Try online

You can try out pyOpenMS in your browser. Just navigate to a topic you are interested in by clicking in the menu bar. Then click on the “Try online with Binder” button.


Note that the first start of binder might take a bit. While binder is perfect for trying pyOpenMS it only offers a limited amount of memory. You should install the pyOpenMS binaries on your PC for serious data processing.

We recommend to use pyOpenMS in PyCharm as it works well with source code documentation.

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 3.7, 3.8 and 3.9.

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.

You can either directly download the latest nightly build by executing the commands below.

MY_OS="Linux" # or "macOS" or "Windows" (case-sensitive)
mv ${MY_OS}\?status=completed ${MY_OS}

Or manually visit the GitHub page that contains the action to build the nightly wheels:, click on e.g., the newest nightly build on the top to get access to artefacts and download the corresponding wheel for macOS, Linux, or Windows.


Now, unzip the folder and select the supported Python version for your environment. The supported Python version is denoted as cp3X in the wheel file name (e.g. pyopenms_nightly-2.7.0.dev20220111-cp39-cp39-macosx_10_9_x86_64 for python 3.9 and macOS >= 10.9)

Finally, install the package with the following shell command:

pip install your-compatible.whl --no-cache-dir

Note that the Github Action page may contain unstable builds and different operating systems might be in a different state (they even might not be available if the builds for a specific OS did not succeed in a long time).

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.