NEWS

riskassessment 3.1.1

Added navigation controls in Function Explorer tab (#644)
Fixed bug that crashed the Package Dependencies page for pkgs without any dependency info available (#802)
Fixed bug that incorrectly displayed 0 dependencies as 1 (#805)
Fixed bug that kept full list of available packages from populating (#776)
Removed .recording attribute from riskmetric assessments for storage purposes
Ensured tarballs directory existed before returning from initialize_raa()

riskassessment 3.1.0

User Enhancements

Allow users to specify decisions within the CSV file used to upload pkgs (#663)
Drastically shortened waiting time in Code explorer/ Package explorer by reading tarballs in memory (#707)
Added Package Dependencies content to Reports (#721)
Added option to include Suggests pkgs in downloadable Reports (#721)
Added Decision column to Package Dependencies tab's table output (#774)
Added Decision Summary card to Package Dependencies tab (#774)
Added hyperlink on dependencies/reverse dependencies cards, directing users to Package Dependencies page for more detail (#597)
Added new table to display reverse dependencies which highlights pkgs that already exist in the database

Squashed Bugs

Fixed bug causing application to crash when trying to delete zero packages (#781)
Fixed bug where app doesn't reset the decision by and decision date fields when re-scoring/re-weighting packages (#680)
Fixed bug where the user privileges table was not aligned with the available privileges in the application (#697)
Fixed typo in privileges table (#719)
Fixed bug where HTML reports displayed a darker green in the cards' meters
Updated logo in reports to lighter version to match application UI
Updated the Dependency Cards to be slightly more informative

Docs

Added About page to introduce our audience to the project a little better, providing useful resources and attribution that highlights individual contributors
Added more context to the metric score card visuals by inserting tool tips & creating a legend modal that describes & interprets all possible visuals (#652)
Added introjs for file browser & function explorer( #581)
Added {riskmetric} assessment documentation URLs to About tab, on Risk Assessment Criteria page.

For Devs

Added non-shinymanager deployment option so that users may use their Posit Credentials instead (#700)
Moved package upload process to a function, allowing devs to populate the database outside of the application
Added tests for the Code Explorer and Function explorer modules
Added repo specification to configuration file (#701)
Ensured configuration checkers run when configuring the database
Utilized {archive} to parse DESCRIPTION file, increasing speed in package upload process
Updated manifest file and deployments article
Updated version of {riskmetric} being used to v0.2.4.9000
Updated version of R to v4.3.3 & Posit Package Manager snapshot dates to 2024-04-08

riskassessment 3.0.0

Enhancements

Added "Suggests" pkgs to Dependencies tab (#624)
Summarized Package Dependencies (#618)
Integrated the 'Function Explorer' to offer users function-level browsing of source code, unit testing, and automatic rendering of help documentation (#498)
Started showing metric_scores for each assessment's card, using an html meter (#634)
Added default {DT} based filter to Database Overview tab (#586)
Allowed users to create decision automation rules for individual metrics (#483)
Added checkbox to databaseView to select all packages for reportDownload handler (#649)
Allowed users to identify and store preferred elements to include in downloaded reports (#526)
Add "Explore Metrics" button to Uploaded Pkgs Summary tab on Upload Packages tab (#653)
Added comment module to the Function Explorer (#643)
Made color palette used through the app even more colorblind-friendly and created lighter "User Guide" logo (#654)

Squashed Bugs

Fixed the app's logo hyperlink to docs not functioning in the expected "zone" (#633)
Fixed tests showing "Package Downloads" community usage card as a non-metric (#621)
Removed "Suggests" from Riskassessment Criteria weights table (#646)
Forced formation of new lines in cards (#671)
Ensured users couldn't create & select packages from CRAN that don't exist on Upload Packages tab

For Devs

Migrated from {jsTreeR} to {shinyTree} (#585)
Removed some unneeded/unused dependencies
Updated {shinytest2} and {chromote} to more recent versions for testing
Added correct remotes reference in DESCRIPTION file for pharmar/riskmetric & rstudio/chromote
Stopped using CRAN repo snapshot date in renv (#677)

riskassessment 2.0.0

Enhancements

Expand privileges to include commenting on metrics and packages (#564)
Allow admin users to edit roles and privileges (#541)
Download source tarball when uploading package to database so that users can explore source contents of package (#574)
Added card Download Trend and linear trend plot on community usage metrics (#438)
Introduced cards to Database tab, reviewing contents of db (#587)
Prominently display the date a package was added (#486)
Fix issue where the repository being used to gather information was inconsistent
Added Package Dependencies page to "Package Metrics" tab, and two new cards to Maintenance Metrics page (#261)
Identify non-riskmetric cards (#573)

Squashed Bugs

Fixed busted button introduced with #547 (#592)

Docs

Updated riskassessment vignette to reflect new tab structure

For Devs

Disable using the Microsoft R Application Network (MRAN) for restoring packages
Removed legacy code that set the covr_coverage assessment's metric weight to 0 in the assessmentInfo mod and metric table initialization sql file.

