pyOpenMS are the Python bindings to the OpenMS open-source C++ library for LC-MS data management and analyses. The Python bindings cover a large part of the OpenMS API to enable rapid algorithm development and workflow development. pyOpenMS supports the Proteomics Standard Initiative (PSI) formats for MS data.

This repository contains documentation, installation instructions, and example code that show different functions of pyOpenMS.

Installation is best done through PyPI (the Python package index) where binary packages are provided for the release versions of OpenMS, covering Linux/Mac/Windows. Alternatively, it is available on (bio)conda.

For the brave nightly build can be found at our local PyPI server.

The readthedocs pyOpenMS documentation is generated from the master branch of this repository, see docs/README.md

The generated documentation is available here: https://pyopenms.readthedocs.io/en/latest/

Are created by CI and stored in master+ipynb to not clutter the master branch.

Binder uses the Jupyter Notebooks in master+ipynb. The conda environment is described in environment.yml, the post-build event installs the nightly pyopenms wheel. Currently, only environment.yml is used by binder. Note: You can test a branch "jpfeuffer-patch-6" using https://notebooks.gesis.org/binder/v2/gh/OpenMS/pyopenms-docs/jpfeuffer-patch-6