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Merge branch 'main' into 187-blog-post-power-of-partnership-code-collaboration-in-nest
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‎.github/pull_request_template.md

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@@ -3,8 +3,9 @@ Thank you for your Pull Request! We have developed this task checklist to help w
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Please check off each taskbox as an acknowledgment that you completed the task or check off that it is not relevant to your Pull Request. This checklist is part of the Github Action workflows and the Pull Request will not be merged into the `main` branch until you have checked off each task.
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- [ ] Place Closes #<insert_issue_number> into the beginning of your Pull Request Title (Use Edit button in top-right if you need to update), and make sure the corresponding issue is linked in the Development section on the right hand side
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- [ ] Ensure your new post folder is of the form `"posts/zzz_DO_NOT_EDIT_<your post title>"`. This is so that the post date can be auto-updated upon the merge into `main`.
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- [ ] Run the script from `CICD.R` line by line to first check the spelling in your post and then to make sure your code is compatible with our code-style. Address any incongruences by following the instructions in the file!
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- [ ] Choose (possibly several) `tag(s)` or categories from the current list: `c("Metadata", "SDTM", "ADaM", "TLG", "Shiny", "Community", "Conferences", "Submissions", "Technical")` for your blog post. If you cannot find anything that fits your blog post, add your own tag! We occasionally tidy up all `tags` for consistency.
8+
- [ ] Choose (possibly several) `tag(s)` or categories from the current list: ` c("Metadata", "SDTM", "ADaM", "TLG", "Shiny", "Community", "Conferences", "Submissions", "Technical")` for your blog post. If you cannot find anything that fits your blog post, propose a new tag to the maintainers! Note: if you use a tag not from this list, the "Check Post Tags" CICD pipeline will error. We occasionally tidy up all `tags` for consistency.
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- [ ] Add a short description for your blog post in the `description` field at the top of the markdown document.
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- [ ] Blog post is *short*, *personalized*, *reproducible* and *readable*
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- [ ] Add a disclaimer at the top of your post, if appropriate (example: **Disclaimer**

‎.github/workflows/check_post_tags.yml

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@@ -0,0 +1,17 @@
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name: Check post tags
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on:
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pull_request:
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branches:
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- 'main'
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jobs:
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Check-post-tags:
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runs-on: ubuntu-latest
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container:
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image: "rocker/tidyverse:4.2.1"
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steps:
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- uses: actions/checkout@v4
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- name: Run check_post_tags
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run: source("R/check_post_tags.R")
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shell: Rscript {0}

‎.github/workflows/link_check.yml

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@@ -1,20 +1,33 @@
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name: Links (Fail Fast)
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on:
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pull_request: {branches: ['main']}
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pull_request:
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branches:
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- main
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jobs:
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linkChecker:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: switch .qmd to .md
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run: source("R/switch.R")
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shell: Rscript {0}
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- name: Set up R # Install R from CRAN
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uses: r-lib/actions/setup-r@v2
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with:
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r-version: '4.3.3' # You can specify a different R version if needed
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- name: Install R packages
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run: |
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Rscript -e 'install.packages("fs")'
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shell: bash
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- name: Switch .qmd to .md
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run: Rscript R/switch.R
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shell: bash
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- name: Link Checker
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uses: lycheeverse/[email protected]
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with:
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fail: true
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env:
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GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎.github/workflows/publish.yml

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@@ -1,12 +1,40 @@
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name: Quarto Publish
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on:
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workflow_dispatch:
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push:
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branches: [main]
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name: Quarto Publish
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jobs:
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Update-post-dates:
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runs-on: ubuntu-latest
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container:
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image: "rocker/tidyverse:4.2.1"
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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with:
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ref: main
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token: ${{ secrets.PHARMAVERSE_BOT }}
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- name: Run update_post_dates
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run: Rscript R/update_post_dates.R # running the R script with Rscript
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- name: Configure Git safe directory
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run: git config --global --add safe.directory /__w/blog/blog
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- name: Commit and push changes
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uses: stefanzweifel/git-auto-commit-action@v5
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with:
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commit_message: "[skip actions] Auto-update blog post date"
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file_pattern: "."
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commit_user_name: github-actions
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commit_user_email: >-
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41898282+github-actions[bot]@users.noreply.github.com
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continue-on-error: true
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build-deploy:
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needs: Update-post-dates
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runs-on: ubuntu-latest
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permissions:
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contents: write
@@ -32,6 +60,11 @@ jobs:
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janitor
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diffdf
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admiral
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admiralonco
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admiralophtha
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admiralpeds
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admiralvaccine
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admiralmetabolic
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patchwork
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here
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reactable
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pharmaverseadam
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link
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sessioninfo
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rtables
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teal
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riskmetric
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tidyCDISC
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mirai
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sdtm.oak
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dverse
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- name: Install tinytex
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run: quarto install tool tinytex

