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785 implement knit print for subclasses of increments #790

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Puzzled-Face
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Part of #774.

PuzzledFace and others added 21 commits May 9, 2023 15:21
Merge branch 'main' of github.com:Roche/crmPack into main

# Conflicts:
#	README.md
Merge branch 'main' of github.com:Roche/crmPack into main

# Conflicts:
#	R/Samples-methods.R
#	devel/rolling-crm-Simona.Rmd
#	examples/Sample-methods-approximate.R
#	man/approximate.Rd
#	tests/testthat/_snaps/Samples-methods.md
#	tests/testthat/test-Samples-methods.R
Merge branch 'main' of github.com:Roche/crmPack into main

# Conflicts:
#	vignettes/example.Rnw
Merge branch 'main' of github.com:Roche/crmPack into main

# Conflicts:
#	tests/testthat/_snaps/Samples-methods.md
#	tests/testthat/test-Samples-methods.R
Merge branch 'main' of github.com:Roche/crmPack into main

# Conflicts:
#	design/devel/rolling-crm-Simona.Rmd
Merge branch 'main' of github.com:Roche/crmPack into main

# Conflicts:
#	tests/testthat/_snaps/Samples-methods.md
Merge branch 'main' of github.com:Roche/crmPack into main

# Conflicts:
#	tests/testthat/_snaps/Samples-methods.md
Merge branch 'main' of github.com:Roche/crmPack into main
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
@Puzzled-Face Puzzled-Face linked an issue Feb 6, 2024 that may be closed by this pull request
@Puzzled-Face Puzzled-Face enabled auto-merge (squash) February 6, 2024 17:32
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github-actions bot commented Feb 6, 2024

Unit Test Performance Difference

Test Suite $Status$ Time on main $±Time$ $±Tests$ $±Skipped$ $±Failures$ $±Errors$
CrmPackClass-class 💔 $21.71$ $+2.74$ $0$ $0$ $0$ $0$
CrmPackClass-methods 💚 $54.94$ $-8.75$ $0$ $0$ $0$ $0$
Design-methods 💔 $29.35$ $+2.38$ $0$ $0$ $0$ $0$
Rules-methods 💔 $45.06$ $+3.27$ $0$ $0$ $0$ $0$
Samples-methods 💔 $28.56$ $+3.61$ $0$ $0$ $0$ $0$
helpers_knitr 💔 $21.18$ $+8.64$ $+40$ $+1$ $0$ $0$
Additional test case details
Test Suite $Status$ Time on main $±Time$ Test Case
CrmPackClass-class 💔 $21.59$ $+2.73$ CrmPackClass_correctly_identifies_crmPack_classes
CrmPackClass-methods 💚 $29.48$ $-7.75$ tidy_methods_exist_for_all_relevant_classes
Rules-methods 💔 $12.82$ $+1.09$ stopTrial_works_correctly_for_StoppingTDCIRatio_when_samples_are_not_provided
Samples-methods 💔 $0.22$ $+1.67$ size_Samples_returns_correct_number_of_samples
helpers_knitr 💔 $20.67$ $+8.47$ asis_parameter_works_correctly_for_all_implemented_methods
helpers_knitr 👶 $+0.16$ knit_print.IncrementsRelativeParts_works_correctly

Results for commit 6637fa8

♻️ This comment has been updated with latest results.

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thanks @Puzzled-Face !

Merge branch '785-implement-knit_print-for-subclasses-of-increments' of github.com:Roche/crmPack into 785-implement-knit_print-for-subclasses-of-increments

# Conflicts:
#	R/helpers_kintr_Increments.R
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github-actions bot commented Feb 7, 2024

Unit Tests Summary

    1 files     40 suites   4m 4s ⏱️
1 280 tests 1 124 ✅ 156 💤 0 ❌
6 935 runs  6 741 ✅ 194 💤 0 ❌

Results for commit bea9cc4.

♻️ This comment has been updated with latest results.

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github-actions bot commented Feb 8, 2024

