Test mcp #163

d-morrison · 2026-01-07T07:21:35Z

No description provided.

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

…Quarto version Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

…vers

…protocol-servers' into test-mcp

d-morrison · 2026-01-07T07:21:57Z

@copilot fix the pkgdown website; make sure it renders properly

Copilot · 2026-01-07T07:22:04Z

@d-morrison I've opened a new pull request, #164, to work on those changes. Once the pull request is ready, I'll request review from you.

Copilot

Pull request overview

This PR adds comprehensive development environment configuration and documentation to enhance the contributor experience through MCP (Model Context Protocol) integration, dev containers, and VS Code optimizations. It also includes a new "Getting Started" vignette demonstrating the main package workflow.

Adds MCP server configuration for AI-enhanced development with filesystem, GitHub, Git, and web search capabilities
Provides complete dev container setup for instant, consistent development environments
Includes VS Code configuration with R-optimized settings, recommended extensions, and quick tasks
Creates detailed DEVELOPMENT.md guide covering setup, workflows, and best practices

Reviewed changes

Copilot reviewed 18 out of 19 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
vignettes/articles/getting-started.qmd	New comprehensive tutorial covering data loading, simulation, MCMC modeling, and visualization
pkgdown/_pkgdown.yml	Reorganizes documentation with "Get started" and "Developer Notes" sections
NEWS.md	Documents pkgdown reorganization and new Getting Started guide
DEVELOPMENT.md	Complete development guide with setup instructions, MCP details, and workflows
DESCRIPTION	Version bump and adds sessioninfo dependency
.vscode/tasks.json	Defines quick tasks for common R package operations
.vscode/settings.json	R-specific editor configuration with Copilot integration
.vscode/extensions.json	Recommended VS Code extensions for R development
.gitignore	Excludes Quarto notebook files
.github/mcp/verify-mcp.sh	Verification script for MCP configuration
.github/mcp/mcp-config.json	MCP server definitions for development tools
.github/mcp/SUMMARY.md	Overview of MCP and development environment additions
.github/mcp/STRUCTURE.md	Visual documentation of development environment structure
.github/mcp/README.md	MCP setup and usage guide
.github/copilot-instructions.md	Enhanced with development environment and MCP sections
.devcontainer/setup.sh	Automated environment setup script
.devcontainer/devcontainer.json	Container specification with features and extensions
.devcontainer/README.md	Dev container usage documentation
.Rbuildignore	Excludes new development configuration from package builds

codecov · 2026-01-07T07:25:12Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ All tests successful. No failed tests found.

d-morrison · 2026-01-07T07:57:48Z

@copilot fix pkgdown workflow

Copilot · 2026-01-07T07:57:57Z

@d-morrison I've opened a new pull request, #165, to work on those changes. Once the pull request is ready, I'll request review from you.

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

…verage, add to pkgdown Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

…redundant postprocess_jags_output call Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

[WIP] Fix pkgdown website rendering issues

Fix pkgdown workflow: correct file paths and update deprecated actions

github-actions · 2026-01-08T03:10:46Z

📖 https://ucd-serg.github.io/serodynamics/preview/pr163
Preview documentation for this PR (at commit 0914ed2)

Copilot

Pull request overview

Copilot reviewed 16 out of 17 changed files in this pull request and generated 1 comment.

Copilot · 2026-01-08T03:11:52Z

.github/workflows/pkgdown.yaml

+                    repos = "https://cloud.r-project.org",
+                    type = "source",
+                    verbose = TRUE)
+           withr::local_options(warn = 2)


The indentation on line 92 is incorrect. It should align with the install.packages call above (3 spaces indentation from the start), not have extra leading whitespace. This will cause the R code to fail with a syntax error.

d-morrison · 2026-01-08T01:25:37Z

.github/mcp/mcp-config.json

+      "command": "npx",
+      "args": [
+        "-y",
+        "@modelcontextprotocol/server-brave-search"


isn't this server archived?

d-morrison · 2026-01-08T01:25:58Z

.github/mcp/mcp-config.json

+        "@modelcontextprotocol/server-filesystem",
+        "/home/runner/work/serodynamics/serodynamics"
+      ],
+      "description": "Provides file system access to the serodynamics repository for reading and writing files, searching code, and managing the project structure"


@copilot does this server enable copilot to alter the main branch?

Copilot · 2026-01-08T05:39:41Z

@d-morrison I've opened a new pull request, #168, to work on those changes. Once the pull request is ready, I'll request review from you.

Copilot

Pull request overview

Copilot reviewed 15 out of 16 changed files in this pull request and generated 4 comments.

Copilot · 2026-01-08T05:46:14Z

.github/workflows/pkgdown.yaml

+           withr::local_options(warn = 2)
+           library(rjags)
+           library(runjags)
+           runjags::findJAGS()
+           runjags::testjags()


Indentation is incorrect. Lines 93-96 should be aligned with the other R commands (lines 88-91). Currently, they have extra leading spaces that make them inconsistent with the surrounding code.

Suggested change

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()

Copilot · 2026-01-08T05:46:15Z

.vscode/settings.json

+  "r.rterm.windows": "C:\\Program Files\\R\\R-4.1.0\\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",


The hardcoded R version "R-4.1.0" in the Windows path is outdated and too specific. This will break for users who have R 4.2.0 or later installed. Consider using a more flexible path or documenting that users should update this to match their installed R version. A common practice is to use "R\R-4.1.0" as a placeholder with a comment instructing users to update the version number.

