Ensure no unit tests create data outside of testthat framework, possibly write custom lintr to police this

[manciniedoardo]

Background Information

@bms63 - please can you fill this section in with the background as mentioned during yesterday's retro? I couldn't find any after a cursory look.

Definition of Done

• Any unit tests identified which create test data outside of the testthat framwork
• Custom lintr written to ensure no new unit tests do this in future.

[manciniedoardo]

@adcascone please feel free to self-assign if you want to take a look at this.

[bms63]

This is a good first candidate

https://github.com/pharmaverse/admiral/blob/main/tests/testthat/test-derive_vars_dt.R

[adcascone]

Thanks @manciniedoardo @bms63! I'll look into this

[adcascone]

PROGRESS: wrote a little function to ID which files in /tests/testthat have code that is run outside of test_that({}) chunks - dumped the information here

code_outside_testthat_2026-02-18.txt

TO DO: Sanity check this output, move code to proper test_that({}) chunks

[adcascone]

Also, general details on why it's important to keep tests self-contained, for future reference! https://r-pkgs.org/testing-design.html#self-sufficient-tests

Whole section is relevant, but especially this -

[adcascone]

UPDATE:

• 22 files have code outside of test_that({}):

[1] "tests/testthat/test-create_query_data.R"            "tests/testthat/test-derive_merged.R"               
[3] "tests/testthat/test-derive_param_bmi.R"             "tests/testthat/test-derive_param_bsa.R"            
[5] "tests/testthat/test-derive_param_exist_flag.R"      "tests/testthat/test-derive_param_exposure.R"       
[7] "tests/testthat/test-derive_param_framingham.R"      "tests/testthat/test-derive_param_map.R"            
[9] "tests/testthat/test-derive_var_anrind.R"            "tests/testthat/test-derive_var_atoxgr.R"           
[11] "tests/testthat/test-derive_var_extreme_date.R"      "tests/testthat/test-derive_var_extreme_flag.R"     
[13] "tests/testthat/test-derive_var_joined_exist_flag.R" "tests/testthat/test-derive_var_trtemfl.R"          
[15] "tests/testthat/test-derive_vars_cat.R"              "tests/testthat/test-derive_vars_dt.R"              
[17] "tests/testthat/test-derive_vars_dtm_to_tm.R"        "tests/testthat/test-derive_vars_dtm.R"             
[19] "tests/testthat/test-derive_vars_transposed.R"       "tests/testthat/test-dt_level.R"                    
[21] "tests/testthat/test-filter_joined.R"                "tests/testthat/test-filter_relative.R" 

@manciniedoardo @bms63 - Trying to think through the best way to stay organized here. Should I make 22 separate issues so that these updates can be tackled file-by-file? Thanks, Ben, for that suggestion

If so, what level of detail should go in each issue? The file linked above shows which lines of code in each file exist outside of a test_that({}) chunk, so would probably be good to include - unless we can link this main issue to all the others

[bms63]

Also, general details on why it's important to keep tests self-contained, for future reference! https://r-pkgs.org/testing-design.html#self-sufficient-tests

Whole section is relevant, but especially this -

Yes agree with the advice - happens when you have 40 people work on a project and now we have to clean up the mess!! :)

I would follow the master issue that @manciniedoardo for doc rework - #2700 - this way folks can create a sub-issue from it when they want to work on it.

[bms63]

Also wondering on having specific datasets we can reference for the tests - minimize copy and pasting of data and making the tests long

https://testthat.r-lib.org/articles/special-files.html?q=data#other-files-and-folders

[manciniedoardo]

@adcascone maybe you can try making the function you wrote into a custom linter as well?

[adcascone]

@bms63 @manciniedoardo I looked into using copilot to address this issue in one of the above files, per the action from our last deep dive meeting (#2953 (comment))

I can't use copilot to do any tasks! Check out this screenshot - I can only ask it things, since I'm on the free plan.

I think one of you mentioned there was some # of free actions users get? Where did you see that?