211 [.teal_data S3 method

[m7pr]

Companion to insightsengineering/teal.code#216

Introduces [.teal_data S3 method for teal_data that is based on [.qenv but also limits join_keys.

[github-actions]

Code Coverage Summary

Filename                     Stmts    Miss  Cover    Missing
-------------------------  -------  ------  -------  --------------------
R/cdisc_data.R                   1       0  100.00%
R/deprecated.R                  71      65  8.45%    19-380
R/dummy_function.R               2       2  0.00%    14-15
R/formatters_var_labels.R       61       0  100.00%
R/join_key.R                    38       0  100.00%
R/join_keys-c.R                 12       0  100.00%
R/join_keys-extract.R          128       0  100.00%
R/join_keys-names.R             15       0  100.00%
R/join_keys-parents.R           30       0  100.00%
R/join_keys-print.R             45       0  100.00%
R/join_keys-utils.R             73       3  95.89%   35-38
R/join_keys.R                   21       0  100.00%
R/teal_data-class.R             35       4  88.57%   71, 119-121
R/teal_data-constructor.R       31      16  48.39%   33, 36-42, 52-58, 61
R/teal_data-extract.R            3       0  100.00%
R/teal_data-get_code.R          13       8  38.46%   114-120, 124
R/teal_data-names.R              8       1  87.50%   31
R/teal_data-show.R               4       4  0.00%    14-19
R/testhat-helpers.R             26       0  100.00%
R/topological_sort.R            32       0  100.00%
R/verify.R                      42      11  73.81%   67, 97-101, 104-108
TOTAL                          691     114  83.50%

Diff against main

Filename                     Stmts    Miss  Cover
-------------------------  -------  ------  --------
R/teal_data-class.R            +21      +4  -11.43%
R/teal_data-constructor.R      +31     +16  +48.39%
R/teal_data-extract.R           +3       0  +100.00%
TOTAL                          +55     +20  -0.01%

Results for commit: a24bac3

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

  1 files   13 suites   1s ⏱️
162 tests 162 ✅ 0 💤 0 ❌
219 runs  219 ✅ 0 💤 0 ❌

Results for commit 967c1c5.

[github-actions]

Unit Tests Summary

  1 files   14 suites   1s ⏱️
161 tests 161 ✅ 0 💤 0 ❌
216 runs  216 ✅ 0 💤 0 ❌

Results for commit a24bac3.

♻️ This comment has been updated with latest results.

[llrs-roche]

Once I read in detail the code and documentation I have some feedback.
I think the examples will be very helpful, I am not sure if the current changes on documentation have the desired consequences.

More importantly matching base's generic argument and take advantage of the S3 methods used here will probably make developing and maintaining the code easier.

When I checked locally the examples failed (It could be my setup), but running interactively shows it too (so there might be some undeclared expectations/dependencies):

d> data["a"]
Error en get(x, envir = ns, inherits = FALSE): 
  objeto '[.qenv' no encontrado
d> traceback()
4: get(x, envir = ns, inherits = FALSE)
3: utils::getFromNamespace("[.qenv", "teal.code") at teal_data-extract.R#33
2: `[.teal_data`(data, "a")
1: data["a"]
d> packageVersion("teal.code")
[1] '0.5.0.9011'
d> packageVersion("teal.data")
[1] '0.6.0.9015'

[m7pr]

@llrs-roche

objeto '[.qenv' no encontrado

Any chance you can change your local setup to English : P ?

Sys.setlocale("LC_ALL","English")

https://stackoverflow.com/questions/16347731/how-to-change-the-locale-of-r

[m7pr]

@llrs-roche you need to install teal.code from 211_subset@main, the same as teal.data from 211_subset@main. Looks like you did not had teal.code installed from 211_subset@main, hence you could not find a function [.qenv.
This is how we prepare PRs for multiple repositories - if functionality is shared between multiple packages, then you need to install all packages from a specific branch to run and check the code.

