resolve merge conflicts

.Rbuildignore

@@ -22,6 +22,7 @@ _\.new\.png$
 ^pkgdown$
 ^Crashpad$
 ^tarballs$
-^source$
 ^revdep
 ^revdep$
+^manifest\.json$
+^\.rscignore$

.github/workflows/R-CMD-check.yaml

@@ -34,6 +34,7 @@ jobs:
           sudo apt-get install -y libcurl4-openssl-dev
           sudo apt-get install -y libharfbuzz-dev
           sudo apt-get install -y libfribidi-dev
+          sudo apt-get install -y texlive-xetex
           
       - uses: actions/checkout@v3
 

.github/workflows/test-coverage.yaml

@@ -17,6 +17,13 @@ jobs:
       RENV_CONFIG_SANDBOX_ENABLED: false
 
     steps:
+      - name: Install TexLive
+        if: runner.os == 'Linux'
+        shell: bash
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y texlive-xetex
+      
       - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-pandoc@v2

.github/workflows/write-manifest.yaml

@@ -0,0 +1,53 @@
+# Workflow derived from https://solutions.posit.co/operations/deploy-methods/ci-cd/github-actions/#overview-of-deploying-to-connect
+
+name: write-manifest
+on:
+  pull_request:
+    branches: [dev]
+    types: [review_requested]
+  workflow_dispatch:
+
+
+jobs:
+  write-manifest:
+    if: ${{ !github.event.pull_request.draft }}
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Move to branch
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.pull_request.head.ref }}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'renv'
+          use-public-rspm: false
+      - uses: r-lib/actions/setup-renv@v2
+
+      - name: Install required packages
+        run: Rscript -e 'renv::install("rsconnect")'
+
+      - name: Create manifest.json
+        run: Rscript -e 'rsconnect::writeManifest()'
+
+      - name: Commit results
+        id: commit-results
+        run: |
+          git config --local user.name "Github Actions"
+          git config --local user.email "actions@github.com"
+          git add manifest.json || echo "WARN: manifest.json was not updated"
+          git commit -m 'Re-build manifest file' || echo "No changes to commit"
+          git push origin || echo "No changes to commit"
+          echo "commit-sha=$(git rev-parse HEAD)" >> "$GITHUB_OUTPUT"
+          
+      - name: Set status
+        run: |
+          gh api \
+            --method POST \
+            -H "Accept: application/vnd.github+json" \
+            -H "X-GitHub-Api-Version: 2022-11-28" \
+            /repos/pharmaR/riskassessment/statuses/${{ steps.commit-results.outputs.commit-sha }} \
+              -f "state=success" -f "description=manifest.json build succeeded!" -f "context=manifest-built"

.gitignore

@@ -14,5 +14,5 @@ docs/
 *.sqlite
 !*demo.sqlite
 tarballs/
-source/
 report_preferences/
+.Renviron

.rscignore

@@ -4,3 +4,4 @@ tests
 revdep
 dev
 man
+.Rprofile

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: riskassessment
 Title: A web app designed to interface with the `riskmetric` package
-Version: 3.0.0
+Version: 3.1.0
 Authors@R: c( 
-    person("Aaron", "Clark", role = c("aut", "cre"), email = "aaron.clark@biogen.com"),
+    person("Aaron", "Clark", role = c("aut", "cre"), email = "clark.aaronchris@gmail.com"),
     person("Robert", "Krajcik", role = "aut", email = "robert.krajcik@biogen.com"),
     person("Jeff", "Thompson", role = "aut", email = "jeff.thompson51317@gmail.com"),
     person("Lars", "Andersen", role = "aut", email = "lars.andersen@boehringer-ingelheim.com"),
@@ -13,6 +13,7 @@ Authors@R: c(
     person("Maya", "Gans", role = "aut", email = "maya.gans@biogen.com"),
     person("Aravind Reddy", "Kallem", role = "aut"),
     person("Eduardo", "Almeida", role = "ctb", email = "eduardoalmeida7393@gmail.com"),
+    person("Narayanan","Iyer",role = "ctb", email = "NarayananSeshan.Iyer@pfizer.com"),
     person(family = "Fission Labs India Pvt Ltd", role = "aut"),
 	  person(family = "PSI special interest group Application and Implementation of Methodologies in Statistics", role = c("cph", "fnd")),
     person(family = "R Validation Hub", role = c("cph", "fnd")),
@@ -32,20 +33,22 @@ Description: A shiny application that allows users to define a list of R
     decisions' can be made at the package level manually or through pre-defined
     automation rules.
 License: MIT + file LICENSE
-URL: https://github.com/pharmaR/riskassessment
+URL: https://github.com/pharmaR/riskassessment, https://pharmar.github.io/riskassessment/
 BugReports: https://github.com/pharmaR/riskassessment/issues
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.0
+RoxygenNote: 7.3.1
 Imports: 
+    archive,
     bslib (>= 0.3.0),
     config (>= 0.3.1),
     cranlogs,
     DBI,
     desc,
     dplyr,
     DT,
+    flextable,
     formattable,
     glue,
     golem (>= 0.3.2),
@@ -73,12 +76,14 @@ Suggests:
     kableExtra,
     knitr,
     pkgload,
+    png,
     rjson,
     rstudioapi,
     shinytest2,
     spelling,
     testthat (>= 3.0.0),
-    tinytex
+    tinytex,
+    withr
 Config/testthat/edition: 3
 Language: en-US
 Depends: 

