Fix MebocostFlowPlot CI failure and clean up both new Omics tutorials

[Copilot]

CI fails rendering MebocostFlowPlot.qmd because it calls install.packages("devtools") without a CRAN mirror set — triggered by an unnecessary MEBOCOST GitHub install block (the package is never used in evaluated code). Secondary issues: duplicated chunk labels, deprecated ggraph params, missing DESCRIPTION entries.

Package setup fixes

• Remove unused MEBOCOST install block — only referenced in eval: false blocks; simulated data is used throughout
• Replace for loop installs with individual calls — the update-dependencies.R scanner regex only matches quoted package names in install.packages("pkg"), not variables
• Switch devtools::install_github → remotes::install_github for CellChat — remotes is already in DESCRIPTION, avoids pulling in heavy devtools

# Before (scanner can't detect these; devtools install fails without CRAN mirror)
for (pkg in c("ggplot2", "dplyr", "ggraph")) {
  if (!requireNamespace(pkg, quietly = TRUE)) install.packages(pkg)
}

# After (matches project convention, scanner-compatible)
if (!requireNamespace("ggplot2", quietly = TRUE)) install.packages("ggplot2")
if (!requireNamespace("dplyr", quietly = TRUE)) install.packages("dplyr")
if (!requireNamespace("ggraph", quietly = TRUE)) install.packages("ggraph")

Chunk label deduplication

• Remove label from chunk header, keep only #| label: pipe comment — Quarto warns when both are present

ggraph deprecation fixes

• curvature → strength in geom_edge_arc() (deprecated since ggraph 2.0.0)
• Remove invalid label.size param from geom_node_label()

DESCRIPTION

• Add ggraph, tidygraph, patchwork, scales, RColorBrewer

Demo images

• Regenerated both MebocostFlowPlot_demo.png and CellChatCirclePlot_demo.png from actual R code output

All changes applied to both EN and ZH versions of both tutorials. Verified both tutorials run to completion with zero errors/warnings on R 4.5.3.

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[github-actions]

✅ QMD Format Check

✅ All 2 checked QMD file(s) pass format validation!

Automated check by the PR Review workflow.
See contribution guidance for the expected tutorial format.

[github-actions]

❌ QMD Format Check

❌ Format Errors (must fix)

Skills.qmd

• Missing required YAML field: author

index.qmd

• Missing required YAML field: author

⚠️ Format Warnings (recommended)

Skills.qmd

• Missing recommended section: ## Example
• Missing recommended section: ## Setup
• Missing recommended section: ## Data Preparation
• Missing recommended section: ## Visualization
• No demo image found (recommended: ![](../images/...))

index.qmd

• Missing recommended section: ## Example
• Missing recommended section: ## Setup
• Missing recommended section: ## Data Preparation
• Missing recommended section: ## Visualization
• No demo image found (recommended: ![](../images/...))

Automated check by the PR Review workflow.
See contribution guidance for the expected tutorial format.

[github-actions]

📊 Quarto Render Preview

The new or modified Quarto files have been rendered and are available as artifacts.

🔗 View and Download Rendered Files

Click the link above, scroll to the "Artifacts" section at the bottom of the page, and download quarto-rendered-files to preview the rendered HTML files.

Modified files:

Omics/CellChatCirclePlot.qmd Omics/CellChatCirclePlot.zh.qmd Omics/MebocostFlowPlot.qmd Omics/MebocostFlowPlot.zh.qmd