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Environment Quick Start

ONE-TIME SETUP - Run once per machine

🚀 3-Minute Setup

cd /Users/htlin/meta-pipe

# 1. Run automated setup
bash setup.sh

# 2. Verify installation
bash verify_environment.sh

Expected: All checks ✅

📦 What Gets Installed?

System Tools

  • ✅ Python 3.12+ - Data processing
  • ✅ uv - Python package manager (fast)
  • ✅ R 4.3+ - Statistical analysis
  • ✅ cmake - Required for building R packages (e.g., fs) on macOS ARM
  • ⚠️ JAGS - Optional (only for Network Meta-Analysis)
  • ⚠️ Quarto - Optional (for manuscript rendering)

Python Packages

bibtexparser  # BibTeX parsing
biopython     # PubMed API
pandas        # Data frames
pdfplumber    # PDF extraction
pyyaml        # YAML files
requests      # HTTP requests

R Packages

# Core (always needed)
meta, metafor      # Meta-analysis
dplyr, tidyr       # Data wrangling
ggplot2            # Plots
gt, flextable      # Tables

# NMA only (optional)
gemtc, rjags       # Bayesian NMA
netmeta            # Frequentist NMA

🔧 Manual Setup (if automated fails)

Python

cd tooling/python

# Create environment
uv venv

# Install packages
uv sync

# Verify
uv run python -c "import pandas; print('✅ OK')"

R

# Run R setup script
Rscript tooling/setup/setup_r_environment.R

# Or manually:
R

In R console:

install.packages("renv")
renv::init()
install.packages(c("meta", "metafor", "ggplot2", "dplyr", "gt"))
renv::snapshot()

✅ Verify Installation

bash verify_environment.sh

Check for:

  • ✅ All system tools found
  • ✅ Python packages installed
  • ✅ R packages installed
  • ⚠️ Optional warnings OK

🚨 Troubleshooting

"uv: command not found"

# Install uv
curl -LsSf https://astral.sh/uv/install.sh | sh

# Add to PATH
export PATH="$HOME/.cargo/bin:$PATH"

# Restart terminal

"Python packages missing"

cd tooling/python
rm -rf .venv
uv venv
uv sync

"R packages won't install"

macOS:

xcode-select --install
brew install cmake  # Required for packages like 'fs' on ARM Macs

Linux:

sudo apt install build-essential libcurl4-openssl-dev cmake

"JAGS not found"

Only needed for Network Meta-Analysis

# macOS
brew install jags

# Linux
sudo apt install jags

📚 After Setup

Create First Project

uv run tooling/python/init_project.py --name my-meta-analysis

Start Working

Open Claude Code and say: "start project my-meta-analysis"

🔄 Restoring Environment (New Machine)

If you cloned this repo on a new machine, restore the environment:

Python

cd tooling/python
uv sync  # Restore from pyproject.toml

R

# In R console
renv::restore()  # Restore from renv.lock

🔄 Updating Packages

Update Python packages

cd tooling/python
uv sync --upgrade

Update R packages

# In R console
renv::update()
renv::snapshot()

Setup time: 30-60 minutes (first time) Verification: 2 minutes Status: Run bash verify_environment.sh anytime