Thanks for the attempt!

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
extract	👶		$+0.09$	$+6$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
extract	👶		$+0.02$	_._preserves_verified_field
extract	👶		$+0.04$	_._subsets_join_keys_also
extract	👶		$+0.03$	_._warns_and_subsets_if_names_are_present_in_code
teal_data	👶		$+0.01$	empty_teal_data_returns_empty_code_and_verified_TRUE
teal_data	💀	$0.02$	$-0.02$	empty_teal_data_returns_empty_code_id_wartnings_and_messages_and_verified_TRUE
verify	👶		$+0.03$	verify_raises_error_if_code_does_not_restore_objects_in_.xData
verify	💀	$0.01$	$-0.01$	verify_raises_error_if_code_does_not_restore_objects_in_env

Results for commit 9c92975

♻️ This comment has been updated with latest results.

[llrs-roche]

Thanks for the changes. I think this is mostly ready for merging, I just added a petition to have a test for a numeric and NA_character_.

I think, the workaround with NextMethod() come from defining it differently than the generic, but seem easy enough.

I tried loading teal.code@211_subset@main and running [.qenv exampels still got the same problems object 'parsed_code' not found, so it might be something related to my environment.

[m7pr]

I tried loading teal.code@211_subset@main and running [.qenv exampels still got the same problems object 'parsed_code' not found, so it might be something related to my environment.

And you did good. I actually left teal.code in unstable state yesterday when I left the office insightsengineering/teal.code#216 (comment) so it was broken. You got the very same error as I got : )

[gogonzo]

Minor comments

[llrs-roche]

Feel free to merge but I still have problems with executing the code with the latest update from teal.code@211_subset@main:

d> data <- teal_data()
d> data <- eval_code(data, "a <- 1;b<-2")
Error in parse(text = code_split[[i]], keep.source = FALSE) : 
  <text>:1:12: unexpected symbol
1: a <- 1;b<-2a
               ^
d> data["a"]
✅︎ verified teal_data object
<environment: 0x00000171ebb781d0> [L]
Parent: <environment: devtools_shims>
Warning message:
In `[.teal_data`(data, "a") :
  None of `names` elements exist in `teal_data`. Returning empty `teal_data`.
d> data[c("a", "b")]
✅︎ verified teal_data object
<environment: 0x00000171ea8c9710> [L]
Parent: <environment: devtools_shims>
Warning message:
In `[.teal_data`(data, c("a", "b")) :
  None of `names` elements exist in `teal_data`. Returning empty `teal_data`.
d> 
d> session_info()
─ Session info ───────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14 ucrt)
 os       Windows 11 x64 (build 22631)
 system   x86_64, mingw32
 ui       RStudio
 language en
 collate  Spanish_Spain.utf8
 ctype    Spanish_Spain.utf8
 tz       Europe/Madrid
 date     2024-10-30
 rstudio  2024.09.0+375 Cranberry Hibiscus (desktop)
 pandoc   3.5 @ C:\\Users\\sanchosl\\AppData\\Local\\Pandoc\\pandoc.exe

