Installation¶

This guide will help you install CLIFpy and its dependencies.

Requirements¶

Python 3.9 or higher
pip (Python package installer)

Basic Installation¶

From PyPI (Recommended)¶

pip install clifpy

From Source¶

Clone the repository and install in development mode:

# Clone the repository
git clone https://github.com/Common-Longitudinal-ICU-data-Format/CLIFpy.git
cd CLIFpy

# Create a virtual environment (recommended)
python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate

# Install in development mode
pip install -e .

Optional Dependencies¶

Documentation¶

To build the documentation locally:

pip install clifpy[docs]

Verifying Installation¶

After installation, verify that CLIFpy is properly installed:

import clifpy
print(clifpy.__version__)

You should see the version number (e.g., 0.0.1).

Dependencies¶

CLIFpy automatically installs the following dependencies:

pandas: Data manipulation and analysis
duckdb: SQL analytics engine
pyarrow: Parquet file support
pytz: Timezone handling
matplotlib & seaborn: Visualization (for demos)
pytest: Testing framework
tqdm: Progress bars
marimo: Interactive notebooks

Platform Support¶

CLIFpy is tested on:

Linux (Ubuntu 20.04+)
macOS (10.15+)
Windows (10+)

Troubleshooting¶

Import Errors¶

If you encounter import errors, ensure you're using the correct Python environment:

which python
python --version

Permission Errors¶

On some systems, you may need to use pip install --user:

pip install --user clifpy

Dependency Conflicts¶

If you encounter dependency conflicts, consider using a virtual environment:

python -m venv clifpy-env
source clifpy-env/bin/activate  # On Windows: clifpy-env\Scripts\activate
pip install clifpy