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Code Coverage Summary

Filename                        Stmts    Miss  Cover    Missing
----------------------------  -------  ------  -------  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/checkmate.R                      73       1  98.63%   72
R/crmPack-package.R                 4       0  100.00%
R/CrmPackClass-methods.R            5       0  100.00%
R/Data-class.R                    147       5  96.60%   43, 564-565, 571-576
R/Data-methods.R                  203       0  100.00%
R/Data-validity.R                 144       1  99.31%   21
R/Design-class.R                  391       0  100.00%
R/Design-methods.R               2775     771  72.22%   563-567, 591-594, 602-621, 626-655, 659-660, 662, 677-685, 689, 701-720, 1122-1126, 1253, 1267-1271, 1333, 1523, 1740, 1767-1770, 1779-1790, 1794-1813, 1824-1828, 1834-1846, 2109, 2134-2137, 2144-2155, 2159-2178, 2190-2194, 2200-2212, 2496-2499, 2527-2530, 2538-2550, 2553-2564, 2568-2604, 2621-2630, 2636-2651, 2676, 2717-2718, 2981-3451, 3546-3557, 3560-3571, 3575-3611, 3628-3637, 3645-3660, 3698, 3740-3741, 4020, 4022-4023, 4082, 4118, 4155-4158, 4177-4181, 4242-4249, 4277-4281, 4289-4307, 4333-4352, 4355, 4388, 4410-4428, 4697, 4792
R/Design-validity.R                38      10  73.68%   47-56
R/fromQuantiles.R                 176      67  61.93%   238-378
R/helpers_broom.R                  74      10  86.49%   30, 34-35, 37-38, 40, 81, 102-104
R/helpers_covr.R                   23       0  100.00%
R/helpers_data.R                   96       1  98.96%   139
R/helpers_design.R                126      41  67.46%   77-129, 250, 255-259
R/helpers_jags.R                   77       0  100.00%
R/helpers_kintr_Increments.R      156       2  98.72%   191, 278
R/helpers_knitr_CohortSize.R      100       0  100.00%
R/helpers_model.R                  85       4  95.29%   38, 89-90, 139
R/helpers_rules.R                 428       0  100.00%
R/helpers_samples.R                 5       0  100.00%
R/helpers_simulations.R            27       0  100.00%
R/helpers.R                       214      61  71.50%   107-127, 162-178, 200-304, 339-353
R/logger.R                         11       0  100.00%
R/mcmc.R                          290      18  93.79%   92-97, 376-377, 387, 389-390, 393-396, 579-580, 669, 675, 733
R/McmcOptions-class.R              22       0  100.00%
R/McmcOptions-methods.R             8       1  87.50%   43
R/McmcOptions-validity.R           42       0  100.00%
R/Model-class.R                  1062     166  84.37%   145-147, 216-218, 222-224, 283-285, 357-359, 363-365, 444-446, 513-515, 577-581, 584-587, 690-693, 697-698, 813-817, 937-939, 943-951, 1096-1098, 1103-1106, 1110-1113, 1229-1233, 1235-1238, 1242-1245, 1248, 1409-1419, 1424-1430, 1585-1588, 1594-1601, 1758, 1767, 1776, 1785, 1794-1799, 1935, 1944, 1953, 1961-1963, 2807-2836, 2840-2846, 2853-2857, 2862, 2969-2982, 3008, 3104-3106, 3110, 3203-3205, 3209, 3278-3290, 3308, 3368-3370, 3372-3373, 3376-3381
R/Model-methods.R                 472      38  91.95%   78, 233-238, 809-854, 1175-1184
R/Model-validity.R                443      16  96.39%   430-433, 442-445, 596-604
R/ModelParams-class.R              17       0  100.00%
R/ModelParams-validity.R           21       0  100.00%
R/Rules-class.R                   458       0  100.00%
R/Rules-methods.R                1541     184  88.06%   889, 892, 895, 1010, 1013, 1016, 1136-1139, 1173, 1276-1279, 1314, 2582-2590, 2614-2621, 2784-2793, 3073-3082, 3215-3458, 3745, 3749, 3794, 3798
R/Rules-validity.R                448      30  93.30%   684-723
R/Samples-class.R                   6       0  100.00%
R/Samples-methods.R              1188      21  98.23%   410-420, 648, 1665-1666, 1698, 1711, 1893, 2223-2228
R/Samples-validity.R               10       0  100.00%
R/Simulations-class.R             208       5  97.60%   784-787, 1043
R/Simulations-methods.R          1617    1473  8.91%    65-350, 406, 416-435, 448-453, 500-509, 674-2969
R/Simulations-validity.R           75      75  0.00%    20-168
R/utils.R                           6       0  100.00%
TOTAL                           13312    3001  77.46%

Diff against main

Filename                        Stmts    Miss  Cover
----------------------------  -------  ------  --------
R/helpers_kintr_Increments.R     +156      +2  +98.72%
R/helpers_knitr_CohortSize.R       +1       0  +100.00%
TOTAL                            +157      +2  +0.25%

Results for commit: bea9cc4

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

@Puzzled-Face
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Please check the test results for IncrementsRelativeParts (in /_snaps/helpers_knitr) carefully. I'm not absolutely certain I've understood what the class is attempting to do.

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Thanks @Puzzled-Face , just double checked the html output you mentioned and it looks right to me.

@Puzzled-Face Puzzled-Face merged commit efe3035 into main Feb 8, 2024
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@Puzzled-Face Puzzled-Face deleted the 785-implement-knit_print-for-subclasses-of-increments branch February 8, 2024 15:39
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Implement knit_print for subclasses of Increments
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