─ Packages ───────────────────────────────────────────────────────────────────────────
 !  package     * version    date (UTC) lib source
    backports     1.5.0      2024-05-23 [2] CRAN (R 4.4.0)
    brio          1.1.5      2024-04-24 [2] CRAN (R 4.4.1)
    cachem        1.1.0      2024-05-16 [2] CRAN (R 4.4.1)
    callr         3.7.6      2024-03-25 [2] CRAN (R 4.4.1)
    checkmate     2.3.2      2024-07-29 [2] CRAN (R 4.4.1)
    cli           3.6.3      2024-06-21 [2] CRAN (R 4.4.1)
    curl          5.2.3      2024-09-20 [2] CRAN (R 4.4.1)
    desc          1.4.3      2023-12-10 [2] CRAN (R 4.4.1)
    devtools    * 2.4.5      2022-10-11 [2] CRAN (R 4.4.1)
    digest        0.6.37     2024-08-19 [2] CRAN (R 4.4.1)
    ellipsis      0.3.2      2021-04-29 [2] CRAN (R 4.4.1)
    fastmap       1.2.0      2024-05-15 [2] CRAN (R 4.4.1)
    fs            1.6.4      2024-04-25 [2] CRAN (R 4.4.1)
    glue          1.8.0      2024-09-30 [2] CRAN (R 4.4.1)
    htmltools     0.5.8.1    2024-04-04 [2] CRAN (R 4.4.1)
    htmlwidgets   1.6.4      2023-12-06 [2] CRAN (R 4.4.1)
    httpuv        1.6.15     2024-03-26 [2] CRAN (R 4.4.1)
    later         1.3.2      2023-12-06 [2] CRAN (R 4.4.1)
    lifecycle     1.0.4      2023-11-07 [2] CRAN (R 4.4.1)
    magrittr      2.0.3      2022-03-30 [2] CRAN (R 4.4.1)
    memoise       2.0.1      2021-11-26 [2] CRAN (R 4.4.1)
    mime          0.12       2021-09-28 [2] CRAN (R 4.4.0)
    miniUI        0.1.1.1    2018-05-18 [2] CRAN (R 4.4.1)
    pkgbuild      1.4.4      2024-03-17 [2] CRAN (R 4.4.1)
    pkgload       1.4.0      2024-06-28 [2] CRAN (R 4.4.1)
    processx      3.8.4      2024-03-16 [2] CRAN (R 4.4.1)
    profvis       0.4.0      2024-09-20 [2] CRAN (R 4.4.1)
    promises      1.3.0      2024-04-05 [2] CRAN (R 4.4.1)
    ps            1.8.0      2024-09-12 [2] CRAN (R 4.4.1)
    purrr         1.0.2      2023-08-10 [2] CRAN (R 4.4.1)
    R6            2.5.1      2021-08-19 [2] CRAN (R 4.4.1)
    Rcpp          1.0.13     2024-07-17 [2] CRAN (R 4.4.1)
    remotes       2.5.0      2024-03-17 [2] CRAN (R 4.4.1)
    rlang         1.1.4      2024-06-04 [2] CRAN (R 4.4.1)
    rprojroot     2.0.4      2023-11-05 [2] CRAN (R 4.4.1)
    rstudioapi    0.17.1     2024-10-22 [2] CRAN (R 4.4.1)
    sessioninfo   1.2.2      2021-12-06 [2] CRAN (R 4.4.1)
    shiny         1.9.1      2024-08-01 [2] CRAN (R 4.4.1)
    teal.code   * 0.5.0.9012 2024-10-30 [1] Github (insightsengineering/teal.code@a32939c)
 VP teal.data   * 0.6.0.9015 2024-10-21 [?] Github (insightsengineering/teal.data@b5ccb1d) (on disk 0.6.0.9012)
    testthat    * 3.2.1.1    2024-04-14 [2] CRAN (R 4.4.1)
    urlchecker    1.0.1      2021-11-30 [2] CRAN (R 4.4.1)
    usethis     * 3.0.0      2024-07-29 [2] CRAN (R 4.4.1)
    vctrs         0.6.5      2023-12-01 [2] CRAN (R 4.4.1)
    withr         3.0.1      2024-07-31 [2] CRAN (R 4.4.1)
    xtable        1.8-4      2019-04-21 [2] CRAN (R 4.4.1)

 [1] C:/Users/sanchosl/R-dev
 [2] C:/Users/sanchosl/AppData/Local/R/win-library/4.4
 [3] C:/Program Files/R/R-4.4.1/library

 V ── Loaded and on-disk version mismatch.
 P ── Loaded and on-disk path mismatch.

too early

[m7pr]

Since insightsengineering/teal.code#216 is ready, I open this PR for the review. Let's see results of CI/CD checks

[gogonzo]

🔥 🧯