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Add helpful instructions to direct user if cmdstanr is not installed #292

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merged 6 commits into from
Mar 25, 2024

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gowerc
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@gowerc gowerc commented Mar 22, 2024

Closes #285

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gowerc commented Mar 22, 2024

Just to add, I wasn't really sure how to actually automate testing this but I did do a local test by deleting my local cmdstanr library and it appears to work as expected.

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github-actions bot commented Mar 22, 2024

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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%   245
R/DataSubject.R                      69       1  98.55%   124
R/DataSurvival.R                     77       0  100.00%
R/defaults.R                         10       6  40.00%   18-57, 84
R/generics.R                         23       1  95.65%   49
R/JointModel.R                      122       8  93.44%   142-144, 194, 198, 240, 286, 292
R/JointModelSamples.R                55       0  100.00%
R/Link.R                             55       4  92.73%   159-162
R/LinkComponent.R                    47       5  89.36%   100, 118, 132-149
R/LongitudinalGSF.R                  64       0  100.00%
R/LongitudinalModel.R                35      12  65.71%   68-83
R/LongitudinalQuantities.R           85       8  90.59%   100-107
R/LongitudinalRandomSlope.R          27       0  100.00%
R/LongitudinalSteinFojo.R            57       8  85.96%   113-135
R/Parameter.R                        14       0  100.00%
R/ParameterList.R                    42       1  97.62%   184
R/Prior.R                           236       8  96.61%   480, 576, 588-606
R/Quantities.R                      105       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               51       0  100.00%
R/SimLongitudinalRandomSlope.R       42       0  100.00%
R/SimLongitudinalSteinFojo.R         48       0  100.00%
R/SimSurvival.R                     104       0  100.00%
R/StanModel.R                        15       0  100.00%
R/StanModule.R                      177       6  96.61%   199-200, 242, 253, 388, 416
R/SurvivalExponential.R              10       0  100.00%
R/SurvivalLoglogistic.R              11       0  100.00%
R/SurvivalModel.R                    19       0  100.00%
R/SurvivalQuantities.R              155       6  96.13%   178-183
R/SurvivalWeibullPH.R                11       0  100.00%
R/utilities.R                       146       1  99.32%   13
R/zzz.R                              28      25  10.71%   3, 8-12, 14-35, 47
TOTAL                              2395     118  95.07%

Diff against main

Filename         Stmts    Miss  Cover
-------------  -------  ------  -------
R/utilities.R       +1       0  +0.00%
R/zzz.R            +26     +23  +10.71%
TOTAL              +27     +23  -0.92%

Results for commit: 89b508a

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

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github-actions bot commented Mar 22, 2024

Unit Tests Summary

  1 files   40 suites   5m 20s ⏱️
120 tests  89 ✅ 31 💤 0 ❌
849 runs  818 ✅ 31 💤 0 ❌

Results for commit 89b508a.

♻️ This comment has been updated with latest results.

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github-actions bot commented Mar 22, 2024

Unit Test Performance Difference

Test Suite $Status$ Time on main $±Time$ $±Tests$ $±Skipped$ $±Failures$ $±Errors$
JointModelSamples 💚 $33.28$ $-2.01$ $0$ $0$ $0$ $0$
LongitudinalQuantiles 💚 $44.63$ $-5.23$ $0$ $0$ $0$ $0$
LongitudinalRandomSlope 💚 $35.00$ $-1.35$ $0$ $0$ $0$ $0$
SurvivalExponential 💚 $28.59$ $-1.63$ $0$ $0$ $0$ $0$
SurvivalLoglogistic 💚 $30.77$ $-1.95$ $0$ $0$ $0$ $0$
compile 💚 $16.20$ $-2.50$ $0$ $0$ $0$ $0$
model_multi_chain 💚 $39.67$ $-1.09$ $0$ $0$ $0$ $0$
stan_functions 💚 $50.10$ $-3.84$ $0$ $0$ $0$ $0$
Additional test case details
Test Suite $Status$ Time on main $±Time$ Test Case
JointModelSamples 💚 $33.28$ $-2.01$ print_works_as_expected_for_JointModelSamples
LongitudinalQuantiles 💚 $37.26$ $-5.04$ Test_that_LongitudinalQuantities_works_as_expected
SurvivalExponential 💚 $28.50$ $-1.64$ SurvivalExponential_can_recover_true_parameter_including_covariates_
SurvivalLoglogistic 💚 $30.59$ $-1.95$ SurvivalLogLogistic_can_recover_known_values
compile 💚 $16.20$ $-2.50$ compileStanModel_doesn_t_error_if_the_directory_doesn_t_exist
model_multi_chain 💚 $39.67$ $-1.09$ Can_recover_known_distribution_parameters_from_random_slope_model_when_using_multiple_chains
stan_functions 💚 $17.79$ $-2.75$ GSF_SLD_function_works_as_expected

Results for commit ef998bc

♻️ This comment has been updated with latest results.

@gowerc gowerc merged commit e4fe089 into main Mar 25, 2024
8 of 16 checks passed
@gowerc gowerc deleted the feature/easy_install_cmdstanr branch March 25, 2024 15:09
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Provide more support for installing cmdstan
2 participants