feat: binder

Author: phdpablo

.binder/.dockerignore

@@ -0,0 +1,39 @@
+# Local development
+docker/
+
+# Git and GitHub
+.git/
+.github/
+
+# Generated outputs
+*. pdf
+docs/
+_site/
+
+# Quarto cache
+.quarto/
+_freeze/
+
+# renv cache (will be recreated in container)
+renv/library/
+renv/local/
+renv/cellar/
+renv/sandbox/
+renv/python/
+renv/staging/
+
+# R temporary files
+.Rhistory
+. RData
+.Rproj. user/
+
+# Python
+__pycache__/
+*.pyc
+. venv/
+.pytest_cache/
+
+# OS files
+.DS_Store
+Thumbs.db
+

.binder/Dockerfile

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+# This file defines how to build a custom Docker image
+# based on the rocker/binder image for MyBinder.org compatibility. 
+# Unlike the docker/Dockerfile (for local development with RStudio),
+# this image is designed for ephemeral, read-only reproducibility checks.
+
+# --- Base Image ---
+# Use the official rocker/binder version 4.4.2 as the starting point. 
+# This image includes R, RStudio Server, Quarto, Pandoc, and JupyterHub
+# pre-installed, and is specifically designed for MyBinder.org. 
+FROM rocker/binder:4.4.2
+
+# --- Image Metadata ---
+# Add labels to the image for identification and documentation purposes.
+# These are useful metadata but do not affect the container's functionality. 
+LABEL maintainer="Pablo Rogers <[email protected]>" \
+      description="MyBinder environment for ARTE"
+
+# --- renv Configuration ---
+# Set environment variables to configure where renv stores its cache
+# and the installed package library.
+# These paths are used to ensure renv functions correctly inside the container.
+ENV RENV_PATHS_CACHE=/home/rstudio/renv/cache
+# Path for the global renv cache (stores . tar.gz of downloaded packages).
+ENV RENV_PATHS_LIBRARY=/home/rstudio/renv/library
+# Path for the R package library installed by renv for this project. 
+
+# --- Copy renv Configuration Files ---
+# Copy necessary renv files from the build context (your local system)
+# to the home directory inside the container.
+# These files are essential for renv to function correctly.
+COPY --chown=rstudio renv.lock /home/rstudio/renv.lock
+# The lock file defining the exact versions of R packages. 
+COPY --chown=rstudio .Rprofile /home/rstudio/.Rprofile
+# The profile file that activates renv when R starts.
+COPY --chown=rstudio renv/activate.R /home/rstudio/renv/activate.R
+# The renv activation script. 
+
+# --- Copy Project Files ---
+# Copy the entire project to the container's home directory. 
+# This includes all source files, data, and documentation. 
+COPY --chown=rstudio .  /home/rstudio
+
+# --- Restore R Packages via renv ---
+# Run the R command to restore R packages listed in renv.lock.
+# This installs the packages at the versions specified into the directory
+# defined by RENV_PATHS_LIBRARY. 
+# The -s flag makes the R execution quieter. 
+RUN R -s -e "renv::restore()"
+
+# --- Install TinyTeX via Quarto ---
+# Install TinyTeX using Quarto's built-in installer.
+# This provides a lightweight LaTeX distribution (~150MB) that is
+# compatible with current CTAN repositories and automatically installs
+# missing LaTeX packages during PDF rendering.
+# Note: rocker/binder comes with TeX Live, but it may have version
+# incompatibilities with remote repositories.  TinyTeX from Quarto
+# ensures a consistent and up-to-date LaTeX environment. 
+RUN quarto install tinytex
+
+# Note: Unlike docker/Dockerfile, this image does not require
+# explicit port exposure or CMD instructions, as rocker/binder
+# already configures JupyterHub and RStudio Server for MyBinder.org. 
+# This environment is ephemeral (max ~12h) and non-persistent,
+# intended only for reproducibility verification, not active development.

