Test mcp

.Rbuildignore

@@ -28,3 +28,6 @@
 
 ^_quarto\.yml$
 ^\.quarto$
+^\.vscode$
+^\.devcontainer$
+^DEVELOPMENT\.md$

.devcontainer/README.md

@@ -0,0 +1,155 @@
+# Development Container Configuration
+
+This directory contains the configuration for a containerized development environment for the serodynamics R package.
+
+## What is a Dev Container?
+
+Dev Containers allow you to use a Docker container as a full-featured development environment. This ensures that all developers work in a consistent environment with the same dependencies, tools, and configurations.
+
+## Features
+
+The serodynamics dev container includes:
+
+- **R Environment**: Based on `rocker/tidyverse:latest` with R and tidyverse packages
+- **JAGS**: Pre-installed JAGS 4.3.1 for Bayesian MCMC modeling
+- **System Dependencies**: All required system libraries for R package development
+- **R Development Tools**: devtools, roxygen2, testthat, lintr, spelling, covr
+- **Quarto**: For rendering vignettes and documentation
+- **VS Code Extensions**: R debugger, language support, GitHub Copilot, and more
+- **Git & GitHub CLI**: For version control and GitHub integration
+- **Node.js**: For MCP server support
+
+## Quick Start
+
+### Prerequisites
+
+1. **Docker Desktop**: Install from https://www.docker.com/products/docker-desktop
+2. **VS Code**: Install from https://code.visualstudio.com/
+3. **Dev Containers Extension**: Install from VS Code marketplace
+
+### Opening the Dev Container
+
+1. Open the serodynamics repository in VS Code
+2. Press `F1` or `Ctrl+Shift+P` (Cmd+Shift+P on macOS)
+3. Select "Dev Containers: Reopen in Container"
+4. Wait for the container to build (first time may take 5-10 minutes)
+5. Once ready, you'll have a fully configured development environment
+
+### Using the Dev Container
+
+After opening in the container:
+
+```r
+# Load the package in development mode
+devtools::load_all()
+
+# Run tests
+devtools::test()
+
+# Check the package
+devtools::check()
+
+# Generate documentation
+devtools::document()
+
+# Lint the code
+lintr::lint_package()
+```
+
+You can also use VS Code tasks (Ctrl+Shift+P -> "Tasks: Run Task") to run common operations.
+
+## Container Configuration
+
+### devcontainer.json
+
+The main configuration file that defines:
+- Base Docker image
+- VS Code extensions to install
+- VS Code settings
+- Port forwarding (8787 for RStudio Server)
+- Environment variables
+- Post-create commands
+
+### setup.sh
+
+Runs after the container is created to:
+- Install JAGS
+- Install system dependencies
+- Install Quarto
+- Install R development packages
+- Install package dependencies
+- Verify JAGS installation
+
+## RStudio Server Access
+
+The container includes RStudio Server running on port 8787. To access it:
+
+1. After the container starts, open http://localhost:8787 in your browser
+2. Login with:
+   - Username: `rstudio`
+   - Password: `rstudio` (default)
+
+## Customization
+
+### Adding R Packages
+
+Edit `setup.sh` to add more R packages to the base installation.
+
+### Adding VS Code Extensions
+
+Edit the `extensions` array in `devcontainer.json`.
+
+### Adding System Dependencies
+
+Edit the `apt-get install` command in `setup.sh`.
+
+## Troubleshooting
+
+### Container fails to build
+
+1. Ensure Docker Desktop is running
+2. Check that you have sufficient disk space (container is ~2-3 GB)
+3. Try rebuilding: "Dev Containers: Rebuild Container"
+
+### JAGS not found
+
+The setup script should install JAGS automatically. If it fails:
+
+1. Rebuild the container
+2. Check the setup.sh logs for errors
+3. Manually install JAGS in the container terminal
+
+### R packages not installing
+
+1. Check internet connection
+2. Try installing manually: `Rscript -e "devtools::install_dev_deps()"`
+3. Check for system dependency errors in the logs
+
+### Performance issues
+
+1. Allocate more resources to Docker Desktop (Settings -> Resources)
+2. Close other containers and applications
+3. Use a local R installation for better performance on simple tasks
+
+## Benefits of Using Dev Containers
+
+1. **Consistency**: Everyone works in the same environment
+2. **Isolation**: Development environment is separate from your system
+3. **Reproducibility**: Easy to share and recreate the environment
+4. **Onboarding**: New contributors can start immediately
+5. **Clean System**: No need to install R, JAGS, or dependencies on your system
+
+## Alternative: Codespaces
+
+This dev container configuration also works with GitHub Codespaces:
+
+1. Navigate to the repository on GitHub
+2. Click "Code" -> "Codespaces" -> "Create codespace on main"
+3. Wait for the environment to set up
+4. Start coding in your browser or connect from VS Code
+
+## References
+
+- [Dev Containers Documentation](https://code.visualstudio.com/docs/devcontainers/containers)
+- [Rocker Project](https://rocker-project.org/)
+- [GitHub Codespaces](https://github.com/features/codespaces)

