Closes #245 - Replace scattered install.packages() with DESCRIPTION + r-lib/actions/setup-r-dependencies

.github/workflows/check_post_tags.yml

@@ -8,10 +8,16 @@ on:
 jobs:
   Check-post-tags:
     runs-on: ubuntu-latest
-    container:
-      image: "rocker/tidyverse:4.2.1"
     steps:
       - uses: actions/checkout@v4
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+      - name: Install packages
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          packages: |
+            any::rmarkdown
+            any::cli
       - name: Run check_post_tags
         run: source("R/check_post_tags.R")
         shell: Rscript {0}

.github/workflows/link_check.yml

@@ -11,15 +11,13 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up R  # Install R from CRAN
+      - name: Set up R
         uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: '4.3.3' # You can specify a different R version if needed
 
       - name: Install R packages
-        run: |
-          Rscript -e 'install.packages("fs")'
-        shell: bash
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          packages: any::fs
 
       - name: Switch .qmd to .md
         run: Rscript R/switch.R

.github/workflows/pr-preview.yml

@@ -19,37 +19,20 @@ jobs:
   build-preview:
     name: Build & Deploy PR Preview
     runs-on: ubuntu-latest
-    container:
-      image: "ghcr.io/pharmaverse/docker_pharmaverse:4.5.1"
     steps:
       - name: Check out repository
         uses: actions/checkout@v4
 
-      - name: Configure Git safe directory
-        run: git config --global --add safe.directory /__w/blog/blog
-
       - name: Set up Quarto
         uses: quarto-dev/quarto-actions/setup@v2
         with:
           version: 1.9.12
 
-      - name: Install R Packages
-        run: |
-          R -e "install.packages(c(
-            'admiral',
-            'diffdf',
-            'patchwork',
-            'here',
-            'filters',
-            'janitor',
-            'link',
-            'sessioninfo',
-            'renv',
-            'riskmetric',
-            'sdtm.oak',
-            'mirai',
-            'dverse',
-            'autoslider.core'))"
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Setup R Dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
 
       - name: Install tinytex
         run: quarto install tool tinytex

.github/workflows/publish.yml

@@ -8,46 +8,26 @@ on:
 jobs:
   build-deploy:
     runs-on: ubuntu-latest
-    container:
-      image: "ghcr.io/pharmaverse/docker_pharmaverse:4.5.1"
     permissions:
       contents: write
     steps:
       - name: Check out repository
         uses: actions/checkout@v4
 
-      - name: Configure Git safe directory
-        run: git config --global --add safe.directory /__w/blog/blog
-
       - name: Set up Quarto
         uses: quarto-dev/quarto-actions/setup@v2
         with:
             version: 1.9.12
 
-      - name: Install R Packages
-        run: |
-          R -e "install.packages(c(
-            'admiral',
-            'diffdf',
-            'patchwork',
-            'here',
-            'filters',
-            'janitor',
-            'link',
-            'sessioninfo',
-            'renv',
-            'riskmetric',
-            'sdtm.oak',
-            'mirai',
-            'dverse',
-            'autoslider.core'))"
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Setup R Dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
 
       - name: Install tinytex
         run: quarto install tool tinytex
 
-      - name: Mark repo directory as safe
-        run: git config --global --add safe.directory /__w/blog/blog
-
       - name: Publish
         uses: quarto-dev/quarto-actions/publish@v2
         with:

.github/workflows/spellcheck.yml

@@ -5,18 +5,20 @@ on:
 jobs:
   Spelling:
     runs-on: ubuntu-latest
-    container:
-      image: "rocker/tidyverse:4.3.1"
     steps:
       - name: Checkout repo
         uses: actions/checkout@v4
 
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+
       - name: Install packages
-        run: |
-          if (!require("roxygen2")) install.packages("roxygen2")
-          if (!require("spelling")) install.packages("spelling")
-          if (!require("testthat")) install.packages("testthat")
-        shell: Rscript {0}
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          packages: |
+            any::spelling
+            any::testthat
+            any::readr
 
