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

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

Python 3.13 (via Jupyter server)

Run a manual pip install:

cd package python3 -m pip install --user .

Python3.7 (outdated since update)

Do this from my Python Environment (loaded with envpython37). Then switch to the correct folder and build the extensions 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 the head node (probably due to resource constraints). In that case, delete intermediate files and try again. Mid-term to-do: Need to build a batchable script.

Python 3.8 (outdated since update):

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