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Merge pull request #17 from Boehringer-Ingelheim/fix-r-cmd
Fix r cmd + pipeline updates
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‎.github/ISSUE_TEMPLATE/hotfix-candidate.md‎

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---
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name: Hotfix candidate
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about: Create a new hotfix candidate issue
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title: "[hotfix] hf/vx.x.x"
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labels: hotfix
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assignees: ''
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---
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Please check that your version number is correct in the title.
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Shortly a comment below will appear with the branch and PR for the new hotfix candidate

‎.github/ISSUE_TEMPLATE/release-candidate.md‎

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---
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name: Release candidate
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about: Create a new release candidate issue
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title: "[release] rc/vx.x.x"
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labels: release
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assignees: ''
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---
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Please check that your version number is correct in the title.
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Shortly a comment below will appear with the branch and PR for the new release candidate

‎.github/PULL_REQUEST_TEMPLATE/hotfix_pull_request_teamplate.md‎

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# Hotfix checklist
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- [ ] Bumped minor version number on both DESCRIPTION and NEWS.md
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- [ ] Build passes pipeline checks
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- [ ] The new changes do not affect the API
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- [ ] The new changes do not affect the documentation (including screenshots)
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- [ ] The new changes do not impact the QC report

‎.github/PULL_REQUEST_TEMPLATE/release_pull_request_template.md‎

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# Critical checks
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- [ ] Is the version number correct?
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- [ ] DESCRIPTION file
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- [ ] [NEWS.md](http://news.md/)
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- [ ] Does the build pass?
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---
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## Documentation
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Does it include the following sections?
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- [ ] Module introduction with features
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- [ ] (O) Screenshots
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- [ ] Installation details
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- [ ] Explanation of function arguments
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- [ ] Data specifications and requirements
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- [ ] Different possible visualizations
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- [ ] Are the changes/new features included in [NEWS.md?](http://news.md/)
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- [ ] (O) Screenshots
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- [ ] (O) Explanation of input menus
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- [ ] (O) Short articles on building the app, compatibility with other modules, known bugs,...
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---
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## QC Report
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- [ ] Does it include a QC Report?
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---
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## API conventions
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- [ ] Follows API convention

‎.github/workflows/hotfix_pr.yml‎

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name: Create a PR link for hotfix issues
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on:
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issues:
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types: [opened, labeled, edited]
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jobs:
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create-pr:
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if: contains(github.event.issue.labels.*.name, 'hotfix') # This ensures the job only runs if the 'hotfix' label is present
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runs-on: ubuntu-latest
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permissions:
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issues: write
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Create PR link and post in comment
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id: pr-link-creation
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env:
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GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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ISSUE: ${{ github.event.issue.html_url }}
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run: |
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version=$(echo "${{ github.event.issue.title }}" | sed -n 's/.*rc\/\(v[0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p')
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# Early return if issue name is not correct
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if [ -z "$version" ]; then
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gh issue comment ${{ github.event.issue.number }} --body "Version number is not present or incorrect."
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exit 1
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fi
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branch_name="hf/$version"
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branch_text="Expected branch name: \`$branch_name\`"
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echo "Creating PR link"
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title=$(echo ${{ github.event.issue.title }} | jq -sRr @uri)hotfix
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pr_url_text="https://github.com/${{github.repository}}/compare/main...${branch_name}?quick_pull=1&template=hotfix_pull_request_template.md&title=${title}&labels=hotfix"
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body_url="PR Link: [pull request](<${pr_url_text}>)."
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body="$branch_text $body_url"
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echo "Creating comment"
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gh issue comment ${{ github.event.issue.number }} --body "$body"

‎.github/workflows/release_pr.yml‎

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name: Create a PR link for release issues
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on:
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issues:
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types: [opened, labeled, edited]
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jobs:
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create-pr:
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if: contains(github.event.issue.labels.*.name, 'release') # This ensures the job only runs if the 'release' label is present
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runs-on: ubuntu-latest
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permissions:
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issues: write
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Create PR link and post in comment
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id: pr-link-creation
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env:
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GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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ISSUE: ${{ github.event.issue.html_url }}
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run: |
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version=$(echo "${{ github.event.issue.title }}" | sed -n 's/.*rc\/\(v[0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p')
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# Early return if issue name is not correct
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if [ -z "$version" ]; then
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gh issue comment ${{ github.event.issue.number }} --body "Version number is not present or incorrect."
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exit 1
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fi
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branch_name="rc/$version"
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branch_text="Expected branch name: \`$branch_name\`"
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echo "Creating PR link"
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title=$(echo ${{ github.event.issue.title }} | jq -sRr @uri)hotfix
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pr_url_text="https://github.com/${{github.repository}}/compare/main...${branch_name}?quick_pull=1&template=release_pull_request_template.md&title=${title}&labels=hotfix"
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body_url="PR Link: [pull request](<${pr_url_text}>)."
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body="$branch_text $body_url"
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echo "Creating comment"
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gh issue comment ${{ github.event.issue.number }} --body "$body"

‎.lintr.R‎

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, object_length_linter = NULL # we don't type long var names just because
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, pipe_continuation_linter = NULL # wickham being overly prescriptive
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, trailing_blank_lines_linter = NULL # natural extension of trailing_whitespace_linter, present on the template
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, return_linter = NULL # wickham being overly prescriptive
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)
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if(identical(Sys.getenv('CI'), "true")){

‎DESCRIPTION‎

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Package: dv.edish
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Type: Package
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Title: eDISH Plot Module for DILI assessment
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Version: 1.2.0-9000
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Version: 1.2.0-9001
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Authors@R:
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c(
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person("Boehringer-Ingelheim Pharma GmbH & Co.KG", role = c("cph", "fnd")),
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Suggests:
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knitr (>= 1.43),
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pharmaverseadam (>= 0.2.0),
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rmarkdown (>= 2.25),
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shinytest2 (>= 0.2.0),
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testthat (>= 3.0.2),
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tibble (>= 3.2.1)
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stats (>= 4.2.2),
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tidyr (>= 1.3.0),
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dv.manager (>= 2.1.4),
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rmarkdown (>= 2.25)
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shinyWidgets
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Depends: R (>= 4.0)
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Remotes: boehringer-ingelheim/dv.manager@main
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VignetteBuilder: knitr

‎NEWS.md‎

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# dv.edish 1.2.0-9000
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# dv.edish 1.2.0-9001
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- Add jumping feature.
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‎_pkgdown.yml‎

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home:
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title: dv.edish
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links:
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- text: Browse source code
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href: https://github.com/Boehringer-Ingelheim/dv.edish/
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reference:
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- title: "Modules and utils"

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