PartSegCore_compiled_backend

This is a package with all cython/c++ backend for ParSeg

Current release extracted from PartSegCore module to avoid building multiple wheels for the main package and speedup tests.

This package requires libomp for build. On linux it can be installed with apt install libomp-dev or yum install libomp-devel. On macOS it can be installed with brew install libomp.

As clang version created on macOS do not have native openmp brew do not set libomp as default visible. If you install libomp with brew and want to build package from source you need to set OMP variable to libomp location.

For example:

export OMP="$(brew --prefix libomp)"
pip install .

As currently there is no wheel for macOS ARM64 it is required to build package from source.

Development in Clion

To install Python build dependencies, run:

pip install scikit-build-core cython cython-cmake numpy setuptools-scm

Then, install the package in development mode:

pip install --no-build-isolation --config-settings=editable.rebuild=true\
 -Cbuild-dir=build -ve .

vendor FindCython.cmake from cython-cmake to cmake directory.

mkdir cmake && cython-cmake vendor cmake

Set CUSTOM_MODULE_PATH environment variable to full path to cmake directory.

Set it in Settings → Build, Execution, Deployment → CMake → Environment

Cite as

Bokota, G., Sroka, J., Basu, S. et al. PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies. BMC Bioinformatics 22, 72 (2021). https://doi.org/10.1186/s12859-021-03984-1