v0.15.2

Bug fixes

• Fixed a bug in handling datanames of modules that crashed module-specific applications when filtering child datasets.

What's Changed

• 1110 when no filters provided, report card should notify about it by @m7pr in #1111
• add options for strict testing by @pawelru in #1102
• Use teal.data::get_code instead of teal.data:::get_code_dependency by @m7pr in #1090
• name specific lintr in utils.R by @m7pr in #1118
• audit linter exceptions by @chlebowa in #1119
• 1125 bug fix@main by @chlebowa in #1126
• describe last patch in NEWS by @chlebowa in #1129
• Enables module-specific filters on init example by @averissimo in #1133
• [skip vbump] upversion v0.15.2 by @donyunardi in #1137

Full Changelog: v0.15.1...v0.15.2

v0.15.1

Bug fixes

• Fixed a bug that stopped the module_specific feature when a teal module specified datanames of length more than 1.

Miscellaneous

• Updated links in vignettes

v0.15.0

New features

• Added landing_popup_module function which creates a module that will display a popup when the app starts. The popup will block access to the app until it is dismissed.
• Filter state snapshots can now be uploaded from file. See ?snapshot.
• Added as_tdata function to facilitate migration of modules to the new teal_data class.
• Added build_app_title function to facilitate adding favicons to app title.

Breaking changes

• data argument in init now accepts only teal_data and teal_data_module.
• tdata has been deprecated and replaced with teal_data. Support for tdata passed to the data argument in module(server) will be removed in the next release.
• module(ui) argument no longer accepts data and datasets arguments. All data dependent logic should be set in the server function.
• module(server) argument deprecated datasets argument. teal_modules' server functions should accept data (teal_data) instead.
• Changed the order of formal arguments in init. filter now comes directly after modules, before title.

Miscellaneous

• Enhanced a module validation checks so that it won't throw messages about data argument unnecessarily.
• Added argument to teal_slices and made modifications to init to enable tagging teal_slices with an app id to safely upload snapshots from disk.
• FilteredData no longer stores pre-processing code in specific slots. Code is now attached as attribute. Adjusted appropriately.

Bug fixes

• Removed Report previewer module from mapping matrix display in filter manager.
• Specified minimal version of package dependencies.

v0.14.0

New features

• Enabled module specific filter panel. See module_specific in teal::teal_slices documentation.
• Enabled capturing and resetting application filter state with snapshots. See ?snapshot.
• Enabled reporter_previewer_module to customize default values through srv_args.
• Enabled passing own reporter_previewer_module in a list of modules to override default one.

Breaking changes

• Specifying filter argument in teal::init requires teal_slices object now. Details in documentation of teal::init.
• Soft deprecated filters argument in module and replaced it with datanames. Details in documentation of teal::module

Miscellaneous

• Removed scda package dependency from examples.

What's Changed

• 835 - get_rcode_*() starts new code chunks in newlines by @m7pr in #836
• documentation typo in get_rcode by @m7pr in #841
• Update workflows by @walkowif in #820
• Update workflows by @walkowif in #842
• Rewrite unclear sentence in creating-custom-modules.Rmd by @m7pr in #854
• Workflow propagations by @walkowif in #855
• Decouple scda by @gogonzo in #858
• extend default report previewer by @gogonzo in #849
• Refactor of the filter panel by @gogonzo in #851
• 355 rename module_add to allow_add by @kartikeyakirar in #863
• Move TealReportCard to teal by @gogonzo in #865
• 298 reset button by @chlebowa in #859
• typo in creating-custom-modules.Rmd by @m7pr in #853
• 382 rename internal functions by @chlebowa in #868
• restart auto by @gogonzo in #873
• restart auto by @gogonzo in #874
• fix r-universe deployment by @gogonzo in #875
• Update install by @gogonzo in #876
• 870 some bugs@main by @chlebowa in #872
• 818 documentation cleanup by @m7pr in #869
• 867 modify mapping matrix by @chlebowa in #879
• 769 replace filters argument by @chlebowa in #877
• handling initial teal_slice by @gogonzo in #880
• fix by @gogonzo in #881
• 884 disappear cog icon by @chlebowa in #886
• add placeholders to managers by @chlebowa in #887
• 410 note experimental by @chlebowa in #888
• update install guide; add getting help; pkg name lowercase by @pawelru in #890
• move gif to man dir by @pawelru in #894
• release 0.14.0 [skip vbump] [skip spelling] by @donyunardi in #897

Full Changelog: v0.13.0...v0.14.0

v0.13.0

Breaking changes

• The use of datasets argument in modules has been deprecated and will be removed in a future release. Please use data argument instead. data is of type tdata; see "Creating custom modules" vignettes and function documentation of teal::new_tdata for further details.
• Due to deprecation of chunks in teal.code, the teal framework now uses their replacement (qenv) instead. The documentation in teal has been updated to reflect this and custom modules written with chunks should be updated to use qenv.
• Due to deprecation of chunks in teal.code, get_rcode, get_rcode_srv, and get_rcode_ui have been removed.

