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addons
 
 
converters
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extra_includes
extra_includes
 
 
pxds
pxds
 
 
pyTOPP
pyTOPP
 
 
pyopenms
pyopenms
 
 
tests
tests
 
 
CMakeLists.txt
CMakeLists.txt
 
 
Jenkinsfile
Jenkinsfile
 
 
MANIFEST.in
MANIFEST.in
 
 
README.md
README.md
 
 
README.rst
README.rst
 
 
README_WRAPPING_NEW_CLASSES
README_WRAPPING_NEW_CLASSES
 
 
check_test_coverage.py
check_test_coverage.py
 
 
create_cpp_extension.py
create_cpp_extension.py
 
 
doCythonCompileOnly.py
doCythonCompileOnly.py
 
 
docompile.py
docompile.py
 
 
env.py.in
env.py.in
 
 
fix_pyi_imports.py
fix_pyi_imports.py
 
 
mac_fix_dependencies.rb
mac_fix_dependencies.rb
 
 
performance.rst
performance.rst
 
 
pyopenms-docs
pyopenms-docs
 
 
pyopenms_copy_deps.cmake
pyopenms_copy_deps.cmake
 
 
requirements_bld.txt
requirements_bld.txt
 
 
requirements_check.py
requirements_check.py
 
 
run_valgrind.sh
run_valgrind.sh
 
 
setup.py
setup.py
 
 
valgrind-python.supp
valgrind-python.supp
 
 

README.md

General

pyopenms is a Python library for the analysis of mass spectrometry data. It is mainly based on Cython wrappers around the OpenMS C++ library. To see which classes and functions are currently wrapped, please check the pxd files under "./pxds" or consult our API documentation. Additionally, it provides some convenience functions for plotting or converting from/to dataframes or numpy arrays.

Wrapping new classes

See README_WRAPPING_NEW_CLASSES

Build instructions

  1. (optional) Create a virtual python environment:

    python -m venv /path/to/myenv

# ... and activate it, e.g.
# Linux:
source <venv>/bin/activate
# Windows:
c:\path\to\myenv\Scripts\activate.bat

  2. Get Python 3.7+ and the following Python libraries:

    pip install -r requirements_bld.txt

  3. If running from an OpenMS build tree (recommended), just reconfigure with

    cmake -DPYOPENMS=ON .

    If it does not find the python that you just installed or complains about libraries not located although you just installed them, help it find the correct python executable by adding -DPython_EXECUTABLE="/path/to/python(.exe)" If your computer has a lot of RAM (16GB+) you can add -DPY_NUM_THREADS=2 (or up to the number of split modules, which are by default PY_NUM_MODULES=8).

    Building with an existing, installed OpenMS library is possible but not well-tested. All you need is the current pyOpenMS directory (where this README is located). Configure CMake in a build dir of your choice with general CMake and pyopenms-related options only. It will try to find OpenMS based on its CMake config files that should be installed with newer versions of OpenMS (around 2.8+) and hopefully parse all necessary options and find OpenMS' transitive dependencies. The rest is the same.

  4. Build CMake target "pyopenms" build-system agnostic with

    cmake --build . --target pyopenms

  5. Run tests with

    ctest -R pyopenms

    "-R" to restrict to pyopenms* tests. If running out of the OpenMS build tree, this should not be necessary.

  6. Install locally (and in-place for live edits [option -e]) into current Python with

    pip install -e pyopenms --no-cache-dir --no-binary=pyopenms

    --no-binary is used because the binaries are/were built with CMake.