README.md

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pybedlite

See documentation on pybedlite.readthedocs.org.

pip install pybedlite

OR

conda install -c bioconda pybedlite

OR

conda create -n pybedlite pybedlite
conda activate pybedlite

Requires python 3.8+ (for python < 3.8, please use pybedlite <= 0.0.3)

Getting Setup for Development Work

Clone the repository to your local machine. Note that pybedlite >= 0.0.4 includes cgranges as a submodule, so you must use the --recurse-submodules option:

git clone --recurse-submodules https://github.com/fulcrumgenomics/pybedlite.git

Poetry is used to manage the python development environment.

A simple way to create an environment with the desired version of python and poetry is to use conda. E.g.:

conda create -n pybedlite python=3.8 poetry
conda activate pybedlite
poetry install

If the methods listed above do not work try the following:

mamba create -n pybedlite -c conda-forge "python=3.9.16" "poetry=1.6.1"
mamba activate pybedlite
poetry install

If, during poetry install on Mac OS X errors are encountered running gcc/clang to build pybedtools or other packages with native code, try setting the following and re-running poetry install:

export CFLAGS="-stdlib=libc++"

Checking the Build

Run all checks with:

./ci/check.sh