ancIBD

This GitHub repository contains development code for the Python package ancIBD that is available via PyPi. Please find the official documentation on readthedocs.

This github repository contains the development code (in ./package/), and also the code underlying the ancIBD publication (in particular in ./notebook/).

The notes below are only for developers of this package who run development versions.

Produce C extension

In order to run the code, you need to have the C extension that implements the forward/backward pass. When installing the Python package, this is done automatically. However, if you are a developer and want to test the latest changes to the packages you will have to do that manually.

On Leipzig Cluster

Simply cd into the python folder, and then cythonize:

cd package/ancIBD/ cythonize -a -i cfunc.pyx

On o2 cluster with Python3.7

Do this from my Python Environment (loaded with envpython37).

Then switch to th correct folder and build the extensions via using the following commands:

envpython37 #load the python environment cd package/ancIBD/ # or path where the cfunc.pyx file is located module load gcc/6.2.0 module load python/3.7.4 cythonize -a -i cfunc.pyx

Warning: cythonizing can be killed on head node (prob. ressources). In that case delete intermediate files and try again. Mid-term todo: Need to build batchable script.

On O2 with Python 3.8:

cd package/ancIBD module load gcc/9.2.0 module load python/3.8.12 cythonize -a -i cfunc.pyx