add R example

InstituteforDiseaseModeling · Sep 24, 2024 · 3e26d0e · 3e26d0e
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diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -24,6 +24,15 @@
 //    "mounts": [
 //    "source=${localWorkspaceFolder},target=/workspaces/${localWorkspaceFolder},type=bind,consistency=cached"
 //    ],
-    "postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh",
+    "portsAttributes": {
+        "8888": {
+            "label": "Jupyter Lab",
+            "onAutoForward": "always",
+        },
+        "8787": {
+          "label": "R studio",
+          "onAutoForward": "always"
+        }
+    },
     "forwardPorts": [8787, 8888]
 }
diff --git a/.devcontainer/postCreateCommand.sh b/.devcontainer/postCreateCommand.sh
@@ -13,6 +13,9 @@ if [ -f "R/renv.lock" ]; then
     cd R && R -e 'renv::restore()'
 fi
 
+# change the default working directory for RStudio
+echo "session-default-working-dir=$localworkspace" >> /etc/rstudio/rsession.conf
+
 rstudio-server start && jupyter lab --ip=0.0.0.0 --no-browser --allow-root --NotebookApp.token=''
 
 echo "Dev environment setup completed!"
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -0,0 +1,99 @@
+name: Render Quarto Files and Deploy to GitHub Pages
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch: # Manual trigger
+
+jobs:
+  render_quarto:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    - name: Build Docker image
+      run: |
+        docker build -t demo-quarto-image .
+
+    - name: Run Quarto in Docker container
+      run: |
+        docker run --rm -v ${{ github.workspace }}:/workspace -w /workspace my-quarto-image bash -c "
+          echo 'Creating gallery directory...'
+          mkdir -p gallery && \
+          echo 'gallery directory created.'
+
+          FOLDERS=(python, R)
+          echo 'Folders to process: ${FOLDERS[@]}'
+
+          for FOLDER in \"\${FOLDERS[@]}\"; do
+            echo 'Searching for .qmd and .ipynb files in $FOLDER...'
+            find \"\$FOLDER\" \( -name '*.qmd' -o -name '*.ipynb' \) | while read file; do
+              
+              echo 'Processing file: $file'
+              target_dir='gallery/$(dirname \"$file\")'
+              echo 'Creating target directory: $target_dir'
+              mkdir -p \"\$target_dir\" && echo 'Directory $target_dir created.'
+
+              echo 'Attempting to render $file with execution...'
+              if quarto render \"\$file\" --to html --output-dir \"\$target_dir\"; then
+                echo 'Successfully rendered $file with execution.'
+              else
+                echo 'Failed to render $file with execution. Rendering without execution...'
+                if quarto render \"\$file\" --to html --no-execute --output-dir \"\$target_dir\"; then
+                  echo 'Successfully rendered $file without execution.'
+                else
+                  echo 'Rendering failed for $file, even without execution.'
+                fi
+              fi
+
+            done
+          done"
+
+
+    - name: Generate Index HTML
+      run: |
+        echo "<html><body><h1>Gallery Index</h1><ul>" > gallery/index.html
+        find gallery -name "*.html" | while read file; do
+          file_name=$(basename "$file")
+          echo "<li><a href=\"./$file\">$file_name</a></li>" >> gallery/index.html
+        done
+        echo "</ul></body></html>" >> gallery/index.html
+        
+    - name: Upload HTML output
+      uses: actions/upload-artifact@v3
+      with:
+        name: gallery
+        path: gallery
+
+    - name: Set up Git user
+      run: |
+        git config --global user.name 'github-actions[bot]'
+        git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+
+    - name: Commit and Push to docs branch
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        # Fetch all branches
+        git fetch origin
+
+        # Check if the docs branch exists, create it if not
+        if git show-ref --quiet refs/heads/docs; then
+          git checkout docs
+        else
+          git checkout --orphan docs
+        fi
+
+        # Copy the gallery folder to the root of the docs branch
+        cp -r gallery/* .
+
+        # Add, commit, and push changes
+        git add gallery
+        git commit -m "Update rendered Quarto files for GitHub Pages (commit: ${{ github.sha:0:7 }})"
+        git push origin docs --force
diff --git a/Dockerfile b/Dockerfile
@@ -19,6 +19,7 @@ RUN apt-get update && apt-get install -y \
     libxt-dev \
     gdebi-core \
     software-properties-common \
+    ffmpeg \
     && apt-get clean
 
