Pre-release activities

[kartikeyakirar]

part of insightsengineering/nestdevs-tasks#48

• Review and update:
  - README.md (check example code)
  - NEWS.md
• Run urlchecker::url_check() to identify broken links and fix
• Review functions:
  - @example tag, make sure it runs, fix if otherwise
  - Make sure functions has @return tag to document the return value
  - no \dontrun tag, replace with if(interactive()) if needed
• Sanity check of all vignettes, make sure there is no typo, no wrong format, etc.
• Run R CMD check --as-cran make sure everything pass
• Package Title is not duplicated in Package Description in DESCRIPTION file (e.g. this happens in teal.slice currently)
• All package names in Title and Description fields of DESCRIPTION file are quoted with '
• You have checked the Package Release Template https://github.com/insightsengineering/teal.reporter/pull/205/files
• Make sure there are no ::: in examples
• Make sure all teal.* mentions are lower-cased and quoted
• Make Sure inst/WORDLIST is minimalized
• Make sure non-exported functions do not have examples
• Make sure each link to our documentation hosted with pkgdown on github pages do not have /main/ in the address but it has /latest/ instead, so we always expose the documentation of the latest release and not what's currently on main branch but not yet released
• switch from title case into sentence case for title and description of functions.
• remove old rd syntax

[github-actions]

Code Coverage Summary

Filename                        Stmts    Miss  Cover    Missing
----------------------------  -------  ------  -------  -------------------------------------------------------------------------------------------------------------------------------------------------
R/calls_combine_by.R                7       0  100.00%
R/choices_labeled.R                49      14  71.43%   25, 36, 41, 51-56, 68, 72-76
R/count_labels.R                   97       0  100.00%
R/filter_panel_api.R               29       1  96.55%   134
R/FilteredData-utils.R             68      25  63.24%   17-20, 23-26, 48-53, 146, 168-177
R/FilteredData.R                  554     218  60.65%   181, 323, 395, 502-511, 535, 556-597, 615-618, 634, 676-709, 725-727, 731-737, 764-792, 816-818, 822-824, 827-838, 842-851, 853-891, 932, 955-977
R/FilteredDataset-utils.R          23       1  95.65%   112
R/FilteredDataset.R               176      67  61.93%   49, 149, 192-198, 226-283, 322-324
R/FilteredDatasetDataframe.R      121       8  93.39%   82, 144, 154, 230-234
R/FilteredDatasetDefault.R         18       4  77.78%   94-107
R/FilteredDatasetMAE.R            134      37  72.39%   49, 110-115, 154-159, 163-164, 182-204
R/FilterPanelAPI.R                 10       0  100.00%
R/FilterState-utils.R             101       2  98.02%   256, 286
R/FilterState.R                   361      61  83.10%   86, 210, 228-232, 239-240, 254-255, 261-262, 310, 312, 314, 366, 410, 642, 685-710, 721-740, 775-781, 790-796
R/FilterStateChoices.R            338     106  68.64%   309-312, 324, 367, 391-398, 402-419, 448, 463-474, 486-494, 498-527, 548-551, 554-557, 568-589, 602-603, 613
R/FilterStateDate.R               212     129  39.15%   226, 279-437
R/FilterStateDatettime.R          309     199  35.60%   266, 319-551
R/FilterStateEmpty.R               53      31  41.51%   89, 99-104, 118, 132-173
R/FilterStateExpr.R                75      62  17.33%   143-267
R/FilterStateLogical.R            196     144  26.53%   135, 158, 218, 222-409
R/FilterStateRange.R              410     105  74.39%   260, 384, 512-516, 519-529, 532, 544-550, 561-573, 577-587, 591-593, 607-634, 649, 652, 667-684, 719-724, 734-736
R/FilterStates-utils.R             70       9  87.14%   106, 125, 185-191, 213, 242
R/FilterStates.R                  364      30  91.76%   78-82, 191, 317-326, 414-417, 460, 545-549, 594, 715-718
R/FilterStatesDF.R                  5       0  100.00%
R/FilterStatesMAE.R                10       1  90.00%   40
R/FilterStatesMatrix.R              3       0  100.00%
R/FilterStatesSE.R                211     157  25.59%   36, 71-73, 83-85, 109-116, 124-131, 154-302
R/include_css_js.R                  5       5  0.00%    12-16
R/teal_slice.R                    107       4  96.26%   134, 188-189, 200
R/teal_slices.R                    84       5  94.05%   146-151
R/test_utils.R                     21       0  100.00%
R/utils.R                          18       0  100.00%
R/variable_types.R                 48      33  31.25%   45-50, 60, 73-108
R/zzz.R                            16      16  0.00%    3-46
TOTAL                            4303    1474  65.74%