       - name: Remove links from .qmd files (Bash)
         run: |

.github/workflows/style_check.yml

@@ -5,13 +5,15 @@ on:
 jobs:
   Style:
     runs-on: ubuntu-latest
-    container: {image: "rocker/tidyverse:4.2.1"}
     steps:
       - name: Checkout repo
         uses: actions/checkout@v4
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
       - name: Install styler
-        run: install.packages("styler")
-        shell: Rscript {0}
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          packages: any::styler
       - name: styler version
         run: packageVersion("styler")
         shell: Rscript {0}

DESCRIPTION

@@ -0,0 +1,70 @@
+Package: pharmaverse.blog
+Type: Book
+Title: Pharmaverse Blog
+Version: 0.1
+Authors@R:
+    person("pharmaverse", "Blog Team", role = c("aut", "cre"))
+Description: This is not a package, but we use this file to declare
+    the dependencies of the blog site.
+URL: https://github.com/pharmaverse/blog
+Imports:
+    admiral,
+    admiraldev,
+    admiralmetabolic,
+    admiralneuro,
+    admiralonco,
+    admiralophtha,
+    admiralpeds,
+    admiralvaccine,
+    autoslider.core,
+    dataviewR,
+    diffdf,
+    dplyr,
+    dverse,
+    DT,
+    filters,
+    forcats,
+    haven,
+    here,
+    janitor,
+    jsonlite,
+    knitr,
+    link,
+    lubridate,
+    logrx,
+    magrittr,
+    metacore,
+    metatools,
+    mirai,
+    nestcolor,
+    patchwork,
+    pharmaverseadam,
+    pharmaverseraw,
+    pharmaversesdtm,
+    reactable,
+    readr,
+    readxl,
+    riskmetric,
+    rlistings,
+    rtables,
+    sdtm.oak,
+    sessioninfo,
+    sparkline,
+    spelling,
+    stringr,
+    teal,
+    teal.data,
+    teal.modules.clinical,
+    teal.modules.general,
+    tern,
+    tibble,
+    tidyverse,
+    xportr,
+    yaml
+Suggests:
+    rmarkdown,
+    roxygen2,
+    styler,
+    testthat
+Encoding: UTF-8
+Language: en-US

R/create_blogpost.R

@@ -1,6 +1,10 @@
 # You can easily create a new blog post skeleton using the create_post() function.
 # First, we load the helping function and the allowed post tags:
 
+# If you have not already installed the blog's dependencies, you can do so using pak:
+# install.packages("pak")
+# pak::pak() # installs all packages listed in the DESCRIPTION file
+
 source("R/help_create_blogpost.R")
 source("R/allowed_tags.R")
 

README.md

@@ -86,49 +86,18 @@ Most importantly:
 
 ## Tips and Tricks
 
-* You can use this code snippet to install all packages needed for the blog site or use the docker image cited below.
-```
-install.packages(
-  c(
-    "jsonlite",
-    "tidyverse",
-    "spelling",
-    "janitor",
-    "diffdf",
-    "admiral",
-    "patchwork",
-    "here",
-    "reactable",
-    "pharmaversesdtm",
-    "metacore",
-    "metatools",
-    "xportr",
-    "pharmaverseadam",
-    "link",
-    "sessioninfo",
-    "rtables",
-    "teal",
-    "riskmetric",
-    "tidyCDISC",
-    "mirai",
-    "dverse",
-    "DT",
-    "xportr",
-    "sdtm.oak",
-    "teal",
-    "riskmetric",
-    "tidyCDISC",
-    "admiralonco",
-    "admiralophtha",
-    "admiralpeds",
-    "admiralvaccine",
-    "admiralmetabolic",
-    "autoslider.core",
-    "filters"
-    "logrx"
-  )
-)
+* All packages needed for the blog site are declared in the [`DESCRIPTION`](DESCRIPTION) file at the root of the repository. You can install them all at once using `pak` (recommended for speed, as it uses binary packages and caching):
+
+```r
+# Install pak if you don't have it
+install.packages("pak")
+
+# Install all blog dependencies from the DESCRIPTION file
+pak::pak()
 ```
+
+Alternatively, you can use the Docker image described below.
+
 ## How to Use the `blog` Docker Image for Local Development
 
 Contributors can benefit from using the [`blog` Docker image](https://github.com/pharmaverse/blog/pkgs/container/blog) when creating their blog posts.