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jonthegeekjonthegeek
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Remove special tibblify version checks (#104)
Also apply air, and update workflows
1 parent 9a1a731 commit 499d903

34 files changed

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‎.Rbuildignore‎

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^\.positai$
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^\.claude$
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^AGENTS\.md$
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^[.]?air[.]toml$
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^\.vscode$

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

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any::testthat
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any::usethis
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any::withr
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Gilead-BioStats/qcthat
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local::.
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- name: Install air

‎.github/workflows/format-suggest.yaml‎

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

‎.github/workflows/pkgdown-cleanup.yaml‎

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

‎.github/workflows/pkgdown.yaml‎

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

‎.github/workflows/qcthat.yaml‎

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

‎.vscode/extensions.json‎

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{
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"recommendations": [
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"Posit.air-vscode"
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]
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}

‎.vscode/settings.json‎

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{
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"[r]": {
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"editor.formatOnSave": true,
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"editor.defaultFormatter": "Posit.air-vscode"
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},
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"[quarto]": {
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"editor.formatOnSave": true,
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"editor.defaultFormatter": "quarto.quarto"
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}
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}

‎DESCRIPTION‎

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snakecase,
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stbl (>= 0.3.0),
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tibble,
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tibblify (>= 0.3.2),
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tibblify (>= 0.4.0),
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xml2,
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yaml
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Suggests:

‎R/components-schema.R‎

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description = character_scalar_property("description"),
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format = character_scalar_property("format")
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),
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constructor = function(type = c(
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"string", "number", "integer",
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"boolean", "array", "object"
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),
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...,
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nullable = FALSE,
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description = character(),
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format = character()) {
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constructor = function(
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type = c(
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"string",
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"number",
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"integer",
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"boolean",
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"array",
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"object"
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),
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...,
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nullable = FALSE,
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description = character(),
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format = character()
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) {
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check_dots_empty()
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if (missing(type)) {
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type <- character()

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