New features

• Added the validate_inputs function that transfers input validation messages to app output.
• modules argument of init accepts teal_module type of object. There is no need to wrap up a single module in modules() or list().
• Updated module_nested_tabs so that only active modules are calculated in a teal app.

Miscellaneous

• Updated examples to use scda.2022.
• Added R session information into a link in the footer of teal applications.
• Added data hashing step using rlang instead of digest package to calculate the hash (which has been moved from teal.data and teal.slice). There is now an explicit hashing check in the reproducible code output.
• Removed deprecated functions: root_modules, default_filter, bookmarkableShinyApp, as well as deprecated logging mechanism, including the functions log_app_usage and .log.
• Updated the "Teal and Bootstrap Themes" vignette to provide more details customizing a teal app with bslib::run_with_themer.
• Removed outdated diagram from srv_nested_tabs documentation.
• Changed default values of header and footer arguments in init to empty text.

What's Changed

• [skip vbump] Dev version with 9xxx by @arkadiuszbeer in #763
• use scda.2022 by @nikolas-burkoff in #766
• Add sessionInfo by @nikolas-burkoff in #767
• Teal refactor by @nikolas-burkoff in #768
• Add coverage badge by @walkowif in #772
• Enable checks for workflow_dispatch event by @walkowif in #773
• add hashing by @mhallal1 in #774
• Fix failing test by @gogonzo in #777
• 757 remove deprecated@main by @chlebowa in #780
• remove root_modules function by @donyunardi in #754
• Remove soft-deprecated function log_app_usage and .log by @chlebowa in #781
• Remove soft deprecated function bookmarkableShinyApp by @chlebowa in #782
• shinyvalidate improvements by @chlebowa in #786
• shinyvalidate improvements reopened by @chlebowa in #788
• Badges and contribution guidelines by @insights-engineering-bot in #790
• docs by @mhallal1 in #791
• convert check to assert by @pawelru in #795
• Update bootstrap vignette by @asbates in #798
• Fix deprecation warning in tests by @nikolas-burkoff in #797
• fix failing tests on R 4.3 by @gogonzo in #800
• fix bug in validate_inputs by @chlebowa in #793
• Add diagram, update NEWS by @donyunardi in #801
• Update check as-cran and default landing page by @walkowif in #805
• teal reactivity solution 2 by @mhallal1 in #806
• add teal.gallery ref to readme by @pawelru in #810
• Documentation fixes for release review by @asbates in #819
• 723 default header@main by @chlebowa in #824
• Revert removal of get_rcode by @asbates in #828
• release 0.13.0 [skip vbump] by @donyunardi in #832

New Contributors

• @walkowif made their first contribution in #772
• @donyunardi made their first contribution in #754
• @asbates made their first contribution in #798

Full Changelog: v0.12.0...v0.13.0

v0.12.0

New features

• Added the support for custom bslib bootstrap themes in teal::init apps, please read more in the new teal-bs-themes vignette.

Enhancements

• Added the option to choose which variables can be filtered in the filter panel by using the filterable attributes for the per-dataset lists in the filter argument of init.
• Updated teal_module to have data argument which receives a list of reactive filter data with "code" and "join_keys" attributes.
• Updated teal_module to have filter_panel_api argument which receives a FilterPanelAPI object.
• Updated the internals of module_teal to reflect changes in teal.slice.
• Updated vignettes and README content.

Breaking changes

• Updated teal_module to no longer receive datasets object in the ... argument. In order to use datasets in the teal_module please specify datasets explicitly.
• Deprecated merge_expression argument in get_rcode_srv function and removed it in get_rcode function.
• Deprecated session argument in get_rcode function.

Miscellaneous

• Enhanced the burger button so it is disabled when the filter panel is not used.

