Remove special tibblify version checks

.Rbuildignore

@@ -14,3 +14,5 @@
 ^\.positai$
 ^\.claude$
 ^AGENTS\.md$
+^[.]?air[.]toml$
+^\.vscode$

.github/workflows/copilot-setup-steps.yml

@@ -45,6 +45,7 @@ jobs:
             any::testthat
             any::usethis
             any::withr
+            Gilead-BioStats/qcthat
             local::.
 
       - name: Install air

.github/workflows/format-suggest.yaml

@@ -0,0 +1,46 @@
+# Workflow derived from https://github.com/posit-dev/setup-air/tree/main/examples
+
+on:
+  # Using `pull_request_target` over `pull_request` for elevated `GITHUB_TOKEN`
+  # privileges, otherwise we can't set `pull-requests: write` when the pull
+  # request comes from a fork, which is our main use case (external contributors).
+  #
+  # `pull_request_target` runs in the context of the target branch (`main`, usually),
+  # rather than in the context of the pull request like `pull_request` does. Due
+  # to this, we must explicitly checkout `ref: ${{ github.event.pull_request.head.sha }}`.
+  # This is typically frowned upon by GitHub, as it exposes you to potentially running
+  # untrusted code in a context where you have elevated privileges, but they explicitly
+  # call out the use case of reformatting and committing back / commenting on the PR
+  # as a situation that should be safe (because we aren't actually running the untrusted
+  # code, we are just treating it as passive data).
+  # https://securitylab.github.com/resources/github-actions-preventing-pwn-requests/
+  pull_request_target:
+
+name: format-suggest.yaml
+
+jobs:
+  format-suggest:
+    name: format-suggest
+    runs-on: ubuntu-latest
+
+    permissions:
+      # Required to push suggestion comments to the PR
+      pull-requests: write
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+
+      - name: Install
+        uses: posit-dev/setup-air@v1
+
+      - name: Format
+        run: air format .
+
+      - name: Suggest
+        uses: reviewdog/action-suggester@v1
+        with:
+          level: error
+          fail_level: error
+          tool_name: air

.github/workflows/pkgdown-cleanup.yaml

@@ -0,0 +1,33 @@
+# This workflow removes the pkgdown preview directory when a PR is closed.
+name: Clean up pkgdown preview
+
+on:
+  pull_request:
+    types: [closed]
+
+permissions:
+  contents: write
+
+jobs:
+  clean-pr-preview:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v6
+        with:
+          repository: ${{ github.repository }}
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ref: gh-pages
+
+      - name: Remove PR preview directory
+        run: |
+          pr_dir="pr/${{ github.event.number }}"
+          if [ -d "$pr_dir" ]; then
+            git config --local user.name "$GITHUB_ACTOR"
+            git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+            git rm -rf "$pr_dir"
+            git commit -m "Remove preview for PR #${{ github.event.number }}"
+            git push
+          else
+            echo "Directory $pr_dir does not exist, skipping cleanup."
+          fi

.github/workflows/pkgdown.yaml

@@ -32,7 +32,7 @@ jobs:
           use-container: "true"
           token: ${{ secrets.GITHUB_TOKEN }}
           needs: website
-          extra-packages: any::pkgdown gilead-biostats/qcthat local::.
+          extra-packages: any::pkgdown gilead-biostats/qcthat local::. any::glue
 
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
@@ -54,7 +54,7 @@ jobs:
           strOwner <- tolower(qcthat::GetGHOwner())
           strRepo <- qcthat::GetGHRepo()
           strURL <- glue::glue(
-            "https://{strOwner}.github.io/{strRepo}/pr/{intPRNumber}/dev"
+            "https://{strOwner}.github.io/{strRepo}/pr/{intPRNumber}"
           )
           print(paste("🌐 URL:", strURL))
           qcthat::CommentIssue(

