lkirk/ts-two-locus-proto

Prototype code for two-locus stats in tskit

2-site stats

Prototype code for 2-site statistics in tskit

Installation

To use this code/notebook, you'll need to recreate the conda environment like so:

conda env create -n <name-of-your-env> --file dev-conda-env.yml
pip install -e .

To build the c code:

cd c
meson setup build

Note: if you don't have ninja or meson installed on your system, they are installed in the conda environment. You can source the conda environment to perform all actions in this codebase.

Running Tests

There are two test suites: a python and a c test suite for running the python prototype and c prototype tests.

To run the c tests:

cd c
ninja -C build test

To run the python tests:

conda activate <name-of-your-env>
pytest -v test

These tests are also run in github actions. The c code coverage can be viewed here

If you'd like to generate code coverage locally:

conda activate <name-of-your-env>
meson setup -Db_coverage=true build  # you might want to remove previous build dir
ninja -C build test coverage