What's Changed

• [skip vbump] by @gogonzo in #666
• Contribution guide updates by @insights-engineering-bot in #671
• 443 rcycle@main by @Polkas in #637
• changes for filter panel constuctor by @nikolas-burkoff in #670
• docs: replaced links to github with links to API pkgdown sites by @kpagacz in #675
• revert - full input cycle by @Polkas in #677
• 654 pass reactive data@main by @gogonzo in #674
• DESC and README by @denisovan31415 in #684
• Update Rbuildignore and add auto-updates by @insights-engineering-bot in #685
• fix test by @mhallal1 in #688
• filter_panel_api by @mhallal1 in #692
• Fix when module(..., filters = NULL) by @gogonzo in #694
• feat: added support for events from the filter panel by @kpagacz in #681
• Update pre-commit config to detect _pkgdown.y[a]ml by @insights-engineering-bot in #699
• Update staged_dependencies.yaml for teal.modules.helios by @danielinteractive in #696
• pass join keys object into the module by @nikolas-burkoff in #697
• Update font awesome icon labels for FA 6 by @cicdguy in #704
• Remove _FILTERED by @nikolas-burkoff in #702
• Update documentation workflow by @insights-engineering-bot in #706
• review css by @Polkas in #703
• update vignettes by @mhallal1 in #705
• Update including-mae-data-in-teal.Rmd by @nikolas-burkoff in #725
• add set filter by @nikolas-burkoff in #724
• Update check.yaml by @arkadiuszbeer in #723
• fix R cmd check --as-cran by @nikolas-burkoff in #730
• teal - bs345 by @Polkas in #727
• NEWS by @mhallal1 in #745
• Update teal.Rmd by @Polkas in #759
• [skip vbump] Release for version 0.12.0 by @insights-engineering-bot in #761

Full Changelog: v0.11.1...v0.12.0

v0.11.1

Enhancements

• Added new function reporter_previewer_module to wrap the teal.reporter package previewer functionality as a teal module.
• Updated teal to support modules which include reporting. If any module which supports reporting is included then a reporter_previewer_module is included.
• Added default arguments to module() and the server argument is now a function where the second argument can be ... or datasets.

Breaking changes

• Deprecated bookmarkableShinyApp. In future releases the teal framework will stop supporting shiny bookmarking (which has not officially been supported); it may be officially supported in the future. Note the filter panel in teal.slice retains its ability to save and restore its state if used in a standalone shiny app with bookmarking.

Miscellaneous

• Added a template to the pkgdown configuration.
• Removed unneeded shinytest app tests.
• Updated package authors.
• Added package vignettes.

v0.10.1

Breaking changes

• Changed the HTML identifiers of teal modules - now each nested module receives its own shiny namespace.
• Deprecated all functions related to connectors that have been moved to their own separate packages.
• Removed raw_dataset, raw_dataset_connector, named_dataset, named_dataset_file, named_dataset_connector, relational_dataset, relational_dataset_file, relational_dataset_connector, key, as_cdisc, as_cdisc_relational.
• Removed rcd_connection and rcd_data; scda_dataset_connectors can be passed into cdisc_data and teal_data directly.
• Replaced rcd_dataset_connector and rcd_cdisc_dataset_connector with scda_dataset_connector and scda_cdisc_dataset_connector respectively.
• Renamed teal_show_js_log option into teal.show_js_log to match options naming convention.
• Removed %is_in% and stop_shiny internal utility functions.

New features

Logging

• Added support for logging using the logger package.
• Added a new function register_logger, which registers a logger in a given namespace.
• Added trace and info levels log messages to the teal framework.
• Added pid and shiny session token into footnote so app developers can identify logs for apps.

Other

• Added print methods to the DatasetConnector, RelationalData, RelationalDataconnector and JoinKeys classes and added input validation to the implementation of the print method that was already in the Dataset object.

• Added public facing constructor functions for CDISCDataConnector, RelationalDataConnector, and DataConnection classes.

• Modified data_extract_spec to allow both the filter and select parameters to be NULL, which results in the data_extract_ui acting as if a filter_spec with all variables as possible choices had been supplied as the filter argument and a select_spec with the multiple parameter set to TRUE had been supplied as the select argument.

• Added support of the full screen for a module when the filters argument is equal NULL.

• Added support for shiny::moduleServer passed to the server parameter of teal::module.

• Added teal.threshold_slider_vs_checkboxgroup as an R option: if a categorical variable has more than this number of unique values, the filter panel uses a drop-down select input instead of a checkbox group.

• Extended the FilteredData API to allow managing filter states programmatically and not only from the UI of a teal application.

• Hid the buttons to remove filters from all datasets and each dataset when there are no active filters.

• Updated init to accept RelationalData, data.frame, MultiAssayExperiment, Dataset, DatasetConnector, list or a function returning a named list as data input.