‎.github/workflows/spellcheck.yml

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@@ -4,27 +4,28 @@ on:
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jobs:
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Spelling:
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runs-on: ubuntu-latest
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container: {image: "rocker/tidyverse:4.2.1"}
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container: {image: "rocker/tidyverse:4.3.1"}
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steps:
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- name: Checkout repo
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uses: actions/checkout@v4
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- name: Install spelling
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run: if (!require("spelling")) install.packages("spelling")
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- name: Install packages
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run: |
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if (!require("roxygen2")) install.packages("roxygen2")
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if (!require("spelling")) install.packages("spelling")
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if (!require("testthat")) install.packages("testthat")
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shell: Rscript {0}
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- name: Install roxygen2
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run: if (!require("roxygen2")) install.packages("roxygen2")
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shell: Rscript {0}
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- name: Run Spelling Check test
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run: spelling::spell_check_files(list.files(pattern = ".*.qmd$", recursive = TRUE), ignore = readr::read_lines("inst/WORDLIST.txt"))
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shell: Rscript {0}
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- name: Install testthat
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run: if (!require("testthat")) install.packages("testthat")
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shell: Rscript {0}
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- name: test typos
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run: testthat::test_that(desc = "No Typo", code = testthat::expect_equal(object = spelling::spell_check_files(list.files(pattern = ".*.qmd$", recursive = TRUE), ignore = readr::read_lines("inst/WORDLIST.txt")), expected = spelling::spell_check_files(path = "inst/WORDLIST.txt", ignore = readr::read_lines("inst/WORDLIST.txt"))))
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- name: Check spelling
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run: |
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testthat::test_that(desc = "Check spelling",
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code = {
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typos <- spelling::spell_check_files(list.files(pattern = ".*.qmd$", recursive = TRUE), ignore = readr::read_lines("inst/WORDLIST.txt"))
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print(typos)
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testthat::expect_equal(
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object = typos,
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expected = spelling::spell_check_files(path = "inst/WORDLIST.txt", ignore = readr::read_lines("inst/WORDLIST.txt"))
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)
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}
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)
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shell: Rscript {0}

‎.lycheeignore

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@@ -18,3 +18,6 @@ file:///home/runner/work/blog/blog/posts/2024-03-01_rhino_shiny_app_validation/A
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https://rsc.niaid.nih.gov/clinical-research-sites/daids-adverse-event-grading-tables
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https://gowerc.github.io/diffdf/reference/diffdf.html](https://gowerc.github.io/diffdf/reference/diffdf.html)
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https://gowerc.github.io/diffdf/reference/diffdf.html
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https://tel.meet/kyw-gdga-civ?pin=3167654532438
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https://meet.google.com/kyw-gdga-civ
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https://insightsengineering.github.io/roxy.shinylive/

‎Dockerfile

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@@ -4,9 +4,20 @@ RUN apt-get update \
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&& apt-get install -y --no-install-recommends \
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ca-certificates \
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curl \
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libxml2-dev \
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libcurl4-openssl-dev \
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zlib1g-dev \
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libfontconfig1-dev \
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libharfbuzz-dev libfribidi-dev \
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libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev \
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libmbedtls-dev cmake \
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libnng-dev xz-utils\
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libcairo2-dev \
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libgit2-dev \
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pkgconf \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* \
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&& curl -o quarto.deb -L https://github.com/quarto-dev/quarto-cli/releases/download/v1.4.550/quarto-1.4.550-linux-amd64.deb \
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&& curl -o quarto.deb -L https://github.com/quarto-dev/quarto-cli/releases/download/v1.6.42/quarto-1.6.42-linux-arm64.deb \
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&& dpkg --install quarto.deb \
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&& rm -f quarto.deb \
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&& R -e 'install.packages(c( \
@@ -23,4 +34,23 @@ RUN apt-get update \
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"metacore", \
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"metatools", \
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"xportr", \
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"pharmaverseadam"))'
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"pharmaverseadam", \
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"link", \
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"sessioninfo", \
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"rtables", \
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"teal", \
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"riskmetric", \
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"tidyCDISC", \
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"mirai", \
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"dverse", \
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"DT", \
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"xportr", \
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"sdtm.oak", \
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"teal", \
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"riskmetric", \
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"tidyCDISC", \
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"admiralonco", \
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"admiralophtha", \
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"admiralpeds", \
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"admiralvaccine", \
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"admiralmetabolic"))'

‎R/CICD.R

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@@ -14,7 +14,11 @@ words <- spelling::spell_check_files(list.files(pattern = ".*.qmd$", recursive =
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)
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# now you can add words to the wordlist
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#-- uncomment the following line
17-
write(words[[1]], file = "inst/WORDLIST.txt", append = TRUE)
17+
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# write(words[[1]], file = "inst/WORDLIST.txt", append = TRUE)
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# sort_words <- sort(readr::read_lines("inst/WORDLIST.txt"))
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# readr::write_lines(sort_words, "inst/WORDLIST.txt")
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1923
spelling::spell_check_files(list.files(pattern = ".*.qmd$", recursive = TRUE),
2024
ignore = readr::read_lines("inst/WORDLIST.txt")