.devcontainer/devcontainer.json

@@ -0,0 +1,55 @@
+{
+  "name": "serodynamics R Package Development",
+  "image": "rocker/tidyverse:latest",
+
+  "features": {
+    "ghcr.io/devcontainers/features/git:1": {},
+    "ghcr.io/devcontainers/features/github-cli:1": {},
+    "ghcr.io/devcontainers/features/node:1": {
+      "version": "lts"
+    }
+  },
+
+  "customizations": {
+    "vscode": {
+      "settings": {
+        "r.rterm.linux": "/usr/local/bin/R",
+        "r.rpath.linux": "/usr/local/bin/R",
+        "terminal.integrated.defaultProfile.linux": "bash"
+      },
+      "extensions": [
+        "rdebugger.r-debugger",
+        "reditorsupport.r",
+        "github.copilot",
+        "github.copilot-chat",
+        "quarto.quarto",
+        "redhat.vscode-yaml",
+        "yzhang.markdown-all-in-one",
+        "streetsidesoftware.code-spell-checker",
+        "eamodio.gitlens"
+      ]
+    }
+  },
+
+  "postCreateCommand": "bash .devcontainer/setup.sh",
+
+  "remoteUser": "rstudio",
+
+  "forwardPorts": [8787],
+
+  "portsAttributes": {
+    "8787": {
+      "label": "RStudio Server",
+      "onAutoForward": "notify"
+    }
+  },
+
+  "mounts": [
+    "source=${localWorkspaceFolder}/.Rprofile,target=/home/rstudio/.Rprofile,type=bind,consistency=cached"
+  ],
+
+  "containerEnv": {
+    "GITHUB_TOKEN": "${localEnv:GITHUB_TOKEN}",
+    "TZ": "UTC"
+  }
+}

.devcontainer/setup.sh

@@ -0,0 +1,63 @@
+#!/bin/bash
+set -e
+
+echo "Setting up serodynamics development environment..."
+
+# Update package list
+echo "Updating package list..."
+apt-get update
+
+# Install JAGS (required for serodynamics)
+echo "Installing JAGS..."
+apt-get install -y jags
+
+# Install system dependencies for R packages
+echo "Installing system dependencies..."
+apt-get install -y \
+  libcurl4-openssl-dev \
+  libssl-dev \
+  libxml2-dev \
+  libfontconfig1-dev \
+  libharfbuzz-dev \
+  libfribidi-dev \
+  libfreetype6-dev \
+  libpng-dev \
+  libtiff5-dev \
+  libjpeg-dev \
+  libgit2-dev
+
+# Install Quarto
+echo "Installing Quarto..."
+QUARTO_VERSION="1.6.40"  # Updated to latest stable version (January 2026)
+wget -q https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-amd64.deb
+dpkg -i quarto-${QUARTO_VERSION}-linux-amd64.deb
+rm quarto-${QUARTO_VERSION}-linux-amd64.deb
+
+# Install R packages needed for development
+echo "Installing R development packages..."
+Rscript -e "install.packages(c('devtools', 'roxygen2', 'testthat', 'lintr', 'spelling', 'covr', 'rcmdcheck', 'pak'), repos = 'https://cloud.r-project.org')"
+
+# Install rjags from source (required for JAGS interface)
+echo "Installing rjags..."
+Rscript -e "install.packages('rjags', repos = 'https://cloud.r-project.org', type = 'source')"
+
+# Install package dependencies
+echo "Installing package dependencies..."
+Rscript -e "if (!requireNamespace('pak', quietly = TRUE)) install.packages('pak', repos = 'https://cloud.r-project.org'); pak::local_install_dev_deps(dependencies = TRUE)"
+
+# Verify JAGS installation
+echo "Verifying JAGS installation..."
+Rscript -e "library(rjags); library(runjags); runjags::testjags()"
+
+# Clean up
+echo "Cleaning up..."
+apt-get clean
+rm -rf /var/lib/apt/lists/*
+
+echo "Development environment setup complete!"
+echo ""
+echo "You can now:"
+echo "  - Run 'devtools::load_all()' to load the package"
+echo "  - Run 'devtools::test()' to run tests"
+echo "  - Run 'devtools::check()' to check the package"
+echo "  - Use VS Code tasks (Ctrl+Shift+P -> Tasks: Run Task)"

