Installing ancIBD

You can find ancIBD on the official Python package repository (PyPI). It can be installed using pip:

python3 -m pip install ancIBD

The software package distributes all source code that pip then compiles automatically during installation.

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

Upgrading ancIBD

If you already have a ancIBD release installed and wish to upgrade to the latest release, you can do so with pip 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 will be automatically installed without any further 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 need those, import errors will alert you. You can then install missing packages manually via pip (as above for ancIBD).