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, we will configure the CMake-based OpenMS build system to enable the pyOpenMS target with the configuration option -DPYOPENMS=ON. If your are using virtualenv or 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 now configure pyOpenMS (inside your build folder) with:


Remember, that you can pass the other options as described above to the first command by adding -DOPTION=VALUE statements if you need them.

Now build pyOpenMS (now there should be pyOpenMS specific build targets). If you are still inside your build folder, you can use “.” as the build folder parameter.

cmake --build $YOURBUILDFOLDER --target pyopenms --config Release

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.