Installation

Prerequisites

PyEnzyme requires Python 3.10 or higher. You can install PyEnzyme using either pip (the standard Python package manager) or uv (a faster, modern alternative).

Install with pip

The standard way to install PyEnzyme is using pip:

pip install pyenzyme

This installs PyEnzyme with all core dependencies, including support for reading and writing EnzymeML documents, database fetchers, visualization tools, and unit handling.

Install with uv

uv is a fast Python package manager written in Rust. It’s significantly faster than pip and provides better dependency resolution. If you don’t have uv installed, you can install it first:

# Install uv
curl -LsSf https://astral.sh/uv/install.sh | sh

Then install PyEnzyme:

uv pip install pyenzyme

Install from source

To install the latest development version or contribute to PyEnzyme, clone the repository and install in editable mode:

git clone https://github.com/EnzymeML/PyEnzyme.git
cd PyEnzyme
pip install -e .

Installing in editable mode (-e) allows you to make changes to the source code that will be immediately reflected without reinstalling.

Optional dependencies

PyEnzyme provides optional dependency groups for extended functionality. The available groups are:

Excel support (excel)

Enables reading and writing Excel files (.xlsx). Installs openpyxl.

With pip:

pip install "pyenzyme[excel]"

With uv:

uv pip install "pyenzyme[excel]"

PySCeS integration (pysces)

Enables kinetic modeling and parameter fitting using PySCeS. Installs pysces and lmfit.

With pip:

pip install "pyenzyme[pysces]"

With uv:

uv pip install "pyenzyme[pysces]"

See the mathematical modeling guide for details on using PySCeS with PyEnzyme.

COPASI support (copasi)

Enables using COPASI for kinetic modeling and parameter fitting. Installs copasi-basico.

With pip:

pip install "pyenzyme[copasi]"

With uv:

uv pip install "pyenzyme[copasi]"

See the COPASI integration guide for details on using COPASI with PyEnzyme.

Development dependencies (tests)

Includes testing tools for development and running the test suite. Installs pytest, pytest-httpx, and pytest-sugar.

With pip:

pip install "pyenzyme[tests]"

With uv:

uv pip install "pyenzyme[tests]"

Legacy API support (v1)

Provides backward compatibility with PyEnzyme v1.x. Installs seaborn, numexpr, python-libcombine, deepdiff, and deprecation.

With pip:

pip install "pyenzyme[v1]"

With uv:

uv pip install "pyenzyme[v1]"

The legacy API is available via pyenzyme.v1. New projects should use the current API.

Installing multiple extras

You can install multiple optional dependencies at once:

With pip:

pip install "pyenzyme[excel,pysces]"

With uv:

uv pip install "pyenzyme[excel,pysces]"

Using uv dependency groups

When using uv, you can also leverage dependency groups directly when installing from source:

git clone https://github.com/EnzymeML/PyEnzyme.git
cd PyEnzyme
uv pip install -e ".[pysces,excel,tests,v1]"

Verify installation

After installation, verify that PyEnzyme is working correctly:

import pyenzyme as pe
print(pe.__version__)

If you see the version number printed, PyEnzyme is installed successfully.

Next steps

Once PyEnzyme is installed, proceed to the next guide to learn how to create EnzymeML documents.