Bug fixes

• choices_selected now correctly removes duplicates from the array passed to its choices parameter.
• Fixed call returned by FilterState in case of using MultiAssayExperiment::subsetByColData. Now single condition for variable containing NA values is !is.na(var) & var == <condition>.
• Fixed data loading of DatasetConnector being dependent on other Dataset or DatasetConnector objects.
• Fixed restoring a bookmarked filter state of teal application.
• Refactored module_nested_tabs to fix the issue with the filter panel not reacting to an input change in a nested module.
• updateOptionalSelectInput no longer sets input to NULL when logical value is passed to selected.
• Fixed setting JoinKeys when key name between two Dataset object differs.
• Fixed printing of the JavaScript console logs to the R console when teal.show_js_log = TRUE.

Miscellaneous

• Soft-deprecate mae_dataset() in favor of more general dataset() constructor.
• Added a vignette describing the modifications to teal applications users can apply using R options.
• Added default values to the label argument of select_spec and filter_spec.
• Added validation to FilteredDataset::get_data to accept logical input only.
• Changed references to outdated functions of teal.devel in the documentation.
• Introduced a Teal prefix to all public R6 classes to avoid name collisions with other packages.
• Removed dependency on utils.nest and replaced its functionality in teal with equivalents from the checkmate package and base R.
• Replaced the old shiny server functions of DataConnection, RelationalDataConnector, DatasetConnector, and RelationalData with the shiny::moduleServer equivalents.
• Running a teal application via ui_teal_with_splash and srv_teal_with_splash is now no longer recommended because it doesn't support new features (e.g. logging, bookmarking). Use init instead.
• Updated the R version requirement to >= 4.0.
• Updated the "filter panel collapse" icon to remove warnings when using shiny version >= 1.7.
• Removed some of the non-exported, debugging modules.
• Updated the footer tag style to be less visible.

v0.10.0

New features

• Allow passing MultiAssayExperiment to the teal::init using mae_dataset function or through
  the connectors.
• Refactored filter panel to use MultiAssayExperiment objects. Filters can be set on a subject level
  (colData of MAE object) and on a experiment level (colData and rowData of an assay).
• Added cdse_dataset_connector to create delayed data objects from CDSE.
• Added datasetdb_dataset_connector to create delayed data objects from DataSetDB.
• Added ricepass_connection to create delayed data objects from entimICE via ricepass.
• Refactor of the filter panel:
  • Simplified setting of initial filter state without need to specify "choices" or "range" named list element depending on the variable class.
  • Dataset type determines an appearance and a functionality of related filters and filters summary.
  • Datasets are passed (by reference) from DDL to FilteredData skipping extracting data and
    their attributes.
  • Redesigned variable filter labels in "Active Filter Variables" panel.
  • Fully testable server functions.

Bug fixes

• Fixed the bug caused by calling mutate_dataset multiple times on the same DatasetConnector or Dataset object.
• Fixed a bug that caused the output of get_code function to not reproduce its raw data set.
• Changed filter_spec to allow no variable selection upon app initialization, where the first possible value was previously selected.

Enhancements

• modules parameter of teal::init function can also receive a list except root_modules
  function call.
• Added split and merge methods to the JoinKeys object.
• Added all_choices() as a possible argument to the selected parameter of filter_spec, select_spec and choices_selected indicating that all choices are selected.
• The append method of a CodeClass object has been modified to print a warning message when the argument does not result in any code being added because it is duplicated.
• Implemented delayed functionality to the mutate method of the Dataset and DatasetConnector objects.
• Modified teal_data to return a CDISCData object whenever any of its arguments is a type of CDISCData object.
• Updated filters to show both levels of a logical variable TRUE/FALSE even if one is missing from the original array.

Miscellaneous

• Updated LICENCE and README with new package references.
• Added a method get_hash to the Dataset class returning the MD5 hash of the object stored inside the Dataset object.
• Replaced random.cdisc.data with scda in examples and tests.
• Implemented functionality to store JoinKeys in Dataset and DatasetConnector classes.
• Added error_on_lintr: TRUE to .lintr
• The pipe operator %>% is now exported such that downstream code and packages can use it.
• Removed hyperlinks to the rice package from the documentation.

v0.9.5

• Added informational stop message when using mutate_data with RelationalDataConnector.
• Modified as_cdisc to behave similarly to cdisc_dataset when called on a Dataset object.
• Changed the displayed format of the data name and the column name in data_extract_spec UI elements. Both are now compressed to <data name>.<column name> if they don't change during runtime of the app.
• Added ADSAFTTE to the list of recognized ADaM dataset names.
• Added another example to data_extract_spec's doc string showcasing app users can choose a variable used for filtering in the encoding panel.
• Added CSS styling to tool tips in teal modules.
• Fixed an edge case error when creating a filter on variable with all missing values crashed the app.
• Fixed a bug that crashes app whenever a Date or datetime column is selected from a filter_spec.