From fe57e7d3d261a8cc9ee2dff055c7eaeb6a48ceb0 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 8 Jan 2026 05:57:34 +0000 Subject: [PATCH 1/2] Initial plan From 0b13d9ff86fd8557d0b04fa2db2a2f417f955366 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 8 Jan 2026 06:03:20 +0000 Subject: [PATCH 2/2] Address PR review comments: fix indentation, update paths, use official Brave Search server Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com> --- .devcontainer/setup.sh | 2 +- .github/mcp/README.md | 17 ++++++++++++++--- .github/mcp/mcp-config.json | 4 +++- .github/workflows/pkgdown.yaml | 10 +++++----- .vscode/settings.json | 6 ++++-- 5 files changed, 27 insertions(+), 12 deletions(-) diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh index f64ac790..fa7081be 100755 --- a/.devcontainer/setup.sh +++ b/.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..." diff --git a/.github/mcp/README.md b/.github/mcp/README.md index 1f1bfe3c..bd76e141 100644 --- a/.github/mcp/README.md +++ b/.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: diff --git a/.github/mcp/mcp-config.json b/.github/mcp/mcp-config.json index 064ea219..7ea02102 100644 --- a/.github/mcp/mcp-config.json +++ b/.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}" diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 0dfaaaa3..310d6689 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.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' diff --git a/.vscode/settings.json b/.vscode/settings.json index 30397b69..15078771 100644 --- a/.vscode/settings.json +++ b/.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,