fix pipe

[m7pr]

Looks like merge module from teal.transform calls %>% here

teal.transform/R/get_dplyr_call.R

Line 172 in 45d962e

function(x, y) call("%>%", x, y),

and this leads to issues on CI/CD like in teal.modules.clinical, where teal_data does not attach dplyr but the magrittr or dplyr are needed to use %>% , so we need to attach it in teal.transform

https://github.com/insightsengineering/teal.modules.clinical/actions/runs/19731200858/job/56532457344

[github-actions]

Unit Tests Summary

  1 files   24 suites   6s ⏱️
194 tests 194 ✅ 0 💤 0 ❌
698 runs  698 ✅ 0 💤 0 ❌

Results for commit 8433b47.

♻️ This comment has been updated with latest results.

[llrs-roche]

Nice addition! I think this will help a lot, in the past I was manually adding it when I thought it was needed. Adding them automatically is a huge improvement.

I could test locally with the examples of merge_datasets() but that only covers the is.list() code branch but not the . Could you add test to cover all the function (the is.call() code branch too)?

Also note that this has the potential to break many snapshots that check for code on modules (but fix others :D).

[github-actions]

Code Coverage Summary

Filename                          Stmts    Miss  Cover    Missing
------------------------------  -------  ------  -------  ------------------------------------------------------------------------------
R/call_utils.R                      163     125  23.31%   19-28, 65, 67, 69, 102-345, 405
R/check_selector.R                   33       0  100.00%
R/choices_labeled.R                 157      27  82.80%   67, 73, 78, 85, 101, 218-222, 226-231, 354-355, 357, 363, 390-397
R/choices_selected.R                 81      11  86.42%   211-237, 274
R/column_functions.R                  3       3  0.00%    15-18
R/data_extract_datanames.R           30       8  73.33%   15-19, 80-82
R/data_extract_filter_module.R      105      47  55.24%   95-108, 110-111, 113-130, 146-165
R/data_extract_module.R             305      67  78.03%   139, 144, 161, 164-169, 171, 190-193, 223-269, 507, 512, 688, 699-700, 778-783
R/data_extract_read_module.R        137       7  94.89%   34, 39-41, 43, 138, 155
R/data_extract_select_module.R       32      18  43.75%   29-46
R/data_extract_single_module.R       60       2  96.67%   30, 43
R/data_extract_spec.R                32       0  100.00%
R/delayed_choices.R                  34       6  82.35%   86, 95-99
R/filter_spec.R                     186       1  99.46%   279
R/format_data_extract.R              16       1  93.75%   48
R/get_dplyr_call.R                  297       0  100.00%
R/get_merge_call.R                  278      29  89.57%   31-37, 48, 214-223, 388, 404-416
R/input_checks.R                     11       2  81.82%   15-16
R/merge_data_utils.R                  2       0  100.00%
R/merge_datasets.R                  137       6  95.62%   122, 254-258
R/merge_expression_module.R          60      11  81.67%   160-165, 183, 359-364
R/Queue.R                            23       0  100.00%
R/resolve_delayed.R                  16       4  75.00%   76-79
R/resolve.R                         115      45  60.87%   46, 180-286
R/select_spec.R                      64       8  87.50%   98, 178-185
R/utils.R                            37      24  35.14%   31-44, 172-185
R/zzz.R                               3       3  0.00%    2-4
TOTAL                              2417     455  81.18%

Diff against main

Filename              Stmts    Miss  Cover
------------------  -------  ------  -------
R/call_utils.R           +7      +1  +2.80%
R/merge_datasets.R       +3       0  +0.10%
TOTAL                   +10      +1  +0.04%

Results for commit: 8433b47

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[osenan]

LGTM.
I checked specialy call utils. The test are difficult for me to review. However, it is good that the checks, except lintr, pass.