Add reporter

[mhallal1]

closes #238

Add reporter to all modules including:

1. plot/table
2. all selected encodings
3. filter panel

the PCA correlation plot depends on this PR: insightsengineering/teal.reporter#113

[github-actions]

Code Coverage Summary

Filename              Stmts    Miss  Cover    Missing
------------------  -------  ------  -------  --------------------------------------------------------------------------------------------------------------------------
R/adtteSpec.R           157      11  92.99%   308-312, 358-362, 364
R/assaySpec.R            44      36  18.18%   102-142
R/barplot.R             170     132  22.35%   40-64, 127-257
R/boxplot.R             173     140  19.08%   41-65, 124-260
R/checkmate.R            18       9  50.00%   110-118
R/experimentSpec.R       92      58  36.96%   99, 214-285
R/forestplot.R          201     171  14.93%   60-91, 151-315
R/geneSpec.R            255     136  46.67%   153-168, 297-448
R/km.R                  190     154  18.95%   63-92, 157-306
R/pca.R                 347     264  23.92%   35-55, 162-453
R/quality.R             299     224  25.08%   18-109, 207-430
R/sampleVarSpec.R       221     100  54.75%   296-302, 314-321, 323, 331-342, 344-345, 347, 350, 358-362, 364-379, 384-407, 410-414, 416, 423-433, 435-436, 444, 489-506
R/scatterplot.R         168     133  20.83%   40-64, 126-257
R/utils.R                16       5  68.75%   75-79
R/volcanoplot.R         195     160  17.95%   35-56, 115-280
R/zzz.R                   1       1  0.00%    2
TOTAL                  2547    1734  31.92%

Results for commit: 3712b0e

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

  1 files  15 suites   25s ⏱️
58 tests 36 ✔️ 22 💤 0 ❌
85 runs  63 ✔️ 22 💤 0 ❌

Results for commit 38e085a.

♻️ This comment has been updated with latest results.

[danielinteractive]

Thanks a lot @mhallal1 ! I did not try it out yet, but trust @Polkas that he will and give feedback on the user experience. One ask, can you please run the shiny tests manually with testing depth 5 and make sure they pass / make any adjustments as needed for the reporter to make them pass. Thanks a lot!

[Polkas]

Modules combined teal.gallery::launch_app("RNA-seq")

Modules separately:

• tm_g_barplot
• tm_g_boxplot
• tm_g_forest_tte
• tm_g_km
• tm_g_pca
• tm_g_quality
• tm_g_scatterplot
• tm_g_volcanoplot

[Polkas]

Please do not print the Encoding elements if they are optional and empty.

[Polkas]

It is surprising that only one module is using plot_with_settings/table_with_settings.
#61

[Polkas]

Please regenarate the _snaps directory in the testthat.
We have some Errors under the testing depth 5 nevertheless they are already on the main branch.

[mhallal1]

Please regenarate or remove the _snaps directory in the testthat. We have some Errors under the testing depth 5 nevertheless they are already on the main branch.

Issue created as it existed on main already: #266

[mhallal1]

@danielinteractive we had to update the snaps folder to pass the test with a depth of 5:

[mhallal1]

Please do not print the Encoding elements if they are optional and empty.

fixed.

[Polkas]

Great work:)
Please create an issue for checking the plot with settings (empty returned height and width) in forest plot, thanks.

[Polkas]

Suggested change

	card$append_plot(forest_plot())
	card$append_plot(forest_plot(), dim = pws$dim())

[mhallal1]

issue created: #267