 # Install Python 3.12.5
@@ -49,5 +50,8 @@ RUN /opt/venv/bin/python -m ipykernel install --user --name=venv --display-name
 EXPOSE 8787
 EXPOSE 8888
 
+# Install renv globally for all users
+RUN R -e "install.packages('renv', repos='https://cran.rstudio.com/')"
+
 # CMD to start both Jupyter and RStudio
 #CMD ["bash", "-c", "rstudio-server start; jupyter lab --ip=0.0.0.0 --no-browser --allow-root --NotebookApp.token=''"]
diff --git a/r/README.md b/r/README.md
@@ -0,0 +1,103 @@
+
+## Before you start creating an example for others, please read the renv best-practices to make sure your code can be easily run and repro by others
+
+`renv` is a good practice to manage R package dependencies. Follow the steps below to restore the project environment, 
+start working, add libraries as needed, and create a snapshot of the dependencies for version control. This will ensure that whoever checkout the code from this repo will be
+working with the same package versions as your original environment.
+
+### 1. Restore the Environment with `renv`
+
+To restore the R environment with the exact packages used in this project, use the `renv` lock file.
+This ensures that you are working with the same package versions as the original environment when it was created.
+
+1. Open R or RStudio within the project folder.
+2. Restore the environment by running:
+
+```r
+# Make sure you have the renv package installed
+install.packages("renv")
+
+# Restore the environment
+renv::restore()
+```
+
+This will install all the required packages as installed as listed in the `renv.lock` file.
+
+### 2. Add Libraries as Needed
+
+As you work on the project, you might need to install additional R libraries. You can do this with `install.packages()` as usual. For example:
+
+```r
+install.packages("ggplot2")
+```
+
+After installing new packages, be sure to update the environment snapshot to capture these new changes.
+
+### 3. Snapshot the Environment
+
+Once you have added or updated any packages, you need to create a new snapshot to update the `renv.lock` file. This ensures that any new dependencies are tracked.
+
+1. Create the snapshot with the following command in R:
+
+```r
+renv::snapshot()
+```
+
+This will update the `renv.lock` file to reflect the current state of your project’s package library.
+
+2.Commit the changes to version control:
+
+```bash
+git add renv.lock
+git commit -m "Updated renv.lock after adding new libraries"
+git push origin <branch-name>
+```
+
+This ensures that others working on the project can restore the environment with the new packages you added.
+
+### 4. Optional: Start a New `renv` Environment
+
+If you are starting a new project or want to reset the environment, you can initialize a new `renv` environment:
+
+```r
+# Initialize renv when there is no existing environment in the project
+renv::init()
+```
+
+This will generate a new `renv` setup, including a fresh `renv.lock` file for you to manage the project’s dependencies.
+
+---
+
+## Use Quarto to Create Interactive Documents
+
+In this folder we show an example that you can share code and ideas with others using a quarto document. See
+[simple_example.qmd](./simple_example.qmd).
+
+To begin with the example, you can open the `simple_example.qmd` file in Rstudio or other IDEs such as VS Code with the Quarto extension installed.
+
+### 1.How to Run the Example
+
+Since we use shinylive to showcase a shiny app in the quarto document, you need to install the `shinylive` package first. 
+This should already be included in the renv.lock file if you follow the above instructions.
+
+```bash
+quarto install extension quarto-ext/shinylive
+```
+
+Then you can preview and render the quarto document by running the following command in the terminal:
+
+```bash
+quarto preview simple_example.qmd --port 4321
+```
+This will start a local server at port 4321 and open the document in your default browser. 
+Any changes you make to the document will be automatically re-rendered in the browser. 
+When you are satisfied with the document, you can render it to a standalone HTML file by running:
+
+```bash
+quarto render simple_example.qmd
+```
+
+This will use the `_quarto.yaml_` configuration file to render the document to an HTML file in the `output-dir` directory defined.
+
+For more implementation details, please refer to the [Quarto documentation](https://quarto.org/).
+
diff --git a/r/_quarto.yml b/r/_quarto.yml
@@ -0,0 +1,16 @@
+project:
+  type: website
+  output-dir: _site
+  resources: 
+  - shinylive-sw.js
+
+website:  
+  title: "r-shinylive in Quarto"
+
+format:
+  html:
+    grid: 
+      body-width: 1350px
+      sidebar-width: 200px
+      margin-width: 200px
+    toc: true