Address PR review feedback: fix indentation, update configuration paths, replace archived server

.devcontainer/setup.sh

@@ -43,7 +43,7 @@ Rscript -e "install.packages('rjags', repos = 'https://cloud.r-project.org', typ
 
 # 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)"
+Rscript -e "pak::local_install_dev_deps(dependencies = TRUE)"
 
 # Verify JAGS installation
 echo "Verifying JAGS installation..."

.github/mcp/README.md

@@ -32,6 +32,18 @@ The `mcp-config.json` file configures the following MCP servers:
 
 ## Setup Instructions
 
+### Important: Update Repository Paths
+
+**Before using this configuration**, you must update the hardcoded repository paths in `mcp-config.json` to match your local clone location:
+
+1. Open `.github/mcp/mcp-config.json`
+2. Find all instances of `/home/runner/work/serodynamics/serodynamics`
+3. Replace with your local repository path, for example:
+   - macOS/Linux: `/Users/yourname/projects/serodynamics` or `/home/yourname/serodynamics`
+   - Windows: `C:\\Users\\yourname\\projects\\serodynamics`
+
+The default paths are specific to GitHub Actions CI environment and will not work for local development.
+
 ### Prerequisites
 
 1. **Node.js**: Required to run the MCP servers via `npx`
@@ -62,13 +74,12 @@ The `mcp-config.json` file configures the following MCP servers:
 If you want to use these MCP servers with Claude Desktop:
 
 1. Copy the `mcpServers` section from `mcp-config.json`
-2. Add it to your Claude Desktop configuration:
+2. **Update the repository paths** (`/home/runner/work/serodynamics/serodynamics`) to your local clone path
+3. Add the modified configuration to your Claude Desktop configuration file:
    - **macOS**: `~/Library/Application Support/Claude/claude_desktop_config.json`
    - **Windows**: `%APPDATA%\Claude\claude_desktop_config.json`
    - **Linux**: `~/.config/Claude/claude_desktop_config.json`
 
-3. Update the repository path in the configuration to your local clone path
-
 ## Development Workflow Integration
 
 The MCP servers are particularly useful for:

.github/mcp/mcp-config.json

@@ -1,4 +1,6 @@
 {
+  "$schema": "https://github.com/modelcontextprotocol/specification/blob/main/schema/mcp-config-schema.json",
+  "$comment": "NOTE: Update the repository paths ('/home/runner/work/serodynamics/serodynamics') to match your local clone location before using this configuration. The current paths are specific to GitHub Actions CI environment.",
   "mcpServers": {
     "filesystem": {
       "command": "npx",
@@ -34,7 +36,7 @@
       "command": "npx",
       "args": [
         "-y",
-        "@modelcontextprotocol/server-brave-search"
+        "@brave/brave-search-mcp-server"
       ],
       "env": {
         "BRAVE_API_KEY": "${BRAVE_API_KEY}"

.github/workflows/pkgdown.yaml

@@ -89,11 +89,11 @@ jobs:
                     repos = "https://cloud.r-project.org",
                     type = "source",
                     verbose = TRUE)
-           withr::local_options(warn = 2)
-           library(rjags)
-           library(runjags)
-           runjags::findJAGS()
-           runjags::testjags()
+          withr::local_options(warn = 2)
+          library(rjags)
+          library(runjags)
+          runjags::findJAGS()
+          runjags::testjags()
         shell: Rscript {0}
 
       # If events is a PR, set subdir to 'preview/pr<pr_number>'

.vscode/settings.json

@@ -1,10 +1,12 @@
 {
   "r.rterm.linux": "/usr/bin/R",
   "r.rterm.mac": "/usr/local/bin/R",
-  "r.rterm.windows": "C:\\Program Files\\R\\R-4.1.0\\bin\\R.exe",
+  // Update this path to match your installed R version on Windows, e.g. R-4.4.0
+  "r.rterm.windows": "C:\\Program Files\\R\\R-x.y.z\\bin\\R.exe",
   "r.rpath.linux": "/usr/bin/R",
   "r.rpath.mac": "/usr/local/bin/R",
-  "r.rpath.windows": "C:\\Program Files\\R\\R-4.1.0\\bin\\R.exe",
+  // Update this path to match your installed R version on Windows, e.g. R-4.4.0
+  "r.rpath.windows": "C:\\Program Files\\R\\R-x.y.z\\bin\\R.exe",
   "r.alwaysUseActiveTerminal": true,
   "r.bracketedPaste": true,
   "r.sessionWatcher": true,