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Genentech / jmpost

https://genentech.github.io/jmpost/
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Change the URL checker to lychee #337

Closed cicdguy closed 5 months ago

cicdguy commented 5 months ago

Instead of the urlchecker R package. Also remove unnecessary exec permissions on files.

github-actions[bot] commented 5 months ago

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Code Coverage Summary

Filename                           Stmts    Miss  Cover    Missing
-------------------------------  -------  ------  -------  --------------------------------
R/brier_score.R                      166       0  100.00%
R/DataJoint.R                         76       2  97.37%   264, 270
R/DataLongitudinal.R                 119       1  99.16%   244
R/DataSubject.R                       85       1  98.82%   142
R/DataSurvival.R                      98       0  100.00%
R/defaults.R                          10       6  40.00%   18-57, 84
R/generics.R                          31       4  87.10%   51, 395, 414, 449
R/Grid.R                              27       1  96.30%   170
R/GridEven.R                          32       0  100.00%
R/GridFixed.R                         30       0  100.00%
R/GridGrouped.R                       52       0  100.00%
R/GridManual.R                        23       3  86.96%   78-80
R/GridObserved.R                      20       0  100.00%
R/GridPopulation.R                    31       4  87.10%   61, 69-71
R/GridPrediction.R                    36       6  83.33%   83, 91-95
R/JointModel.R                       123       8  93.50%   141-143, 193, 197, 239, 285, 291
R/JointModelSamples.R                 59       0  100.00%
R/link_generics.R                     13       3  76.92%   59, 76, 91
R/Link.R                              62       4  93.55%   200-203
R/LinkComponent.R                     19       3  84.21%   88, 120-121
R/LongitudinalGSF.R                   82       0  100.00%
R/LongitudinalModel.R                 19       0  100.00%
R/LongitudinalQuantities.R            71       0  100.00%
R/LongitudinalRandomSlope.R           41       5  87.80%   93-97
R/LongitudinalSteinFojo.R             75       5  93.33%   143-147
R/Parameter.R                         14       0  100.00%
R/ParameterList.R                     42       1  97.62%   184
R/Prior.R                            236       8  96.61%   481, 577, 589-607
R/Promise.R                           25       0  100.00%
R/Quantities.R                        60       0  100.00%
R/QuantityGeneratorPopulation.R       22       0  100.00%
R/QuantityGeneratorPrediction.R       48       0  100.00%
R/QuantityGeneratorSubject.R          19       0  100.00%
R/settings.R                          12      12  0.00%    55-69
R/SimGroup.R                           5       0  100.00%
R/SimJointData.R                      72       1  98.61%   103
R/SimLongitudinal.R                    5       2  60.00%   22, 40
R/SimLongitudinalGSF.R                53       0  100.00%
R/SimLongitudinalRandomSlope.R        42       0  100.00%
R/SimLongitudinalSteinFojo.R          50       0  100.00%
R/SimSurvival.R                      104       0  100.00%
R/StanModel.R                         15       0  100.00%
R/StanModule.R                       176       6  96.59%   192-193, 235, 246, 383, 411
R/SurvivalExponential.R               10       0  100.00%
R/SurvivalLoglogistic.R               11       0  100.00%
R/SurvivalModel.R                     19       0  100.00%
R/SurvivalQuantities.R               170       1  99.41%   125
R/SurvivalWeibullPH.R                 11       0  100.00%
R/utilities.R                        143       1  99.30%   13
R/zzz.R                               28      25  10.71%   3, 8-12, 14-35, 47
TOTAL                               2792     113  95.95%

Diff against main

Filename      Stmts    Miss  Cover
----------  -------  ------  --------
TOTAL             0       0  +100.00%

Results for commit: 1a8268b52bfda1c54247d8966ca9cef379f1088d

Minimum allowed coverage is 80%

:recycle: This comment has been updated with latest results

github-actions[bot] commented 5 months ago

Unit Tests Summary

  1 files  132 suites   1m 42s :stopwatch: 124 tests  96 :white_check_mark: 27 :zzz: 0 :x: 1 :fire: 891 runs  858 :white_check_mark: 32 :zzz: 0 :x: 1 :fire:

For more details on these errors, see this check.

Results for commit 1a8268b5.

