default_variant_is_produced_correctly
table_lbt02	💚	$2.73$	$-1.41$	LBT02_default_variant_is_produced_correctly
table_lbt04	💚	$5.85$	$-4.60$	LBT04_default_variant_is_produced_correctly
table_lbt05	💚	$13.86$	$-11.33$	LBT05_variant_1_is_produced_correctly
table_lbt05	💚	$12.15$	$-10.17$	LBT05_variant_2_is_produced_correctly
table_lbt05	💚	$11.07$	$-8.88$	LBT05_variant_4_is_produced_correctly
table_lbt07	💚	$7.01$	$-4.61$	LBT07_is_produced_correctly
table_lbt13	💚	$2.73$	$-1.86$	LBT13_variant_1_LOW_works_as_expected
table_lbt14	💚	$38.32$	$-31.83$	LBT14_variant_1_HIGH_works_as_expected
table_lbt14	💚	$36.28$	$-30.37$	LBT14_variant_2_LOW_works_as_expected
table_lbt14	💚	$11.89$	$-7.81$	LBT14_variant_3_LOW_without_baseline_missing_works_as_expected
table_lbt14	💚	$33.17$	$-27.48$	LBT14_variant_4_LOW_and_force_1_missing_both_baseline_and_post_baseline_then_force_the_missing_baseline_as_0_as_expected
table_lbt14	💚	$55.44$	$-46.36$	LBT14_variant_5_HIGH_with_fillings_works_as_expected
table_lbt15	💚	$2.20$	$-1.43$	LBT15_variant_1_works_as_expected
table_lbt15	💚	$1.95$	$-1.25$	LBT15_variant_2_works_as_expected
table_pkpt03	💚	$2.25$	$-1.17$	PKPT03_Drug_X_is_produced_correctly

Results for commit 62d28e7

♻️ This comment has been updated with latest results.

[Melkiades]

from checks:

Found the following significant warnings:
  Warning: replacing previous import ‘formatters::var_relabel’ by ‘random.cdisc.data::var_relabel’ when loading ‘scda.test’

We need to fix #129 too here

[zdz2101]

With regard to the pharmaverseadam stuff, looks great! See my other comments as well. Also wondering why the 10 new "<- NULL" error stuff is showing up, they don't show up when I'm testing each file individually but it shows up when I click the "test" button on the top right of the rstudio ui

[Melkiades]

With regard to the pharmaverseadam stuff, looks great! See my other comments as well. Also wondering why the 10 new "<- NULL" error stuff is showing up, they don't show up when I'm testing each file individually but it shows up when I click the "test" button on the top right of the rstudio ui

I have no idea! I will investigate ;)

[Melkiades]

@zdz2101 @edelarua @shajoezhu, now the tests should all work. Testing time reduced to < 10min (it says 256s) and snap file size reduced to <=100 KB (one was 1.4Mb before) ;)

[zdz2101]

LGTM