.github/workflows/qcthat.yaml

@@ -0,0 +1,157 @@
+# Workflow derived from
+# https://github.com/Gilead-BioStats/qcthat/tree/v1.1.1/inst/workflows/qcthat.yaml.
+on:
+  pull_request:
+    types: [opened, edited, reopened, synchronize, milestoned]
+  release:
+    types: [released]
+  issues:
+    types: [closed]
+  workflow_dispatch:
+    inputs:
+      pr:
+        description: PR number to which reports should be added (leave blank for none).
+        required: false
+      milestone:
+        description: Milestone name to use for the milestone report (leave blank for none).
+        required: false
+      tag:
+        description: Release tag to which the report should be attached (leave blank for none).
+        required: false
+      issueNumber:
+        description: The closed issue number to process to update user acceptance testing information.
+        required: false
+
+name: qcthat Quality Control
+
+permissions:
+  # read: Required for generating reports and updating UAT status.
+  # write: Required for initiating the UAT process.
+  issues: write
+  # read: Required for updating UAT status.
+  # write: Required for adding reports to pull requests.
+  pull-requests: write
+  # write: Required for attaching reports to releases.
+  contents: write
+  # write: Required for updating UAT status.
+  actions: write
+
+# Configuration variables for controlling workflow behavior
+env:
+  qcthat_UAT: true
+  qcthat_PR_REPORT: true
+  qcthat_COMPLETED_REPORT: true
+  qcthat_MILESTONE_REPORT: true
+  qcthat_RELEASE_REPORT: true
+  qcthat_FAIL_FOR_TEST_FAILURES: true
+
+jobs:
+  qcthat:
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/api2r/pkgskills-ci:release
+    if: >-
+      (github.event_name == 'issues' && contains(github.event.issue.labels.*.name, 'qcthat-uat')) ||
+      github.event_name != 'issues'
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: api2r/actions/install@v1
+        with:
+          use-container: "true"
+          token: ${{ secrets.GITHUB_TOKEN }}
+          extra-packages: Gilead-BioStats/qcthat@main local::.
+
+      - name: Manage User Acceptance Testing
+        if: >-
+          env.qcthat_UAT == 'true' && (
+            (github.event_name == 'issues' && contains(github.event.issue.labels.*.name, 'qcthat-uat')) ||
+            (github.event_name == 'workflow_dispatch' && inputs.issueNumber != '')
+          )
+        run: |
+          Rscript -e "qcthat::TriggerUAT()"
+
+      - name: Generate Issue-Test Matrix
+        if: >-
+          (env.qcthat_PR_REPORT == 'true' || env.qcthat_RELEASE_REPORT == 'true' || env.qcthat_FAIL_FOR_TEST_FAILURES == 'true') && (
+            github.event_name == 'pull_request' ||
+            github.event_name == 'release' ||
+            (github.event_name == 'workflow_dispatch' && inputs.issueNumber == '')
+          )
+        run: |
+          # Generate the full matrix for the package
+          IssueTestMatrix <- qcthat::QCPackage()
+          print(IssueTestMatrix)
+
+          # Save the matrix and UAT data for subsequent steps
+          saveRDS(IssueTestMatrix, "ITM.rds")
+          qcthat::SaveUATIssues()
+        shell: Rscript {0}
+
+      - name: Update PR Reports
+        if: >-
+          env.qcthat_PR_REPORT == 'true' && (
+            github.event_name == 'pull_request' ||
+            (github.event_name == 'workflow_dispatch' && inputs.pr != '')
+          )
+        run: |
+          issueTestMatrix <- readRDS("ITM.rds")
+          qcthat::LoadUATIssues()
+          qcthat::CommentAllReports(
+            dfITM = issueTestMatrix,
+            lglPR = as.logical("${{ env.qcthat_PR_REPORT }}"),
+            lglMilestone = as.logical("${{ env.qcthat_MILESTONE_REPORT }}"),
+            lglCompleted = as.logical("${{ env.qcthat_COMPLETED_REPORT }}"),
+            lglUAT = as.logical("${{ env.qcthat_UAT }}")
+          )
+        shell: Rscript {0}
+
+      - name: Update Release Reports
+        if: >-
+          env.qcthat_RELEASE_REPORT == 'true' && (
+            github.event_name == 'release' || inputs.tag != ''
+          )
+        run: |
+          issueTestMatrix <- readRDS("ITM.rds")
+          qcthat::LoadUATIssues()
+          qcthat::AttachReleaseReports(
+            dfITM = issueTestMatrix,
+            lglCompleted = as.logical("${{ env.qcthat_COMPLETED_REPORT }}"),
+            lglMilestone = as.logical("${{ env.qcthat_MILESTONE_REPORT }}")
+          )
+        shell: Rscript {0}
+
+      - name: Flag failure for PR
+        if: >-
+          env.qcthat_FAIL_FOR_TEST_FAILURES == 'true' && (
+            github.event_name == 'pull_request' ||
+            (github.event_name == 'workflow_dispatch' && inputs.pr != '')
+          )
+        run: |
+          issueTestMatrix <- readRDS("ITM.rds")
+          dfPR <- qcthat::QCPR(dfITM = issueTestMatrix)
+          if (any(dfPR$Disposition == "fail", na.rm = TRUE)) {
+            cli::cli_abort(
+              "One or more tests failed or were skipped for PR-associated issues."
+            )
+          }
+        shell: Rscript {0}
+
+      - name: Flag failure for completed
+        if: >-
+          env.qcthat_FAIL_FOR_TEST_FAILURES == 'true' && (
+            github.event_name == 'pull_request' ||
+            github.event_name == 'release' ||
+            (github.event_name == 'workflow_dispatch' && inputs.issueNumber == '')
+          )
+        run: |
+          issueTestMatrix <- readRDS("ITM.rds")
+          dfCompleted = qcthat::QCCompletedIssues(dfITM = issueTestMatrix)
+          if (any(dfCompleted$Disposition == "fail", na.rm = TRUE)) {
+            cli::cli_abort(
+              "One or more tests failed or were skipped for completed issues."
+            )
+          }
+        shell: Rscript {0}

