Installation

The software ancIBD is on the official Python package repository (PyPI). One can install it using pip:

python3 -m pip install ancIBD

This package distributes source code that is compiled during installation with pip.

Expert note: The file setup.py contains the relevant installation information. In specific cases, you can also manually compile the relevant C code using Cython.

Upgrading

If you already have a ancIBD release installed via pip and wish to upgrade to the latest stable release, you can do so by adding --upgrade:

pip install --upgrade ancIBD

c Extension

For performance reasons, the heavy lifting of the algorithms is coded into C methods (cfunc.c). This “extension” is built automatically during installation from cfunc.pyx via the package cython (when CYTHON=True in setup.py, the default setting). If you set CYTHON=False, the extension is directly compiled from cfunc.c (experimental, not tested on all platforms).

Dependencies

The basic Python package dependencies are sufficient for the core functions of ancIBD. We kept the required dependencies minimal to avoid creating dependency conflicts. When ancIBD is installed, the following dependent Python packages should be automatically installed without any action on your part:

• numpy for calculations with numerical arrays at C speed

• pandas for handling databases and tables at C speed

• h5py for handling hdf5, a file format with partial I/O

• psutil for process monitoring

Some downstream and advanced functionalities require additional packages, such as matplotlib` for specific plots. If you are missing those, import errors will alert you. You can then install missing packages manually via ``pip.