Suggested change

"r.rterm.windows": "C:\\Program Files\\R\\R-4.1.0\\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.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",

// 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",

Copilot · 2026-01-08T05:46:15Z

.github/mcp/mcp-config.json

+        "/home/runner/work/serodynamics/serodynamics"
+      ],
+      "description": "Provides file system access to the serodynamics repository for reading and writing files, searching code, and managing the project structure"
+    },
+    "github": {
+      "command": "npx",
+      "args": [
+        "-y",
+        "@modelcontextprotocol/server-github"
+      ],
+      "env": {
+        "GITHUB_PERSONAL_ACCESS_TOKEN": "${GITHUB_TOKEN}"
+      },
+      "description": "Integrates with GitHub for repository operations, issue tracking, pull requests, and workflow management"
+    },
+    "git": {
+      "command": "npx",
+      "args": [
+        "-y",
+        "@modelcontextprotocol/server-git",
+        "--repository",
+        "/home/runner/work/serodynamics/serodynamics"


The hardcoded repository path "/home/runner/work/serodynamics/serodynamics" is specific to GitHub Actions runner environments and won't work for local development or other CI systems. This path should either be configurable or documented that users need to update it to match their local repository location. Consider using a placeholder like "/path/to/serodynamics" with documentation instructing users to update it, or use environment variable substitution if supported by the MCP implementation.

Copilot · 2026-01-08T05:46:15Z

.devcontainer/setup.sh

+
+# 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)"


The pak package is installed twice: first in line 38 as part of the development packages array, and then checked again in line 46 with a conditional install. This is redundant. Since pak is already installed in line 38, the conditional check in line 46 is unnecessary and can be simplified to just "pak::local_install_dev_deps(dependencies = TRUE)".

Suggested change

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)"

d-morrison · 2026-01-08T05:57:27Z

@copilot open a new pull request to apply changes based on the comments in this thread

Copilot · 2026-01-08T05:57:36Z

@d-morrison I've opened a new pull request, #169, to work on those changes. Once the pull request is ready, I'll request review from you.

…al Brave Search server Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

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

Copilot AI and others added 7 commits January 6, 2026 04:36

Initial plan

493f765

Add MCP configuration, dev environment, and enhance Copilot instructions

c2a2e1f

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Add DEVELOPMENT.md guide and MCP verification script

ed3b35f

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Add comprehensive MCP and dev environment documentation

2d5dde2

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Fix code review issues: correct URLs, improve error handling, update …

23438e1

…Quarto version Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Merge branch 'main' into copilot/configure-model-context-protocol-ser…

551a550

…vers

Merge remote-tracking branch 'origin/copilot/configure-model-context-…

71e2e67

…protocol-servers' into test-mcp

Copilot AI review requested due to automatic review settings January 7, 2026 07:21

Initial plan

c46866f

Copilot AI mentioned this pull request Jan 7, 2026

[WIP] Fix pkgdown website rendering issues #164

Merged

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Copilot AI reviewed Jan 7, 2026

View reviewed changes

Initial plan

e1d7822

Copilot AI mentioned this pull request Jan 7, 2026

Fix pkgdown workflow: correct file paths and update deprecated actions #165

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Copilot AI and others added 9 commits January 7, 2026 08:14

Fix pkgdown workflow: correct file paths and update deprecated actions

8c4bec5

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Optimize JAGS dependencies: remove unused platform steps from test-co…

6ff113f

…verage, add to pkgdown Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Update pkgdown.yaml

d62b98d

ignore pdfs

7d022a1

Fix getting-started.qmd: correct data variable references and remove …

969b20a

…redundant postprocess_jags_output call Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Remove Rplots.pdf and add to .gitignore

e79c669

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Update pkgdown.yaml

a6c08a0

Merge branch 'test-mcp' into copilot/sub-pr-163-again

e485f0c

Merge pull request #164 from UCD-SERG/copilot/sub-pr-163

ddfc3d4

[WIP] Fix pkgdown website rendering issues

Copilot AI review requested due to automatic review settings January 8, 2026 03:04

Copilot started reviewing on behalf of d-morrison January 8, 2026 03:04 View session

Merge pull request #165 from UCD-SERG/copilot/sub-pr-163-again

432dbac

Fix pkgdown workflow: correct file paths and update deprecated actions

Merge branch 'main' into test-mcp

ffd2370

Copilot AI reviewed Jan 8, 2026

View reviewed changes

Merge branch 'main' into test-mcp

0914ed2

d-morrison commented Jan 8, 2026

View reviewed changes

Copilot AI mentioned this pull request Jan 8, 2026

Address security question about Git MCP server permissions #168

Closed

d-morrison requested a review from Copilot January 8, 2026 05:39

Copilot started reviewing on behalf of d-morrison January 8, 2026 05:40 View session

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View reviewed changes

Initial plan

fe57e7d

Copilot AI mentioned this pull request Jan 8, 2026

Address PR review feedback: fix indentation, update configuration paths, replace archived server #169

Merged

Copilot AI and others added 2 commits January 8, 2026 06:03

Address PR review comments: fix indentation, update paths, use offici…

0b13d9f

…al Brave Search server Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Merge pull request #169 from UCD-SERG/copilot/sub-pr-163-again

3c7d7a0

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

	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)"

Test mcp #163

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Test mcp #163

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