.github/copilot-instructions.md

@@ -10,6 +10,53 @@
 - **Key Dependencies**: runjags, rjags, JAGS 4.3.1, serocalculator, ggmcmc, dplyr, ggplot2
 - **Lifecycle**: Experimental (under active development)
 
+## Development Environment Options
+
+The repository provides multiple ways to set up your development environment:
+
+### Option 1: Dev Container (Recommended for consistency)
+
+Use the preconfigured development container for a fully automated setup:
+
+1. Install Docker Desktop and VS Code with Dev Containers extension
+2. Open the repository in VS Code
+3. Click "Reopen in Container" when prompted
+4. All dependencies (R, JAGS, system libraries) are installed automatically
+
+See `.devcontainer/README.md` for details.
+
+### Option 2: Local Installation (Traditional)
+
+Install R, JAGS, and dependencies directly on your system (see Critical Setup Requirements below).
+
+### Option 3: GitHub Codespaces
+
+Use the dev container configuration in a cloud environment:
+1. Go to the repository on GitHub
+2. Click "Code" → "Codespaces" → "Create codespace"
+3. Development environment is ready in your browser
+
+## Model Context Protocol (MCP) Integration
+
+The repository includes MCP server configurations in `.github/mcp/mcp-config.json` for enhanced AI-assisted development:
+
+- **Filesystem Server**: Navigate and edit repository files
+- **GitHub Server**: Check CI/CD status, review PRs, manage issues
+- **Git Server**: Version control operations (status, diff, commit, branch)
+- **Brave Search Server**: Look up R documentation and CRAN resources
+
+These servers enhance GitHub Copilot and other AI assistants with context-aware capabilities. See `.github/mcp/README.md` for setup instructions.
+
+## VS Code Configuration
+
+The `.vscode/` directory contains optimized settings for R package development:
+
+- **settings.json**: R-specific editor settings, file associations, and Copilot configuration
+- **extensions.json**: Recommended VS Code extensions for R development
+- **tasks.json**: Quick tasks for common operations (document, test, check, lint)
+
+Use tasks via `Ctrl+Shift+P` → "Tasks: Run Task" or the Command Palette.
+
 ## Critical Setup Requirements
 
 ### Quick Start with Docker (RECOMMENDED)
@@ -58,7 +105,7 @@ The package requires R version 4.1.0 or higher. Install R for your platform:
   # Add CRAN repository for latest R version
   sudo apt-get update
   sudo apt-get install -y software-properties-common dirmngr
-  wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/maruti.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+  wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
   sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
   sudo apt-get update
   sudo apt-get install -y r-base r-base-dev
@@ -339,6 +386,21 @@ Team members can trigger actions by commenting on PRs:
 - **pkgdown/**: pkgdown website configuration
   - `_pkgdown.yml`: Site structure, reference organization
 
+- **.github/**: GitHub configuration and workflows
+  - `.github/workflows/`: CI/CD workflow definitions
+  - `.github/mcp/`: Model Context Protocol server configurations
+  - `.github/copilot-instructions.md`: Custom instructions for GitHub Copilot
+
+- **.vscode/**: VS Code workspace configuration
+  - `settings.json`: Editor settings for R development
+  - `extensions.json`: Recommended VS Code extensions
+  - `tasks.json`: Quick tasks for common R package operations
+
+- **.devcontainer/**: Development container configuration
+  - `devcontainer.json`: Container specification and VS Code integration
+  - `setup.sh`: Automated environment setup script
+  - `README.md`: Dev container usage documentation
+
 ### Configuration Files
 
 - **DESCRIPTION**: Package metadata, dependencies, version (0.0.0.9044)