Adding copilot environment

.devcontainer/.vscode/settings.json

@@ -0,0 +1,4 @@
+{
+    "r.plot.useHttpgd": true,
+    "r.alwaysUseActiveTerminal": true
+}

.devcontainer/Containerfile

@@ -0,0 +1,11 @@
+FROM rocker/tidyverse:4.5.1
+
+# Adding R packages for development
+RUN install2.r --error roxygen2 tinytest devtools covr rmarkdown knitr
+
+RUN install2.r --error languageserver && \
+  installGithub.r nx10/httpgd
+
+RUN install2.r --error XML igraph servr htmlwidgets
+
+CMD ["bash"]

.devcontainer/devcontainer.json

@@ -0,0 +1,36 @@
+// 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": "rgexf",
+	"build": {
+		"dockerfile": "Containerfile"
+	},
+	"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"
+}

.github/workflows/ci.yml

@@ -69,8 +69,9 @@ jobs:
           error-on: '"warning"'
 
       # Upload the built package as an artifact
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         if: ${{ matrix.config.os == 'ubuntu-latest' && matrix.config.r == 'release' }}
         with:
           name: ${{ matrix.config.os }}-pkg
           path: ${{ github.workspace }}/*.tar.gz
+

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

@@ -0,0 +1,42 @@
+name: "Copilot Setup Steps"
+
+# Automatically run the setup steps when they are changed to allow for easy validation, and
+# allow manual testing through the repository's "Actions" tab
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+  pull_request:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+
+jobs:
+  # The job MUST be called `copilot-setup-steps` or it will not be picked up by Copilot.
+  copilot-setup-steps:
+    runs-on: ubuntu-latest
+
+    # Set the permissions to the lowest permissions possible needed for your steps.
+    # Copilot will be given its own token for its operations.
+    permissions:
+      # If you want to clone the repository as part of your setup steps, for example to install dependencies, you'll need the `contents: read` permission. If you don't clone the repository in your setup steps, Copilot will do this for you automatically after the steps complete.
+      contents: read
+
+    # You can define any steps you want, and they will run before the agent starts.
+    # If you do not check out your code, Copilot will do this for you.
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::rcmdcheck
+            any::tinytest
+          needs: check

.github/workflows/website.yml

@@ -1,27 +1,86 @@
-name: rgexf website
+# 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:
 
-on: [push, pull_request]
+name: pkgdown
 
-env:
-  cntr: gvegayon/rgexf:latest
+# Sets permissions of the GITHUB_TOKEN
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+  pull-requests: write
+  actions: read
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
 
 jobs:
   build:
-    runs-on: Ubuntu-latest
-
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
 
-      - name: Container
-        run: docker pull ${cntr}
+      # Upload artifact for GitHub Pages deployment (only for pushes to main/master)
+      - name: Upload Pages artifact
+        if: github.event_name != 'pull_request' && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master')
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs
 
-      - name: Building website
-        run: |
-          docker run --rm -i -v ${PWD}:/home/mnt -w /home/mnt ${cntr} Rscript -e 'pkgdown::build_site()'
-          sudo cp -r lesmiserables docs/ 
+      # Upload artifact for PR preview (only for pull requests)
+      - name: Upload PR artifact
+        if: github.event_name == 'pull_request'
+        uses: actions/upload-artifact@v4
+        with:
+          name: pkgdown-site
+          path: docs
 
-      - name: Deploy
-        uses: peaceiris/actions-gh-pages@v3
+      # Post comment with link to artifact on PRs
+      - name: Post artifact link to PR
+        if: github.event_name == 'pull_request'
+        uses: CDCgov/cfa-actions/post-artifact@v1.2.0
         with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./docs
+          artifact-name: pkgdown-site
+          gh-token: ${{ secrets.GITHUB_TOKEN }}
+          message: 'Thank you for your contribution @${{ github.actor }} :rocket:! The pkgdown site preview is ready for review :point_right: [Download here]({ artifact-url }) :point_left:!'
+
+  # Deployment job - only runs on pushes to main/master
+  deploy:
+    if: github.event_name != 'pull_request' && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master')
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

README.qmd

@@ -6,6 +6,7 @@ format: gfm
 knitr::opts_chunk$set(fig.path = "man/figures/", warning = FALSE)
 ```
 
+```{=markdown}
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/rgexf)](https://cran.r-project.org/package=rgexf)
 [![Downloads](https://cranlogs.r-pkg.org/badges/rgexf)](https://cran.r-project.org/package=rgexf)
 [![Downloads](https://cranlogs.r-pkg.org/badges/grand-total/rgexf)](https://cran.r-project.org/package=rgexf)
@@ -14,6 +15,7 @@ knitr::opts_chunk$set(fig.path = "man/figures/", warning = FALSE)
 [![Coverage Status](https://img.shields.io/codecov/c/github/gvegayon/rgexf/master.svg)](https://app.codecov.io/github/gvegayon/rgexf?branch=master)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.03456/status.svg)](https://doi.org/10.21105/joss.03456)
 [![Sponsor](https://img.shields.io/badge/-Sponsor-fafbfc?logo=GitHub%20Sponsors)](https://github.com/sponsors/gvegayon)
+```
 
 # rgexf: Build, Import and Export GEXF Graph Files <img src="man/figures/logo.svg" align="right" height="200"/>