Skip to content

Code style: black

PYggdrasil/workflows

Implements workflows to test and evaluate PYggdrasil using snakemake.

Usage

Before running any rules, set the WORKDIR in Snakefile and the path to the PYggdrasil package in the tree_inference.smk file.

Shared and experimental workflows are implemented. Shared workflows can be called upon by string matching i.e. 

    snakemake -c <n_cores> <WORKDIR>/<EXPERIMENT>/T_r_34_23.json
which runs created a random Tree of 34 nodes and generation seed 23, see tree_inference._file_id for details. Where <n_cores> is the number of cores to use, and <WORKDIR>/<EXPERIMENT> is the directory of the output.

Or run full experiments, titled m markXX by

    snakemake -c <n_cores> markXX

To inspect the DAG of the snakemake rule, e.g. mark00, run 

snakemake --dag mark00 | dot -Tpng > dag.png

Environment

Whilst we use Poetry as a dependency manager, we recommend to used Conda to as the environment manager.

PYggdrasil's dependencies are best installed via Poetry in an envrioment created by Conda.

This seperation allows to disect the dependencies of the package from the dependencies of the workflows, such as snakemake.

We recommend a setup via mini-conda., i.e on linux:

mkdir -p ~/miniconda3
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
rm -rf ~/miniconda3/miniconda.sh
~/miniconda3/bin/conda init bash
~/miniconda3/bin/conda init zsh
Note that the above installs miniconda in your home directory.

Further, enhance by adding mamba to the conda environment, for faster resolving of dependencies: 

conda install mamba -n base -c conda-forge

Then, create a new environment for the project: 

cd PYggdrasil/
mamba env create -f environment.yml

Then add in all project specific dependencies via: 

cd PYggdrasil/
conda activate PYggdrasil
pip install -e .
This should install all the dependencies, and make the package available in the environment PYggdrasil that is currently active by running the prior command.