Build from Source

To install pyOpenMS from source, you will first have to compile OpenMS successfully on your platform of choice (note that for MS Windows you will need to match your compiler and Python version). Please follow the official documentation in order to compile OpenMS for your platform. Next you will need to install the following software packages

On Microsoft Windows: you need the 64 bit C++ compiler from Visual Studio 2015 to compile the newest pyOpenMS for Python 3.5, 3.6 or 3.7. This is important, else you get a clib that is different than the one used for building the Python executable, and pyOpenMS will crash on import. The OpenMS wiki has detailed information on building pyOpenMS on Windows.

You can install all necessary Python packages on which pyOpenMS depends through

pip install -U setuptools
pip install -U pip
pip install -U autowrap
pip install -U pytest
pip install -U numpy
pip install -U wheel

Depending on your systems setup, it may make sense to do this inside a virtual environment

virtualenv pyopenms_venv
source pyopenms_venv/bin/activate

Next, configure OpenMS with pyOpenMS: execute cmake as usual, but with parameters DPYOPENMS=ON. Also, if using virtualenv or using a specific Python version, add -DPYTHON_EXECUTABLE:FILEPATH=/path/to/python to ensure that the correct Python executable is used. Compiling pyOpenMS can use a lot of memory and take some time, however you can reduce the memory consumption by breaking up the compilation into multiple units and compiling in parallel, for example -DPY_NUM_THREADS=2 -DPY_NUM_MODULES=4 will build 4 modules with 2 threads. You can then configure pyOpenMS:

cmake -DPYOPENMS=ON
make pyopenms

Build pyOpenMS (now there should be pyOpenMS specific build targets). Afterwards, test that all went well by running the tests:

ctest -R pyopenms

Which should execute all the tests and return with all tests passing.

Further Questions

In case the above instructions did not work, please refer to the Wiki Page, contact the development team on github or send an email to the OpenMS mailing list.