:recycle: This comment has been updated with latest results.

github-actions[bot] commented 5 months ago

Unit Test Performance Difference

Test Suite $Status$ Time on main $±Time$ $±Tests$ $±Skipped$ $±Failures$ $±Errors$
Grid 💀 $0.00$ $-0.00$ $-1$ $0$ $0$ $0$
JointModelSamples 💚 $5.46$ $-4.15$ $0$ $0$ $0$ $0$
compile 💚 $14.86$ $-11.00$ $0$ $0$ $0$ $0$
extract_quantities 💚 $16.45$ $-16.10$ $0$ $0$ $0$ $0$
model_multi_chain 💚 $70.83$ $-65.65$ $0$ $0$ $0$ $0$
Additional test case details | Test Suite | $Status$ | Time on `main` | $±Time$ | Test Case | |:-----|:----:|:----:|:----:|:-----| | DataSurvival | 👶 | | $+21.50$ | _unnamed_ | | Grid | 💀 | $0.00$ | $-0.00$ | GridFixed_bug_has_been_fixed | | Grid | 💀 | $0.01$ | $-0.01$ | GridObservered_Constructs_correct_quantities | | Grid | 💀 | $0.00$ | $-0.00$ | GridPopulation_doesn_t_work_with_SurvivalQuantities | | Grid | 💀 | $0.01$ | $-0.01$ | GridPopulation_works_as_expected_for_GSF_models | | Grid | 💀 | $0.01$ | $-0.01$ | GridPopulation_works_as_expected_for_Longitudinal_models | | Grid | 💀 | $152.80$ | $-152.80$ | Grid_objects_work_with_QuantityGenerator_and_QuantityCollapser | | Grid | 💀 | $0.01$ | $-0.01$ | coalesceGridTime_works_as_expected | | Grid | 💀 | $0.01$ | $-0.01$ | subjects_to_list_works_as_expected | | GridPrediction | 💚 | $150.53$ | $-147.32$ | GridPrediction_works_as_expected_for_Survival_models | | JointModelSamples | 💚 | $5.46$ | $-4.15$ | print_works_as_expected_for_JointModelSamples | | LinkComponent | 💚 | $2.93$ | $-1.22$ | all_link_files_pass_stan_s_syntax_checker | | LongitudinalGSF | 💚 | $5.26$ | $-4.99$ | LongitudinalGSF_works_as_expected_with_default_arguments | | LongitudinalQuantiles | 💚 | $30.09$ | $-8.62$ | Test_that_LongitudinalQuantities_works_as_expected | | LongitudinalRandomSlope | 💚 | $56.89$ | $-56.47$ | Print_method_for_LongitudinalRandomSlope_works_as_expected | | LongitudinalSteinFojo | 💚 | $375.02$ | $-372.17$ | LongitudinalSteinFojo_works_as_expected_with_default_arguments | | SimSurvival | 💚 | $3.11$ | $-1.19$ | SimSurvivalExponential_creates_a_dataset_with_the_correct_parameter | | SurvivalExponential | 💚 | $26.77$ | $-21.48$ | SurvivalExponential_can_recover_true_parameter_including_covariates_ | | SurvivalLoglogistic | 💚 | $46.34$ | $-45.77$ | sim_os_loglogistic_is_consistant_with_flexsurv | | SurvivalQuantities | 💚 | $79.88$ | $-71.75$ | SurvivalQuantities_and_autoplot.SurvivalQuantities_works_as_expected | | SurvivalWeibullPH | 💚 | $10.09$ | $-2.52$ | Print_method_for_SurvivalWeibullPH_works_as_expected | | compile | 💚 | $14.86$ | $-11.00$ | compileStanModel_doesn_t_error_if_the_directory_doesn_t_exist | | extract_quantities | 💚 | $16.45$ | $-16.10$ | extract_quantities_works_as_expected | | model_multi_chain | 💚 | $70.83$ | $-65.65$ | Can_recover_known_distribution_parameters_from_random_slope_model_when_using_multiple_chains | | stan_functions | 💚 | $68.32$ | $-66.23$ | GSF_SLD_function_works_as_expected |

Results for commit 6529af599947420064c78b1e7ede91c9476544e8

♻️ This comment has been updated with latest results.