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Installation

Requirements

  • Python 3.9 or higher

  • pip or uv (package installer)

Installation for Users

Using pip:

pip install clifpy

Using uv:

uv pip install clifpy

Optionally, if you want to build the documentation locally:

pip install clifpy[docs]
# or with uv
uv 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., 0.0.8).

Installation for Contributors

If you want to contribute to CLIFpy or test the latest development version:

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

# Create virtual environment (if using uv, it handles this automatically)
uv venv  # or: python -m venv venv
source .venv/bin/activate  # On Windows: .venv\Scripts\activate (or venv\Scripts\activate)

# Install in editable mode with dev dependencies
uv pip install -e .
# or with pip
pip install -e .
For testing and documentation development, install the dev dependency group:

# Using uv (reads from pyproject.toml [dependency-groups])
uv pip install -e . --group dev

# Or manually install dev dependencies
pip install marimo mkdocs mkdocs-material mkdocstrings[python] nbformat pytest-doctestplus sybil

Dev dependencies include:

  • sybil: For markdown documentation testing

  • mkdocs + mkdocs-material: For building documentation

  • mkdocstrings: For API reference generation

  • pytest-doctestplus: For enhanced docstring testing

  • marimo: For interactive notebook development

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, use a fresh virtual environment:

# With uv
uv venv --python 3.9
source .venv/bin/activate

# With venv
python -m venv fresh-env
source fresh-env/bin/activate

# Then install
uv pip install clifpy  # or: pip install clifpy