Installation

Command Line

To install pyOpenMS from the command line using the binary wheels, you can type

pip install numpy
pip install pyopenms

We have binary packages for OSX, Linux and Windows (64 bit only) available from PyPI. Make sure to download the 64bit Python release for Windows. Currently we only support Python 3.9, 3.10, 3.11, 3.12 and 3.13.

You can install Python first from here, again make sure to download the 64bit release. You can then open a shell and type the two commands above (on Windows you may potentially have to use C:\Python37\Scripts\pip.exe in case pip is not in your system path).

Nightly/ CI wheels

If you want the newest features you can also install nightly builds of pyOpenMS with the following shell command:

pip install --index-url https://pypi.cs.uni-tuebingen.de/simple/ pyopenms

Source (advanced users)

To install pyOpenMS from source, you will first have to compile OpenMS successfully on your platform of choice and then follow the building from source instructions. Note that this may be non-trivial and is not recommended for most users.

Wrap Classes (advanced users)

In order to wrap new classes in pyOpenMS, read the following guide.