Installation

Installation

Requirements

• Python 3.12, 3.13, or 3.14
• numpy >= 1.24
• pandas >= 2.0

No R installation required at runtime.

---

Install options

From PyPI

pip install harmonizepy

From GitHub (latest development version)

pip install git+https://github.com/LangeLab/HarmonizePy.git

Development install with uv

uv python install 3.12.13
uv sync --dev --python 3.12.13

The --dev flag installs pytest, mypy, and ruff alongside the package.

---

Optional extras

Extra	Install command	What it adds
io	pip install harmonizepy[io]	Parquet output support and faster CSV/TSV reading via pyarrow >= 14.0
config	pip install harmonizepy[config]	YAML config files via pyyaml >= 6.0. JSON and TOML work without this extra.
completion	pip install harmonizepy[completion]	Shell tab-completion for the CLI via argcomplete >= 3.0
all	pip install harmonizepy[all]	All three extras above

Parquet is the recommended output format for large datasets. Install the io extra if you plan to use --output-format parquet or write .parquet files directly from Python.

---

Verify the install

harmonizepy --version

Or from Python:

import harmonizepy
print(harmonizepy.__version__)

Expected output: 0.3.2