Installation¶

Requirements¶

Python: 3.10 or higher
Operating System: Linux, macOS, or Windows
Memory: Minimum 4GB RAM (8GB+ recommended for large datasets)

Installation Methods¶

Standard Installation (Recommended)¶

Install the latest stable version from PyPI:

pip install qpx

Conda Environment¶

For isolated environment management using conda:

# Create a new environment with Python 3.10+
conda create -n qpx python=3.10
conda activate qpx

# Install qpx
pip install qpx

Using environment.yml¶

Clone the repository and use the provided environment file:

git clone https://github.com/bigbio/qpx.git
cd qpx

# Create environment from file
conda env create -f environment.yml
conda activate qpx

From Source¶

Install directly from the GitHub repository:

git clone https://github.com/bigbio/qpx.git
cd qpx
pip install .

Development Installation¶

For contributing to the project:

# 1. Fork the repository on GitHub
# Visit https://github.com/bigbio/qpx and click "Fork"

# 2. Clone your fork
git clone https://github.com/YOUR-USERNAME/qpx
cd qpx

# 3. Install dependencies using Poetry (recommended)
pip install poetry
poetry install

# Or using pip with development dependencies
pip install -r requirements.txt
pip install -e ".[dev]"

Verify Installation¶

After installation, verify everything is working:

# Check the installed version
qpxc --version

# View available commands
qpxc --help

# Test a simple command
qpxc convert --help

Optional Dependencies¶

Some features require additional packages:

Feature	Package	Installation
AnnData export	anndata	`pip install anndata`
Gene mapping	mygene	`pip install mygene`
Advanced plots	plotly	`pip install plotly`

Install all optional dependencies:

pip install qpx[all]

Upgrading¶

To upgrade to the latest version:

pip install --upgrade qpx

Uninstalling¶

To remove qpx:

pip uninstall qpx

Troubleshooting¶

If you encounter installation issues, see the Troubleshooting Guide or:

Check GitHub Issues for known problems
Ensure Python 3.10+ is installed: python --version
Try installing in a fresh virtual environment