‎R/allowed_tags.R

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#' This is a vector of all the allowed blog post tags. It is stored in a separate file so that it can be referenced
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#' by `create_blogpost.R` and `check_post_tags.R`.
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allowed_tags <- c("Metadata", "SDTM", "ADaM", "TLG", "Shiny", "Community", "Conferences", "Submissions", "Technical")

‎R/appendix.R

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library(dplyr)
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suppressMessages(library(dplyr))
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# markdown helpers --------------------------------------------------------
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markdown_appendix <- function(name, content) {

‎R/check_post_tags.R

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# Get list of blog posts ----
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posts <- list.files("posts", recursive = TRUE, pattern = "*.qmd")
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4+
# Get vector of allowed tags ----
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source("R/allowed_tags.R")
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7+
# Function to extract tags from a post and check them against the allowed list ----
8+
check_post_tags <- function(post, allowed_post_tags = allowed_tags) {
9+
post_tags <- rmarkdown::yaml_front_matter(file.path("posts", post))$categories
10+
cross_check <- post_tags %in% allowed_post_tags
11+
problematic_tags <- post_tags[!cross_check]
12+
13+
if (!all(cross_check)) {
14+
cli::format_message("The tag(s) {.val {problematic_tags}} in the post {.val {post}} are not from the allowed list of tags.")
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}
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}
17+
18+
# Apply check_post_tags to all blog posts and find problem posts ----
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check_results <- lapply(posts, check_post_tags)
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error_messages <- unlist(Filter(Negate(is.null), check_results))
21+
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# Construct error message if one or more posts have problematic tags ----
23+
if (length(error_messages) > 0) {
24+
error_messages <- c(error_messages, "Please select from the following tags: {.val {allowed_tags}}, or contact one of the maintainers.")
25+
names(error_messages) <- rep("x", length(error_messages) - 1)
26+
27+
concatenated_error_messages <- cli::cli_bullets(error_messages)
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cli::cli_abort(concatenated_error_messages)
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}

‎R/create_blogpost.R

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# You can easily create a new blog post skeleton using the create_post() function.
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# First, we load the helping function:
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# First, we load the helping function and the allowed post tags:
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source("R/help_create_blogpost.R")
5-
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source("R/allowed_tags.R")
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## The available images are at the moment:
88
list.files("media") %>% tools::file_path_sans_ext()
99
## Please choose (possibly multiple) from this tags list:
10-
c("Metadata", "SDTM", "ADaM", "TLG", "Shiny", "Community", "Conferences", "Submissions", "Technical")
10+
print(allowed_tags)
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# Fill in the info, e.g.:
1313
create_post(
14-
post_name = "Code collaboration in NEST", # needs to be character vector (length 1)
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post_date = "2025-03-11", # needs to be character vector (length 1)
16-
description = "", # you can fill the description in later as well
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author = c("Ilse Augustyns", "Nicholas Masel", "Tad Lewandowski", "Gabriel Becker"), # one or more authors are permitted
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cover_image = "rtables", # chose one of the above (see line 8)
1914
tags = c("TLG", "ADaM") # chose (multiple) from line 10
15+
post_name = "My Blog", # needs to be character vector (length 1)
16+
post_date = "2024-12-01", # needs to be length 1 character vector and will be auto-updated when your post is merged
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description = "", # you can fill the description in later as well
18+
author = c("My Name"), # one or more authors are permitted
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cover_image = "pharmaverse", # chose one of the above (see line 8)
20+
tags = c("Metadata", "SDTM", "ADaM", "TLG", "Shiny", "Community", "Conferences", "Submissions", "Technical") # chose (multiple) from line 10
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)
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22-
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# Remove that post:
2424
# unlink("posts/2023-06-15_lbla", recursive = TRUE)
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‎R/help_create_blogpost.R

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# Prepare values
4747
snake_name <- gsub(" ", "_", tolower(gsub("(.)([A-Z])", "\\1 \\2", post_name)))
48-
short_name <- paste(post_date, snake_name, sep = "_")
48+
short_name <- paste("zzz_DO_NOT_EDIT", snake_name, sep = "_")
4949

5050
if (short_name != short_name %>% stringr::str_trunc(30)) {
5151
message("For the folder creation:")

‎R/readme.md

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@@ -4,7 +4,10 @@ Some of these files help in creating/developing blog-posts, others are used by o
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- `create_blogpost.R`: use this script to create a new blogpost based on our blogpost template.
66
- `CICD.R`: use this script to spellcheck and stylecheck your blogpost.
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- `allowed_tags.R`: contains vector of allowed blog post tags
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## development files
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- `help_create_blogpost.R`: script containing the function(s) used by `create_blogpost.R`
1011
- `switch.R`: Used by CICD spellcheck workflow.
12+
- `check_post_tags.R`: Used by Check-Post-Tags CICD workflow
13+
- `update_post_dates.R`: Used by Update-Post-Dates CICD workflow

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