.vscode/extensions.json

@@ -0,0 +1,5 @@
+{
+    "recommendations": [
+        "Posit.air-vscode"
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,10 @@
+{
+    "[r]": {
+        "editor.formatOnSave": true,
+        "editor.defaultFormatter": "Posit.air-vscode"
+    },
+    "[quarto]": {
+        "editor.formatOnSave": true,
+        "editor.defaultFormatter": "quarto.quarto"
+    }
+}

DESCRIPTION

@@ -26,7 +26,7 @@ Imports:
     snakecase,
     stbl (>= 0.3.0),
     tibble,
-    tibblify (>= 0.3.2),
+    tibblify (>= 0.4.0),
     xml2,
     yaml
 Suggests:

R/components-schema.R

@@ -41,14 +41,20 @@ class_schema <- S7::new_class(
     description = character_scalar_property("description"),
     format = character_scalar_property("format")
   ),
-  constructor = function(type = c(
-                           "string", "number", "integer",
-                           "boolean", "array", "object"
-                         ),
-                         ...,
-                         nullable = FALSE,
-                         description = character(),
-                         format = character()) {
+  constructor = function(
+    type = c(
+      "string",
+      "number",
+      "integer",
+      "boolean",
+      "array",
+      "object"
+    ),
+    ...,
+    nullable = FALSE,
+    description = character(),
+    format = character()
+  ) {
     check_dots_empty()
     if (missing(type)) {
       type <- character()

R/components-security_scheme-api_key.R

@@ -30,8 +30,10 @@ class_api_key_security_scheme <- S7::new_class(
     parameter_name = character_scalar_property("parameter_name"),
     location = character_scalar_property("location")
   ),
-  constructor = function(parameter_name = character(),
-                         location = c("query", "header", "cookie")) {
+  constructor = function(
+    parameter_name = character(),
+    location = c("query", "header", "cookie")
+  ) {
     if (length(parameter_name)) {
       location <- rlang::arg_match(location)
     } else {
@@ -75,10 +77,12 @@ S7::method(length, class_api_key_security_scheme) <- function(x) {
 #' @export
 #' @family components_security_schemes
 #' @family components
-as_api_key_security_scheme <- function(x,
-                                       ...,
-                                       arg = caller_arg(x),
-                                       call = caller_env()) {
+as_api_key_security_scheme <- function(
+  x,
+  ...,
+  arg = caller_arg(x),
+  call = caller_env()
+) {
   as_api_object(
     x,
     class_api_key_security_scheme,

R/components-security_scheme-oauth2-authorization_code_flow.R

@@ -36,11 +36,13 @@ class_oauth2_authorization_code_flow <- S7::new_class(
     authorization_url = character_scalar_property("authorization_url"),
     token_url = character_scalar_property("token_url")
   ),
-  constructor = function(authorization_url = character(),
-                         token_url = character(),
-                         ...,
-                         refresh_url = character(),
-                         scopes = class_scopes()) {
+  constructor = function(
+    authorization_url = character(),
+    token_url = character(),
+    ...,
+    refresh_url = character(),
+    scopes = class_scopes()
+  ) {
     check_dots_empty()
     S7::new_object(
       S7::S7_object(),
@@ -84,10 +86,12 @@ S7::method(length, class_oauth2_authorization_code_flow) <- function(x) {
 #' @export
 #' @family components_security_schemes
 #' @family components
-as_oauth2_authorization_code_flow <- function(x,
-                                              ...,
-                                              arg = caller_arg(x),
-                                              call = caller_env()) {
+as_oauth2_authorization_code_flow <- function(
+  x,
+  ...,
+  arg = caller_arg(x),
+  call = caller_env()
+) {
   as_api_object(
     x,
     class_oauth2_authorization_code_flow,