Diff against main

Filename                    Stmts    Miss  Cover
------------------------  -------  ------  --------
R/calls_combine_by.R           -1       0  +100.00%
R/count_labels.R               -1       0  +100.00%
R/filter_panel_api.R           -6       0  -0.59%
R/FilteredData-utils.R        -30      -4  -7.17%
R/FilterStateDatettime.R       +2       0  +0.42%
R/utils.R                      -7      -2  +8.00%
TOTAL                         -43      -6  -0.20%

Results for commit: 5ecbaa9

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

  1 files   29 suites   22s ⏱️
359 tests 359 ✅ 0 💤 0 ❌
822 runs  822 ✅ 0 💤 0 ❌

Results for commit 5ecbaa9.

♻️ This comment has been updated with latest results.

[m7pr]

Hey @kartikeyakirar I left few minor comments, but I would like them to be resolved before we merge

[m7pr]

Hey, just to summarize what's going on during this PR.
@kartikeyakirar did a great job eliminating ~20 cleanup issues from the pre-release checklist.

Changes in repository included

• addition of new CRAN badges to README
• changing installation instructions to regular installation from CRAN
• addition of the CRAN RELEASE issue template
• cleanup of pkgdown titles

During this PR @chlebowa proposed we move internal examples to a special vignette (with an addition to documentation with @seealso tag pointing to this vignette). Later on we also discussed if we should move them to inst/demo() part of the package. At the end of the day, we decided to use getFromNamespace() function to overcome limitation of ::: usage in the documentation, which is discouraged by CRAN policy. The vignette was discarded.

Other main changes included

• examples and vignettes were run and verified for compliteness
• refinement of roxygen2 @title, @description and @details sections/tags
• WORDLIST cleanup and typos verification
• review of cleanness of the documentation
  • mostly classes of parameters
  • addition of @internal tags to some pages so they are not listed in the index of the package
  • quoting package names and R with backticks
• removal of :: prefixing and library(shiny) calls from examples since shiny is in Depends and prefixing in examples clutters the picture
• tests:
  • adding prefixes in tests/ and substitution of ::: usage with getFromNamespace()
  • we added a skip flow in case some packages are missing on a run (since they are only in Suggests)
    • testthat::skip_if_not_installed("MultiAssayExperiment")
    • @averissimo started a discussion about this in here Pre-release activities #506 (comment) and provided a change for that in here 3220aac
    • this will be required by IDR GHA flows anyway https://github.com/insightsengineering/idr-tasks/issues/713
• vignettes:
  • filter panel for developer vignettes had it's graph of dependencies refreshed
  • classes were renamed (e.g. DefaultFilteredDatase to DataframeFilteredDataset, FilteredDatasetMAE to MAEFilteredDataset) and their appearance in the proper place of the vignettes was reviewed

Final remarks

• Last review changes required was raised by @chlebowa Pre-release activities #506 (review) and is now satisfied.
• @pawelru found a NOTE in R CMD CHECK Pre-release activities #506 (comment) that @kartikeyakirar claims to be resolved once we land teal on CRAN so I believe this is minor
  Pre-release activities #506 (comment)
• I believe there is one more thing that is not yet covered Pre-release activities #506 (comment) but I created a new issue for that remove filters for columns: ARRAY_TYPE excluded from mae warning  #531

Multiple people were involved in this PR, kudos to @kartikeyakirar @chlebowa and @averissimo
A lot of things have been provided in this PR (112 files changed!) and I think it's time to merge this. DONE is better than PERFECT. We can tackle other small things outside of this PR. It can not grow any longer and I state it's in good shape to be merged.

this is resolved!

[kartikeyakirar]

Thank you, @m7pr, for your excellent summary of the PR and approving it. I concur that it contains numerous changes, and as you suggested any additional change requests should be separate issue. Reviewing the entire pull request in one go could be challenging. I plan to merge this pull request in 3 hours, which should provide enough time for any final comments or feedback.

thanks everyone.