riskassessment 1.0.0

Enhancements

Updated the version of {riskmetric} used to V0.2.2
Implemented usage of configuration file instead of passing arguments in run_app() (#459)
- Added decision categories (#459)
- Added decision automation rules (#459)
- Added log file designation (#463)
- Implemented user roles/privileges to allow for more granular access to actions in the application (#527)
- Allow metric weights to be initialized (#482)
From a computational speed perspective, we made the following improvements that users should feel
- During package upload, inserting community metrics into database (#516)
- When metric weights are changed, we re-score instead of re-assess, saving huge amounts of time (#537)
The Database View got a few updates:
- Added Decision-related columns like the decision time stamp & decision source
- Introduced the decision category table
Enhanced (what was formerly known as) the "Report Preview" tab to include:
- A more holistic Report Builder. This allows users to define what content shows up in the report (#348).
- Users can now compose a long form "Package Summary" to keep track of more pertinent items (perhaps items less central to {riskmetric} output) for a more rounded package review (#348).
Allowed the certain users to set a custom color for decision categories (#465)
Added a code coverage (covr_coverage) card and add optimized the card layout logic (#533)

Squashed Bugs

Fixed Chromote error (#477)
Fixed bug preventing icons from displaying on admin tab (#427)
Fixed button alignment issues (#514)
Re-positioned footer to be at the bottom of the visible page (#518)
Added a new check that conditionally delivers message about differing pkg versions ONLY when CSV file is loaded (#515)
Fixed broken links in docs

Docs

Updated help files for build_comm_plotly() to include example output (#409).
Created new (and updated some) user guides to explain how to precisely control the app deployment using a configuration file.
Retired some pertinent "old"" user guides in case users are still running old versions of {riskassessment}

For Devs

Utilized glue::glue_sql() inside of update and select functions (#520)
Improved speed of inserting community metrics into database (#516)
Re-score instead of re-assess when metric weights are changed, meaning we are now storing the pkg assessment (#537)
Pass warning instead of error when default privilege config gets combined with another config (#547)

riskassessment 0.1.1

Enhancements

Upgraded to leverage {riskmetric} to v0.2.0 which impacts risk score calculations
Add button that redirects to pkg metrics
Added 'search' capability to database view tab
Added Excel & CSV export options on Database View tab
Added hyperlink to the documentation site / user guide within the application
Added check that URLs needed to upload packages are reachable, just in case!
Added riskassessment logo for docx and pdf reports
Some general aesthetic improvements, for example: made sure tab headers were a consistent size

Squashed Bugs

Fixed bug where card displaying "Number of downloads in last 12 months" was faulty, summing all months from previous year and none from current year.
Report headings were changed to "asis" sentence case to avoid altering case on package names in reports
Fix failing tests: prefix AppDriver$new with 'shinytest2::'
Fix for Chromote error provided by Winston Chang

Docs

Added User Feedback survey to README (#411)
Fixed broken R-CMD-CHECK badge in README
Updated a few vignettes to describe new 'Decision Automation' feature

For Devs

Removed {golem} testing option pre_auth_user from the arguments of run_app()
Improved stability and ease-of-use for testing introJS module
Preload information for a select list of packages to improve tests utilizing shinytest2
Upgraded to R Version v4.2.2

riskassessment 0.1.0

All New Features

Allowed users to type in package names to be assessed in the app, instead of uploading CSV file. Also allow point-and-click deletion of packages.
Added decision automation capabilities where the user can set decision rules for uploaded packages to be auto-assigned.

Enhancements

Added "PDF report" download option (#280)
Added risk score to the Report Preview tab and downloaded reports (#264).
Exported generate_comm_data() to help users build the community usage data needed run build_comm_plotly() (also exported) to produce the "downloads by month"" plot as seen on the Community Usage tab of the application. (#266).

For deployment

Created a argument for run_app() called login_note which allows users deploying the app to add custom log-in notes on the authentication screen. By default, it displays a note about how to use default usernames and passwords to gain entry for the first time.
Engineered a new argument to run_app() called app_version which allows users deploying the application to publish their own custom text string in the app's authentication screen and any downloaded reports. By default, it will display the installed version.

Docs

Updated README to include more description, 'Usage' info, including how to install & run the app for the first time. Last, included links to the demo app & a short video walk-through. Very brief notes were included regarding deployment environments.
Added several vignettes to documentation site, including:
- "Get started with riskassessment" vignette
- "Administrative Tools and Options" vignette
Designed hex logo
updated documentation to reflect new repo name 'riskassessment' without the '_' to separate the two words.
suggest installation of riskmetric from GitHub, and not CRAN (for now)

Squashed Bugs

Fixed bug causing Community Usage metrics to fail on Mac computers
Fixed bug causing the report to fail when no Community Metrics were available for a package.
Add founders/copyright holders to DESCRIPTION file
Fixed bug where Assessment Criteria tables were failing to render.
Improved metric 'card' aesthetics in order to remove scroll bars (#198).
Added console warnings, log-in note, and modals to warn user there is a bug with {fontawesome} v0.4.0. For more info, the bug status can be tracked here.
Fixed summary of community usage data when there was more than one package version released in the same month
Fixed bug where the logging file was not being set
Fixed package delete button shadow; fix introjs for admin/non-admin roles
Fixed display of 'Report Bugs' metric to align with current riskmetric presentation as 0 or 1

For Devs

Some general re-organizing of the package's infrastructure to make testing and development easier.
Added unit tests to attain test coverage >85% (#295).
Added renv and a renv.lock file as well as corresponding vignette for developers/contributors to align on.
Reduce number of package dependencies from 33 to 26
Changed risk-based color gradient to use colorblind-friendly color palette (#324).
Adopt (temporary) CRAN-first data collection method for pkg info via riskmetric::pkg_ref()

riskassessment 0.0.1

Initiated simple app.R for easier deployment using runURL("https://github.com/pharmaR/riskassessment/archive/master.zip") and shiny::runGitHub('riskassessment', 'pharmaR')

riskassessment 0.0.0.9000

Added a NEWS.md file to track changes to the package.
Used {golem} to complete "packagization" of {riskassessment}