gvegayon's patch to Dev specify versions description mpw

.devcontainer/Containerfile

@@ -0,0 +1,40 @@
+FROM docker.io/rocker/r-ver:4.4.1
+
+# Will copy the package to the container preserving the directory structure
+RUN mkdir -p pkg
+
+COPY ./DESCRIPTION pkg/
+
+# Installing missing dependencies (removing pandoc-citeproc install)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    libcurl4-openssl-dev
+RUN install2.r pak
+# dependencies = TRUE means we install `suggests` too
+RUN Rscript -e 'pak::local_install_deps("pkg", upgrade = FALSE, dependencies = TRUE)'
+# The cmdstan version will need to be incrementally updated
+# Must also manually bump cmdstan version `.github/workflows` when updating
+RUN Rscript -e 'cmdstanr::install_cmdstan(version="2.36.0")'
+# This requires access to the Azure Container Registry
+# FROM ghcr.io/cdcgov/cfa-epinow2-pipeline:${TAG}
+
+# Will copy the package to the container preserving the directory structure
+COPY . pkg/
+
+# Install the full package while leaving the tar.gz file in the
+# container for later use.
+RUN R CMD build --no-build-vignettes --no-manual pkg && \
+    R CMD INSTALL CFAEpiNow2Pipeline_*.tar.gz
+
+# Ensure the package is working properly
+ARG CHECK_PKG=true
+RUN if [ "$CHECK_PKG" = "true" ]; then \
+        R CMD check --no-build-vignettes --no-manual CFAEpiNow2Pipeline_*.tar.gz; \
+    else \
+        echo "Skipping package check (CHECK_PKG=$CHECK_PKG)"; \
+    fi
+
+ARG DEVELOPMENT=false
+COPY ./extra.sh extra.sh
+RUN chmod +x extra.sh && ./extra.sh && rm -rf extra.sh pkg/
+
+CMD ["bash"]

.devcontainer/devcontainer.json

@@ -0,0 +1,40 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/cpp
+{
+	"name": "epinow2-pipeline",
+	"build": {
+		"dockerfile": "../Dockerfile",
+		"args": {
+			"CHECK_PKG": "false",
+			"DEVELOPMENT": "true"
+		}
+	},
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"reditorsupport.r",
+				"rdebugger.r-debugger",
+				"quarto.quarto",
+				"tianyishi.rmarkdown"
+			]
+		}
+	},
+	"mounts": [
+        // Mount the .vscode configuration into the container
+        "source=${localWorkspaceFolder}/.devcontainer/.vscode,target=/workspaces/${localWorkspaceFolderBasename}/.vscode,type=bind,consistency=cached"
+    ]
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	// "postCreateCommand": "gcc -v",
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

.devcontainer/extra.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+# If the development mode is true, then install the extra packages
+if [ "$DEVELOPMENT" = "true" ]; then
+    echo "Development mode is enabled";
+
+    # Setting up dependencies
+    apt-get update && apt-get install \
+        libharfbuzz-dev libfribidi-dev libfontconfig1-dev \
+        libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev \
+        --no-install-recommends -y && \
+    install2.r --error devtools roxygen2 testthat languageserver && \
+
+    # Installing the httpgd package (requires libcairo)
+    apt-get install -y --no-install-recommends libcairo2-dev && \
+    installGithub.r nx10/httpgd;
+
+    # Installing pre-commit and uv
+    apt-get install pipx -y --no-install-recommends
+    echo 'PATH=/root/.local/bin:$PATH' >> ~/.bashrc
+    source ~/.bashrc
+    pipx install uv
+    pipx install pre-commit
+    pipx inject pre-commit pre-commit-uv
+else
+    echo "Development mode is disabled";
+fi

.github/workflows/containers-and-az-pool.yaml

@@ -94,6 +94,10 @@ jobs:
     needs: build-pipeline-image
     uses: ./.github/workflows/test-documentation.yaml
 
+  pkgdown:
+    needs: build-pipeline-image
+    uses: ./.github/workflows/pkgdown.yaml
+
   acr-import:
     needs: build-pipeline-image
     runs-on: ubuntu-latest

.github/workflows/pkgdown.yaml

@@ -1,19 +1,43 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
-  push:
-    branches: [main, master]
-  pull_request:
-    branches: [main, master]
-  release:
-    types: [published]
-  workflow_dispatch:
+  workflow_call:
 
 name: pkgdown website
 
 jobs:
+  get-image-name:
+    runs-on: ubuntu-latest
+    outputs:
+      IMAGE: ${{ steps.image-name.outputs.image_name }}
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Extract branch name
+        id: branch-name
+        run: |
+          echo "branch=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}" >> $GITHUB_OUTPUT
+
+      - name: Figure out tag (either latest if it is main or the branch name)
+        id: image-tag
+        run: |
+          if [ "${{ steps.branch-name.outputs.branch }}" = "main" ]; then
+            echo "tag=latest" >> $GITHUB_OUTPUT
+          else
+            echo "tag=${{ steps.branch-name.outputs.branch }}" >> $GITHUB_OUTPUT
+          fi
+
+      - name: Build Docker Image String
+        id: image-name
+        run: echo "image_name=ghcr.io/cdcgov/cfa-epinow2-pipeline:${{ steps.image-tag.outputs.tag }}" >> $GITHUB_OUTPUT
+
   pkgdown:
     runs-on: ubuntu-latest
+    needs: get-image-name
+    container:
+      image: ${{ needs.get-image-name.outputs.IMAGE }}
     # Only restrict concurrency for non-PR jobs
     concurrency:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
@@ -22,24 +46,30 @@ jobs:
     permissions:
       contents: write
       pull-requests: write
+
     steps:
       - uses: actions/checkout@v5
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
-          r-version: "4.4.3"
+      # Setting up gh CLI (cached)
+      - name: Setup GH CLI
+        uses: cli/gh-extension-precompile@v2
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      # Installs python using a cached version
+      - uses: actions/setup-python@v5
         with:
-          extra-packages: any::pkgdown, local::.
-          needs: website
+          python-version: '3.13'
+
+      # Installing pkgdown (won't be cached)
+      - name: Install pkgdown
+        run: |
+          install2.r pkgdown
 
       - name: Build site
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
+        run: |
+          pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
 
       - name: Save artifact
         if: ${{ github.event_name == 'pull_request' }}

DESCRIPTION

@@ -56,5 +56,5 @@ Additional_repositories:
 	https://stan-dev.r-universe.dev
 URL: https://cdcgov.github.io/cfa-epinow2-pipeline/
 Depends:
-    R (>= 3.50)
+    R (>= 3.5.0)
 LazyData: true

Makefile

@@ -2,7 +2,11 @@ REGISTRY=cfaprdbatchcr.azurecr.io/
 IMAGE_NAME=cfa-epinow2-pipeline
 BRANCH=$(shell git branch --show-current)
 CONFIG_CONTAINER=rt-epinow2-config
+
+ifndef CNTR_MGR
 CNTR_MGR=docker
+endif
+
 ifeq ($(BRANCH), main)
 TAG=latest
 else

NEWS.md

@@ -1,6 +1,7 @@
 # CFAEpiNow2Pipeline v0.2.0
 
 ## Features
+
 * Adjust run trigger for time change
 * Move first run earlier in the day
 * Removing duplicative r-cmd-check.yaml file (already checking in Dockerfile)