503 shinytest2 : migrate test to shinytest2 using TealAppDriver

[kartikeyakirar]

part of https://github.com/insightsengineering/coredev-tasks/issues/503

• Test if the example for the modules tm_* can be run without shiny errors
• Test if the sample_tm_* can be run without shiny errors
• Test if the examples these helper shiny modules can be run without shiny errors
• adtteSpec
• assaySpec
• experimentSpec
• geneSpec
• sampleVarSpec

[github-actions]

Code Coverage Summary

Filename              Stmts    Miss  Cover    Missing
------------------  -------  ------  -------  -------------------------------------------------------------------------------------------------------------------------------
R/adtteSpec.R           170     123  27.65%   253-400
R/assaySpec.R            53      39  26.42%   104-146
R/barplot.R             187     151  19.25%   39-66, 129-279
R/boxplot.R             189     158  16.40%   40-67, 125-278
R/checkmate.R            18       9  50.00%   110-118
R/experimentSpec.R       90      57  36.67%   97, 215-283
R/forestplot.R          213     185  13.15%   58-92, 152-326
R/geneSpec.R            256     153  40.23%   154-169, 296-480
R/km.R                  207     173  16.43%   61-92, 156-325
R/pca.R                 366     283  22.68%   34-56, 165-476
R/quality.R             319     246  22.88%   18-110, 208-453
R/sampleVarSpec.R       236     104  55.93%   299, 318-327, 333-340, 342, 350-362, 364-365, 367, 370, 378-382, 384-399, 404-428, 431-435, 437, 444-454, 456-457, 465, 510-527
R/scatterplot.R         180     147  18.33%   39-65, 127-272
R/utils.R                16       0  100.00%
R/volcanoplot.R         203     173  14.78%   34-57, 113-292
R/zzz.R                   2       2  0.00%    2-3
TOTAL                  2705    2003  25.95%

Diff against main

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

Results for commit: fb6f8e3

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

  1 files   16 suites   11s ⏱️
 56 tests  43 ✅ 13 💤 0 ❌
538 runs  525 ✅ 13 💤 0 ❌

Results for commit fb6f8e3.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
shinytest2-adtteSpec	👶		$+0.01$	$+1$	$+1$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
adtteSpec	💀	$0.03$	$-0.03$	adtteSpecServer_module_works_as_expected_in_the_test_app
shinytest2-adtteSpec	👶		$+0.01$	adtteSpecServer_module_works_as_expected_in_the_test_app

Results for commit 0a542d1

♻️ This comment has been updated with latest results.

[danielinteractive]

Hi @kartikeyakirar , what is the state of this PR?

[kartikeyakirar]

Hey @danielinteractive,
cc @donyunardi

Just wanted to update you on a couple of PRs:

https://github.com/insightsengineering/teal.modules.helios/pull/130
#375
Both were aimed at modifying shiny test2 using tealAppDriver. However, they're currently on hold due to discussions regarding the addition of a method for selecting MAE dataset in insightsengineering/teal#1190. It was decided later that this wouldn't be part of tealAppDriver and will instead be tested in teal.slice itself.

we're prioritized the addition of shinytest2 in tmc and tmg. I'll be picking these PRs back up shortly, but until then, they're on hold.

[Copilot]

Pull Request Overview

This PR migrates module tests from shinytest to shinytest2 by removing old test scripts and adding new end-to-end tests powered by TealAppDriver.

• Removed obsolete app scripts and legacy test-*.R files that used the old framework
• Deleted corresponding snapshots and helper functions for shinytest
• Introduced test-shinytest2-*.R files covering all modules (volcanoplot, scatterplot, barplot, boxplot, pca, quality, km, forest, geneSpec, sampleVarSpec, assaySpec, adtteSpec, experimentSpec)

Reviewed Changes

Copilot reviewed 48 out of 68 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
tests/testthat/volcanoplot/app.R	Removed old Shiny app script for the volcano plot example
tests/testthat/test-volcanoplot.R	Deleted legacy unit and integration tests for volcanoplot
tests/testthat/test-shinytest2-volcanoplot.R	Added shinytest2-based e2e tests for the volcanoplot module
tests/testthat/test-shinytest2-scatterplot.R	Added shinytest2-based e2e tests for the scatterplot module
tests/testthat/test-shinytest2-barplot.R	Added shinytest2-based e2e tests for the barplot module

Comments suppressed due to low confidence (3)

tests/testthat/test-shinytest2-barplot.R:56

• The input ID "genes" doesn't match the later use of "x-genes". Update this to get_active_module_input("x-genes") for consistency.

  res <- app$get_active_module_input("genes")

tests/testthat/test-shinytest2-boxplot.R:12

• The .test argument is referring to an undefined variable. It should be set explicitly (e.g., .test = TRUE).

        .test = .test

tests/testthat/test-shinytest2-barplot.R:13

• The .test parameter is undefined here. Use .test = TRUE (or another literal) to enable test mode.

        .test = .test

[Copilot]

The data argument in TealAppDriver$new() is using a new teal_data() call instead of the data variable defined on the previous line. Replace with data = data to use the intended dataset.

Suggested change

	data = teal_data(MAE = helios::large_helios_data),
	data = data,