.binder/README.md

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+# Binder Configuration
+
+This folder contains the configuration files needed to run ARTE on [MyBinder.org](https://mybinder.org/), a free cloud service that creates executable environments from GitHub repositories.
+
+## Purpose
+
+Unlike the `docker/` folder (designed for local development with persistent storage), the `.binder/` configuration creates an **ephemeral environment** for reproducibility verification. This allows anyone to:
+
+- Verify that the ARTE environment is fully reproducible
+- Explore the project structure and outputs without local setup
+- Test the Quarto rendering process in a clean environment
+
+> **Note:** MyBinder sessions are temporary (maximum ~12 hours) and non-persistent. Any changes made will be lost when the session ends.  This environment is intended for verification and exploration, not active development.
+
+## Launching ARTE on MyBinder
+
+Click the badge below to launch ARTE in your browser:
+
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/phdpablo/article-template/main)
+
+### Step-by-Step Instructions
+
+#### 1. Wait for the Environment to Build
+
+After clicking the badge, MyBinder will build the Docker image and start your session. **Please be patient** — the first build can take **10-15 minutes** as it needs to: 
+
+- Download the base image
+- Restore all R packages from `renv.lock`
+- Install TinyTeX for PDF rendering
+
+#### 2. Open RStudio from JupyterHub
+
+Once the environment loads, you will see **JupyterHub** in your browser. To access RStudio: 
+
+- Look for the **RStudio** button/icon in the JupyterHub launcher
+- Click it to open RStudio in a **new browser tab**
+
+#### 3. Open the Project in RStudio
+
+When RStudio opens: 
+
+- The ARTE project should already be loaded
+- If not, go to `File > Open Project... ` and select the `.Rproj` file
+
+#### 4. Render the Project with Quarto
+
+Open the **Terminal** tab in RStudio (next to Console) and run:
+
+```bash
+quarto render
+```
+
+This will render all Quarto documents and generate the outputs in the `docs/` folder. The rendering process may take a few minutes.
+
+#### 5. View the Rendered ARTE
+
+After rendering completes: 
+
+1. Navigate to the `docs/` folder in the RStudio Files pane
+2. Click on `index.html`
+3. Select **"View in Web Browser"** to open it in a new browser tab
+4. Navigate through the ARTE to explore all sections and outputs
+
+## Files in This Folder
+
+| File | Description |
+|------|-------------|
+| `Dockerfile` | Defines the Docker image based on `rocker/binder:4.4.2` with renv packages and TinyTeX |
+
+## Differences from docker/Dockerfile
+
+| Aspect | docker/Dockerfile | .binder/Dockerfile |
+|--------|-------------------|-------------------|
+| **Base image** | `rocker/verse:4.5.1` | `rocker/binder:4.4.2` |
+| **Purpose** | Local development | Reproducibility verification |
+| **Persistence** | Volumes for data persistence | Ephemeral (no persistence) |
+| **LaTeX** | TeX Live (pre-installed) | TinyTeX (via Quarto) |
+| **Interface** | RStudio Server only | JupyterHub + RStudio |
+| **Duration** | Unlimited | Max ~12 hours |
+
+## Troubleshooting
+
+### Build is taking too long
+
+The build takes longer because MyBinder needs to create the image from scratch.
+
+### Session timed out
+
+MyBinder sessions expire after ~10-20 minutes of inactivity or ~12 hours maximum. Simply relaunch by clicking the badge again.
+
+### PDF rendering fails
+
+If `quarto render` fails for PDF output, try rendering only HTML:
+
+```bash
+quarto render --to html
+```
+
+## Learn More
+
+- [MyBinder Documentation](https://mybinder.readthedocs.io/)
+- [Rocker Binder Images](https://rocker-project.org/images/versioned/binder.html)
+- [Quarto Documentation](https://quarto.org/)

.github/workflows/README.md

@@ -38,6 +38,6 @@ This workflow file (`deploy.yml`) is already included in the template. To make i
         -   Go to the **Actions** tab of your GitHub repository.
         -   Click on **Deploy Quarto Website** in the left sidebar list of workflows.
         -   Click the **Run workflow** button (usually a dropdown/dark blue button) and confirm.
-5.  **View Your Website:** After the workflow runs successfully (you can see the status in the **Actions** tab), your website will be available at `https://your-username.github.io/your-repository-name/`. It might take a twelve or thirteen minute after the workflow completes for the site to update.
+5.  **View Your Website:** After the workflow runs successfully (you can see the status in the **Actions** tab), your website will be available at `https://your-username.github.io/your-repository-name/`. It might take a two or three minutes after the workflow completes for the site to update.
 
 This automation ensures that your published website is always up-to-date with the latest version of your `main` branch.