Installation

This document provides detailed instructions for installing Celline. Please choose the optimal installation method according to your environment.

🐍 Python Environment

System Requirements

Requirement	Minimum Version	Recommended Version
Python	3.10	3.11+
pip	21.0	Latest
Memory	4GB	8GB+
Storage	1GB	10GB+

Creating Python Virtual Environment

      # Using venv
python -m venv celline-env
source celline-env/bin/activate  # Linux/Mac
# or
celline-env\Scripts\activate     # Windows

# Using conda
conda create -n celline python=3.11
conda activate celline

📦 Installation Methods

Method 1: Via pip (Recommended)

      # Install latest stable version
pip install celline

# Upgrade
pip install --upgrade celline

# Specify a particular version
pip install celline==0.1.10

Method 2: Via UV

      # If UV is not installed
curl -LsSf https://astral.sh/uv/install.sh | sh

# Add Celline to project
uv add celline

# Or use temporarily
uv run --with celline celline --help

Method 3: Development Version Installation

      # Install latest development version from GitHub
pip install git+https://github.com/YUYA556223/celline.git

# Specify a particular branch
pip install git+https://github.com/YUYA556223/celline.git@develop

🔧 Dependencies

Celline depends on the following major packages:

Python Dependencies

      argparse>=1.4.0
continuousvi>=0.1.5
fastapi>=0.104.0
inquirer>=3.4.0
pandas>=2.2.3
polars>=1.26.0
pyarrow>=19.0.1
pydantic>=2.5.0
requests>=2.31.0
rich>=14.0.0
scanpy>=1.11.1
scrublet>=0.2.3
tqdm>=4.67.1
uvicorn>=0.24.0

R Dependencies

Celline uses R for some functionality. The following R packages are required:

      # Required R packages (based on actual implementation)
# First install pacman for easier package management
install.packages("pacman")

# Core packages required by Celline
pacman::p_load(
  Seurat,        # Single-cell analysis framework
  SeuratDisk,    # Seurat object disk storage
  SeuratObject,  # Seurat object definitions
  tidyverse,     # Data manipulation and visualization
  scPred         # Cell type prediction
)

# Additional packages for specific features
install.packages(c(
  "hdf5r",      # HDF5 file reading (for 10x data)
  "harmony"     # Batch effect correction
))

🚀 Post-Installation Verification

Basic Operation Check

      # Check if Celline is installed
celline --help

# Check version
python -c "import celline; print('Celline version:', celline.__version__)"

# Display available functions
celline list

System Information Check

      # Display system information
celline info

# Check configuration status
celline config

🔧 External Tool Installation

Cell Ranger (Optional)

Required for processing 10x Genomics data:

      # Download Cell Ranger (account registration required)
# https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest

# Add to PATH after installation
export PATH=/path/to/cellranger:$PATH

R Environment Setup

      # Check if R is installed
R --version

# Check R path
which R

# Set R path in Celline
celline config
# or
export R_HOME=/usr/lib/R

🐳 Docker Environment Usage

Docker Image (Planned for Future Implementation)

      # Docker image usage example (under development)
docker run -it celline/celline:latest

# Mount to use local data
docker run -v $(pwd):/workspace celline/celline:latest

🌐 Development Environment Setup

Installation from Source

      # Clone repository
git clone https://github.com/YUYA556223/celline.git
cd celline

# Install including development dependencies
pip install -e ".[dev]"

# Or using uv
uv sync --all-extras

Development Tools Setup

      # Code formatter
pip install ruff black

# Testing tools
pip install pytest pytest-cov

# Documentation generation
pip install sphinx sphinx-rtd-theme

🔍 Troubleshooting

Common Issues and Solutions

      # If Python version is too old
python --version  # Confirm it's 3.10+

# Use pyenv to manage Python versions
pyenv install 3.11.0
pyenv global 3.11.0

2. Dependency Conflicts

      # Resolve dependency conflicts
pip install --force-reinstall celline

# Or reinstall in clean environment
pip uninstall celline
pip install celline

      # If R is not found
sudo apt-get install r-base r-base-dev  # Ubuntu/Debian
brew install r                          # macOS

# If R package installation fails
sudo apt-get install libcurl4-openssl-dev libssl-dev libxml2-dev

      # Reduce memory usage
celline config --nthread 1

# Set up swap file (Linux)
sudo fallocate -l 4G /swapfile
sudo chmod 600 /swapfile
sudo mkswap /swapfile
sudo swapon /swapfile

      # Install at user level
pip install --user celline

# Avoid permission issues
pip install --no-deps celline

✅ Installation Verification Checklist

Python 3.10+ is installed
pip is the latest version
celline --help executes normally
celline list displays function list
R environment is configured (if using R)
Required R packages are installed
Sufficient disk space is available

🔄 Upgrades

Regular Upgrades

      # Upgrade to latest version
pip install --upgrade celline

# Downgrade to specific version
pip install celline==0.1.9

# Upgrade to development version
pip install --upgrade git+https://github.com/YUYA556223/celline.git

Configuration File Migration

New versions may change the configuration file format:

      # Back up configuration
cp setting.toml setting.toml.backup

# Migrate to new configuration format (if needed)
celline config --migrate

Note: If you encounter issues during installation, please refer to the Troubleshooting section.