NAMESPACE

@@ -25,12 +25,23 @@ importFrom(DT,selectRows)
 importFrom(DT,styleEqual)
 importFrom(RSQLite,SQLite)
 importFrom(RSQLite,sqliteCopyDatabase)
+importFrom(archive,archive)
+importFrom(archive,archive_read)
 importFrom(bslib,bs_theme)
+importFrom(bslib,card)
+importFrom(bslib,card_body)
+importFrom(bslib,card_header)
+importFrom(bslib,card_image)
+importFrom(bslib,card_title)
+importFrom(bslib,layout_column_wrap)
+importFrom(bslib,page_fluid)
+importFrom(bslib,tooltip)
 importFrom(cranlogs,cran_downloads)
-importFrom(desc,desc_fields)
-importFrom(desc,desc_get_field)
-importFrom(desc,desc_get_list)
+importFrom(desc,description)
 importFrom(dplyr,case_when)
+importFrom(flextable,colformat_char)
+importFrom(flextable,flextable)
+importFrom(flextable,set_table_properties)
 importFrom(formattable,as.datatable)
 importFrom(formattable,csscolor)
 importFrom(formattable,formattable)
@@ -88,20 +99,24 @@ importFrom(rvest,html_node)
 importFrom(rvest,html_table)
 importFrom(rvest,html_text)
 importFrom(rvest,read_html)
+importFrom(shiny,HTML)
 importFrom(shiny,NS)
 importFrom(shiny,actionButton)
+importFrom(shiny,em)
 importFrom(shiny,icon)
 importFrom(shiny,modalDialog)
 importFrom(shiny,removeModal)
 importFrom(shiny,shinyApp)
 importFrom(shiny,showModal)
+importFrom(shiny,tagAppendAttributes)
 importFrom(shiny,tagList)
 importFrom(shinyAce,aceEditor)
 importFrom(shinyAce,updateAceEditor)
 importFrom(shinyTree,get_selected)
 importFrom(shinyTree,renderTree)
 importFrom(shinyTree,shinyTree)
 importFrom(shinyTree,updateTree)
+importFrom(shinyWidgets,actionBttn)
 importFrom(shinyWidgets,colorPickr)
 importFrom(shinyWidgets,materialSwitch)
 importFrom(shinyWidgets,prettyCheckboxGroup)
@@ -129,6 +144,7 @@ importFrom(sortable,sortable_js)
 importFrom(sortable,sortable_js_capture_input)
 importFrom(sortable,sortable_options)
 importFrom(stats,lm)
+importFrom(stats,na.omit)
 importFrom(stats,predict)
 importFrom(stringr,regex)
 importFrom(stringr,str_extract)
@@ -141,6 +157,7 @@ importFrom(tools,Rd2HTML)
 importFrom(tools,package_dependencies)
 importFrom(utils,adist)
 importFrom(utils,available.packages)
+importFrom(utils,capture.output)
 importFrom(utils,download.file)
 importFrom(utils,getParseData)
 importFrom(utils,head)

NEWS.md

@@ -1,3 +1,44 @@
+# 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
@@ -14,16 +55,18 @@
 * Made color palette used through the app even more colorblind-friendly and created lighter "User Guide" logo (#654)
 
 ### Squashed Bugs
-* Fixed tests showing "Package Downloads" community usage card as non-metric (#621)
-* Fixed bug with the logo's hyperlink not functioning in the expected zone (#633)
-* Removed suggests from riskcalc weights table (#646)
-* Forced new lines in card paragraphs (#671)
+* 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